Ensembl Compara
Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.
Description
More detailed information about this field from each metasource.
Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:36.128941
Webpage:
http://www.ensembl.org/info/genome/compara/index.htmlWebpage
More detailed information about this field from each metasource.
http://www.ensembl.org/info/genome/compara/index.html
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:36.128941
Licence:
Name: UnlicenseLicence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
PMID: 19029536
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:36.128941
Publications
More detailed information about this field from each metasource.
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
PMID: 19029536
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:36.128941
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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
PubMed citations: 615.
615 articles citing: EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding. PMID:35851624
Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts. PMID:35710325
Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. PMID:35698132
Genetic Diversity and Genetic Differentiation of Populations of Golden-Backed Carp (Cyprinus carpio var. Jinbei) in Traditional Rice Fields in Guizhou, China. PMID:35681841
Patterns of genomic divergence in sympatric and allopatric speciation of three Mihoutao (Actinidia) species. PMID:35591930
Mutations in Growth-Related Genes Induced by EMS Treatment in Scallops. PMID:35559043
The Quest for Orthologs orthology benchmark service in 2022. PMID:35552456
Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. PMID:35508966
Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding. PMID:35484301
Chromosome-level genome assembly and characterization of Sophora Japonica. PMID:35466378
Two Cladosporium Fungi with Opposite Functions to the Chinese White Wax Scale Insect Have Different Genome Characters. PMID:35330288
AutoCoEv-A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution. PMID:35328772
G-quadruplex occurrence and conservation: more than just a question of guanine-cytosine content. PMID:35261973
The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. PMID:35189950
The Evolution of Oxytocin and Vasotocin Receptor Genes in Jawed Vertebrates: A Clear Case for Gene Duplications Through Ancestral Whole-Genome Duplications. PMID:35185783
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
Translational relevance of forward genetic screens in animal models for the study of psychiatric disease. PMID:35124155
Evolutionary history of type II transmembrane serine proteases involved in viral priming. PMID:35122525
Minc03328 effector gene downregulation severely affects Meloidogyne incognita parasitism in transgenic Arabidopsis thaliana. PMID:35050413
Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum. PMID:35013486
Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards. PMID:34919713
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (Trapa spp., Lythraceae). PMID:34861095
Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry. PMID:34847934
Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors. PMID:34792170
Ensembl 2022. PMID:34791404
Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change. PMID:34689746
PIC-Me: paralogs and isoforms classifier based on machine-learning approaches. PMID:34674638
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip. PMID:34535071
Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome. PMID:34469736
The bowfin genome illuminates the developmental evolution of ray-finned fishes. PMID:34462605
Genetic diversity and main functional composition of Lingzhi strains from main producing areas in China. PMID:34417676
Environmental impacts of COVID-19 treatment: Toxicological evaluation of azithromycin and hydroxychloroquine in adult zebrafish. PMID:34380260
Exploring the genomic resources and analysing the genetic diversity and population structure of Chinese indigenous rabbit breeds by RAD-seq. PMID:34311701
Response to sulfur in Schizosaccharomyces pombe. PMID:34279603
In vivo and in vitro human gene essentiality estimations capture contrasting functional constraints. PMID:34268495
The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts. PMID:34253727
A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis. PMID:34230458
The complete chloroplast genome of Cymbidium dayanum (Orchidaceae). PMID:34151012
Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.). PMID:34082694
Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. PMID:34079582
Region-specific expression of young small-scale duplications in the human central nervous system. PMID:33882820
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow. PMID:33787929
Molecular characteristics of Brucella melitensis isolates from humans in Qinghai Province, China. PMID:33771234
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau. PMID:33753478
Biological impact of mutually exclusive exon switching. PMID:33651795
Genomic Evidence for Convergent Molecular Adaptation in Electric Fishes. PMID:33638979
The utilization of small non-mammals in traumatic brain injury research: A systematic review. PMID:33539662
Integration of metabolomics and transcriptomics reveals convergent pathways driving radiation-induced salivary gland dysfunction. PMID:33522389
The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia. PMID:33487168
Characterization of the complete chloroplast genome of Musella lasiocarpa. PMID:33474300
The complete chloroplast genome of Catalpa 'Bairihua', a hybrid variety with multi season flowering. PMID:33457939
Characterization of the complete chloroplast genome of Tilia taishanensis S. B. Liang (Tiliaceae). PMID:33457919
Zebrafish models of acute leukemias: Current models and future directions. PMID:33340278
The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy. PMID:33328438
Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress. PMID:33304549
MobiDB: intrinsically disordered proteins in 2021. PMID:33237329
A generalized Robinson-Foulds distance for labeled trees. PMID:33208096
A novel systems biology approach to evaluate mouse models of late-onset Alzheimer's disease. PMID:33172468
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
The structural variation landscape in 492 Atlantic salmon genomes. PMID:33056985
Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics. PMID:33010949
Genomic analyses of diverse wild and cultivated accessions provide insights into the evolutionary history of jujube. PMID:32946650
The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2'-O-Me sites. PMID:32912962
Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken. PMID:32883984
Comparative transcriptomics of primary cells in vertebrates. PMID:32718981
Exploring Protein Intrinsic Disorder with MobiDB. PMID:32696355
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. PMID:32619550
Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. PMID:32616020
A scalable SCENIC workflow for single-cell gene regulatory network analysis. PMID:32561888
Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic. PMID:32555586
Comparative population genomics dissects the genetic basis of seven domestication traits in jujube. PMID:32528701
Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. PMID:32499537
Gapless assembly of maize chromosomes using long-read technologies. PMID:32434565
Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing. PMID:32377359
Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development. PMID:32374726
Loss of Arabidopsis β-COP Function Affects Golgi Structure, Plant Growth and Tolerance to Salt Stress. PMID:32351533
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. PMID:32343307
Molecular Characteristics of Brucella Isolates Collected From Humans in Hainan Province, China. PMID:32292391
Patterns of gene evolution following duplications and speciations in vertebrates. PMID:32266119
Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica. PMID:32242238
A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. PMID:32208137
Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders. PMID:32183904
Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China. PMID:32161618
Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals. PMID:32123117
Sympatric speciation of wild emmer wheat driven by ecology and chromosomal rearrangements. PMID:32123089
Spatiