VISTA

Names
More detailed information about this field from each metasource.

VISTA
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

vista
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

Other names: vista

Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

Webpage:

http://genome.lbl.gov/vista/index.shtml

Publications: (8)

Publications
More detailed information about this field from each metasource.

VISTA: computational tools for comparative genomics
PMID: 15215394
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

VISTA Enhancer Browser--a database of tissue-specific human enhancers
PMID: 17130149
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
PMID: 12654723
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

VISTA : visualizing global DNA sequence alignments of arbitrary length
PMID: 11159318
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

AVID: A global alignment program
PMID: 12529311
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

Glocal alignment: finding rearrangements during alignment
PMID: 12855437
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments
PMID: 15033870
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

Multiple whole genome alignments and novel biomedical applications at the VISTA portal
PMID: 17488840
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

VISTA: computational tools for comparative genomics PubMed citations: 959.

959 articles citing: VISTA: computational tools for comparative genomics

Disjunction and Vicariance Between East and West Asia: A Case Study on Euonymus sect. Uniloculares Based on Plastid Genome Analysis. PMID:35360330
Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests. PMID:35336757
Complete chloroplast genome studies of different apple varieties indicated the origin of modern cultivated apples from Malus sieversii and Malus sylvestris. PMID:35321410
Characteristics and comparative analysis of Mesona chinensis Benth chloroplast genome reveals DNA barcode regions for species identification. PMID:35318559
Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis. PMID:35291941
Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships. PMID:35287585
Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus. PMID:35283921
Comparative chloroplast genome analysis of medicinally important Veratrum (Melanthiaceae) in China: Insights into genomic characterization and phylogenetic relationships. PMID:35281123
Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species. PMID:35280541
Genetic and chemical markers for authentication of three Artemisia species: A. capillaris, A. gmelinii, and A. fukudo. PMID:35271607
The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L. PMID:35271574
The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes, Structural Characterization, Comparative Analysis, Phylogenomics and Time Divergence. PMID:35269924
The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus. PMID:35255817
Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae). PMID:35252450
Identification of Medicinal Bidens Plants for Quality Control Based on Organelle Genomes. PMID:35242042
An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin. PMID:35241112
Comparative analyses of chloroplast genomes in 'Red Fuji' apples: low rate of chloroplast genome mutations. PMID:35223207
The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. PMID:35222983
The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications. PMID:35221575
Characterization of the complete chloroplast genome of Brassica oleracea var. italica and phylogenetic relationships in Brassicaceae. PMID:35202392
Comparative Analysis of the Complete Chloroplast Genomes of Nine Paphiopedilum Species. PMID:35186004
The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species. PMID:35183127
The comparative studies of complete chloroplast genomes in Actinidia (Actinidiaceae): novel insights into heterogenous variation, clpP gene annotation and phylogenetic relationships. PMID:35175427
Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion. PMID:35161429
Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans. PMID:35149731
Plastid genome data provide new insights into the phylogeny and evolution of the genus Epimedium. PMID:35127172
Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate. PMID:35119932
The complete chloroplast genome sequencing analysis revealed an unusual IRs reduction in three species of subfamily Zygophylloideae. PMID:35108324
Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes. PMID:35096026
Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae). PMID:35086490
Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae. PMID:35086477
Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China. PMID:35082807
A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex. PMID:35064146
Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). PMID:35053061
Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species. PMID:35052453
Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus. PMID:34991463
The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships. PMID:34975990
Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis. PMID:34975932
Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis. PMID:34966403
Variation in Plastome Sizes Accompanied by Evolutionary History in Monogenomic Triticeae (Poaceae: Triticeae). PMID:34966398
The First Two Complete Mitochondrial Genomes of Neoephemeridae (Ephemeroptera): Comparative Analysis and Phylogenetic Implication for Furcatergalia. PMID:34946823
Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.). PMID:34940902
Complete chloroplast genome sequencing support Angelica decursiva is an independent species from Peucedanum praeruptorum. PMID:34924707
Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium. PMID:34895202
Authentication of Zingiber Species Based on Analysis of Metabolite Profiles. PMID:34880881
Dissection of the Regulatory Elements of the Complex Expression Pattern of Puckered, a Dual-Specificity JNK Phosphatase. PMID:34830088
Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes. PMID:34828383
Chloroplast genome characteristics and phylogenetic analysis of the medicinal plant Blumea balsamifera (L.) DC. PMID:34826835
Non-coding regulatory elements: Potential roles in disease and the case of epilepsy. PMID:34820881
Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution. PMID:34816061
Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). PMID:34814832
Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae. PMID:34804117
Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae. PMID:34777305
Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships. PMID:34733586
A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas). PMID:34732792
Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae. PMID:34707858
On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology. PMID:34707629
Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles (Hosta; Asparagaceae) in East Asia. PMID:34685791
Development of a LAMP-Based Molecular Species Diagnosis Method for Four Major Agricultural Pests in the Genus Spodoptera (Lepidoptera: Noctuidae). PMID:34680652
Comparative plastid genomics of Mazaceae: focusing on a new recognized genus, Puchiumazus. PMID:34665332
Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass. PMID:34630493
Comparative Chloroplast Genomics and Phylogenetic Analysis of Zygophyllum (Zygophyllaceae) of China. PMID:34630471
Complete plastid genome of Gentiana leucomelaena Maxim. (Gentianaceae) and phylogenetic analysis. PMID:34553055
The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold. PMID:34541615
Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives. PMID:34521343
Comparative and Evolutionary Analyses on the Complete Plastomes of Five Kalanchoe Horticultural Plants. PMID:34512691
The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time. PMID:34493218
Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers. PMID:34485770
The bowfin genome illuminates the developmental evolution of ray-finned fishes. PMID:34462605
Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). PMID:34459920
The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae). PMID:34451562
siRNA Mediate RNA Interference Concordant with Early On-Target Transient Transcriptional Interference. PMID:34440463
Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny. PMID:34439948
Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae). PMID:34422006
Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region. PMID:34421963
Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships. PMID:34386040
The complete plastid genome of Cotinus coggygria and phylogenetic analysis of the Anacardiaceae. PMID:34342605
Characterizing chloroplast genomes and inferring maternal divergence of the Triticum-Aegilops complex. PMID:34321524
Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications. PMID:34303345
Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae. PMID:34282194
The Conservation of Chloroplast Genome Structure and Improved Resolution of Infrafamilial Relationships of Crassulaceae. PMID:34276716
Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. PMID:34256850
Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer. PMID:34255978
A duplicated amh is the master sex-determining gene for Sebastes rockfish in the Northwest Pacific. PMID:34255977
Evolution of Developmental Programs for the Midline Structures in Chordates: Insights From Gene Regulation in the Floor Plate and Hypochord Homologues of Ciona Embryos. PMID:34235159
Both microRNA-455-5p and -3p repress hypoxia-inducible factor-2α expression and coordinately regulate cartilage homeostasis. PMID:34230481
Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria. PMID:34225754
Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. PMID:34219317
Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution. PMID:34204211
Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS). PMID:34200260
Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau. PMID:34195504
Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement. PMID:34194461
Complete plastomes of six species of Wikstroemia (Thymelaeaceae) reveal paraphyly with the monotypic genus Stellera. PMID:34193929
Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars. PMID:34188842
Comparative analyses of Mikania (Asteraceae: Eupatorieae) plastomes and impact of data partitioning and inference methods on phylogenetic relationships. PMID:34168241
Phylogenomic Analyses of Hepatica Species and Comparative Analyses Within Tribe Anemoneae (Ranunculaceae). PMID:34149746
Coordination of two enhancers drives expression of olfactory trace amine-associated receptors. PMID:34145235
Comparative genome analysis revealed gene inversions, boundary expansions and contractions, and gene loss in the Stemona sessilifolia (Miq.) Miq. chloroplast genome. PMID:34143785
Temporal evolution of cellular heterogeneity during the progression to advanced AR-negative prostate cancer. PMID:34099734
High promoter sequence variation in subgroup 6 members of R2R3-MYB genes is involved in different floral anthocyanin color patterns in Lilium spp. PMID:34052932
Plastome structure and phylogenetic relationships of Styracaceae (Ericales). PMID:34049486
Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner. PMID:34009390
Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays. PMID:34003345
Comparative analysis of chloroplast genome structure and molecular dating in Myrtales. PMID:33992095
Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola. PMID:33976800
Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Lactuca raddeana and Lactuca sativa. PMID:33969207
The complete chloroplast genome of Photinia davidsoniae: molecular structures and comparative analysis. PMID:33969192
Complete chloroplast genome of Myracrodruon urundeuva and its phylogenetics relationships in Anacardiaceae family. PMID:33967463
Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. PMID:33964091
Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae. PMID:33932143
Plasticity of Naturally Occurring Regulatory T Cells in Allergic Airway Disease Is Modulated by the Transcriptional Activity of Il-6. PMID:33925531
Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships. PMID:33911961
Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex. PMID:33910529
Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species. PMID:33903715
Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae). PMID:33888057
Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. PMID:33846596
Lineage-specific plastid degradation in subtribe Gentianinae (Gentianaceae). PMID:33841784
Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae). PMID:33841465
Structure and comparative analysis of the mitochondrial genomes of Liolaemus lizards with different modes of reproduction and ploidy levels. PMID:33828904
The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci. PMID:33827918
Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes. PMID:33794772
Development of genomic resources for the genus Celtis (Cannabaceae) based on genome skimming data. PMID:33778224
Plastome phylogenomics of the East Asian endemic genus Dobinea. PMID:33778223
Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae). PMID:33778222
Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae). PMID:33778221
Characteration and comparative analysis of the whole chloroplast genomes of five common millet (Panicum miliaceum). PMID:33763565
Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes. PMID:33736599
Complete chloroplast genome sequence of Adenophora racemosa (Campanulaceae): Comparative analysis with congeneric species. PMID:33735287
Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PMID:33711072
The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China. PMID:33676415
Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line. PMID:33674697
Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. PMID:33669616
Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera. PMID:33665028
Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis. PMID:33649234
Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia. PMID:33637038
Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes. PMID:33619356
Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements. PMID:33584746
ARF2 represses expression of plant GRF transcription factors in a complementary mechanism to microRNA miR396. PMID:33580700
Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae. PMID:33574434
Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis. PMID:33573201
Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. PMID:33540810
The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts. PMID:33533895
Dbx2 regulation in limbs suggests interTAD sharing of enhancers. PMID:33497014
Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan. PMID:33441744
Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae). PMID:33419221
Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea. PMID:33413130
Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences. PMID:33413107
Modeling by disruption and a selected-for partner for the nude locus. PMID:33369874
Complete plastid genome of Gentiana trichotoma (Gentianaceae) and phylogenetic analysis. PMID:33365723
Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships. PMID:33362846
Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae). PMID:33343605
A region of the sex chromosome associated with population differences in diapause induction contains highly divergent alleles at clock genes. PMID:33340097
Comparative Genomics Studies on the dmrt Gene Family in Fish. PMID:33281869
Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications. PMID:33267775
Comparative Analysis of Complete Chloroplast Genome Sequences of Wild and Cultivated Bougainvillea (Nyctaginaceae). PMID:33260641
Development of a Species Diagnostic Molecular Tool for an Invasive Pest, Mythimna loreyi, Using LAMP. PMID:33228220
Plastid Phylogenomics of Dendroseris (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands. PMID:33224173
The origin and evolution of a distinct mechanism of transcription initiation in yeasts. PMID:33219055
Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes. PMID:33218207
Mammalian-specific ectodermal enhancers control the expression of Hoxc genes in developing nails and hair follicles. PMID:33199643
Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea. PMID:33198274
dbCNS: A New Database for Conserved Noncoding Sequences. PMID:33196844
Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Paeonia Section Moutan Species (Paeoniaceae). PMID:33193580
Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae). PMID:33188288
Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships. PMID:33187470
Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses. PMID:33178241
Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes. PMID:33171839
An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification. PMID:33105814
PhycoCosm, a comparative algal genomics resource. PMID:33104790
Characteristics of Organellar Genomes and Nuclear Internal Transcribed Spacers in the Tertiary Relict Genus Dipelta and Their Phylogenomic Implications. PMID:33101393
Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae). PMID:33088627
Plastome structure and adaptive evolution of Calanthe s.l. species. PMID:33083127
Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae. PMID:33066261
Chloroplast Genome Sequences and Comparative Analyses of Combretaceae Mangroves with Related Species. PMID:33062686
Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification. PMID:33050285
Unexpected mutual regulation underlies paralogue functional diversification and promotes epithelial tissue maturation in Tribolium. PMID:33020571
The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes. PMID:33005000
Comparative analysis of chloroplast genomes in Vasconcellea pubescens A.DC. and Carica papaya L. PMID:32978465
Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot. PMID:32912160
Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae). PMID:32899372
Deep Convergence, Shared Ancestry, and Evolutionary Novelty in the Genetic Architecture of Heliconius Mimicry. PMID:32883703
Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny. PMID:32878602
The Complete Chloroplast Genome Sequences of 14 Curcuma Species: Insights Into Genome Evolution and Phylogenetic Relationships Within Zingiberales. PMID:32849804
Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia. PMID:32824526
COVID-19, SARS-CoV-2, and Export Controls. PMID:32816590
The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae. PMID:32808964
Complete Chloroplast Genomes and Comparative Analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae). PMID:32785156
Genetic and Epigenetic Regulation of the Smoothened Gene (SMO) in Cancer Cells. PMID:32784501
Fagopyrum esculentum ssp. ancestrale-A Hybrid Species Between Diploid F. cymosum and F. esculentum. PMID:32765557
Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L. PMID:32756391
Complete Chloroplast Genome of Rhipsalis baccifera, the only Cactus with Natural Distribution in the Old World: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies. PMID:32752116
Plastome comparative genomics in maples resolves the infrageneric backbone relationships. PMID:32742784
Complete chloroplast genomes of Zingiber montanum and Zingiber zerumbet: Genome structure, comparative and phylogenetic analyses. PMID:32735595
Characteristics and Mutational Hotspots of Plastomes in Debregeasia (Urticaceae). PMID:32733543
The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis. PMID:32719421
Complete Chloroplast Genome Characterization of Oxalis Corniculata and Its Comparison with Related Species from Family Oxalidaceae. PMID:32717796
Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling. PMID:32699274
Characterization and Comparative Analysis of Two Rheum Complete Chloroplast Genomes. PMID:32685515
A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains. PMID:32685287
Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species. PMID:32651417
Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies. PMID:32636853
Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences. PMID:32626767
Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species. PMID:32616875
Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots. PMID:32596045
Olig2-Induced Semaphorin Expression Drives Corticospinal Axon Retraction After Spinal Cord Injury. PMID:32564090
The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica). PMID:32545897
Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae. PMID:32532210
Genome-Wide Analysis Identifies NURR1-Controlled Network of New Synapse Formation and Cell Cycle Arrest in Human Neural Stem Cells. PMID:32522891
Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). PMID:32466556
Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses. PMID:32462024
The transcription factor HAND2 up-regulates transcription of the IL15 gene in human endometrial stromal cells. PMID:32444497
rps3 as a Candidate Mitochondrial Gene for the Molecular Identification of Species from the Colletotrichum acutatum Species Complex. PMID:32422999
Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution. PMID:32420321
Plastome Evolution in Saxifragaceae and Multiple Plastid Capture Events Involving Heuchera and Tiarella. PMID:32391025
Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. PMID:32384622
Comparative analysis of the complete chloroplast genomes from six Neotropical species of Myrteae (Myrtaceae). PMID:32384134
Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae). PMID:32379799
Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species. PMID:32365609
Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae. PMID:32353023
Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses. PMID:32351518
Complete Chloroplast Genome Sequence of Hibiscus cannabinus and Comparative Analysis of the Malvaceae Family. PMID:32256523
Characteristics analysis of the complete Wurfbainia villosa chloroplast genome. PMID:32255937
Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences. PMID:32239179
The complete chloroplast genome of Myriophyllum spicatum reveals a 4-kb inversion and new insights regarding plastome evolution in Haloragaceae. PMID:32211179
Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. PMID:32194972
Organization of the Addax Major Histocompatibility Complex Provides Insights Into Ruminant Evolution. PMID:32161588
Initial Characterization of the Chloroplast Genome of Vicia sepium, an Important Wild Resource Plant, and Related Inferences About Its Evolution. PMID:32153639
Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata. PMID:32127603
Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis. PMID:32121524
Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae. PMID:32102387
The chloroplasts genomic analyses of Rosa laevigata, R. rugosa and R. canina. PMID:32082412
Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes. PMID:32077945
Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance. PMID:32071921
Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution. PMID:32071806
Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny. PMID:32033491
-Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae). PMID:32025370
Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships. PMID:31997112
The complete chloroplast genome of Microcycas calocoma (Miq.) A. DC. (Zamiaceae, Cycadales) and evolution in Cycadales. PMID:31976174
Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution. PMID:31973113
Plastome sequencing of Myripnois dioica and comparison within Asteraceae. PMID:31934676
Caudal-dependent cell positioning directs morphogenesis of the C. elegans ventral epidermis. PMID:31923384
The Complete Chloroplast Genomes of Two Lespedeza Species: Insights into Codon Usage Bias, RNA Editing Sites, and Phylogenetic Relationships in Desmodieae (Fabaceae: Papilionoideae). PMID:31906237
Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. PMID:31903688
Comparative and Functional Genomic Resource for Mechanistic Studies of Human Blood Pressure-Associated Single Nucleotide Polymorphisms. PMID:31902252
Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid. PMID:31886246
Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing. PMID:31867041
Species Identification of Dracaena Using the Complete Chloroplast Genome as a Super-Barcode. PMID:31849682
A transposable element insertion is associated with an alternative life history strategy. PMID:31848330
Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences. PMID:31844573
Intra-individual heteroplasmy in the Gentiana tongolensis plastid genome (Gentianaceae). PMID:31799070
Sequencing and analyses on chloroplast genomes of Tetrataenium candicans and two allies give new insights on structural variants, DNA barcoding and phylogeny in Apiaceae subfamily Apioideae. PMID:31772837
Tasks, Techniques, and Tools for Genomic Data Visualization. PMID:31768085
Complete Chloroplast Genomes of Vachellia nilotica and Senegalia senegal: Comparative Genomics and Phylogenomic Placement in a New Generic System. PMID:31765416
Gene Losses and Variations in Chloroplast Genome of Parasitic Plant Macrosolen and Phylogenetic Relationships within Santalales. PMID:31752332
Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul. PMID:31747873
Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny. PMID:31744457
The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension. PMID:31719172
Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae). PMID:31717580
A New Chloroplast DNA Extraction Protocol Significantly Improves the Chloroplast Genome Sequence Quality of Foxtail Millet (Setaria italica (L.) P. Beauv.). PMID:31700055
Sow Thistle Chloroplast Genomes: Insights into the Plastome Evolution and Relationship of Two Weedy Species, Sonchus asper and Sonchus oleraceus (Asteraceae). PMID:31683955
Comparison of chloroplast genomes of Gynura species: sequence variation, genome rearrangement and divergence studies. PMID:31664913
Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae). PMID:31653891
Developing Chloroplast Genomic Resources from 25 Avena Species for the Characterization of Oat Wild Relative Germplasm. PMID:31652703
Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'. PMID:31644545
Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis. PMID:31614980
Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PMID:31607787
Draft Genome Sequence of Sporolactobacillus inulinus NBRC 111894, Isolated from Kôso, a Japanese Sugar-Vegetable Fermented Beverage. PMID:31601658
Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula. PMID:31581648
Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species. PMID:31579601
The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species. PMID:31578450
Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. PMID:31572496
Characterization and Activity Analyses of the FLOWERING LOCUS T Promoter in Gossypium Hirsutum. PMID:31561427
Comparison of Whole Plastome Sequences between Thermogenic Skunk Cabbage Symplocarpus renifolius and Nonthermogenic S. nipponicus (Orontioideae; Araceae) in East Asia. PMID:31547213
Chloroplast Genomes and Comparative Analyses among Thirteen Taxa within Myrsinaceae s.str. Clade (Myrsinoideae, Primulaceae). PMID:31540236
Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships. PMID:31532782
Genome Comparison Reveals Mutation Hotspots in the Chloroplast Genome and Phylogenetic Relationships of Ormosia Species. PMID:31531364
The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene. PMID:31531272
Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes. PMID:31497389
Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. PMID:31467890
Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses. PMID:31439882
Comparison and Phylogenetic Analysis of Chloroplast Genomes of Three Medicinal and Edible Amomum Species. PMID:31430862
Development of Plastid Genomic Resources for Discrimination and Classification of Epimedium wushanense (Berberidaceae). PMID:31426439
Comparative and Phylogenetic Analyses of Ginger (Zingiber officinale) in the Family Zingiberaceae Based on the Complete Chloroplast Genome. PMID:31409043
Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing. PMID:31406227
Structure and features of the complete chloroplast genome of Melastoma dodecandrum. PMID:31404219
Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics. PMID:31382526
Plant Defenses Against Pests Driven by a Bidirectional Promoter. PMID:31379907
Expansion of a core regulon by transposable elements promotes Arabidopsis chemical diversity and pathogen defense. PMID:31371717
Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes. PMID:31330852
Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae. PMID:31328036
CsTFL1 inhibits determinate growth and terminal flower formation through interaction with CsNOT2a in cucumber. PMID:31320327
Determination of the evolutionary pressure on Camellia oleifera on Hainan Island using the complete chloroplast genome sequence. PMID:31289703
Modular tissue-specific regulation of doublesex underpins sexually dimorphic development in Drosophila. PMID:31285355
Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae). PMID:31275342
Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales. PMID:31242865
Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species. PMID:31234777
The Human TET2 Gene Contains Three Distinct Promoter Regions With Differing Tissue and Developmental Specificities. PMID:31231651
TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data. PMID:31164077
The Complete Chloroplast Genome of Euphrasia regelii, Pseudogenization of ndh Genes and the Phylogenetic Relationships Within Orobanchaceae. PMID:31156705
Gibberellins Act Downstream of Arabis PERPETUAL FLOWERING1 to Accelerate Floral Induction during Vernalization. PMID:31097676
Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis. PMID:31071159
Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb "Bang-Poong". PMID:31060231
Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways. PMID:31053165
A homeotic shift late in development drives mimetic color variation in a bumble bee. PMID:31043564
The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development. PMID:31036599
Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill. PMID:30987216
The plastid genome and its implications in barcoding specific-chemotypes of the medicinal herb Pogostemon cablin in China. PMID:30986249
Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach. PMID:30947707
Identification and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Ephedra Herbs Containing Ephedrine. PMID:30941367
Identification of regulatory elements recapitulating early expression of L-plastin in the zebrafish enveloping layer and embryonic periderm. PMID:30940554
Metagenomes of a Freshwater Charavirus from British Columbia Provide a Window into Ancient Lineages of Viruses. PMID:30934644
Calcineurin inhibitors reduce NFAT-dependent expression of antifungal pentraxin-3 by human monocytes. PMID:30934147
Evidence of mitochondrial DNA in the chloroplast genome of Convallaria keiskei and its subsequent evolution in the Asparagales. PMID:30903007
Sequencing and Comparative Analysis of the Chloroplast Genome of Angelica polymorpha and the Development of a Novel Indel Marker for Species Identification. PMID:30875988
Evolutionary Comparison of the Chloroplast Genome in the Woody Sonchus Alliance (Asteraceae) on the Canary Islands. PMID:30875850
Interspecific delimitation and relationships among four Ostrya species based on plastomes. PMID:30866795
Comparative genomics reveals origin of MIR159A-MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae. PMID:30840147
Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species. PMID:30823362
Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation. PMID:30808310
Combining Strengths for Multi-genome Visual Analytics Comparison. PMID:30783378
The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae). PMID:30740573
Venous endothelin modulates responsiveness of cardiac sympathetic axons to arterial semaphorin. PMID:30735130
Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis. PMID:30699955
The Complete Chloroplast Genomes of Echinacanthus Species (Acanthaceae): Phylogenetic Relationships, Adaptive Evolution, and Screening of Molecular Markers. PMID:30687376
The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species. PMID:30641990
The Plastid Genome of Deschampsia cespitosa (Poaceae). PMID:30634385
First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees. PMID:30629590
Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children. PMID:30626342
A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula. PMID:30610167
Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae). PMID:30609873
Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications. PMID:30598104
Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids. PMID:30563463
Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships. PMID:30558106
Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses. PMID:30533315
Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes. PMID:30505665
A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates. PMID:30499775
Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq. PMID:30479362
Complete Chloroplast Genome Sequence of Malus hupehensis: Genome Structure, Comparative Analysis, and Phylogenetic Relationships. PMID:30413097
Comparative Chloroplast Genome Analysis of Rhubarb Botanical Origins and the Development of Specific Identification Markers. PMID:30380708
Pantoea Bacteriophage vB_PagS_Vid5: A Low-Temperature Siphovirus That Harbors a Cluster of Genes Involved in the Biosynthesis of Archaeosine. PMID:30366363
Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars. PMID:30352068
The Genomic Basis of Tumor Regression in Tasmanian Devils (Sarcophilus harrisii). PMID:30321343
Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens. PMID:30295986
Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis. PMID:30271968
Identification of a limb enhancer that is removed by pathogenic deletions downstream of the SHOX gene. PMID:30250174
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus. PMID:30248930
Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae. PMID:30242472
Immediate-Early Promoter-Driven Transgenic Reporter System for Neuroethological Research in a Hemimetabolous Insect. PMID:30225346
Plastome characteristics of Cannabaceae. PMID:30175293
First reported chloroplast genome sequence of Punica granatum (cultivar Helow) from Jabal Al-Akhdar, Oman: phylogenetic comparative assortment with Lagerstroemia. PMID:30159822
Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships. PMID:30154353
Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species. PMID:30149578
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima. PMID:30126202
Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships. PMID:30120274
Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae). PMID:30104517
Comparative Analysis of Complete Chloroplast Genomes of Anemoclema, Anemone, Pulsatilla, and Hepatica Revealing Structural Variations Among Genera in Tribe Anemoneae (Ranunculaceae). PMID:30100915
Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae. PMID:30089144
The Floral C-Lineage Genes Trigger Nectary Development in Petunia and Arabidopsis. PMID:30087206
A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties. PMID:30083466
First chloroplast genomics study of Phoenix dactylifera (var. Naghal and Khanezi): A comparative analysis. PMID:30063732
Spatial regulation of expanded transcription in the Drosophila wing imaginal disc. PMID:30063727
Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus. PMID:29989238
Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers. PMID:29976857
Whole-Genome Comparison Reveals Divergent IR Borders and Mutation Hotspots in Chloroplast Genomes of Herbaceous Bamboos (Bambusoideae: Olyreae). PMID:29949900
Phylogenetic comparison of Epstein-Barr virus genomes. PMID:29948828
Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage. PMID:29925900
Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae. PMID:29915292
Presomitic mesoderm-specific expression of the transcriptional repressor Hes7 is controlled by E-box, T-box, and Notch signaling pathways. PMID:29895619
Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species. PMID:29876074
Comparative Chloroplast Genomics of Dipsacales Species: Insights Into Sequence Variation, Adaptive Evolution, and Phylogenetic Relationships. PMID:29875791
Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable. PMID:29874832
The Chloroplast Genome of Lilium henrici: Genome Structure and Comparative Analysis. PMID:29861452
The complete chloroplast genome sequence of Actinidia arguta using the PacBio RS II platform. PMID:29795601
The Complete Plastome Sequences of Seven Species in Gentiana sect. Kudoa (Gentianaceae): Insights Into Plastid Gene Loss and Molecular Evolution. PMID:29765380
Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea. PMID:29747436
Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences. PMID:29743507
Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species. PMID:29701675
The chloroplast genome of Cerasus humilis: Genomic characterization and phylogenetic analysis. PMID:29694421
The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae. PMID:29694416
Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae. PMID:29693617
Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana. PMID:29686078
The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. PMID:29684203
Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis. PMID:29642545
The Complete Chloroplast Genome of Heimia myrtifolia and Comparative Analysis within Myrtales. PMID:29642470
Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny. PMID:29619041
Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data. PMID:29618324
Molecular and Antigenic Characterization of Piscine orthoreovirus (PRV) from Rainbow Trout (Oncorhynchus mykiss). PMID:29614838
Comparative Plastid Genomes of Primula Species: Sequence Divergence and Phylogenetic Relationships. PMID:29614787
Evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation. PMID:29610331
Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species. PMID:29601535
Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species. PMID:29596414
Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. PMID:29549088
The complete chloroplast genome sequence of Epipremnum aureum and its comparative analysis among eight Araceae species. PMID:29529038
A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene. PMID:29527594
The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis. PMID:29518967
Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution. PMID:29498674
The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske. PMID:29494552
Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing. PMID:29463014
Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis. PMID:29462921
Plastid Genome Comparative and Phylogenetic Analyses of the Key Genera in Fagaceae: Highlighting the Effect of Codon Composition Bias in Phylogenetic Inference. PMID:29449857
The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species. PMID:29439505
Characterization of TTN Novex Splicing Variants across Species and the Role of RBM20 in Novex-Specific Exon Splicing. PMID:29438341
An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time. PMID:29431097
Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements. PMID:29416569
Conserved Upstream Regulatory Regions in Mammalian Tyrosine Hydroxylase. PMID:29404959
Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences. PMID:29396532
Stat3 and CCAAT enhancer-binding protein β (C/ebpβ) activate Fanconi C gene transcription during emergency granulopoiesis. PMID:29382715
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii. PMID:29373520
Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes. PMID:29293597
The complete chloroplast genome sequence of Asian Palmyra palm (Borassus flabellifer). PMID:29246263
Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution. PMID:29216844
De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. PMID:29216381
Characterization of a Novel Bat Adenovirus Isolated from Straw-Colored Fruit Bat (Eidolon helvum). PMID:29207524
Integral Phylogenomic Approach over Ilex L. Species from Southern South America. PMID:29165335
The Complete Chloroplast Genome Sequences of Aconitum pseudolaeve and Aconitum longecassidatum, and Development of Molecular Markers for Distinguishing Species in the Aconitum Subgenus Lycoctonum. PMID:29160852
Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism. PMID:29142288
Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data. PMID:29119144
The Complete Amomum kravanh Chloroplast Genome Sequence and Phylogenetic Analysis of the Commelinids. PMID:29104233
Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus. PMID:29099062
Identification of genome-wide targets of Olig2 in the adult mouse spinal cord using ChIP-Seq. PMID:29049317
Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids. PMID:29046685
The complete chloroplast genome sequence of strawberry (Fragaria × ananassa Duch.) and comparison with related species of Rosaceae. PMID:29038765
VICTOR: genome-based phylogeny and classification of prokaryotic viruses. PMID:29036289
Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species. PMID:29026168
A long-range cis-regulatory element for class I odorant receptor genes. PMID:29026079
SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development. PMID:29021530
Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates. PMID:28961967
Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships. PMID:28955369
Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. PMID:28955348
Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis. PMID:28925932
Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species. PMID:28905330
The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria. PMID:28902130
Long noncoding RNAs in the model species Brachypodium distachyon. PMID:28900227
The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species. PMID:28863163
Complete Chloroplast Genome Sequence of Decaisnea insignis: Genome Organization, Genomic Resources and Comparative Analysis. PMID:28855603
Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice. PMID:28846681
Molecular Structure and Phylogenetic Analyses of Complete Chloroplast Genomes of Two Aristolochia Medicinal Species. PMID:28837061
Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species. PMID:28809950
A kidney-specific genetic control module in mice governs endocrine regulation of the cytochrome P450 gene Cyp27b1 essential for vitamin D3 activation. PMID:28808057
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua. PMID:28800082
Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family. PMID:28793854
Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis. PMID:28790364
Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species. PMID:28763486
Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences. PMID:28747666
The Complete Chloroplast Genome of Chinese Bayberry (Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales. PMID:28713393
Maize YABBY Genes drooping leaf1 and drooping leaf2 Regulate Plant Architecture. PMID:28698237
Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. PMID:28683832
Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting. PMID:28659711
Real-time monitoring of PtaHMGB activity in poplar transactivation assays. PMID:28638438
Cytoplasmic Form of Carlr lncRNA Facilitates Inflammatory Gene Expression upon NF-κB Activation. PMID:28626066
The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species. PMID:28608849
Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny. PMID:28575004
Characterization of basal and lipopolysaccharide-induced microRNA expression in equine peripheral blood mononuclear cells using Next-Generation Sequencing. PMID:28552958
Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium. PMID:28422071
Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae). PMID:28421090
Contrasting evolutionary genome dynamics between domesticated and wild yeasts. PMID:28416820
Odorant Sensory Input Modulates DNA Secondary Structure Formation and Heterogeneous Ribonucleoprotein Recruitment on the Tyrosine Hydroxylase and Glutamic Acid Decarboxylase 1 Promoters in the Olfactory Bulb. PMID:28411275
The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species. PMID:28326093
Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression. PMID:28320313
The Complete Chloroplast Genome Sequences of Six Rehmannia Species. PMID:28294981
Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at FLC orthologues. PMID:28261921
The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes. PMID:28241056
A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically Important Brassica Species Comprising the Triangle of U. PMID:28210266
Elevated HMGN4 expression potentiates thyroid tumorigenesis. PMID:28186538
Mitochondrial AtTrxo1 is transcriptionally regulated by AtbZIP9 and AtAZF2 and affects seed germination under saline conditions. PMID:28184497
Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies. PMID:28182646
Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies. PMID:28178222
Foxn1-β5t transcriptional axis controls CD8+ T-cell production in the thymus. PMID:28176764
Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes. PMID:28154574
Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives. PMID:28152978
Complete Chloroplast Genomes of Erianthus arundinaceus and Miscanthus sinensis: Comparative Genomics and Evolution of the Saccharum Complex. PMID:28125648
Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail. PMID:28122988
The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses. PMID:28119727
The Thyroid Na+/I- Symporter: Molecular Characterization and Genomic Regulation. PMID:28117294
Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny. PMID:28111577
Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes. PMID:28018385
Phylogenetic Relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island Based on Chloroplast Genome Sequencing. PMID:28009803
An ensemble of regulatory elements controls Runx3 spatiotemporal expression in subsets of dorsal root ganglia proprioceptive neurons. PMID:28007784
Construction of a Dual-Fluorescence Reporter System to Monitor the Dynamic Progression of Pluripotent Cell Differentiation. PMID:27999597
Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae. PMID:27995013
The genome of the Gulf pipefish enables understanding of evolutionary innovations. PMID:27993155
Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae). PMID:27965698
Rice SNP-seek database update: new SNPs, indels, and queries. PMID:27899667
Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). PMID:27867769
Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript. PMID:27856735
Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape. PMID:27856734
In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus. PMID:27856528
Lineage diversification, homo- and heterologous reassortment and recombination shape the evolution of chicken orthoreoviruses. PMID:27830770
Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species. PMID:27790228
Bcr-abl regulates Stat5 through Shp2, the interferon consensus sequence binding protein (Icsbp/Irf8), growth arrest specific 2 (Gas2) and calpain. PMID:27769062
Diabetes-linked transcription factor HNF4α regulates metabolism of endogenous methylarginines and β-aminoisobutyric acid by controlling expression of alanine-glyoxylate aminotransferase 2. PMID:27752141
Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. PMID:27729060
The complete chloroplast genome sequence of Gentiana lawrencei var. farreri (Gentianaceae) and comparative analysis with its congeneric species. PMID:27703869
Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals. PMID:27698483
MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species. PMID:27594782
Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice. PMID:27589600
Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads. PMID:27558458
The Complete Chloroplast Genome Sequence of the Medicinal Plant Swertia mussotii Using the PacBio RS II Platform. PMID:27517885
In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide a framework for future studies of their origin and function. PMID:27507266
Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs. PMID:27466206
Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives. PMID:27452401
Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species. PMID:27446185
Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis. PMID:27442423
Chloroplast genome structures in Gentiana (Gentianaceae), based on three medicinal alpine plants used in Tibetan herbal medicine. PMID:27422574
Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle. PMID:27412606
The Complete Chloroplast Genome of Ye-Xing-Ba (Scrophularia dentata; Scrophulariaceae), an Alpine Tibetan Herb. PMID:27391235
Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species. PMID:27379132
Chloroplast genome structure in Ilex (Aquifoliaceae). PMID:27378489
Revisiting the Plastid Phylogenomics of Pinaceae with Two Complete Plastomes of Pseudolarix and Tsuga. PMID:27352945
Conservation of the role of INNER NO OUTER in development of unitegmic ovules of the Solanaceae despite a divergence in protein function. PMID:27350128
Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals. PMID:27296695
Paralogous Regulators ArsR1 and ArsR2 of Pseudomonas putida KT2440 as a Basis for Arsenic Biosensor Development. PMID:27208139
Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae). PMID:27206980
Black perithecial pigmentation in Fusarium species is due to the accumulation of 5-deoxybostrycoidin-based melanin. PMID:27193384
Synteny Portal: a web-based application portal for synteny block analysis. PMID:27154270
StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform. PMID:27138013
The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms. PMID:27047519
The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses. PMID:27014326
Cell-to-cell movement of mitochondria in plants. PMID:26951647
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. PMID:26950095
TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. PMID:26940763
Organization and characteristics of the major histocompatibility complex class II region in the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). PMID:26932528
Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies. PMID:26930606
Biosynthesis of the acetyl-CoA carboxylase-inhibiting antibiotic, andrimid in Serratia is regulated by Hfq and the LysR-type transcriptional regulator, AdmX. PMID:26914969
Ensembl comparative genomics resources. PMID:26896847
Physiological evidence for diversification of IFNα- and IFNβ-mediated response programs in different autoimmune diseases. PMID:26882897
A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. PMID:26829752
RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PMID:26808730
Cis-regulatory programs in the development and evolution of vertebrate paired appendages. PMID:26783722
Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis. PMID:26668304
Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction. PMID:26658285
Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies. PMID:26574686
Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications. PMID:26566230
Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting. PMID:26543346
Spatially differentiated expression of quadruplicated green-sensitive RH2 opsin genes in zebrafish is determined by proximal regulatory regions and gene order to the locus control region. PMID:26537431
Identification of a novel cis-regulatory element essential for immune tolerance. PMID:26527800
Functionally conserved enhancers with divergent sequences in distant vertebrates. PMID:26519295
Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective. PMID:26513163
A novel miR-371a-5p-mediated pathway, leading to BAG3 upregulation in cardiomyocytes in response to epinephrine, is lost in Takotsubo cardiomyopathy. PMID:26512958
Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. PMID:26506948
Superinfection exclusion and the long-term survival of honey bees in Varroa-infested colonies. PMID:26505829
Alterations in Mc1r gene expression are associated with regressive pigmentation in Astyanax cavefish. PMID:26462499
Functional Diversification of Motor Neuron-specific Isl1 Enhancers during Evolution. PMID:26447474
A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells. PMID:26440894
Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor. PMID:26429922
Whole-Genome Sequencing of Kaposi's Sarcoma-Associated Herpesvirus from Zambian Kaposi's Sarcoma Biopsy Specimens Reveals Unique Viral Diversity. PMID:26423952
Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae. PMID:26389887
Data integration in biological research: an overview. PMID:26336651
Activation of Six1 Expression in Vertebrate Sensory Neurons. PMID:26313368
A shift in anterior-posterior positional information underlies the fin-to-limb evolution. PMID:26283004
Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus. PMID:26275815
Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model. PMID:26238020
Orthology for comparative genomics in the mouse genome database. PMID:26223881
Parent-progeny sequencing indicates higher mutation rates in heterozygotes. PMID:26176923
A Phox2b BAC Transgenic Rat Line Useful for Understanding Respiratory Rhythm Generator Neural Circuitry. PMID:26147470
Conserved Noncoding Sequences Regulate lhx5 Expression in the Zebrafish Forebrain. PMID:26147098
The achaete-scute complex in Diptera: patterns of noncoding sequence evolution. PMID:26134680
Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome. PMID:26103589
Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome. PMID:26084764
The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis. PMID:26046631
Functional assessment of disease-associated regulatory variants in vivo using a versatile dual colour transgenesis strategy in zebrafish. PMID:26030420
An alignment-free method to find and visualise rearrangements between pairs of DNA sequences. PMID:25984837
Activity of the porcine gonadotropin-releasing hormone receptor gene promoter is partially conferred by a distal gonadotrope specific element (GSE) within an upstream enhancing region, two proximal GSEs and a retinoid X receptor binding site. PMID:25981521
Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum) and Comparative Analysis with Common Buckwheat (F. esculentum). PMID:25966355
A novel large deletion of the ICR1 region including H19 and putative enhancer elements. PMID:25943194
Expression of leukemia inhibitory factor in Müller glia cells is regulated by a redox-dependent mRNA stability mechanism. PMID:25907681
Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats. PMID:25887666
Molecular development of chondrichthyan claspers and the evolution of copulatory organs. PMID:25868783
Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. PMID:25862382
Deep sequencing reveals the complete genome and evidence for transcriptional activity of the first virus-like sequences identified in Aristotelia chilensis (Maqui Berry). PMID:25855242
The evolutionary origination and diversification of a dimorphic gene regulatory network through parallel innovations in cis and trans. PMID:25835988
Temporal regulation of HIF-1 and NF-κB in hypoxic hepatocarcinoma cells. PMID:25823824
Comparative and evolutionary analyses of Meloidogyne spp. Based on mitochondrial genome sequences. PMID:25799071
Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae. PMID:25774672
Nucleotide sequence conservation of novel and established cis-regulatory sites within the tyrosine hydroxylase gene promoter. PMID:25774193
The broad-spectrum antibiotic, zeamine, kills the nematode worm Caenorhabditis elegans. PMID:25767467
Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. PMID:25753587
Lhx4 deficiency: increased cyclin-dependent kinase inhibitor expression and pituitary hypoplasia. PMID:25668206
Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes. PMID:25658309
Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis. PMID:25648715
Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum. PMID:25635040
Full-genome sequencing of a Hungarian canine G3P[3] Rotavirus A strain reveals high genetic relatedness with a historic Italian human strain. PMID:25634124
Overlapping mouse subcongenic strains successfully separate two linked body fat QTL on distal MMU 2. PMID:25613955
Transcriptional control of an essential ribozyme in Drosophila reveals an ancient evolutionary divide in animals. PMID:25569672
Genomic perspectives of transcriptional regulation in forebrain development. PMID:25569346
Transcriptional, posttranscriptional, and posttranslational regulation of SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function in the shoot apex. PMID:25524441
Complete chloroplast genome of Macadamia integrifolia confirms the position of the Gondwanan early-diverging eudicot family Proteaceae. PMID:25522147
An integrative computational approach for prioritization of genomic variants. PMID:25506935
Genetics and timing of sex determination in the East African cichlid fish Astatotilapia burtoni. PMID:25494637
Regulation of tyrosine hydroxylase transcription by hnRNP K and DNA secondary structure. PMID:25493445
Human G3P[9] rotavirus strains possessing an identical genotype constellation to AU-1 isolated at high prevalence in Brazil, 1997-1999. PMID:25467218
Genome sequence comparison reveals a candidate gene involved in male-hermaphrodite differentiation in papaya (Carica papaya) trees. PMID:25416421
The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism. PMID:25409087
Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering. PMID:25365514
The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. PMID:25296686
Alignathon: a competitive assessment of whole-genome alignment methods. PMID:25273068
c-Rel regulates Ezh2 expression in activated lymphocytes and malignant lymphoid cells. PMID:25266721
Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians. PMID:25209999
LCK: a new biomarker candidate for the early diagnosis of acute myocardial infarction. PMID:25209966
Sp6 and Sp8 transcription factors control AER formation and dorsal-ventral patterning in limb development. PMID:25166858
An evaluation of the ecological relationship between Drosophila species and their parasitoid wasps as an opportunity for horizontal transposon transfer. PMID:25146840
An otx/nodal regulatory signature for posterior neural development in ascidians. PMID:25121599
Bacteriophage ϕMAM1, a viunalikevirus, is a broad-host-range, high-efficiency generalized transducer that infects environmental and clinical isolates of the enterobacterial genera Serratia and Kluyvera. PMID:25107968
Ancient nuclear plastid DNA in the yew family (taxaceae). PMID:25084786
Evolutionary relationship of disease resistance genes in soybean and Arabidopsis specific for the Pseudomonas syringae effectors AvrB and AvrRpm1. PMID:25034017
Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea. PMID:24999826
Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes. PMID:24968346
Identification of a transient Sox5 expressing progenitor population in the neonatal ventral forebrain by a novel cis-regulatory element. PMID:24954155
The genome of Eucalyptus grandis. PMID:24919147
Complete sequencing of IncI1 sequence type 2 plasmid pJIE512b indicates mobilization of blaCMY-2 from an IncA/C plasmid. PMID:24890591
GenomeVISTA--an integrated software package for whole-genome alignment and visualization. PMID:24860159
Complete Genome Sequence of the Highly Virulent Aeromonas hydrophila AL09-71 Isolated from Diseased Channel Catfish in West Alabama. PMID:24855300
The chloroplast genome of Hyoscyamus niger and a phylogenetic study of the tribe Hyoscyameae (Solanaceae). PMID:24851862
Genetic association study of adiposity and melanocortin-4 receptor (MC4R) common variants: replication and functional characterization of non-coding regions. PMID:24820477
Species-specific alternative splicing leads to unique expression of sno-lncRNAs. PMID:24734784
The Armc10/SVH gene: genome context, regulation of mitochondrial dynamics and protection against Aβ-induced mitochondrial fragmentation. PMID:24722288
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. PMID:24714809
The brain-uterus connection: brain derived neurotrophic factor (BDNF) and its receptor (Ntrk2) are conserved in the mammalian uterus. PMID:24714156
Cis-regulatory elements are harbored in Intron5 of the RUNX1 gene. PMID:24655352
Combined analysis of the chloroplast genome and transcriptome of the Antarctic vascular plant Deschampsia antarctica Desv. PMID:24647560
Identification of transcriptional regulatory elements for Ntng1 and Ntng2 genes in mice. PMID:24642214
The AtCathB3 gene, encoding a cathepsin B-like protease, is expressed during germination of Arabidopsis thaliana and transcriptionally repressed by the basic leucine zipper protein GBF1. PMID:24600022
hemingway is required for sperm flagella assembly and ciliary motility in Drosophila. PMID:24554765
Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome. PMID:24515595
The vertebrate RCAN gene family: novel insights into evolution, structure and regulation. PMID:24465593
Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f. PMID:24438474
Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription. PMID:24415943
Lampreys have a single gene cluster for the fast skeletal myosin heavy chain gene family. PMID:24376886
Complete mitochondrial genomes of chimpanzee- and gibbon-derived Ascaris isolated from a zoological garden in southwest China. PMID:24358225
Phylogenomics of fescue grass-derived fungal endophytes based on selected nuclear genes and the mitochondrial gene complement. PMID:24330497
Predicting plastid marker variation: can complete plastid genomes from closely related species help? PMID:24312409
NK4 antagonizes Tbx1/10 to promote cardiac versus pharyngeal muscle fate in the ascidian second heart field. PMID:24311985
Comparative genome analysis of Solanum lycopersicum and Solanum tuberosum. PMID:24307771
MycoCosm portal: gearing up for 1000 fungal genomes. PMID:24297253
Genomic, RNAseq, and molecular modeling evidence suggests that the major allergen domain in insects evolved from a homodimeric origin. PMID:24253356
Meis1 regulates Foxn4 expression during retinal progenitor cell differentiation. PMID:24244849
Plasticity of leukocytic exudates in resolving acute inflammation is regulated by MicroRNA and proresolving mediators. PMID:24238341
Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications. PMID:24205264
Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales. PMID:24205047
Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PMID:24204767
Immune-related functions of the Hivep gene family in East African cichlid fishes. PMID:24142922
Looking for CDKN1C enhancers. PMID:24129436
BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton. PMID:24116150
Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. PMID:24086142
SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics. PMID:24053737
Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). PMID:24043829
Regulation of MEIS1 by distal enhancer elements in acute leukemia. PMID:24022755
Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. PMID:23915326
CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae species. PMID:23898041
Expression and sequence evolution of aromatase cyp19a1 and other sexual development genes in East African cichlid fishes. PMID:23883521
Functional evolution of cis-regulatory modules of STMADS11 superclade MADS-box genes. PMID:23860795
Whole-transcriptome shotgun sequencing (RNA-seq) screen reveals upregulation of cellobiose and motility operons of Lactobacillus ruminis L5 during growth on tetrasaccharides derived from barley β-glucan. PMID:23851085
Heterogeneous conservation of Dlx paralog co-expression in jawed vertebrates. PMID:23840829
FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain. PMID:23826354
Genomic organisation of the seven ParaHox genes of coelacanths. PMID:23775937
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
Linking protective GAB2 variants, increased cortical GAB2 expression and decreased Alzheimer's disease pathology. PMID:23724096
Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia. PMID:23690750
Transcriptional repression of BODENLOS by HD-ZIP transcription factor HB5 in Arabidopsis thaliana. PMID:23682118
Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development. PMID:23674602
MicroRNA-22 and promoter motif polymorphisms at the Chga locus in genetic hypertension: functional and therapeutic implications for gene expression and the pathogenesis of hypertension. PMID:23674521
Candidate gene association studies: a comprehensive guide to useful in silico tools. PMID:23656885
Visualizing time-related data in biology, a review. PMID:23585583
Complete plastid genome sequencing of Trochodendraceae reveals a significant expansion of the inverted repeat and suggests a Paleogene divergence between the two extant species. PMID:23577110
Predicting the next eye pathogen: analysis of a novel adenovirus. PMID:23572555
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex. PMID:23550121
Pax6 regulates gene expression in the vertebrate lens through miR-204. PMID:23516376
The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PMID:23460883
Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants. PMID:23460871
STAT3 regulates arginase-I in myeloid-derived suppressor cells from cancer patients. PMID:23454751
Signaling between transforming growth factor β (TGF-β) and transcription factor SNAI2 represses expression of microRNA miR-203 to promote epithelial-mesenchymal transition and tumor metastasis. PMID:23447531
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. PMID:23435085
Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. PMID:23393190
Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences. PMID:23359656
Aging-induced dysregulation of dicer1-dependent microRNA expression impairs angiogenic capacity of rat cerebromicrovascular endothelial cells. PMID:23239824
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PMID:23236275
PGDD: a database of gene and genome duplication in plants. PMID:23180799
Gibberellins regulate the transcription of the continuous flowering regulator, RoKSN, a rose TFL1 homologue. PMID:23175671
A modified UPR stress sensing system reveals a novel tissue distribution of IRE1/XBP1 activity during normal Drosophila development. PMID:23160805
ARID1a-DNA interactions are required for promoter occupancy by SWI/SNF. PMID:23129809
Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits. PMID:23122416
Genome-wide identification of rice class I metallothionein gene: tissue expression patterns and induction in response to heavy metal stress. PMID:23053198
Mobilization of pathogenicity islands by Staphylococcus aureus strain Newman bacteriophages. PMID:23050217
BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border. PMID:23034628
Bacterial biosynthetic gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and anti-oomycete compound, oocydin A. PMID:23012376
Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes. PMID:23009612
Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome. PMID:23008801
Evolutionary history and genome organization of DUF1220 protein domains. PMID:22973535
Identification and characterization of orthologs of AtNHX5 and AtNHX6 in Brassica napus. PMID:22973287
Genetic and genomic toolbox of the chordate Ciona intestinalis. PMID:22964837
pEl1573 Carrying blaIMP-4, from Sydney, Australia, is closely related to other IncL/M plasmids. PMID:22926566
Genomic basis of a polyagglutinating isolate of Neisseria meningitidis. PMID:22904290
A cis-regulatory module upstream of deltaC regulated by Ntla and Tbx16 drives expression in the tailbud, presomitic mesoderm and somites. PMID:22877946
A web-based multi-genome synteny viewer for customized data. PMID:22856879
An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference. PMID:22851613
Promoter-specific expression and imprint status of marsupial IGF2. PMID:22848567
Evolution of the Cdk-activator Speedy/RINGO in vertebrates. PMID:22763696
Insertion-deletions in a FADS2 intron 1 conserved regulatory locus control expression of fatty acid desaturases 1 and 2 and modulate response to simvastatin. PMID:22748975
Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome. PMID:22747999
Definition of genetic events directing the development of distinct types of brain tumors from postnatal neural stem/progenitor cells. PMID:22719073
Evolution of coding and non-coding genes in HOX clusters of a marsupial. PMID:22708672
GenomeRing: alignment visualization based on SuperGenome coordinates. PMID:22689781
Expression of vernalization responsive genes in wheat is associated with histone H3 trimethylation. PMID:22684814
The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene. PMID:22681678
Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PMID:22606302
A regulatory potential of the Xist gene promoter in vole M. rossiaemeridionalis. PMID:22606223
Egr-1 induces DARPP-32 expression in striatal medium spiny neurons via a conserved intragenic element. PMID:22593050
Bmps and id2a act upstream of Twist1 to restrict ectomesenchyme potential of the cranial neural crest. PMID:22589745
Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease. PMID:22543974
Comparative analysis and visualization of multiple collinear genomes. PMID:22536897
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. PMID:22530965
Human invariant natural killer T cells acquire transient innate responsiveness via histone H4 acetylation induced by weak TCR stimulation. PMID:22508835
Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing. PMID:22482802
Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. PMID:22479192
Identification and analysis of conserved cis-regulatory regions of the MEIS1 gene. PMID:22448256
Expression of the central growth regulator BIG BROTHER is regulated by multiple cis-elements. PMID:22433627
Nuclear factor of activated T cells 1 (NFAT1)-induced permissive chromatin modification facilitates nuclear factor-κB (NF-κB)-mediated interleukin-9 (IL-9) transactivation. PMID:22427656
Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant. PMID:22403630
Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors. PMID:22323600
Highly divergent dimorphic alleles of the proteasome subunit beta type-8 (PSMB8) gene of the bichir Polypterus senegalus: implication for evolution of the PSMB8 gene of jawed vertebrates. PMID:22322674
Interleukin-1β modulates smooth muscle cell phenotype to a distinct inflammatory state relative to PDGF-DD via NF-κB-dependent mechanisms. PMID:22318995
Bioinformatics for personal genome interpretation. PMID:22247263
An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement. PMID:22234889
DNaseI hypersensitivity and ultraconservation reveal novel, interdependent long-range enhancers at the complex Pax6 cis-regulatory region. PMID:22220192
Circular DNA intermediate in the duplication of Nile tilapia vasa genes. PMID:22216289
IMG: the Integrated Microbial Genomes database and comparative analysis system. PMID:22194640
Modulation of auxin-binding protein 1 gene expression in maize and the teosintes by transposon insertions in its promoter. PMID:22187004
The Enhancer of split complex arose prior to the diversification of schizophoran flies and is strongly conserved between Drosophila and stalk-eyed flies (Diopsidae). PMID:22151427
Using Sybil for interactive comparative genomics of microbes on the web. PMID:22121156
The genome portal of the Department of Energy Joint Genome Institute. PMID:22110030
Phytozome: a comparative platform for green plant genomics. PMID:22110026
Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals. PMID:22103247
Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. PMID:22060816
A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PMID:22022263
Functional characterization of a genetic polymorphism in the promoter of the ESR2 gene. PMID:21979797
Sequencing and analysis of plastid genome in mycoheterotrophic orchid Neottia nidus-avis. PMID:21971517
RXRα and LXR activate two promoters in placenta- and tumor-specific expression of PLAC1. PMID:21937108
High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PMID:21931804
Genomic sequence around butterfly wing development genes: annotation and comparative analysis. PMID:21909358
Identification of a novel ZIC3 isoform and mutation screening in patients with heterotaxy and congenital heart disease. PMID:21858219
Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. PMID:21841803
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. PMID:21824423
Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs. PMID:21821017
GSV: a web-based genome synteny viewer for customized data. PMID:21810250
Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.). PMID:21799845
Characterization of the human SLC30A8 promoter and intronic enhancer. PMID:21798992
Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes. PMID:21794110
VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies. PMID:21791533
Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony. PMID:21779173
New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits. PMID:21767393
The Wnt3a/β-catenin target gene Mesogenin1 controls the segmentation clock by activating a Notch signalling program. PMID:21750544
Activation of Src and transformation by an RPTPα splice mutant found in human tumours. PMID:21725282
Predicting site-specific human selective pressure using evolutionary signatures. PMID:21685080
In silico characterization of the neural alpha tubulin gene promoter of the sea urchin embryo Paracentrotus lividus by phylogenetic footprinting. PMID:21678058
Functional dissection of the Oct6 Schwann cell enhancer reveals an essential role for dimeric Sox10 binding. PMID:21653862
Expression of miRNAs miR-133b and miR-206 in the Il17a/f locus is co-regulated with IL-17 production in αβ and γδ T cells. PMID:21637854
Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus. PMID:21629789
Rheumatoid arthritis-associated polymorphisms are not protective against Alzheimer's disease. PMID:21595938
Expansion of the Ago gene family in the teleost clade. PMID:21556854
Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. PMID:21518738
Replication and extension of association between common genetic variants in SIM1 and human adiposity. PMID:21512513
Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells. PMID:21486496
Rice-Map: a new-generation rice genome browser. PMID:21450055
SyMAP v3.4: a turnkey synteny system with application to plant genomes. PMID:21398631
Interleukin 12B (IL12B) genetic variation and pulmonary tuberculosis: a study of cohorts from The Gambia, Guinea-Bissau, United States and Argentina. PMID:21339808
A microRNA-dependent program controls p53-independent survival and chemosensitivity in human and murine squamous cell carcinoma. PMID:21293058
Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X. PMID:21282478
Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. PMID:21276790
Proliferation-associated POU4F2/Brn-3b transcription factor expression is regulated by oestrogen through ERα and growth factors via MAPK pathway. PMID:21241485
Differential expression and alternative splicing of rice sulphate transporter family members regulate sulphur status during plant growth, development and stress conditions. PMID:21221698
Plant noncoding RNA gene discovery by "single-genome comparative genomics". PMID:21220549
Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study. PMID:21177773
Genetic variation in the beta2 subunit of the voltage-gated calcium channel and pharmacogenetic association with adverse cardiovascular outcomes in the INternational VErapamil SR-Trandolapril STudy GENEtic Substudy (INVEST-GENES). PMID:21156931
Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. PMID:21056888
Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position. PMID:21047394
Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. PMID:20978766
Two lamprey Hedgehog genes share non-coding regulatory sequences and expression patterns with gnathostome Hedgehogs. PMID:20967201
The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer. PMID:20942803
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. PMID:20924354
The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS. PMID:20844019
Early B-cell factors are required for specifying multiple retinal cell types and subtypes from postmitotic precursors. PMID:20826655
Twist1 promotes heart valve cell proliferation and extracellular matrix gene expression during development in vivo and is expressed in human diseased aortic valves. PMID:20804746
Enhancers of GnRH transcription embedded in an upstream gene use homeodomain proteins to specify hypothalamic expression. PMID:20667983
Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli. PMID:20643337
Myoferlin regulation by NFAT in muscle injury, regeneration and repair. PMID:20571050
Regulation of odor receptor genes in trichoid sensilla of the Drosophila antenna. PMID:20551440
Comparison of homoeolocus organisation in paired BAC clones from white clover (Trifolium repens L.) and microcolinearity with model legume species. PMID:20492736
cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. PMID:20472817
The SNF2H chromatin remodeling enzyme has opposing effects on cytokine gene expression. PMID:20471682
Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. PMID:20471290
Detecting genomic islands using bioinformatics approaches. PMID:20395967
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PMID:20386746
LEF1/beta-catenin complex regulates transcription of the Cav3.1 calcium channel gene (Cacna1g) in thalamic neurons of the adult brain. PMID:20371816
Promoters of the barley germin-like GER4 gene cluster enable strong transgene expression in response to pathogen attack. PMID:20305123
A downstream intergenic cluster of regulatory enhancers contributes to the induction of CYP24A1 expression by 1alpha,25-dihydroxyvitamin D3. PMID:20236932
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon. PMID:20205726
Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication. PMID:20170488
Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements. PMID:20169179
Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. PMID:20139301
Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity. PMID:20122262
Periostin shows increased evolutionary plasticity in its alternatively spliced region. PMID:20109226
A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. PMID:20059953
BMP4 induction of trophoblast from mouse embryonic stem cells in defined culture conditions on laminin. PMID:20033790
Genome-wide profiling of populus small RNAs. PMID:20021695
Association of a functional microsatellite within intron 1 of the BMP5 gene with susceptibility to osteoarthritis. PMID:20021689
Mobile antibiotic resistance encoding elements promote their own diversity. PMID:20019796
A FOXA1-binding enhancer regulates Hoxb13 expression in the prostate gland. PMID:20018680
Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PMID:19956538
Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins. PMID:19951405
delta-EF1 is a negative regulator of Ihh in the developing growth plate. PMID:19948490
Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines. PMID:19917140
Genetic variation in the NBS1, MRE11, RAD50 and BLM genes and susceptibility to non-Hodgkin lymphoma. PMID:19917125
Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. PMID:19893611
Requirement for the basic helix-loop-helix transcription factor Dec2 in initial TH2 lineage commitment. PMID:19881507
The integrated microbial genomes system: an expanding comparative analysis resource. PMID:19864254
CD69 gene is differentially regulated in T and B cells by evolutionarily conserved promoter-distal elements. PMID:19841192
Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes. PMID:19805301
Extensive structural renovation of retrogenes in the evolution of the Populus genome. PMID:19789289
Prediction and identification of tumor-specific noncoding RNAs from human UniGene. PMID:19757216
Alpha-fetoprotein related gene (ARG): a new member of the albumin gene family that is no longer functional in primates. PMID:19733224
Common variants in FLNB/CRTAP, not ARHGEF3 at 3p, are associated with osteoporosis in southern Chinese women. PMID:19727905
Comparative genomics of chondrichthyan Hoxa clusters. PMID:19725973
Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. PMID:19675151
Systemic acquired resistance in soybean is regulated by two proteins, Orthologous to Arabidopsis NPR1. PMID:19656407
Copy number variation influences gene expression and metabolic traits in mice. PMID:19648292
Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. PMID:19602626
Identification of regulatory elements in the Isl1 gene locus. PMID:19598113
Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate. PMID:19596448
Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years. PMID:19583854
Evolution of developmental regulation in the vertebrate FgfD subfamily. PMID:19562753
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. PMID:19561337
Reliable means of diagnosis and serovar determination of blood-borne Salmonella strains: quick PCR amplification of unique genomic loci by novel primer sets. PMID:19535522
Genome-wide analysis of conservation and divergence of microsatellites in rice. PMID:19484264
EDGAR: a software framework for the comparative analysis of prokaryotic genomes. PMID:19457249
Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster. PMID:19451167
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
Comparative genomic analysis of the major histocompatibility complex class I region in the teleost genus Oryzias. PMID:19350233
Transient and transgenic analysis of the zebrafish ventricular myosin heavy chain (vmhc) promoter: an inhibitory mechanism of ventricle-specific gene expression. PMID:19322764
Gene targeting in mouse embryonic stem cells. PMID:19266325
Longevity is associated with increased vascular resistance to high glucose-induced oxidative stress and inflammatory gene expression in Peromyscus leucopus. PMID:19181967
Identification of direct T-box target genes in the developing zebrafish mesoderm. PMID:19158186
Genetic association study for RSV bronchiolitis in infancy at the 5q31 cytokine cluster. PMID:19131452
Giant panda genomic data provide insight into the birth-and-death process of mammalian major histocompatibility complex class II genes. PMID:19127303
Pleiotropic effects in Eya3 knockout mice. PMID:19102749
Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. PMID:19098269
Temporal regulation of Ath5 gene expression during eye development. PMID:19059393
A bioinformatician's guide to metagenomics. PMID:19052320
FoxF1 and FoxL1 link hedgehog signaling and the control of epithelial proliferation in the developing stomach and intestine. PMID:19049965
Conserved genomic structure of the Cyp1a1 and Cyp1a2 loci and their dioxin responsive elements cluster. PMID:19026991
Identification and characterization of new long conserved noncoding sequences in vertebrates. PMID:19015917
Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics. PMID:19003267
Differential gene expression in a coculture model of angiogenesis reveals modulation of select pathways and a role for Notch signaling. PMID:18984672
Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2. PMID:18980692
BRG1-mediated chromatin remodeling regulates differentiation and gene expression of T helper cells. PMID:18852284
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. PMID:18845571
BOV--a web-based BLAST output visualization tool. PMID:18793422
Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans. PMID:18789808
Cyclic AMP-induced chromatin changes support the NFATc-mediated recruitment of GATA-3 to the interleukin 5 promoter. PMID:18772129
Evolution of ventricular myocyte electrophysiology. PMID:18765860
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. PMID:18753151
Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies. PMID:18647405
Hormonal regulation of cardiac KCNE2 gene expression. PMID:18611433
Loss of the transmembrane but not the soluble kit ligand isoform increases testicular germ cell tumor susceptibility in mice. PMID:18593919
A broad analysis of IL1 polymorphism and rheumatoid arthritis. PMID:18576312
Genomic investigation of alpha-synuclein multiplication and parkinsonism. PMID:18571778
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. PMID:18562680
The evolution of the DLK1-DIO3 imprinted domain in mammals. PMID:18532878
Comparative in silico analysis identifies bona fide MyoD binding sites within the Myocyte stress 1 gene promoter. PMID:18489770
Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum. PMID:18488228
Genomic imprinting of IGF2 in marsupials is methylation dependent. PMID:18454865
Laboratory strains of murine cytomegalovirus are genetically similar to but phenotypically distinct from wild strains of virus. PMID:18417589
Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression. PMID:18385377
Chromosomal regions 22q13 and 3p25 may harbor quantitative trait loci influencing both age at menarche and bone mineral density. PMID:18379822
PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes. PMID:18366802
Genomic analysis of Ovis aries (Ovar) MHC class IIa loci. PMID:18322680
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. PMID:18282510
Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence. PMID:18282108
Growth hormone regulation of insulin-like growth factor-I gene expression may be mediated by multiple distal signal transducer and activator of transcription 5 binding sites. PMID:18276757
Natural variation in four human collagen genes across an ethnically diverse population. PMID:18272325
Genetic analysis of chromosome 20-related posterior polymorphous corneal dystrophy: genetic heterogeneity and exclusion of three candidate genes. PMID:18253095
TINF2, a component of the shelterin telomere protection complex, is mutated in dyskeratosis congenita. PMID:18252230
Analysis of the Otd-dependent transcriptome supports the evolutionary conservation of CRX/OTX/OTD functions in flies and vertebrates. PMID:18241855
An enhancer 20 kilobases upstream of the human receptor activator of nuclear factor-kappaB ligand gene mediates dominant activation by 1,25-dihydroxyvitamin D3. PMID:18202151
mef2 activity levels differentially affect gene expression during Drosophila muscle development. PMID:18198273
Widespread genetic incompatibility in C. elegans maintained by balancing selection. PMID:18187622
A novel promoter-tethering element regulates enhancer-driven gene expression at the bithorax complex in the Drosophila embryo. PMID:18045839
TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. PMID:18045502
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. PMID:17986450
Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. PMID:17986329
Structural and functional analysis of the human TAF1/DYT3 multiple transcript system. PMID:17952504
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. PMID:17945028
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782
Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. PMID:17880721
Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species. PMID:17875208
Localization and regulation of mouse pantothenate kinase 2. PMID:17825826
Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer. PMID:17823307
Characterization of the equine 2'-5' oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes. PMID:17822564
Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar). PMID:17651474
Identification of 9 uterine genes that are regulated during mouse pregnancy and exhibit abnormal levels in the cyclooxygenase-1 knockout mouse. PMID:17617897
Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain. PMID:17617896
Ancestral European roots of Helicobacter pylori in India. PMID:17584914
Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages. PMID:17570149
Blueprint for a high-performance biomaterial: full-length spider dragline silk genes. PMID:17565367
Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction. PMID:17559649
Alternative promoters and repetitive DNA elements define the species-dependent tissue-specific expression of the FMO1 genes of human and mouse. PMID:17547558
PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes. PMID:17535443
Single nucleotide polymorphism discovery and haplotype analysis of Ca2+-dependent K+ channel beta-1 subunit. PMID:17496725
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. PMID:17488840
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. PMID:17460045
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes. PMID:17428321
Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. PMID:17395715
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. PMID:17374142
Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements. PMID:17362514
Conserved elements within first intron of aquaporin-5 (Aqp5) function as transcriptional enhancers. PMID:17339032
Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. PMID:17310332
Early embryonic lethality of mice lacking the essential protein SNEV. PMID:17283042
Enhancer identification through comparative genomics. PMID:17276707
GenomeBlast: a web tool for small genome comparison. PMID:17217510
The UBX-regulated network in the haltere imaginal disc of D. melanogaster. PMID:17174297
Identification of long-range regulatory elements in the protocadherin-alpha gene cluster. PMID:17172445
Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss. PMID:17146045
RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. PMID:17142223
Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. PMID:17135569
VISTA Enhancer Browser--a database of tissue-specific human enhancers. PMID:17130149
SwissRegulon: a database of genome-wide annotations of regulatory sites. PMID:17130146
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. PMID:17062155
Genome heterogeneity of SA11 rotavirus due to reassortment with "O" agent. PMID:17059839
Generalized genomic distance-based regression methodology for multilocus association analysis. PMID:17033957
Family-based association study of matrix metalloproteinase-3 and -9 haplotypes with susceptibility to ischemic white matter injury. PMID:17024375
Spreading and mutability of Selenomonas ruminantium plasmids. PMID:17007426
Genetic analysis of the GRIK2 modifier effect in Huntington's disease. PMID:16959037
Patterns of association between PPARgamma genetic variation and indices of adiposity and insulin action in African-Americans and whites: the CARDIA Study. PMID:16955276
Sequence conservation of homeologous bacterial artificial chromosomes and transcription of homeologous genes in soybean (Glycine max L. Merr.). PMID:16888343
Primate-specific evolution of an LDLR enhancer. PMID:16884525
Computational identification of transcriptional regulatory elements in DNA sequence. PMID:16855295
Breakup of a homeobox cluster after genome duplication in teleosts. PMID:16801555
Close sequence comparisons are sufficient to identify human cis-regulatory elements. PMID:16769978
Polymorphisms of the low-density lipoprotein receptor-related protein 5 (LRP5) gene are associated with obesity phenotypes in a large family-based association study. PMID:16723389
MicroRNA enrichment among short 'ultraconserved' sequences in insects. PMID:16698958
Promoter mutations that increase amyloid precursor-protein expression are associated with Alzheimer disease. PMID:16685645
A periodic pattern of mRNA secondary structure created by the genetic code. PMID:16682450
Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters. PMID:16636282
Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PMID:16609730
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. PMID:16509994
Long-term persistence of both functional and non-functional alleles at the leukocyte immunoglobulin-like receptor A3 (LILRA3) locus suggests balancing selection. PMID:16501917
Bone morphogenetic protein-2 induces proinflammatory endothelial phenotype. PMID:16436676
A novel approach to identifying regulatory motifs in distantly related genomes. PMID:16420672
Altered RNA editing in mice lacking ADAR2 autoregulation. PMID:16382140
DBTGR: a database of tunicate promoters and their regulatory elements. PMID:16381930
The integrated microbial genomes (IMG) system. PMID:16381883
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy. PMID:16336695
Tools and strategies for physiological genomics: the Rat Genome Database. PMID:16106031
Genomic multiple sequence alignments: refinement using a genetic algorithm. PMID:16086841
Progressive proximal expansion of the primate X chromosome centromere. PMID:16030148
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. PMID:16024824
Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. PMID:16011797
SVC: structured visualization of evolutionary sequence conservation. PMID:15991338
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. PMID:15790396
The DNA sequence of the human X chromosome. PMID:15772651
VISTA Enhancer Browser--a database of tissue-specific human enhancers PubMed citations: 513.

513 articles citing: VISTA Enhancer Browser--a database of tissue-specific human enhancers

GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data. PMID:35234913
Mouse genomic and cellular annotations. PMID:35124726
Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome. PMID:35027568
Epigenome rewiring in human pluripotent stem cells. PMID:34955367
Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development. PMID:34942352
Transgenic Model Systems Have Revolutionized the Study of Disease. PMID:34941457
Evolving features of human cortical development and the emerging roles of non-coding RNAs in neural progenitor cell diversity and function. PMID:34921638
Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing. PMID:34913122
A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses. PMID:34906355
Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer. PMID:34903763
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era. PMID:34827709
SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning. PMID:34822715
Quantitative spatial and temporal assessment of regulatory element activity in zebrafish. PMID:34796872
Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals. PMID:34784928
A single-cell atlas of chromatin accessibility in the human genome. PMID:34774128
Perfect and imperfect views of ultraconserved sequences. PMID:34764456
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. PMID:34761274
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance. PMID:34663447
From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries. PMID:34659337
Many chronological aging clocks can be found throughout the epigenome: Implications for quantifying biological aging. PMID:34655509
An atlas of gene regulatory elements in adult mouse cerebrum. PMID:34616068
Single-cell epigenomics reveals mechanisms of human cortical development. PMID:34616060
Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development. PMID:34584102
Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients. PMID:34502260
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. PMID:34491989
lncExplore: a database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data. PMID:34464437
The bowfin genome illuminates the developmental evolution of ray-finned fishes. PMID:34462605
Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. PMID:34446581
Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. PMID:34410491
A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome. PMID:34356064
Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH. PMID:34326544
Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective. PMID:34276769
Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. PMID:34256850
Tissue-specific 5-hydroxymethylcytosine landscape of the human genome. PMID:34253716
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. PMID:34252960
Untangling the genetic link between type 1 and type 2 diabetes using functional genomics. PMID:34230558
Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions. PMID:34197622
Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. PMID:34159315
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. PMID:34021236
Cardiac cell type-specific gene regulatory programs and disease risk association. PMID:33990324
Microdeletion of 9q22.3: A patient with minimal deletion size associated with a severe phenotype. PMID:33960642
Fish-Ing for Enhancers in the Heart. PMID:33920121
Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid. PMID:33915225
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. PMID:33888138
The cis-regulatory effects of modern human-specific variants. PMID:33885362
A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. PMID:33850120
A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures. PMID:33849996
hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context. PMID:33824393
Heart Enhancers: Development and Disease Control at a Distance. PMID:33777110
Neuronal enhancers are hotspots for DNA single-strand break repair. PMID:33767446
HAND transcription factors cooperatively specify the aorta and pulmonary trunk. PMID:33757801
Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases. PMID:33747049
Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning. PMID:33686085
An intriguing characteristic of enhancer-promoter interactions. PMID:33685407
Identification of Novel Genetic Regulatory Region for Proprotein Convertase FURIN and Interferon Gamma in T Cells. PMID:33679774
Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers. PMID:33655411
Comprehensive analysis of single cell ATAC-seq data with SnapATAC. PMID:33637727
Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells. PMID:33623376
Annotation of chromatin states in 66 complete mouse epigenomes during development. PMID:33619351
CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues. PMID:33583425
3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders. PMID:33545232
Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. PMID:33531684
Dbx2 regulation in limbs suggests interTAD sharing of enhancers. PMID:33497014
Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression. PMID:33478249
Giant lungfish genome elucidates the conquest of land by vertebrates. PMID:33461212
Enhancer redundancy in development and disease. PMID:33442000
intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data. PMID:33372591
PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence. PMID:33320871
Cell-Type-Specific Gene Regulatory Networks Underlying Murine Neonatal Heart Regeneration at Single-Cell Resolution. PMID:33296652
Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. PMID:33263113
A map of cis-regulatory elements and 3D genome structures in zebrafish. PMID:33239788
Genome-wide association study identifies 16 genomic regions associated with circulating cytokines at birth. PMID:33227023
Prioritizing long range interactions in noncoding regions using GWAS and deletions perturbed TADs. PMID:33209206
dbCNS: A New Database for Conserved Noncoding Sequences. PMID:33196844
Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles. PMID:33193605
A human cell atlas of fetal chromatin accessibility. PMID:33184180
Ensembl 2021. PMID:33137190
VARAdb: a comprehensive variation annotation database for human. PMID:33095866
Analyzing a putative enhancer of optic disc morphology. PMID:33092545
Cell-type-specific 3D epigenomes in the developing human cortex. PMID:33057195
SilencerDB: a comprehensive database of silencers. PMID:33045745
A survey on deep learning in DNA/RNA motif mining. PMID:33005921
Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart. PMID:32993371
Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. PMID:32991838
Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty. PMID:32986727
Tamoxifen-inducible cardiac-specific Cre transgenic mouse using VIPR2 intron. PMID:32983955
Interpreting the impact of noncoding structural variation in neurodevelopmental disorders. PMID:32973355
In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes-Associated Single Nucleotide Polymorphisms. PMID:32912862
NeuroLab Research Experiences: Extending the CURE Design Framework into an Informal Science Setting Dedicated to Pre-College STEM Instruction. PMID:32832882
Enhancer evolutionary co-option through shared chromatin accessibility input. PMID:32778581
Preclinical evidence for the therapeutic value of TBX5 normalization in arrhythmia control. PMID:32777030
Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis. PMID:32772801
Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates. PMID:32747566
Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants. PMID:32732423
The changing mouse embryo transcriptome at whole tissue and single-cell resolution. PMID:32728245
Spatiotemporal DNA methylome dynamics of the developing mouse fetus. PMID:32728242
An atlas of dynamic chromatin landscapes in mouse fetal development. PMID:32728240
Epigenetic and Transcriptional Networks Underlying Atrial Fibrillation. PMID:32717170
Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers That Drive Differentiation of Pancreatic Cells. PMID:32655276
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. PMID:32637041
DNA methylation and hydroxymethylation have distinct genome-wide profiles related to axonal regeneration. PMID:32633672
A Chromatin Accessibility Atlas of the Developing Human Telencephalon. PMID:32610082
Mapping and characterization of structural variation in 17,795 human genomes. PMID:32460305
EpiRegio: analysis and retrieval of regulatory elements linked to genes. PMID:32459338
Progress, Challenges, and Surprises in Annotating the Human Genome. PMID:32421357
A statistical framework for predicting critical regions of p53-dependent enhancers. PMID:32392580
Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate. PMID:32318854
Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia. PMID:32303558
Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits. PMID:32268095
Loss-of-function tolerance of enhancers in the human genome. PMID:32243438
Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies. PMID:32238901
Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction. PMID:32226593
Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants. PMID:32169219
Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. PMID:32094912
Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease. PMID:32032514
GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling. PMID:31989924
Towards a comprehensive catalogue of validated and target-linked human enhancers. PMID:31988385
Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. PMID:31988093
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. PMID:31978042
Chromatin accessibility dynamics in a model of human forebrain development. PMID:31974223
A Pretraining-Retraining Strategy of Deep Learning Improves Cell-Specific Enhancer Predictions. PMID:31969903
A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome. PMID:31956652
Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation. PMID:31943068
The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13. PMID:31896583
A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia. PMID:31891018
Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs. PMID:31856658
Genetic and Epigenetic Control of Heart Development. PMID:31818853
Recapitulation-like developmental transitions of chromatin accessibility in vertebrates. PMID:31807314
Interrogating the Grainyhead-like 2 (Grhl2) genomic locus identifies an enhancer element that regulates palatogenesis in mouse. PMID:31782997
Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant. PMID:31773361
Ranking of non-coding pathogenic variants and putative essential regions of the human genome. PMID:31748530
EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. PMID:31740966
The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension. PMID:31719172
UCSC Genome Browser enters 20th year. PMID:31691824
Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets. PMID:31682597
Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model. PMID:31672653
ENdb: a manually curated database of experimentally supported enhancers for human and mouse. PMID:31665430
A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers. PMID:31659164
Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. PMID:31631012
Identification of atrial fibrillation associated genes and functional non-coding variants. PMID:31628324
Organoid single-cell genomic atlas uncovers human-specific features of brain development. PMID:31619793
Contribution of retrotransposition to developmental disorders. PMID:31604926
Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development. PMID:31591447
Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf. PMID:31533979
Bioinformatics Discovery of Putative Enhancers within Mouse Odorant Receptor Gene Clusters. PMID:31529021
Genomic architecture of Shh-dependent cochlear morphogenesis. PMID:31488567
MPRAnalyze: statistical framework for massively parallel reporter assays. PMID:31477158
Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development. PMID:31417368
Whole genome and transcriptome sequencing of post-mortem cardiac tissues from sudden cardiac death victims identifies a gene regulatory variant in NEXN. PMID:31392414
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. PMID:31367015
Computational Biology Solutions to Identify Enhancers-target Gene Pairs. PMID:31316726
Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation. PMID:31307522
Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea. PMID:31227770
Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function. PMID:31221079
On the traces of tcf12: Investigation of the gene expression pattern during development and cranial suture patterning in zebrafish (Danio rerio). PMID:31188878
Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification. PMID:31127120
RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants. PMID:31106382
Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers. PMID:31080136
Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver. PMID:31067820
Chromatin Conformation Links Putative Enhancers in Intracranial Aneurysm-Associated Regions to Potential Candidate Genes. PMID:30994044
Improved Prediction of Regulatory Element Using Hybrid Abelian Complexity Features with DNA Sequences. PMID:30959806
Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. PMID:30944857
Trim33 is required for appropriate development of pre-cardiogenic mesoderm. PMID:30940539
Predicting enhancers in mammalian genomes using supervised hidden Markov models. PMID:30917778
Hoxa13 regulates expression of common Hox target genes involved in cartilage development to coordinate the expansion of the autopodal anlage. PMID:30895612
Enhancer and super-enhancer: Positive regulators in gene transcription. PMID:30891562
ClinTAD: a tool for copy number variant interpretation in the context of topologically associated domains. PMID:30765865
Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain, Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele. PMID:30765420
Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers. PMID:30753279
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. PMID:30737237
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. PMID:30727967
Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. PMID:30696717
EnhancerDB: a resource of transcriptional regulation in the context of enhancers. PMID:30689845
RAEdb: a database of enhancers identified by high-throughput reporter assays. PMID:30624654
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. PMID:30612741
Functional characterization of the ZEB2 regulatory landscape. PMID:30590588
GWAS Identifies Risk Locus for Erectile Dysfunction and Implicates Hypothalamic Neurobiology and Diabetes in Etiology. PMID:30583798
Association of low-frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts. PMID:30582786
High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human. PMID:30568279
Insertional translocation involving an additional nonchromothriptic chromosome in constitutional chromothripsis: Rule or exception? PMID:30565424
The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental Disorders. PMID:30563709
Dichotomy in redundant enhancers points to presence of initiators of gene regulation. PMID:30563465
TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression. PMID:30538121
Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome. PMID:30524473
Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. PMID:30503521
Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development. PMID:30478328
A neuronal enhancer network upstream of MEF2C is compromised in patients with Rett-like characteristics. PMID:30445463
CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs. PMID:30423099
CNEFinder: finding conserved non-coding elements in genomes. PMID:30423090
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. PMID:30413698
Nervous System Regionalization Entails Axial Allocation before Neural Differentiation. PMID:30343898
Characterization of cis-regulatory elements for Fgf10 expression in the chick embryo. PMID:30325084
An intronic genetic variation of MGMT affects enhancer activity and is associated with glioma susceptibility. PMID:30310321
NG2 expression in NG2 glia is regulated by binding of SoxE and bHLH transcription factors to a Cspg4 intronic enhancer. PMID:30306660
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PMID:30286077
HACER: an atlas of human active enhancers to interpret regulatory variants. PMID:30247654
Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. PMID:30224808
Genomic analysis of transcriptional networks directing progression of cell states during MGE development. PMID:30217225
Enhancer reprogramming in mammalian genomes. PMID:30200877
Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. PMID:30183087
Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation. PMID:30139328
Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. PMID:30137428
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals. PMID:30137416
Genome-wide Identification and Characterization of Enhancers Across 10 Human Tissues. PMID:30123079
Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver. PMID:30069000
Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. PMID:30014848
A promoter interaction map for cardiovascular disease genetics. PMID:29988018
Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks. PMID:29955040
VRTN is Required for the Development of Thoracic Vertebrae in Mammals. PMID:29904281
GWAS reveals loci associated with velopharyngeal dysfunction. PMID:29855589
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods. PMID:29855387
Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes. PMID:29805044
Towards a map of cis-regulatory sequences in the human genome. PMID:29733395
High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. PMID:29719267
An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. PMID:29700473
Mapping genetic variants for cranial vault shape in humans. PMID:29698431
PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition. PMID:29643364
iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization. PMID:29621297
Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. PMID:29618048
Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population. PMID:29608725
Genetic susceptibility to neuroblastoma: current knowledge and future directions. PMID:29589100
De novo mutations in regulatory elements in neurodevelopmental disorders. PMID:29562236
Mapping of Human FOXP2 Enhancers Reveals Complex Regulation. PMID:29515369
An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data. PMID:29514626
Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. PMID:29491135
Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors. PMID:29440260
Lineage specific transcription factors and epigenetic regulators mediate TGFβ-dependent enhancer activation. PMID:29438503
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. PMID:29434377
Enhancer redundancy provides phenotypic robustness in mammalian development. PMID:29420474
Phenotypic interpretation of complex chromosomal rearrangements informed by nucleotide-level resolution and structural organization of chromatin. PMID:29321672
The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. PMID:29307494
Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice. PMID:29301908
Regulatory variants of FOXG1 in the context of its topological domain organisation. PMID:29289958
Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. PMID:29280435
PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets. PMID:29273440
Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains. PMID:29269730
Multiple enhancer regions govern the transcription of CCN2 during embryonic development. PMID:29256171
Noncoding copy-number variations are associated with congenital limb malformation. PMID:29236091
Multiethnic GWAS Reveals Polygenic Architecture of Earlobe Attachment. PMID:29198719
Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience. PMID:29183403
Software for rapid time dependent ChIP-sequencing analysis (TDCA). PMID:29178831
Conserved non-coding elements: developmental gene regulation meets genome organization. PMID:29121339
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. PMID:29106417
The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. PMID:29096072
Appendages and gene regulatory networks: Lessons from the limbless. PMID:29076617
DiseaseEnhancer: a resource of human disease-associated enhancer catalog. PMID:29059320
Genomic Patterns of De Novo Mutation in Simplex Autism. PMID:28965761
A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree. PMID:28952437
Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog). PMID:28846100
Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PMID:28827824
Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. PMID:28735859
Short DNA sequence patterns accurately identify broadly active human enhancers. PMID:28716036
Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits. PMID:28683716
Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development. PMID:28633494
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. PMID:28605766
Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers. PMID:28589862
HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development. PMID:28538179
Perspectives on Gene Regulatory Network Evolution. PMID:28528721
An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. PMID:28506242
Comparative transcriptomics in human and mouse. PMID:28479595
Associations of the Intellectual Disability Gene MYT1L with Helix-Loop-Helix Gene Expression, Hippocampus Volume and Hippocampus Activation During Memory Retrieval. PMID:28470180
Cytosine modifications modulate the chromatin architecture of transcriptional enhancers. PMID:28396520
Potential energy landscapes identify the information-theoretic nature of the epigenome. PMID:28346445
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. PMID:28332981
Improved regulatory element prediction based on tissue-specific local epigenomic signatures. PMID:28193886
eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis. PMID:28161522
New insights from GWAS for the cleft palate among han Chinese population. PMID:28160584
Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq. PMID:28121289
Chromatin dynamics regulate mesenchymal stem cell lineage specification and differentiation to osteogenesis. PMID:28077316
Editing the Neuronal Genome: a CRISPR View of Chromatin Regulation in Neuronal Development, Function, and Plasticity. PMID:28018138
A regulatory sequence from the retinoid X receptor γ gene directs expression to horizontal cells and photoreceptors in the embryonic chicken retina. PMID:28003731
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. PMID:27980086
Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13. PMID:27974206
EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm. PMID:27929098
Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. PMID:27923844
Determinants of orofacial clefting II: Effects of 5-Aza-2'-deoxycytidine on gene methylation during development of the first branchial arch. PMID:27923600
Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data. PMID:27887606
Genomic approaches to the assessment of human spina bifida risk. PMID:27883265
The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances. PMID:27867070
Progressive Loss of Function in a Limb Enhancer during Snake Evolution. PMID:27768887
Formation of new chromatin domains determines pathogenicity of genomic duplications. PMID:27706140
Genome-wide compendium and functional assessment of in vivo heart enhancers. PMID:27703156
Identifying candidate genes for 2p15p16.1 microdeletion syndrome using clinical, genomic, and functional analysis. PMID:27699255
An Ultraconserved Brain-Specific Enhancer Within ADGRL3 (LPHN3) Underpins Attention-Deficit/Hyperactivity Disorder Susceptibility. PMID:27692237
LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines. PMID:27662487
Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring. PMID:27609221
ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells. PMID:27582018
EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. PMID:27515742
Variants in CCL16 are associated with blood plasma and cerebrospinal fluid CCL16 protein levels. PMID:27357396
Genome-wide association study of prolactin levels in blood plasma and cerebrospinal fluid. PMID:27357110
A unique stylopod patterning mechanism by Shox2-controlled osteogenesis. PMID:27287812
IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation. PMID:27282637
Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells. PMID:27197220
Molecular characterization of NRXN1 deletions from 19,263 clinical microarray cases identifies exons important for neurodevelopmental disease expression. PMID:27195815
Evaluation of IRX Genes and Conserved Noncoding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis. PMID:27172222
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
Origin and evolution of developmental enhancers in the mammalian neocortex. PMID:27114548
Jointly characterizing epigenetic dynamics across multiple human cell types. PMID:27095202
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. PMID:27089393
Systematic identification of gene family regulators in mouse and human embryonic stem cells. PMID:27084933
Cis-regulatory architecture of a brain signaling center predates the origin of chordates. PMID:27064252
Distinct epigenetic signatures elucidate enhancer-gene relationships that delineate CIMP and non-CIMP colorectal cancers. PMID:27049830
A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types. PMID:26999799
Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters. PMID:26957309
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. PMID:26950095
Active DNA demethylation at enhancers during the vertebrate phylotypic period. PMID:26928226
Early developmental gene enhancers affect subcortical volumes in the adult human brain. PMID:26890892
Ensembl regulation resources. PMID:26888907
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. PMID:26888867
Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome. PMID:26861146
The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. PMID:26808208
Role of non-coding sequence variants in cancer. PMID:26781813
Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor. PMID:26715627
Genetic Regulation of Sinoatrial Node Development and Pacemaker Program in the Venous Pole. PMID:26682210
Progress and challenges in bioinformatics approaches for enhancer identification. PMID:26634919
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Hemichordate genomes and deuterostome origins. PMID:26580012
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
EMERGE: a flexible modelling framework to predict genomic regulatory elements from genomic signatures. PMID:26531828
CEGA--a catalog of conserved elements from genomic alignments. PMID:26527719
Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PMID:26505748
MEPD: medaka expression pattern database, genes and more. PMID:26450962
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus. PMID:26443638
Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes. PMID:26439399
Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality. PMID:26411685
Sequential Binding of MEIS1 and NKX2-5 on the Popdc2 Gene: A Mechanism for Spatiotemporal Regulation of Enhancers during Cardiogenesis. PMID:26411676
Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. PMID:26382291
Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. PMID:26365491
DENdb: database of integrated human enhancers. PMID:26342387
Activation of Six1 Expression in Vertebrate Sensory Neurons. PMID:26313368
A shift in anterior-posterior positional information underlies the fin-to-limb evolution. PMID:26283004
Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. PMID:26257179
The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape. PMID:26253316
The frequent evolutionary birth and death of functional promoters in mouse and human. PMID:26228054
A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells. PMID:26169177
A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PMID:26131856
Comprehensive identification and analysis of human accelerated regulatory DNA. PMID:26104583
CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus. PMID:26100672
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. PMID:25984238
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. PMID:25972927
Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. PMID:25959816
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. PMID:25959774
ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. PMID:25916854
Human gene-centered transcription factor networks for enhancers and disease variants. PMID:25910213
Widespread macromolecular interaction perturbations in human genetic disorders. PMID:25910212
Long-range regulatory interactions at the 4q25 atrial fibrillation risk locus involve PITX2c and ENPEP. PMID:25888893
The ensembl regulatory build. PMID:25887522
A distinct regulatory region of the Bmp5 locus activates gene expression following adult bone fracture or soft tissue injury. PMID:25886903
The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers. PMID:25857663
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. PMID:25849986
Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. PMID:25791631
Replication of 13q31.1 association in nonsyndromic cleft lip with cleft palate in Europeans. PMID:25786657
Spectacle: fast chromatin state annotation using spectral learning. PMID:25786205
A diverse epigenetic landscape at human exons with implication for expression. PMID:25765649
Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study. PMID:25765133
Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis. PMID:25745175
Identifying transcriptional cis-regulatory modules in animal genomes. PMID:25704908
A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD). PMID:25701871
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. PMID:25697895
Integrative analysis of haplotype-resolved epigenomes across human tissues. PMID:25693566
Intermediate DNA methylation is a conserved signature of genome regulation. PMID:25691127
Genomic perspectives of transcriptional regulation in forebrain development. PMID:25569346
A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. PMID:25569170
Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. PMID:25564442
Identification and computational analysis of gene regulatory elements. PMID:25561628
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs. PMID:25547756
Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain. PMID:25539921
A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential. PMID:25512558
An integrative computational approach for prioritization of genomic variants. PMID:25506935
An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. PMID:25493341
Histone H3 K27 acetylation marks a potent enhancer element on the adipogenic master regulator gene Pparg2. PMID:25485585
HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme. PMID:25453830
GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. PMID:25428361
Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells. PMID:25428352
Monoallelic expression of the human FOXP2 speech gene. PMID:25422445
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation. PMID:25415054
Principles of regulatory information conservation between mouse and human. PMID:25409826
DEEP: a general computational framework for predicting enhancers. PMID:25378307
A large scale expression study associates uc.283-plus lncRNA with pluripotent stem cells and human glioma. PMID:25352916
Deletions of chromosomal regulatory boundaries are associated with congenital disease. PMID:25315429
Genome-wide identification of signaling center enhancers in the developing limb. PMID:25273087
Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. PMID:25249388
Deletions of exons with regulatory activity at the DYNC1I1 locus are associated with split-hand/split-foot malformation: array CGH screening of 134 unrelated families. PMID:25231166
Identification of a face enhancer reveals direct regulation of LIM homeobox 8 (Lhx8) by wingless-int (WNT)/β-catenin signaling. PMID:25190800
Tissue-specific RNA expression marks distant-acting developmental enhancers. PMID:25188404
A 'tool box' for deciphering neuronal circuits in the developing chick spinal cord. PMID:25147209
Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework. PMID:25144359
Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms. PMID:25133983
Dnmt3a regulates global gene expression in olfactory sensory neurons and enables odorant-induced transcription. PMID:25123312
A functional synonymous coding variant in the IL1RN gene is associated with survival in septic shock. PMID:25089931
Integrating diverse datasets improves developmental enhancer prediction. PMID:24967590
UCbase 2.0: ultraconserved sequences database (2014 update). PMID:24951797
Lynx web services for annotations and systems analysis of multi-gene disorders. PMID:24948611
Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence. PMID:24934569
Functional analysis of limb transcriptional enhancers in the mouse. PMID:24920384
Genome-scale functional characterization of Drosophila developmental enhancers in vivo. PMID:24896182
Targeted CNS Delivery Using Human MiniPromoters and Demonstrated Compatibility with Adeno-Associated Viral Vectors. PMID:24761428
Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. PMID:24752179
Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period. PMID:24709821
The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes. PMID:24709820
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. PMID:24658142
Obesity-associated variants within FTO form long-range functional connections with IRX3. PMID:24646999
Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex. PMID:24618363
Transcriptional enhancers: from properties to genome-wide predictions. PMID:24614317
Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits. PMID:24465181
Association of the hepatocyte growth factor gene with keratoconus in an Australian population. PMID:24416191
Functional and topological characteristics of mammalian regulatory domains. PMID:24398455
Ensembl 2014. PMID:24316576
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
EMAGE mouse embryo spatial gene expression database: 2014 update. PMID:24265223
Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses. PMID:24244860
Many human accelerated regions are developmental enhancers. PMID:24218637
The mystery of extreme non-coding conservation. PMID:24218634
Functional characterization of SIM1-associated enhancers. PMID:24203700
Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. PMID:24089456
Functional analysis of limb enhancers in the developing fin. PMID:24068387
The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PMID:24009522
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. PMID:23995138
Pax7 is regulated by cMyb during early neural crest development through a novel enhancer. PMID:23942518
A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. PMID:23917988
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. PMID:23892608
A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. PMID:23867016
Co-segregation of trichorhinophalangeal syndrome with a t(8;13)(q23.3;q21.31) familial translocation that appears to increase TRPS1 gene expression. PMID:23835950
The evolution of lineage-specific regulatory activities in the human embryonic limb. PMID:23827682
Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. PMID:23814184
Machine learning and genome annotation: a match meant to be? PMID:23731483
GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. PMID:23723249
The genomic landscape of cohesin-associated chromatin interactions. PMID:23704192
Candidate gene association studies: a comprehensive guide to useful in silico tools. PMID:23656885
From remote enhancers to gene regulation: charting the genome's regulatory landscapes. PMID:23650632
TRACER: a resource to study the regulatory architecture of the mouse genome. PMID:23547943
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. PMID:23512712
Distinct cis regulatory elements govern the expression of TAG1 in embryonic sensory ganglia and spinal cord. PMID:23469119
Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. PMID:23432897
A high-resolution enhancer atlas of the developing telencephalon. PMID:23375746
Genetic and functional modularity of Hox activities in the specification of limb-innervating motor neurons. PMID:23359544
Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome. PMID:23355428
Function and regulation of AUTS2, a gene implicated in autism and human evolution. PMID:23349641
Dlx1&2-dependent expression of Zfhx1b (Sip1, Zeb2) regulates the fate switch between cortical and striatal interneurons. PMID:23312518
Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. PMID:23307621
Enhancer chip: detecting human copy number variations in regulatory elements. PMID:23284961
Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain. PMID:23267051
Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. PMID:23253453
Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1. PMID:23249738
Cell specific CD44 expression in breast cancer requires the interaction of AP-1 and NFκB with a novel cis-element. PMID:23226410
Ensembl 2013. PMID:23203987
Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements. PMID:23201014
UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks. PMID:23193254
Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. PMID:23159369
Hundreds of conserved non-coding genomic regions are independently lost in mammals. PMID:23042682
A cis-element in the Notch1 locus is involved in the regulation of gene expression in interneuron progenitors. PMID:23022658
Homeotic arm-to-leg transformation associated with genomic rearrangements at the PITX1 locus. PMID:23022097
Annotation of functional variation in personal genomes using RegulomeDB. PMID:22955989
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. PMID:22950945
Sequencing and analysis of a South Asian-Indian personal genome. PMID:22938532
Gene isoform specificity through enhancer-associated antisense transcription. PMID:22937057
POU-III transcription factors (Brn1, Brn2, and Oct6) influence neurogenesis, molecular identity, and migratory destination of upper-layer cells of the cerebral cortex. PMID:22892427
Human developmental enhancers conserved between deuterostomes and protostomes. PMID:22876195
A map of the cis-regulatory sequences in the mouse genome. PMID:22763441
Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. PMID:22759862
Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. PMID:22722344
The cis-regulatory dynamics of the Drosophila CNS determinant castor are controlled by multiple sub-pattern enhancers. PMID:22691242
Evidence for additional FREM1 heterogeneity in Manitoba oculotrichoanal syndrome. PMID:22690109
Axonal patterns and targets of dA1 interneurons in the chick hindbrain. PMID:22539838
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. PMID:22421546
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PMID:22412381
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. PMID:22253291
An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement. PMID:22234889
Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PMID:22215994
Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers. PMID:22208168
Gli2 and MEF2C activate each other's expression and function synergistically during cardiomyogenesis in vitro. PMID:22199256
A distal modular enhancer complex acts to control pituitary- and nervous system-specific expression of the LHX3 regulatory gene. PMID:22194342
Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. PMID:22178994
A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons. PMID:22174821
GWASdb: a database for human genetic variants identified by genome-wide association studies. PMID:22139925
Large-scale discovery of enhancers from human heart tissue. PMID:22138689
Enhancer-driven chromatin interactions during development promote escape from silencing by a long non-coding RNA. PMID:22085535
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. PMID:22058225
Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors. PMID:21963459
VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies. PMID:21791533
Towards resolving the transcription factor network controlling myelin gene expression. PMID:21729871
Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder. PMID:21724599
Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures. PMID:21680890
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. PMID:21632746
Genome-wide identification of conserved regulatory function in diverged sequences. PMID:21628450
Ascl1/Mash1 is a novel target of Gli2 during Gli2-induced neurogenesis in P19 EC cells. PMID:21559470
Genetics of nonsyndromic orofacial clefts. PMID:21545302
Disease and phenotype data at Ensembl. PMID:21400687
Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. PMID:21276790
A unique chromatin signature uncovers early developmental enhancers in humans. PMID:21160473
Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions. PMID:21109530
Motor and dorsal root ganglion axons serve as choice points for the ipsilateral turning of dI3 axons. PMID:21084609
Statistical analysis strategies for association studies involving rare variants. PMID:20940738
ChIP-Seq identification of weakly conserved heart enhancers. PMID:20729851
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. PMID:20647237
The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. PMID:20494938
Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development. PMID:20426846
Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features. PMID:20392819
Translog, a web browser for studying the expression divergence of homologous genes. PMID:20122234
Genome-wide discovery of human heart enhancers. PMID:20075146
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. PMID:19969543
Combinatorial binding predicts spatio-temporal cis-regulatory activity. PMID:19890324
G-compass: a web-based comparative genome browser between human and other vertebrate genomes. PMID:19846439
Conserved expression patterns predict microRNA targets. PMID:19779543
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. PMID:19698106
Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1. PMID:19545367
ChIP-seq accurately predicts tissue-specific activity of enhancers. PMID:19212405
cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. PMID:18718943
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. PMID:18279518
ORegAnno: an open-access community-driven resource for regulatory annotation. PMID:18006570
CONDOR: a database resource of developmentally associated conserved non-coding elements. PMID:17760977
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA PubMed citations: 457.

457 articles citing: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex. PMID:35064146
Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region. PMID:34421963
Evolution of lbx spinal cord expression and function. PMID:34411410
lra: A long read aligner for sequences and contigs. PMID:34153026
Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays. PMID:34003345
Rampant Genome-Wide Admixture across the Heliconius Radiation. PMID:33944917
Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes. PMID:33794772
Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. PMID:33669616
Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ. PMID:33303762
Plastid Phylogenomics of Dendroseris (Cichorieae; Asteraceae): Insights Into Structural Organization and Molecular Evolution of an Endemic Lineage From the Juan Fernández Islands. PMID:33224173
Chloroplast genome data of Luffa acutangula and Luffa aegyptiaca and their phylogenetic relationships. PMID:33195780
Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos. PMID:33191918
Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer. PMID:32958671
Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae). PMID:32912155
Deep Convergence, Shared Ancestry, and Evolutionary Novelty in the Genetic Architecture of Heliconius Mimicry. PMID:32883703
COVID-19, SARS-CoV-2, and Export Controls. PMID:32816590
Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ. PMID:32563153
Whole genome sequencing identifies an allele responsible for clear vs. turbid plaque morphology in a Mycobacteriophage. PMID:32513117
An evolutionarily ancient mechanism for regulation of hemoglobin expression in vertebrate red cells. PMID:32396940
Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses. PMID:32351518
GSAlign: an efficient sequence alignment tool for intra-species genomes. PMID:32093618
Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing. PMID:31867041
Complete genome sequence of fowl adenovirus-8b UPM04217 isolate associated with the inclusion body hepatitis disease in commercial broiler chickens in Malaysia reveals intermediate evolution. PMID:31803810
Sow Thistle Chloroplast Genomes: Insights into the Plastome Evolution and Relationship of Two Weedy Species, Sonchus asper and Sonchus oleraceus (Asteraceae). PMID:31683955
Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae). PMID:31653891
Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias. PMID:31605487
Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PMID:31437150
Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes. PMID:31330852
Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei. PMID:31270201
A homeotic shift late in development drives mimetic color variation in a bumble bee. PMID:31043564
The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development. PMID:31036599
Identification of regulatory elements recapitulating early expression of L-plastin in the zebrafish enveloping layer and embryonic periderm. PMID:30940554
Metagenomes of a Freshwater Charavirus from British Columbia Provide a Window into Ancient Lineages of Viruses. PMID:30934644
Evolutionary Comparison of the Chloroplast Genome in the Woody Sonchus Alliance (Asteraceae) on the Canary Islands. PMID:30875850
A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates. PMID:30867425
The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species. PMID:30641990
Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae). PMID:30609873
Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids. PMID:30563463
Whole-Genome Alignment and Comparative Annotation. PMID:30379572
Identification of a limb enhancer that is removed by pathogenic deletions downstream of the SHOX gene. PMID:30250174
Comparative Analysis of Complete Chloroplast Genomes of Anemoclema, Anemone, Pulsatilla, and Hepatica Revealing Structural Variations Among Genera in Tribe Anemoneae (Ranunculaceae). PMID:30100915
The Floral C-Lineage Genes Trigger Nectary Development in Petunia and Arabidopsis. PMID:30087206
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. PMID:29992260
Genetic characterization and mutation analysis of Qihe547 Aujeszky's disease virus in China. PMID:29980205
Comparative Genomic Analysis of Re-emergent Human Adenovirus Type 55 Pathogens Associated With Adult Severe Community-Acquired Pneumonia Reveals Conserved Genomes and Capsid Proteins. PMID:29922263
Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon. PMID:29675466
Pathogenicity and Whole Genome Sequence Analysis of a Pseudorabies Virus Strain FJ-2012 Isolated from Fujian, Southern China. PMID:29527230
The FBH family of bHLH transcription factors controls ACC synthase expression in sugarcane. PMID:29514290
Conserved Upstream Regulatory Regions in Mammalian Tyrosine Hydroxylase. PMID:29404959
Construction of an infectious horsepox virus vaccine from chemically synthesized DNA fragments. PMID:29351298
seq-seq-pan: building a computational pan-genome data structure on whole genome alignment. PMID:29334898
Integral Phylogenomic Approach over Ilex L. Species from Southern South America. PMID:29165335
Comparative genomic analysis of two emergent human adenovirus type 14 respiratory pathogen isolates in China reveals similar yet divergent genomes. PMID:29089589
Whole Genome Sequence Analysis of Mutations Accumulated in rad27Δ Yeast Strains with Defects in the Processing of Okazaki Fragments Indicates Template-Switching Events. PMID:28974572
Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals. PMID:28922870
Comparative analysis reveals regulatory motifs at the ainS/ainR pheromone-signaling locus of Vibrio fischeri. PMID:28916743
Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. PMID:28683832
Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting. PMID:28659711
BAC Recombineering of the Agouti Loci from Spotted Gar and Zebrafish Reveals the Evolutionary Ancestry of Dorsal-Ventral Pigment Asymmetry in Fish. PMID:28544213
Odorant Sensory Input Modulates DNA Secondary Structure Formation and Heterogeneous Ribonucleoprotein Recruitment on the Tyrosine Hydroxylase and Glutamic Acid Decarboxylase 1 Promoters in the Olfactory Bulb. PMID:28411275
Diversification of spatiotemporal expression and copy number variation of the echinoid hbox12/pmar1/micro1 multigene family. PMID:28350855
Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach. PMID:28347272
Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens. PMID:28257628
Zebrafish transgenic constructs label specific neurons in Xenopus laevis spinal cord and identify frog V0v spinal neurons. PMID:28188691
Genome data on the extinct Bison schoetensacki establish it as a sister species of the extant European bison (Bison bonasus). PMID:28187706
Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion. PMID:28051769
The genome of the Gulf pipefish enables understanding of evolutionary innovations. PMID:27993155
Alternate-locus aware variant calling in whole genome sequencing. PMID:27964746
Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton. PMID:27902701
Developmental mechanisms of stripe patterns in rodents. PMID:27806375
Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards. PMID:27733546
Complete Genome Sequences of the Historical Legionella pneumophila Strains OLDA and Pontiac. PMID:27563044
Conservation of the role of INNER NO OUTER in development of unitegmic ovules of the Solanaceae despite a divergence in protein function. PMID:27350128
Black perithecial pigmentation in Fusarium species is due to the accumulation of 5-deoxybostrycoidin-based melanin. PMID:27193384
Organization and characteristics of the major histocompatibility complex class II region in the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). PMID:26932528
Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2-independent mechanism. PMID:26896392
CEGA--a catalog of conserved elements from genomic alignments. PMID:26527719
Functionally conserved enhancers with divergent sequences in distant vertebrates. PMID:26519295
Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development. PMID:26464005
Functional Diversification of Motor Neuron-specific Isl1 Enhancers during Evolution. PMID:26447474
Clostridium difficile: New Insights into the Evolution of the Pathogenicity Locus. PMID:26446480
Activation of Six1 Expression in Vertebrate Sensory Neurons. PMID:26313368
Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus. PMID:26275815
The LMO2 -25 Region Harbours GATA2-Dependent Myeloid Enhancer and RUNX-Dependent T-Lymphoid Repressor Activity. PMID:26161748
A Phox2b BAC Transgenic Rat Line Useful for Understanding Respiratory Rhythm Generator Neural Circuitry. PMID:26147470
Conserved Noncoding Sequences Regulate lhx5 Expression in the Zebrafish Forebrain. PMID:26147098
The achaete-scute complex in Diptera: patterns of noncoding sequence evolution. PMID:26134680
Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy. PMID:26125617
Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome. PMID:26084764
Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave. PMID:26083419
Population structure of mitochondrial genomes in Saccharomyces cerevisiae. PMID:26062918
Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment. PMID:25983537
Evolution of CONSTANS Regulation and Function after Gene Duplication Produced a Photoperiodic Flowering Switch in the Brassicaceae. PMID:25972346
YOC, A new strategy for pairwise alignment of collinear genomes. PMID:25885358
Deep sequencing reveals the complete genome and evidence for transcriptional activity of the first virus-like sequences identified in Aristotelia chilensis (Maqui Berry). PMID:25855242
The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. PMID:25840857
Nucleotide sequence conservation of novel and established cis-regulatory sites within the tyrosine hydroxylase gene promoter. PMID:25774193
First genome-wide association study in an Australian aboriginal population provides insights into genetic risk factors for body mass index and type 2 diabetes. PMID:25760438
Gene order alignment on trees with multiOrthoAlign. PMID:25572278
Identification and computational analysis of gene regulatory elements. PMID:25561628
Regulation of tyrosine hydroxylase transcription by hnRNP K and DNA secondary structure. PMID:25493445
Insights into the possible role of IFNG and IFNGR1 in Kala-azar and Post Kala-azar Dermal Leishmaniasis in Sudanese patients. PMID:25466928
Evolution of and evolutionary relationships between extant vaccinia virus strains. PMID:25410873
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. PMID:25410596
Intron evolution in Saccharomycetaceae. PMID:25364803
Investigating genomic structure using changept: A Bayesian segmentation model. PMID:25349679
The evolution of comparative genomics. PMID:25333060
The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. PMID:25296686
An evaluation of the ecological relationship between Drosophila species and their parasitoid wasps as an opportunity for horizontal transposon transfer. PMID:25146840
C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison. PMID:25110578
Noncoding origins of anthropoid traits and a new null model of transposon functionalization. PMID:25043600
Evolutionary relationship of disease resistance genes in soybean and Arabidopsis specific for the Pseudomonas syringae effectors AvrB and AvrRpm1. PMID:25034017
Evolutionary conservation of cold-induced antisense RNAs of FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives. PMID:25030056
Transcriptional regulation analysis and the potential transcription regulator site in the extended KAP6.1 promoter in sheep. PMID:24990691
The genome of Eucalyptus grandis. PMID:24919147
GenomeVISTA--an integrated software package for whole-genome alignment and visualization. PMID:24860159
Local similarity search to find gene indicators in mitochondrial genomes. PMID:24833343
The RNA-binding protein ELAV regulates Hox RNA processing, expression and function within the Drosophila nervous system. PMID:24803653
Simultaneous alignment and folding of protein sequences. PMID:24766258
The brain-uterus connection: brain derived neurotrophic factor (BDNF) and its receptor (Ntrk2) are conserved in the mammalian uterus. PMID:24714156
Genome alignment with graph data structures: a comparison. PMID:24712884
MC64-ClustalWP2: a highly-parallel hybrid strategy to align multiple sequences in many-core architectures. PMID:24710354
Cis-regulatory elements are harbored in Intron5 of the RUNX1 gene. PMID:24655352
Identification of transcriptional regulatory elements for Ntng1 and Ntng2 genes in mice. PMID:24642214
Differential LRRK2 expression in the cortex, striatum, and substantia nigra in transgenic and nontransgenic rodents. PMID:24633735
Genome scale patterns of recombination between coinfecting vaccinia viruses. PMID:24574414
Genetic and functional evidence for a locus controlling otitis media at chromosome 10q26.3. PMID:24499112
uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation. PMID:24484385
Appearance of Planktothrix rubescens bloom with [D-Asp3, Mdha7]MC-RR in gravel pit pond of a shallow lake-dominated area. PMID:24351711
Phylogenomics of fescue grass-derived fungal endophytes based on selected nuclear genes and the mitochondrial gene complement. PMID:24330497
Meis1 regulates Foxn4 expression during retinal progenitor cell differentiation. PMID:24244849
Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). PMID:24043829
Cell interactions and patterned intercalations shape and link epithelial tubes in C. elegans. PMID:24039608
Regulation of MEIS1 by distal enhancer elements in acute leukemia. PMID:24022755
Evolutionary dynamics of the accessory genome of Listeria monocytogenes. PMID:23825666
Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications. PMID:23749448
Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. PMID:23674305
FOGSAA: Fast Optimal Global Sequence Alignment Algorithm. PMID:23624407
Predicting the next eye pathogen: analysis of a novel adenovirus. PMID:23572555
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex. PMID:23550121
Development of a singleplex PCR assay for rapid identification and differentiation of Cryptococcus neoformans var. grubii, Cryptococcus neoformans var. neoformans, Cryptococcus gattii, and hybrids. PMID:23536400
Regulatory genomics: Insights from the zebrafish. PMID:23440612
Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. PMID:23393190
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. PMID:23281809
Cell specific CD44 expression in breast cancer requires the interaction of AP-1 and NFκB with a novel cis-element. PMID:23226410
A cis-element in the Notch1 locus is involved in the regulation of gene expression in interneuron progenitors. PMID:23022658
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. PMID:22988817
Unleashing the genome of brassica rapa. PMID:22866056
An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference. PMID:22851613
GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes. PMID:22723889
Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties. PMID:22666536
Complete genome sequence of the European sheatfish virus. PMID:22570241
Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. PMID:22479192
Analysis of human adenovirus type 19 associated with epidemic keratoconjunctivitis and its reclassification as adenovirus type 64. PMID:22467570
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. PMID:22452820
Phylo: a citizen science approach for improving multiple sequence alignment. PMID:22412834
Pregnane X receptor and yin yang 1 contribute to the differential tissue expression and induction of CYP3A5 and CYP3A4. PMID:22292071
Localization of high level of sequence conservation and divergence regions in cotton. PMID:22212344
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. PMID:22168237
Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals. PMID:22103247
Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments. PMID:22086332
Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. PMID:22060816
Genome sequences and characterization of the related Gordonia phages GTE5 and GRU1 and their use as potential biocontrol agents. PMID:22038604
A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PMID:22022263
Multiplex sequencing of seven ocular herpes simplex virus type-1 genomes: phylogeny, sequence variability, and SNP distribution. PMID:22016062
Orthopoxvirus genome evolution: the role of gene loss. PMID:21994715
Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways. PMID:21980306
Genomic analysis of the vaccinia virus strain variants found in Dryvax vaccine. PMID:21976639
Loss of genes for DNA recombination and repair in the reductive genome evolution of thioautotrophic symbionts of Calyptogena clams. PMID:21966992
Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution. PMID:21949720
High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PMID:21931804
Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PMID:21931557
Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment. PMID:21867510
Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes. PMID:21794110
New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits. PMID:21767393
Genetic and functional evidence implicating DLL1 as the gene that influences susceptibility to visceral leishmaniasis at chromosome 6q27. PMID:21742847
Functional analysis of conserved non-coding regions around the short stature hox gene (shox) in whole zebrafish embryos. PMID:21731768
ELAV-mediated 3'-end processing of ewg transcripts is evolutionarily conserved despite sequence degeneration of the ELAV-binding site. PMID:21705751
Predicting site-specific human selective pressure using evolutionary signatures. PMID:21685080
Cactus: Algorithms for genome multiple sequence alignment. PMID:21665927
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. PMID:21646336
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PMID:21637758
Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus. PMID:21629789
Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes. PMID:21554730
Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. PMID:21518738
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. PMID:21470961
Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm. PMID:21445268
Expression of the Distalless-B gene in Ciona is regulated by a pan-ectodermal enhancer module. PMID:21338600
Contribution of rapid evolution of the luxR-luxI intergenic region to the diverse bioluminescence outputs of Vibrio fischeri strains isolated from different environments. PMID:21317265
Inexact Local Alignment Search over Suffix Arrays. PMID:21278916
Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events. PMID:21247963
Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies. PMID:21245917
Evolution of microRNAs and the diversification of species. PMID:21169229
Genetic variation in the beta2 subunit of the voltage-gated calcium channel and pharmacogenetic association with adverse cardiovascular outcomes in the INternational VErapamil SR-Trandolapril STudy GENEtic Substudy (INVEST-GENES). PMID:21156931
Assessing computational methods of cis-regulatory module prediction. PMID:21152003
Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan. PMID:21147954
A family history of DUX4: phylogenetic analysis of DUXA, B, C and Duxbl reveals the ancestral DUX gene. PMID:21110847
Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. PMID:21056888
Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position. PMID:21047394
Two lamprey Hedgehog genes share non-coding regulatory sequences and expression patterns with gnathostome Hedgehogs. PMID:20967201
Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes. PMID:20885980
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model. PMID:20846408
High level of structural polymorphism driven by mobile elements in the Hox genomic region of the Chaetognath Spadella cephaloptera. PMID:20829282
Genome sequences of human adenovirus 14 isolates from mild respiratory cases and a fatal pneumonia, isolated during 2006-2007 epidemics in North America. PMID:20738863
A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities. PMID:20686707
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PMID:20593022
The origin and evolution of ARGFX homeobox loci in mammalian radiation. PMID:20565723
Transcriptional regulation of Elf-1: locus-wide analysis reveals four distinct promoters, a tissue-specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation. PMID:20525788
Comparative assessment of methods for aligning multiple genome sequences. PMID:20495551
Comparison of homoeolocus organisation in paired BAC clones from white clover (Trifolium repens L.) and microcolinearity with model legume species. PMID:20492736
eHive: an artificial intelligence workflow system for genomic analysis. PMID:20459813
Cgaln: fast and space-efficient whole-genome alignment. PMID:20433723
Differential regulation of dopaminergic gene expression by Er81. PMID:20357122
Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes. PMID:20346147
Transcriptome analysis reveals a major impact of JAK protein tyrosine kinase 2 (Tyk2) on the expression of interferon-responsive and metabolic genes. PMID:20338026
Mobile regulatory cassettes mediate modular shuffling in T4-type phage genomes. PMID:20333230
Elucidating genome structure evolution by analysis of isoapostatic gene clusters using statistics of variance of gene distances. PMID:20333218
Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates. PMID:20333173
MISHIMA--a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. PMID:20298584
A novel DFNB1 deletion allele supports the existence of a distant cis-regulatory region that controls GJB2 and GJB6 expression. PMID:20236118
A Study of the Distribution of Phylogenetically Conserved Blocks within Clusters of Mammalian Homeobox Genes. PMID:20209015
Complete genome sequences of avian paramyxovirus serotype 6 prototype strain Hong Kong and a recent novel strain from Italy: evidence for the existence of subgroups within the serotype. PMID:20206652
Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. PMID:20204374
Conservation of gene linkage in dispersed vertebrate NK homeobox clusters. PMID:20112453
Genomic characterization of human adenovirus 36, a putative obesity agent. PMID:20109503
Towards realistic benchmarks for multiple alignments of non-coding sequences. PMID:20102627
Genome-wide prediction of transcription factor binding sites using an integrated model. PMID:20096096
Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PMID:20041216
A new measurement of sequence conservation. PMID:20028539
Mobile antibiotic resistance encoding elements promote their own diversity. PMID:20019796
Early evolution of conserved regulatory sequences associated with development in vertebrates. PMID:20011110
Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites. PMID:19995462
Unique sequence features of the Human adenovirus 31 complete genomic sequence are conserved in clinical isolates. PMID:19939241
Identification and characterization of odorant-binding protein 1 gene from the Asian malaria mosquito, Anopheles stephensi. PMID:19909381
The mouse and human Fli1 genes are similarly regulated by Ets factors in T cells. PMID:19829305
Implications of chimaeric non-co-linear transcripts. PMID:19741701
Comparative genomics of chondrichthyan Hoxa clusters. PMID:19725973
Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus. PMID:19693423
Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. PMID:19675151
Brucella microti: the genome sequence of an emerging pathogen. PMID:19653890
Melanism in peromyscus is caused by independent mutations in agouti. PMID:19649329
CSA: an efficient algorithm to improve circular DNA multiple alignment. PMID:19627599
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. PMID:19589141
Evolution of developmental regulation in the vertebrate FgfD subfamily. PMID:19562753
Computational analysis of human adenovirus type 22 provides evidence for recombination among species D human adenoviruses in the penton base gene. PMID:19553309
Functional and comparative genomics analyses of pmp22 in medaka fish. PMID:19534778
Fast statistical alignment. PMID:19478997
Assessing phylogenetic motif models for predicting transcription factor binding sites. PMID:19478008
Dynamic in vivo binding of STAT5 to growth hormone-regulated genes in intact rat liver. Sex-specific binding at low- but not high-affinity STAT5 sites. PMID:19423653
The difficulty of avoiding false positives in genome scans for natural selection. PMID:19411606
Conservation of core gene expression in vertebrate tissues. PMID:19371447
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. PMID:19293946
Evidence for co-evolution between human microRNAs and Alu-repeats. PMID:19209240
Strategies for reliable exploitation of evolutionary concepts in high throughput biology. PMID:19204813
Lossless filter for multiple repeats with bounded edit distance. PMID:19183438
Learning a prior on regulatory potential from eQTL data. PMID:19180192
Multiple whole-genome alignments without a reference organism. PMID:19176791
Evolution of regulatory sequences in 12 Drosophila species. PMID:19132088
Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. PMID:19121219
A recalibrated molecular clock and independent origins for the cholera pandemic clones. PMID:19115014
nGASP--the nematode genome annotation assessment project. PMID:19099578
Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. PMID:19098269
Shaping skeletal growth by modular regulatory elements in the Bmp5 gene. PMID:19096511
Regulatory potential for concerted modulation of Nrf2- and Nfkb1-mediated gene expression in inflammation and carcinogenesis. PMID:19050705
CoCoNUT: an efficient system for the comparison and analysis of genomes. PMID:19014477
Human adenovirus type 19: genomic and bioinformatics analysis of a keratoconjunctivitis isolate. PMID:19000724
Multiple genome alignment for identifying the core structure among moderately related microbial genomes. PMID:18976470
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. PMID:18971253
Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome. PMID:18957082
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. PMID:18952863
CompMoby: comparative MobyDick for detection of cis-regulatory motifs. PMID:18950538
Genome-wide nucleotide-level mammalian ancestor reconstruction. PMID:18849525
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. PMID:18849524
Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster. PMID:18791732
PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. PMID:18769735
The evolution of epigenetic regulators CTCF and BORIS/CTCFL in amniotes. PMID:18769711
Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PMID:18769675
Conserved secondary structures in Aspergillus. PMID:18665251
Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies. PMID:18647405
Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans. PMID:18633349
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PMID:18584029
Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource. PMID:18580967
An evolutionarily conserved sexual signature in the primate brain. PMID:18566661
The evolution of the DLK1-DIO3 imprinted domain in mammals. PMID:18532878
Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. PMID:18490265
Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum. PMID:18488228
Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism. PMID:18471294
Genome analysis of the platypus reveals unique signatures of evolution. PMID:18464734
Transcription induces strand-specific mutations at the 5' end of human genes. PMID:18463301
Rapid evolution of yeast centromeres in the absence of drive. PMID:18430941
Laboratory strains of murine cytomegalovirus are genetically similar to but phenotypically distinct from wild strains of virus. PMID:18417589
Mapping of small RNAs in the human ENCODE regions. PMID:18394580
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? PMID:18394174
Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle. PMID:18344325
Genomic analysis of Ovis aries (Ovar) MHC class IIa loci. PMID:18322680
Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams. PMID:18305898
ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. PMID:18294369
Addressing chromosome evolution in the whole-genome sequence era. PMID:18293102
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. PMID:18282510
Construction of a fosmid library of cucumber (Cucumis sativus) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon (Cucumis melo). PMID:18273646
Mechanisms of intron gain and loss in Cryptococcus. PMID:18234113
Multiple organism algorithm for finding ultraconserved elements. PMID:18186941
SeqAn an efficient, generic C++ library for sequence analysis. PMID:18184432
Uncertainty in homology inferences: assessing and improving genomic sequence alignment. PMID:18073381
High-throughput sequence alignment using Graphics Processing Units. PMID:18070356
A survey of DNA motif finding algorithms. PMID:18047721
TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. PMID:18045502
The "alternative" choice of constitutive exons throughout evolution. PMID:18020709
MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules. PMID:17997594
Mulan: multiple-sequence alignment to predict functional elements in genomic sequences. PMID:17993678
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PMID:17973026
How accurately is ncRNA aligned within whole-genome multiple alignments? PMID:17963514
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. PMID:17956628
DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage. PMID:17935613
Statistical power of phylo-HMM for evolutionarily conserved element detection. PMID:17919331
Finding regulatory elements and regulatory motifs: a general probabilistic framework. PMID:17903285
Mammalian microRNA prediction through a support vector machine model of sequence and structure. PMID:17895987
Neuroadaptations in human chronic alcoholics: dysregulation of the NF-kappaB system. PMID:17895971
Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni. PMID:17845724
Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer. PMID:17823307
Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. PMID:17822543
CONDOR: a database resource of developmentally associated conserved non-coding elements. PMID:17760977
Extensive parallelism in protein evolution. PMID:17705846
Mammalian comparative sequence analysis of the Agrp locus. PMID:17684549
The evolution of gene expression QTL in Saccharomyces cerevisiae. PMID:17668057
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. PMID:17626050
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. PMID:17571346
Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages. PMID:17570149
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. PMID:17568002
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. PMID:17567995
Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction. PMID:17559649
Frequent gain and loss of functional transcription factor binding sites. PMID:17530920
Single nucleotide polymorphism discovery and haplotype analysis of Ca2+-dependent K+ channel beta-1 subunit. PMID:17496725
G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. PMID:17496117
Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach. PMID:17488849
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. PMID:17488840
Multiple non-collinear TF-map alignments of promoter regions. PMID:17456238
Query-dependent banding (QDB) for faster RNA similarity searches. PMID:17397253
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. PMID:17374142
Extreme genomic variation in a natural population. PMID:17372217
Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements. PMID:17362514
Alternative S2 hinge regions of the myosin rod differentially affect muscle function, myofibril dimensions and myosin tail length. PMID:17316684
Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. PMID:17310332
Enhancer identification through comparative genomics. PMID:17276707
Large-scale discovery of promoter motifs in Drosophila melanogaster. PMID:17238282
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. PMID:17201929
Brn3a target gene recognition in embryonic sensory neurons. PMID:17196582
Transcriptional regulation of the Drosophila melanogaster muscle myosin heavy-chain gene. PMID:17194628
Dynamic use of multiple parameter sets in sequence alignment. PMID:17182633
The ENCODE Project at UC Santa Cruz. PMID:17166863
Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PMID:17132051
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. PMID:17119069
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. PMID:17062155
inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons. PMID:17054788
Large-scale turnover of functional transcription factor binding sites in Drosophila. PMID:17040121
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. PMID:17022809
Genome of horsepox virus. PMID:16940536
Selective promoter recognition by chlamydial sigma28 holoenzyme. PMID:16936033
An integrative method for accurate comparative genome mapping. PMID:16933978
Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments. PMID:16924100
Search for basonuclin target genes. PMID:16919236
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. PMID:16912276
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. PMID:16904011
Graemlin: general and robust alignment of multiple large interaction networks. PMID:16899655
Haplotype block structure is conserved across mammals. PMID:16895449
Primate-specific evolution of an LDLR enhancer. PMID:16884525
Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. PMID:16859531
Computational identification of transcriptional regulatory elements in DNA sequence. PMID:16855295
PromAn: an integrated knowledge-based web server dedicated to promoter analysis. PMID:16845074
Stubb: a program for discovery and analysis of cis-regulatory modules. PMID:16845069
Close sequence comparisons are sufficient to identify human cis-regulatory elements. PMID:16769978
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. PMID:16759380
Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila. PMID:16715176
MicroRNA enrichment among short 'ultraconserved' sequences in insects. PMID:16698958
Heterotachy in mammalian promoter evolution. PMID:16683025
Functional conservation of Pax6 regulatory elements in humans and mice demonstrated with a novel transgenic reporter mouse. PMID:16674807
Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters. PMID:16636282
Identification and classification of conserved RNA secondary structures in the human genome. PMID:16628248
An autoregulatory loop directs the tissue-specific expression of p63 through a long-range evolutionarily conserved enhancer. PMID:16581802
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. PMID:16542424
Choosing the best heuristic for seeded alignment of DNA sequences. PMID:16533404
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. PMID:16509994
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PMID:16477324
Rate of promoter class turn-over in yeast evolution. PMID:16472383
A novel approach to identifying regulatory motifs in distantly related genomes. PMID:16420672
Application of a superword array in genome assembly. PMID:16397298
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. PMID:16381947
Ensembl 2006. PMID:16381931
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. PMID:16344566
Multiple sequence alignment accuracy and evolutionary distance estimation. PMID:16305750
Ancestral sequence alignment under optimal conditions. PMID:16293191
BEGAIN: a novel imprinted gene that generates paternally expressed transcripts in a tissue- and promoter-specific manner in sheep. PMID:16261422
Web-based resources for comparative genomics. PMID:16197736
Functional constraints on the constitutive androstane receptor inferred from human sequence variation and cross-species comparisons. PMID:16197734
De novo discovery of a tissue-specific gene regulatory module in a chordate. PMID:16169925
Using multiple alignments to improve seeded local alignment algorithms. PMID:16100379
Genome-wide promoter extraction and analysis in human, mouse, and rat. PMID:16086854
Genomic multiple sequence alignments: refinement using a genetic algorithm. PMID:16086841
Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. PMID:16077009
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. PMID:16024819
Orthologous repeats and mammalian phylogenetic inference. PMID:15998912
CONREAL web server: identification and visualization of conserved transcription factor binding sites. PMID:15980509
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. PMID:15980508
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. PMID:15980497
Manipulating multiple sequence alignments via MaM and WebMaM. PMID:15980474
transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. PMID:15969769
Distribution and intensity of constraint in mammalian genomic sequence. PMID:15965027
A novel variant of Inpp5f is imprinted in brain, and its expression is correlated with differential methylation of an internal CpG island. PMID:15964807
Cross-species comparison of Drosophila male accessory gland protein genes. PMID:15944345
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. PMID:15933209
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. PMID:15882449
Evolutionary distance estimation and fidelity of pair wise sequence alignment. PMID:15840174
A male-specific quantitative trait locus on 1p21 controlling human stature. PMID:15827092
Silencing of Fshr occurs through a conserved, hypersensitive site in the first intron. PMID:15817654
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. PMID:15790396
The DNA sequence of the human X chromosome. PMID:15772651
An Eulerian path approach to local multiple alignment for DNA sequences. PMID:15668398
MAP2: multiple alignment of syntenic genomic sequences. PMID:15640451
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. PMID:15632085
Highly conserved non-coding sequences are associated with vertebrate development. PMID:15630479
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538
Mulan: multiple-sequence local alignment and visualization for studying function and evolution. PMID:15590941
ABC: software for interactive browsing of genomic multiple sequence alignment data. PMID:15588288
Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. PMID:15545497
Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. PMID:15545496
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. PMID:15511292
Improved hit criteria for DNA local alignment. PMID:15485572
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. PMID:15357878
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. PMID:15345045
MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. PMID:15304649
Incongruent patterns of local and global genome size evolution in cotton. PMID:15256507
Mauve: multiple alignment of conserved genomic sequence with rearrangements. PMID:15231754
VISTA: computational tools for comparative genomics. PMID:15215394
A suite of web-based programs to search for transcriptional regulatory motifs. PMID:15215381
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. PMID:15215346
Building genomic profiles for uncovering segmental homology in the twilight zone. PMID:15173115
Sockeye: a 3D environment for comparative genomics. PMID:15123592
Pegasys: software for executing and integrating analyses of biological sequences. PMID:15096276
Aligning multiple genomic sequences with the threaded blockset aligner. PMID:15060014
MAVID: constrained ancestral alignment of multiple sequences. PMID:15060012
Automated whole-genome multiple alignment of rat, mouse, and human. PMID:15060011
Pash: efficient genome-scale sequence anchoring by Positional Hashing. PMID:15060009
Characterization of evolutionary rates and constraints in three Mammalian genomes. PMID:15059994
MUSCLE: multiple sequence alignment with high accuracy and high throughput. PMID:15034147
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. PMID:14993210
MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. PMID:14993209
Whole-genome shotgun assembly and comparison of human genome assemblies. PMID:14769938
Versatile and open software for comparing large genomes. PMID:14759262
Benchmarking tools for the alignment of functional noncoding DNA. PMID:14736341
Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. PMID:14718377
Fast and sensitive multiple alignment of large genomic sequences. PMID:14693042
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. PMID:14672977
Multi-species sequence comparison: the next frontier in genome annotation. PMID:14659006
Identification and characterization of multi-species conserved sequences. PMID:14656959
Conservation of regulatory elements between two species of Drosophila. PMID:14629780
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. PMID:12824357
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. PMID:12727901
VISTA : visualizing global DNA sequence alignments of arbitrary length PubMed citations: 390.

390 articles citing: VISTA : visualizing global DNA sequence alignments of arbitrary length

The complete chloroplast genome sequence of the medicinal plant Abrus pulchellus subsp. cantoniensis: genome structure, comparative and phylogenetic relationship analysis. PMID:35338406
The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L. PMID:35271574
Plastome phylogenomics and historical biogeography of aquatic plant genus Hydrocharis (Hydrocharitaceae). PMID:35260081
The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. PMID:35222983
The Complete Chloroplast Genome of Carya cathayensis and Phylogenetic Analysis. PMID:35205413
Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes. PMID:35096026
Structural characterization of Platanthera ussuriensis chloroplast genome and comparative analyses with other species of Orchidaceae. PMID:35086477
Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. PMID:34991482
Chloroplast genomes of two Pueraria DC. species: sequencing, comparative analysis and molecular marker development. PMID:34856076
Comparative genomic study on the complete plastomes of four officinal Ardisia species in China. PMID:34782652
Perfect and imperfect views of ultraconserved sequences. PMID:34764456
Development of a LAMP-Based Molecular Species Diagnosis Method for Four Major Agricultural Pests in the Genus Spodoptera (Lepidoptera: Noctuidae). PMID:34680652
Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. PMID:34646478
Differential regulation of mammalian and avian ATOH1 by E2F1 and its implication for hair cell regeneration in the inner ear. PMID:34588543
Characterization of the complete chloroplast genome of Rohdea wattii (Asparagaceae). PMID:34471695
Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus. PMID:34458062
Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny. PMID:34439948
Evolution of lbx spinal cord expression and function. PMID:34411410
Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria. PMID:34225754
The complete chloroplast genome of Lithocarpus hancei (Benth.) Rehd (Fagaceae) from Zhejiang, China. PMID:34212084
Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution. PMID:34204211
Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis. PMID:34083611
Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner. PMID:34009390
Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays. PMID:34003345
Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships. PMID:33911961
Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species. PMID:33903715
Comparative Analysis of Complete Chloroplast Genome Sequences in Edgeworthia (Thymelaeaceae) and New Insights Into Phylogenetic Relationships. PMID:33790948
Complete chloroplast genome sequence and phylogenetic analysis of winter oil rapeseed (Brassica rapa L.). PMID:33763561
Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes. PMID:33736599
Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates. PMID:33669616
Sequencing and comparative analysis of the chloroplast genome of Ribes odoratum provide insights for marker development and phylogenetics in Ribes. PMID:33627964
Complete Chloroplast Genome of Abutilon fruticosum: Genome Structure, Comparative and Phylogenetic Analysis. PMID:33573201
Immune System Effects of Insulin-Like Peptide 5 in a Mouse Model. PMID:33519716
Dbx2 regulation in limbs suggests interTAD sharing of enhancers. PMID:33497014
Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications. PMID:33441833
Complete chloroplast genome of Rhododendron pulchrum, an ornamental medicinal and food tree. PMID:33366070
Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships. PMID:33362846
A region of the sex chromosome associated with population differences in diapause induction contains highly divergent alleles at clock genes. PMID:33340097
The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis. PMID:33276435
Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera. PMID:33252661
Development of a Species Diagnostic Molecular Tool for an Invasive Pest, Mythimna loreyi, Using LAMP. PMID:33228220
Unexpected mutual regulation underlies paralogue functional diversification and promotes epithelial tissue maturation in Tribolium. PMID:33020571
Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer. PMID:32958671
Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot. PMID:32912160
COVID-19, SARS-CoV-2, and Export Controls. PMID:32816590
Complete Chloroplast Genomes and Comparative Analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae). PMID:32785156
Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species. PMID:32616875
Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae. PMID:32532210
Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China. PMID:32513105
Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment. PMID:32509453
The transcription factor HAND2 up-regulates transcription of the IL15 gene in human endometrial stromal cells. PMID:32444497
Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa. PMID:32443835
Quantitative Proteomics Identifies TCF1 as a Negative Regulator of Foxp3 Expression in Conventional T Cells. PMID:32422593
An evolutionarily ancient mechanism for regulation of hemoglobin expression in vertebrate red cells. PMID:32396940
MicroRNA 27a Is a Key Modulator of Cholesterol Biosynthesis. PMID:32071155
The complete chloroplast genome of Microcycas calocoma (Miq.) A. DC. (Zamiaceae, Cycadales) and evolution in Cycadales. PMID:31976174
Characterization of the Complete Chloroplast Genome of Acer truncatum Bunge (Sapindales: Aceraceae): A New Woody Oil Tree Species Producing Nervonic Acid. PMID:31886246
Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium 'Summit'. PMID:31879574
Lampreys, the jawless vertebrates, contain three Pax6 genes with distinct expression in eye, brain and pancreas. PMID:31863055
Complete chloroplast genomes of two Siraitia Merrill species: Comparative analysis, positive selection and novel molecular marker development. PMID:31860647
A transposable element insertion is associated with an alternative life history strategy. PMID:31848330
Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae. PMID:31798674
Tasks, Techniques, and Tools for Genomic Data Visualization. PMID:31768085
Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements. PMID:31632631
Draft Genome Sequence of Sporolactobacillus inulinus NBRC 111894, Isolated from Kôso, a Japanese Sugar-Vegetable Fermented Beverage. PMID:31601658
Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae. PMID:31467890
Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing. PMID:31406227
Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii. PMID:31380427
Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis. PMID:31361757
Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes. PMID:31330852
Determination of the evolutionary pressure on Camellia oleifera on Hainan Island using the complete chloroplast genome sequence. PMID:31289703
A homeotic shift late in development drives mimetic color variation in a bumble bee. PMID:31043564
Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome. PMID:30987338
Sequencing and Structural Analysis of the Complete Chloroplast Genome of the Medicinal Plant Lycium chinense Mill. PMID:30987216
The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data. PMID:30980269
Identification of regulatory elements recapitulating early expression of L-plastin in the zebrafish enveloping layer and embryonic periderm. PMID:30940554
Metagenomes of a Freshwater Charavirus from British Columbia Provide a Window into Ancient Lineages of Viruses. PMID:30934644
Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb. PMID:30911328
Regulatory Diversification of INDEHISCENT in the Capsella Genus Directs Variation in Fruit Morphology. PMID:30827915
Significance of Photosynthetic Characters in the Evolution of Asian Gnetum (Gnetales). PMID:30804953
The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species. PMID:30641990
Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children. PMID:30626342
Comparative Analysis of the Complete Chloroplast Genome Sequences of Three Closely Related East-Asian Wild Roses (Rosa sect. Synstylae; Rosaceae). PMID:30609873
Conserved Noncoding Sequences Boost ADR1 and SP1 Regulated Human Swiprosin-1 Promoter Activity. PMID:30405162
The Genomic Basis of Tumor Regression in Tasmanian Devils (Sarcophilus harrisii). PMID:30321343
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. PMID:30297745
Plastomes of nine hornbeams and phylogenetic implications. PMID:30271544
Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae. PMID:30242472
Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution. PMID:30154814
Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species. PMID:30149578
Molecular characterisation of rotavirus strains detected during a clinical trial of the human neonatal rotavirus vaccine (RV3-BB) in Indonesia. PMID:30145099
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima. PMID:30126202
A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties. PMID:30083466
Increased CD4+ T cell lineage commitment determined by CpG methylation correlates with better prognosis in urinary bladder cancer patients. PMID:30075815
Characterization of the Chloroplast Genome Sequence of Acer miaotaiense: Comparative and Phylogenetic Analyses. PMID:30018192
Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus. PMID:29989238
Presomitic mesoderm-specific expression of the transcriptional repressor Hes7 is controlled by E-box, T-box, and Notch signaling pathways. PMID:29895619
Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L. PMID:29882896
Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species. PMID:29876074
Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae. PMID:29693617
Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon. PMID:29675466
Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses. PMID:29494509
Complete chloroplast genome of the medicinal plant Amomum compactum: gene organization, comparative analysis, and phylogenetic relationships within Zingiberales. PMID:29449878
The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species. PMID:29439505
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii. PMID:29373520
At-MINI ZINC FINGER2 and Sl-INHIBITOR OF MERISTEM ACTIVITY, a Conserved Missing Link in the Regulation of Floral Meristem Termination in Arabidopsis and Tomato. PMID:29298836
Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species. PMID:29186778
The Complete Amomum kravanh Chloroplast Genome Sequence and Phylogenetic Analysis of the Commelinids. PMID:29104233
Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album. PMID:29056940
Comparative analysis reveals regulatory motifs at the ainS/ainR pheromone-signaling locus of Vibrio fischeri. PMID:28916743
Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua. PMID:28800082
Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. PMID:28683832
BAC Recombineering of the Agouti Loci from Spotted Gar and Zebrafish Reveals the Evolutionary Ancestry of Dorsal-Ventral Pigment Asymmetry in Fish. PMID:28544213
The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms. PMID:28500291
A Two-Step Model for de Novo Activation of WUSCHEL during Plant Shoot Regeneration. PMID:28389585
Diversification of spatiotemporal expression and copy number variation of the echinoid hbox12/pmar1/micro1 multigene family. PMID:28350855
Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at FLC orthologues. PMID:28261921
Zebrafish transgenic constructs label specific neurons in Xenopus laevis spinal cord and identify frog V0v spinal neurons. PMID:28188691
Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies. PMID:28178222
Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives. PMID:28152978
The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman. PMID:28085925
Alternative intronic promoters in development and disease. PMID:28078440
Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes. PMID:27999584
The genome of the Gulf pipefish enables understanding of evolutionary innovations. PMID:27993155
Transcriptional programs that control expression of the autoimmune regulator gene Aire. PMID:27941786
Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton. PMID:27902701
A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. PMID:27898393
Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. PMID:27729060
Chloroplast genome structure in Ilex (Aquifoliaceae). PMID:27378489
TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. PMID:26940763
Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2-independent mechanism. PMID:26896392
Parallel Evolution of Polydactyly Traits in Chinese and European Chickens. PMID:26859147
Spatially differentiated expression of quadruplicated green-sensitive RH2 opsin genes in zebrafish is determined by proximal regulatory regions and gene order to the locus control region. PMID:26537431
Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development. PMID:26464005
Clostridium difficile: New Insights into the Evolution of the Pathogenicity Locus. PMID:26446480
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
A shift in anterior-posterior positional information underlies the fin-to-limb evolution. PMID:26283004
Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus. PMID:26275815
Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus. PMID:26100509
Evolution of CONSTANS Regulation and Function after Gene Duplication Produced a Photoperiodic Flowering Switch in the Brassicaceae. PMID:25972346
Expression of leukemia inhibitory factor in Müller glia cells is regulated by a redox-dependent mRNA stability mechanism. PMID:25907681
Molecular development of chondrichthyan claspers and the evolution of copulatory organs. PMID:25868783
Adult Deletion of SRF Increases Epileptogenesis and Decreases Activity-Induced Gene Expression. PMID:25636686
A method for calculating probabilities of fitness consequences for point mutations across the human genome. PMID:25599402
Identification and computational analysis of gene regulatory elements. PMID:25561628
Regulation of CDX4 gene transcription by HoxA9, HoxA10, the Mll-Ell oncogene and Shp2 during leukemogenesis. PMID:25531430
Genetics and timing of sex determination in the East African cichlid fish Astatotilapia burtoni. PMID:25494637
Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species. PMID:25427255
Evening expression of arabidopsis GIGANTEA is controlled by combinatorial interactions among evolutionarily conserved regulatory motifs. PMID:25361953
Comparative assembly hubs: web-accessible browsers for comparative genomics. PMID:25138168
Nkx2-5 regulates cardiac growth through modulation of Wnt signaling by R-spondin3. PMID:25053429
Evolutionary conservation of cold-induced antisense RNAs of FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives. PMID:25030056
Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. PMID:25001059
The brain-uterus connection: brain derived neurotrophic factor (BDNF) and its receptor (Ntrk2) are conserved in the mammalian uterus. PMID:24714156
Appearance of Planktothrix rubescens bloom with [D-Asp3, Mdha7]MC-RR in gravel pit pond of a shallow lake-dominated area. PMID:24351711
Immune-related functions of the Hivep gene family in East African cichlid fishes. PMID:24142922
Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. PMID:24089456
Comparative chloroplast genomes of camellia species. PMID:24009730
Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. PMID:23997651
Increased Fanconi C expression contributes to the emergency granulopoiesis response. PMID:23925293
Unraveling genomic variation from next generation sequencing data. PMID:23885890
Expression and sequence evolution of aromatase cyp19a1 and other sexual development genes in East African cichlid fishes. PMID:23883521
MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis. PMID:23847151
FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain. PMID:23826354
Natural killer cell receptor genes in the family Equidae: not only Ly49. PMID:23724088
Transcriptional repression of BODENLOS by HD-ZIP transcription factor HB5 in Arabidopsis thaliana. PMID:23682118
Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. PMID:23597078
Predicting the next eye pathogen: analysis of a novel adenovirus. PMID:23572555
Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16. PMID:23408978
Genetic determinants of haemolysis in sickle cell anaemia. PMID:23406172
Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. PMID:23393190
Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements. PMID:23201014
Expression and promoter analysis of a highly restricted integrin alpha gene in vascular smooth muscle. PMID:23142384
Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes. PMID:23055411
β-Catenin activates the HOXA10 and CDX4 genes in myeloid progenitor cells. PMID:23038246
BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border. PMID:23034628
Theria-specific homeodomain and cis-regulatory element evolution of the Dlx3-4 bigene cluster in 12 different mammalian species. PMID:22951979
Genomic basis of a polyagglutinating isolate of Neisseria meningitidis. PMID:22904290
An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference. PMID:22851613
Looping mediated interaction between the promoter and 3' UTR regulates type II collagen expression in chondrocytes. PMID:22815835
Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties. PMID:22666536
Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PMID:22606240
The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids. PMID:22555800
Human invariant natural killer T cells acquire transient innate responsiveness via histone H4 acetylation induced by weak TCR stimulation. PMID:22508835
Adaptor protein LNK is a negative regulator of brain neural stem cell proliferation after stroke. PMID:22496561
HoxA10 protein regulates transcription of gene encoding fibroblast growth factor 2 (FGF2) in myeloid cells. PMID:22493287
Contrasted patterns of molecular evolution in dominant and recessive self-incompatibility haplotypes in Arabidopsis. PMID:22457631
EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. PMID:22327739
Overreliance on the hexon gene, leading to misclassification of human adenoviruses. PMID:22301156
Leiomodin 1, a new serum response factor-dependent target gene expressed preferentially in differentiated smooth muscle cells. PMID:22157009
The Enhancer of split complex arose prior to the diversification of schizophoran flies and is strongly conserved between Drosophila and stalk-eyed flies (Diopsidae). PMID:22151427
GenomeView: a next-generation genome browser. PMID:22102585
ETS-dependent regulation of a distal Gata4 cardiac enhancer. PMID:22056786
Functional characterization of human Kindlin-2 core promoter identifies a key role of SP1 in Kindlin-2 transcriptional regulation. PMID:21922223
Genomic sequence around butterfly wing development genes: annotation and comparative analysis. PMID:21909358
A novel mechanism for the transcriptional regulation of Wnt signaling in development. PMID:21856776
Computationally designed adeno-associated virus (AAV) Rep 78 is efficiently maintained within an adenovirus vector. PMID:21844368
Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. PMID:21841803
Smooth muscle calponin: an unconventional CArG-dependent gene that antagonizes neointimal formation. PMID:21817093
ELAV-mediated 3'-end processing of ewg transcripts is evolutionarily conserved despite sequence degeneration of the ELAV-binding site. PMID:21705751
High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PMID:21655229
p53 directly represses Id2 to inhibit the proliferation of neural progenitor cells. PMID:21608079
Informatic and functional approaches to identifying a regulatory region for the cardiac sodium channel. PMID:21566215
Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. PMID:21518738
HoxA10 activates CDX4 transcription and Cdx4 activates HOXA10 transcription in myeloid cells. PMID:21471217
A novel g.-1258G>A mutation in a conserved putative regulatory element of PAX9 is associated with autosomal dominant molar hypodontia. PMID:21443745
Expression of the Distalless-B gene in Ciona is regulated by a pan-ectodermal enhancer module. PMID:21338600
Contribution of rapid evolution of the luxR-luxI intergenic region to the diverse bioluminescence outputs of Vibrio fischeri strains isolated from different environments. PMID:21317265
Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events. PMID:21247963
Genetic variation in the beta2 subunit of the voltage-gated calcium channel and pharmacogenetic association with adverse cardiovascular outcomes in the INternational VErapamil SR-Trandolapril STudy GENEtic Substudy (INVEST-GENES). PMID:21156931
The genomic constellation of a novel avian orthoreovirus strain associated with runting-stunting syndrome in broilers. PMID:21116842
Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans. PMID:21106068
HoxA10 regulates transcription of the gene encoding transforming growth factor beta2 (TGFbeta2) in myeloid cells. PMID:21087928
Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. PMID:21056888
Information Visualization Techniques in Bioinformatics during the Postgenomic Era. PMID:20976032
Two lamprey Hedgehog genes share non-coding regulatory sequences and expression patterns with gnathostome Hedgehogs. PMID:20967201
Direct transcriptional regulation of Gata4 during early endoderm specification is controlled by FoxA2 binding to an intronic enhancer. PMID:20692247
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PMID:20593022
Myoferlin regulation by NFAT in muscle injury, regeneration and repair. PMID:20571050
Transcriptional regulation of Elf-1: locus-wide analysis reveals four distinct promoters, a tissue-specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation. PMID:20525788
Convergence of Notch and beta-catenin signaling induces arterial fate in vascular progenitors. PMID:20404113
Promoters of the barley germin-like GER4 gene cluster enable strong transgene expression in response to pathogen attack. PMID:20305123
Visualizing genomes: techniques and challenges. PMID:20195257
Intronic elements in the Na+/I- symporter gene (NIS) interact with retinoic acid receptors and mediate initiation of transcription. PMID:20123735
Genome-wide profiling of populus small RNAs. PMID:20021695
In silico analysis of human Telomerase Reverse Transcriptase (hTERT) gene: identification of a distant homolog of Melanoma Antigen Family Gene (MAGE). PMID:20011463
Autonomic function in hypertension; role of genetic variation at the catecholamine storage vesicle protein chromogranin B. PMID:20011129
Genome-wide scans for footprints of natural selection. PMID:20008396
Identification and characterization of odorant-binding protein 1 gene from the Asian malaria mosquito, Anopheles stephensi. PMID:19909381
Requirement for the basic helix-loop-helix transcription factor Dec2 in initial TH2 lineage commitment. PMID:19881507
Peptide YY (PYY) gene polymorphisms in the 3'-untranslated and proximal promoter regions regulate cellular gene expression and PYY secretion and metabolic syndrome traits in vivo. PMID:19820027
Exploratory visual analysis of conserved domains on multiple sequence alignments. PMID:19811691
Characterization of the shsp genes in Drosophila buzzatii and association between the frequency of Valine mutations in hsp23 and climatic variables along a longitudinal gradient in Australia. PMID:19806471
The interferon consensus sequence binding protein (ICSBP/IRF8) activates transcription of the FANCF gene during myeloid differentiation. PMID:19801548
Myocardin-dependent activation of the CArG box-rich smooth muscle gamma-actin gene: preferential utilization of a single CArG element through functional association with the NKX3.1 homeodomain protein. PMID:19797053
An endoderm-specific transcriptional enhancer from the mouse Gata4 gene requires GATA and homeodomain protein-binding sites for function in vivo. PMID:19777593
Nuclear factor of activated T cells mediates fluid shear stress- and tensile strain-induced Cox2 in human and murine bone cells. PMID:19748606
Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. PMID:19675151
Melanism in peromyscus is caused by independent mutations in agouti. PMID:19649329
Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years. PMID:19583854
Isl1 is a direct transcriptional target of Forkhead transcription factors in second-heart-field-derived mesoderm. PMID:19580802
Evolution of developmental regulation in the vertebrate FgfD subfamily. PMID:19562753
Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout. PMID:19549339
Reliable means of diagnosis and serovar determination of blood-borne Salmonella strains: quick PCR amplification of unique genomic loci by novel primer sets. PMID:19535522
Functional and comparative genomics analyses of pmp22 in medaka fish. PMID:19534778
Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks. PMID:19443447
Dynamic in vivo binding of STAT5 to growth hormone-regulated genes in intact rat liver. Sex-specific binding at low- but not high-affinity STAT5 sites. PMID:19423653
Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups. PMID:19335879
Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. PMID:19184460
Identification of an ancient Bmp4 mesoderm enhancer located 46 kb from the promoter. PMID:19159624
Identification of direct T-box target genes in the developing zebrafish mesoderm. PMID:19158186
Shaping skeletal growth by modular regulatory elements in the Bmp5 gene. PMID:19096511
Mutation analysis of a large Chinese pedigree with congenital preaxial polydactyly. PMID:19066618
Identification and characterization of new long conserved noncoding sequences in vertebrates. PMID:19015917
Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. PMID:18842825
Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster. PMID:18791732
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. PMID:18753151
The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. PMID:18710514
GATA transcription factors directly regulate the Parkinson's disease-linked gene alpha-synuclein. PMID:18669654
The evolution of the DLK1-DIO3 imprinted domain in mammals. PMID:18532878
Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters. PMID:18493037
Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum. PMID:18488228
Epigenetic blocking of an enhancer region controls irradiation-induced proapoptotic gene expression in Drosophila embryos. PMID:18410726
Cis-regulatory organization of the Pax6 gene in the ascidian Ciona intestinalis. PMID:18342846
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. PMID:18282510
Rescue from oculocutaneous albinism type 4 using medaka slc45a2 cDNA driven by its own promoter. PMID:18245373
Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment. PMID:18218066
Ascorbate peroxidase gene family in tomato: its identification and characterization. PMID:18026995
Mulan: multiple-sequence alignment to predict functional elements in genomic sequences. PMID:17993678
ADAM15 gene structure and differential alternative exon use in human tissues. PMID:17937806
Statistical power of phylo-HMM for evolutionarily conserved element detection. PMID:17919331
Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni. PMID:17845724
Characterization of the equine 2'-5' oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes. PMID:17822564
Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. PMID:17822543
Phylogenomic analyses of KCNA gene clusters in vertebrates: why do gene clusters stay intact? PMID:17697377
Identification of conserved domains in the promoter regions of nitric oxide synthase 2: implications for the species-specific transcription and evolutionary differences. PMID:17686182
SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approach. PMID:17683615
Mechanistic role of a disease-associated genetic variant within the ADAM33 asthma susceptibility gene. PMID:17640346
Blueprint for a high-performance biomaterial: full-length spider dragline silk genes. PMID:17565367
Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction. PMID:17559649
PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes. PMID:17535443
New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. PMID:17534720
Positive selection within the Schizophrenia-associated GABA(A) receptor beta(2) gene. PMID:17520021
Hand is a direct target of the forkhead transcription factor Biniou during Drosophila visceral mesoderm differentiation. PMID:17511863
Single nucleotide polymorphism discovery and haplotype analysis of Ca2+-dependent K+ channel beta-1 subunit. PMID:17496725
G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. PMID:17496117
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. PMID:17488840
Basal and 3,3',4,4',5-pentachlorobiphenyl-induced expression of cytochrome P450 1A, 1B and 1C genes in zebrafish. PMID:17445853
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. PMID:17428329
Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PMID:17426814
Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements. PMID:17362514
Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. PMID:17310332
Somatic sequence alterations in twenty-one genes selected by expression profile analysis of breast carcinomas. PMID:17224074
Comparative genomic analysis of prion genes. PMID:17199895
Brn3a target gene recognition in embryonic sensory neurons. PMID:17196582
Identification of long-range regulatory elements in the protocadherin-alpha gene cluster. PMID:17172445
Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila. PMID:17163987
Mutation of a ubiquitously expressed mouse transmembrane protein (Tapt1) causes specific skeletal homeotic transformations. PMID:17151244
Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. PMID:17135569
Genetic analysis of the GRIK2 modifier effect in Huntington's disease. PMID:16959037
Identification of the ancestral killer immunoglobulin-like receptor gene in primates. PMID:16911775
Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. PMID:16872532
Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. PMID:16859531
FoxA2, Nkx2.2, and PDX-1 regulate islet beta-cell-specific mafA expression through conserved sequences located between base pairs -8118 and -7750 upstream from the transcription start site. PMID:16847327
Phosphodiesterase 4D polymorphisms and the risk of cerebral infarction in a biracial population: the Stroke Prevention in Young Women Study. PMID:16835261
Spatial and temporal divergence of expression in duplicated barley germin-like protein-encoding genes. PMID:16751662
Precraniate origin of cranial motoneurons. PMID:16735475
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles. PMID:16719907
Functional conservation of Pax6 regulatory elements in humans and mice demonstrated with a novel transgenic reporter mouse. PMID:16674807
Duplication and relocation of the functional DPY19L2 gene within low copy repeats. PMID:16526957
Concerted evolution of two novel protein families in Caenorhabditis species. PMID:16415360
An analysis of genetic variation across the MBL2 locus in Dutch Caucasians indicates that 3' haplotypes could modify circulating levels of mannose-binding lectin. PMID:16208516
Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements. PMID:16204191
Web-based resources for comparative genomics. PMID:16197736
Comparative analysis in cereals of a key proline catabolism gene. PMID:16179990
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. PMID:16024819
Distribution and intensity of constraint in mammalian genomic sequence. PMID:15965027
A microRNA polycistron as a potential human oncogene. PMID:15944707
Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels. PMID:15897982
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. PMID:15867430
Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene. PMID:15859353
An inversion involving the mouse Shh locus results in brachydactyly through dysregulation of Shh expression. PMID:15841179
Strong polyadenylation and weak pausing combine to cause efficient termination of transcription in the human Ggamma-globin gene. PMID:15798211
An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. PMID:15778292
Functional evolution of a cis-regulatory module. PMID:15757364
The architecture of mammalian ribosomal protein promoters. PMID:15707503
Organization of the MASP2 locus and its expression profile in mouse and rat. PMID:15672593
Highly conserved non-coding sequences are associated with vertebrate development. PMID:15630479
Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis. PMID:15598802
Mulan: multiple-sequence local alignment and visualization for studying function and evolution. PMID:15590941
ABC: software for interactive browsing of genomic multiple sequence alignment data. PMID:15588288
Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. PMID:15545497
A computational and experimental approach toward a priori identification of alternatively spliced exons. PMID:15525709
Whole-genome analysis of temporal gene expression during foregut development. PMID:15492775
Evolution of programmed ribosomal frameshifting in the TERT genes of Euplotes. PMID:15461427
Core promoter sequences contribute to ovo-B regulation in the Drosophila melanogaster germline. PMID:15371353
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. PMID:15345045
Comparison of the genomic structure and variation in the two human sodium-dependent vitamin C transporters, SLC23A1 and SLC23A2. PMID:15316768
Linkage disequilibrium and association of MAPT H1 in Parkinson disease. PMID:15297935
Nucleotide variation in the Egfr locus of Drosophila melanogaster. PMID:15280235
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. PMID:15215395
VISTA: computational tools for comparative genomics. PMID:15215394
Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. PMID:15198975
eShadow: a tool for comparing closely related sequences. PMID:15173121
A giant novel gene undergoing extensive alternative splicing is severed by a Cornelia de Lange-associated translocation breakpoint at 3q26.3. PMID:15168106
Sockeye: a 3D environment for comparative genomics. PMID:15123592
Automated whole-genome multiple alignment of rat, mouse, and human. PMID:15060011
Organization and expression of the SLC36 cluster of amino acid transporter genes. PMID:15058382
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. PMID:14993211
Both rare and common polymorphisms contribute functional variation at CHGA, a regulator of catecholamine physiology. PMID:14740315
Pattern of diversity in the genomic region near the maize domestication gene tb1. PMID:14701910
Multi-species sequence comparison: the next frontier in genome annotation. PMID:14659006
Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. PMID:14656967
Identification and characterization of multi-species conserved sequences. PMID:14656959
Comparative genomics. PMID:14624258
OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. PMID:12952558
Insights from human/mouse genome comparisons. PMID:12925891
Strong conservation of the human NF2 locus based on sequence comparison in five species. PMID:12925885
A general approach for identifying distant regulatory elements applied to the Gdf6 gene. PMID:12915490
Recent segmental and gene duplications in the mouse genome. PMID:12914656
Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. PMID:12840041
MAVID multiple alignment server. PMID:12824358
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. PMID:12824357
Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence. PMID:12824356
Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. PMID:12724540
A strategy for identifying transcription factor binding sites reveals two classes of genomic c-Myc target sites. PMID:12702757
Comparative genomic tools and databases: providing insights into the human genome. PMID:12697725
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. PMID:12654723
Toucan: deciphering the cis-regulatory logic of coregulated genes. PMID:12626717
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. PMID:12537575
AVID: A global alignment program. PMID:12529311
Strategies and tools for whole-genome alignments. PMID:12529308
Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. PMID:12529304
Reevaluating human gene annotation: a second-generation analysis of chromosome 22. PMID:12529303
Cross-species sequence comparisons: a review of methods and available resources. PMID:12529301
SeqVISTA: a graphical tool for sequence feature visualization and comparison. PMID:12513700
Comparative genomic sequence analysis of the human chromosome 21 Down syndrome critical region. PMID:12213769
Sequence variation and haplotype structure at the human HFE locus. PMID:12196404
Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. PMID:12097338
rVista for comparative sequence-based discovery of functional transcription factor binding sites. PMID:11997350
Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci. PMID:11997341
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. PMID:11997337
Utility and distribution of conserved noncoding sequences in the grasses. PMID:11972021
Multiple regions within the promoter of the murine Ifnar-2 gene confer basal and inducible expression. PMID:11939908
Molecular characterization and mapping of ATOH7, a human atonal homolog with a predicted role in retinal ganglion cell development. PMID:11889557
Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. PMID:11779826
PharmGKB: the Pharmacogenetics Knowledge Base. PMID:11752281
What use is the human genome for understanding the mouse? PMID:11737939
Non-coding RNAs: the architects of eukaryotic complexity. PMID:11713189
Human and mouse alpha-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element. PMID:11156617
AVID: A global alignment program PubMed citations: 153.

153 articles citing: AVID: A global alignment program

A Python-based programming language for high-performance computational genomics. PMID:34282326
A prescient evolutionary model for genesis, duplication and differentiation of MIR160 homologs in Brassicaceae. PMID:34052911
The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts. PMID:33533895
GSAlign: an efficient sequence alignment tool for intra-species genomes. PMID:32093618
Taxogenomics and Systematics of the Genus Pantoea. PMID:31736906
Comparative genomics reveals origin of MIR159A-MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae. PMID:30840147
A fast adaptive algorithm for computing whole-genome homology maps. PMID:30423094
Whole-Genome Alignment and Comparative Annotation. PMID:30379572
Haplotyping of Cornus florida and C. kousa chloroplasts: Insights into species-level differences and patterns of plastic DNA variation in cultivars. PMID:30352068
Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae. PMID:30242472
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points. PMID:29992260
Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus. PMID:29989238
Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage. PMID:29925900
The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. PMID:29684203
The genome of the Gulf pipefish enables understanding of evolutionary innovations. PMID:27993155
Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. PMID:27729060
Spatially differentiated expression of quadruplicated green-sensitive RH2 opsin genes in zebrafish is determined by proximal regulatory regions and gene order to the locus control region. PMID:26537431
Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas. PMID:26276216
The achaete-scute complex in Diptera: patterns of noncoding sequence evolution. PMID:26134680
Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment. PMID:25983537
Adult Deletion of SRF Increases Epileptogenesis and Decreases Activity-Induced Gene Expression. PMID:25636686
GenomeVISTA--an integrated software package for whole-genome alignment and visualization. PMID:24860159
Local similarity search to find gene indicators in mitochondrial genomes. PMID:24833343
Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PMID:24786295
Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. PMID:24089456
Animal models for studying female genital tract infection with Chlamydia trachomatis. PMID:23836817
Genomic organisation of the seven ParaHox genes of coelacanths. PMID:23775937
FOGSAA: Fast Optimal Global Sequence Alignment Algorithm. PMID:23624407
Embryonic stem cell-derived granulosa cells participate in ovarian follicle formation in vitro and in vivo. PMID:23536570
Mir-125a-5p-mediated regulation of Lfng is essential for the avian segmentation clock. PMID:23484856
Regulatory genomics: Insights from the zebrafish. PMID:23440612
A comparative approach to understanding tissue-specific expression of uncoupling protein 1 expression in adipose tissue. PMID:23293654
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. PMID:23110901
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. PMID:22988817
Long read alignment based on maximal exact match seeds. PMID:22962447
Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp. PMID:22911737
Hox genes regulate the onset of Tbx5 expression in the forelimb. PMID:22872086
The molecular mechanism of action of the CR6261-Azichromycin combination found through computational analysis. PMID:22693576
Accounting for alignment uncertainty in phylogenomics. PMID:22272325
Molecular mechanisms of EGF signaling-dependent regulation of pipe, a gene crucial for dorsoventral axis formation in Drosophila. PMID:22198544
Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules. PMID:22115527
A guided tour of large genome size in animals: what we know and where we are heading. PMID:22042526
Genomic sequence around butterfly wing development genes: annotation and comparative analysis. PMID:21909358
Expression of Mirlet7 family microRNAs in response to retinoic acid-induced spermatogonial differentiation in mice. PMID:21430230
A novel Gli3 enhancer controls the Gli3 spatiotemporal expression pattern through a TALE homeodomain protein binding site. PMID:21262763
A genome alignment algorithm based on compression. PMID:21159205
Mugsy: fast multiple alignment of closely related whole genomes. PMID:21148543
Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems. PMID:20565733
Cgaln: fast and space-efficient whole-genome alignment. PMID:20433723
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. PMID:20407027
LEF1/beta-catenin complex regulates transcription of the Cav3.1 calcium channel gene (Cacna1g) in thalamic neurons of the adult brain. PMID:20371816
MISHIMA--a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. PMID:20298584
Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins. PMID:19951405
Deletion of an enhancer near DLX5 and DLX6 in a family with hearing loss, craniofacial defects, and an inv(7)(q21.3q35). PMID:19707792
Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. PMID:19675151
Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. PMID:19602626
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. PMID:19561337
Genome-wide analysis of conservation and divergence of microsatellites in rice. PMID:19484264
MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes. PMID:19430601
Dynamic in vivo binding of STAT5 to growth hormone-regulated genes in intact rat liver. Sex-specific binding at low- but not high-affinity STAT5 sites. PMID:19423653
Strategies for reliable exploitation of evolutionary concepts in high throughput biology. PMID:19204813
Multiple whole-genome alignments without a reference organism. PMID:19176791
Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. PMID:19175934
BEAP: The BLAST Extension and Alignment Program- a tool for contig construction and analysis of preliminary genome sequence. PMID:19159488
Giant panda genomic data provide insight into the birth-and-death process of mammalian major histocompatibility complex class II genes. PMID:19127303
ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets. PMID:19014503
Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics. PMID:19003267
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. PMID:18971253
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. PMID:18849524
Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster. PMID:18791732
ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. PMID:18294369
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. PMID:18282510
A survey of DNA motif finding algorithms. PMID:18047721
TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. PMID:18045502
Mulan: multiple-sequence alignment to predict functional elements in genomic sequences. PMID:17993678
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. PMID:17956628
Identification of conserved domains in the promoter regions of nitric oxide synthase 2: implications for the species-specific transcription and evolutionary differences. PMID:17686182
Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages. PMID:17570149
Blueprint for a high-performance biomaterial: full-length spider dragline silk genes. PMID:17565367
Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction. PMID:17559649
Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene. PMID:17557180
Alternative promoters and repetitive DNA elements define the species-dependent tissue-specific expression of the FMO1 genes of human and mouse. PMID:17547558
Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach. PMID:17488849
The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals. PMID:17333539
Dynamic use of multiple parameter sets in sequence alignment. PMID:17182633
Genomic selective constraints in murid noncoding DNA. PMID:17166057
Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution. PMID:17075697
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. PMID:17062155
inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons. PMID:17054788
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. PMID:17022809
An integrative method for accurate comparative genome mapping. PMID:16933978
Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus. PMID:16884529
Breakup of a homeobox cluster after genome duplication in teleosts. PMID:16801555
MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution. PMID:16762073
Transcription factor map alignment of promoter regions. PMID:16733547
Chaos game representation for comparison of whole genomes. PMID:16677374
Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PMID:16609730
Duplication and relocation of the functional DPY19L2 gene within low copy repeats. PMID:16526957
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. PMID:16509994
A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol. PMID:16465619
Identification of a tandem duplicated array in the Rhox alpha locus on mouse chromosome X. PMID:16465597
A novel approach to identifying regulatory motifs in distantly related genomes. PMID:16420672
Application of a superword array in genome assembly. PMID:16397298
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. PMID:16381947
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy. PMID:16336695
Multiple sequence alignment accuracy and evolutionary distance estimation. PMID:16305750
Specific-pathogen-free pigs as an animal model for studying Chlamydia trachomatis genital infection. PMID:16299329
An analysis of genetic variation across the MBL2 locus in Dutch Caucasians indicates that 3' haplotypes could modify circulating levels of mannose-binding lectin. PMID:16208516
Genomic multiple sequence alignments: refinement using a genetic algorithm. PMID:16086841
The scale of mutational variation in the murid genome. PMID:16024822
CONREAL web server: identification and visualization of conserved transcription factor binding sites. PMID:15980509
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. PMID:15980497
Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method. PMID:15943864
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. PMID:15867430
Evolutionary distance estimation and fidelity of pair wise sequence alignment. PMID:15840174
Silencing of Fshr occurs through a conserved, hypersensitive site in the first intron. PMID:15817654
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. PMID:15790396
Principles of microRNA-target recognition. PMID:15723116
The architecture of mammalian ribosomal protein promoters. PMID:15707503
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. PMID:15632085
GenomeViz: visualizing microbial genomes. PMID:15601465
Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis. PMID:15598802
Mulan: multiple-sequence local alignment and visualization for studying function and evolution. PMID:15590941
Human MicroRNA targets. PMID:15502875
A comprehensive transcript index of the human genome generated using microarrays and computational approaches. PMID:15461792
Evolution of programmed ribosomal frameshifting in the TERT genes of Euplotes. PMID:15461427
Comparative genomics: methods and applications. PMID:15278216
Mauve: multiple alignment of conserved genomic sequence with rearrangements. PMID:15231754
VISTA: computational tools for comparative genomics. PMID:15215394
Building genomic profiles for uncovering segmental homology in the twilight zone. PMID:15173115
GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes. PMID:15128433
Visualization of multiple genome annotations and alignments with the K-BROWSER. PMID:15060015
MAVID: constrained ancestral alignment of multiple sequences. PMID:15060012
Pash: efficient genome-scale sequence anchoring by Positional Hashing. PMID:15060009
MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. PMID:14993209
Whole-genome shotgun assembly and comparison of human genome assemblies. PMID:14769938
Versatile and open software for comparing large genomes. PMID:14759262
Benchmarking tools for the alignment of functional noncoding DNA. PMID:14736341
MicroRNA targets in Drosophila. PMID:14709173
Pattern of diversity in the genomic region near the maize domestication gene tb1. PMID:14701910
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. PMID:14672977
Multi-species sequence comparison: the next frontier in genome annotation. PMID:14659006
Projector: automatic contig mapping for gap closure purposes. PMID:14602937
Insights from human/mouse genome comparisons. PMID:12925891
Computational identification of Drosophila microRNA genes. PMID:12844358
MAVID multiple alignment server. PMID:12824358
SLAM web server for comparative gene finding and alignment. PMID:12824355
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. PMID:12814519
Comparative genomic tools and databases: providing insights into the human genome. PMID:12697725
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. PMID:12654723
SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. PMID:12618381
Strategies and tools for whole-genome alignments. PMID:12529308
Cross-species sequence comparisons: a review of methods and available resources. PMID:12529301

Glocal alignment: finding rearrangements during alignment PubMed citations: 143.

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments PubMed citations: 21.

Multiple whole genome alignments and novel biomedical applications at the VISTA portal PubMed citations: 16.

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gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

transcription factors and regulatory sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

dna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

sequence assembly
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

gene transcripts mapping transcription factors and regulatory sites dna sequence assembly rare diseases

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VISTA

Names
More detailed information about this field from each metasource.

VISTA
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

vista
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

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VISTA Enhancer Browser

LncVar

RegPrecise

UCSC Genome Browser database

PAZAR

SwissRegulon

hTFtarget

GenoList Genome Browser

The Arabidopsis Gene Regulatory Information Server

refTSS

IPD-MHC - Major Histocompatibility Complex Database

PASS2

CRISPRs Database

Animal Transcription Factor Database

Annotated regulatory Binding Sites from Orthologous Promoters

RsHSF

TcoF-DB

FlyFactorSurvey

BacHBerryEXP

RAEdb

VISTA Names More detailed information about this field from each metasource. × VISTA metasource: bio.tools version: extracted_at: 2022-11-04T11:30:57.636780 vista metasource: bio.tools version: extracted_at: 2022-11-04T11:30:57.636780 Close

Webpage:

More to explore:

1/20

VISTA Enhancer Browser

LncVar

RegPrecise

UCSC Genome Browser database

PAZAR

SwissRegulon

hTFtarget

GenoList Genome Browser

The Arabidopsis Gene Regulatory Information Server

refTSS

IPD-MHC - Major Histocompatibility Complex Database

PASS2

CRISPRs Database

Animal Transcription Factor Database

Annotated regulatory Binding Sites from Orthologous Promoters

RsHSF

TcoF-DB

FlyFactorSurvey

BacHBerryEXP

RAEdb

VISTA

Names
More detailed information about this field from each metasource.

VISTA
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

vista
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780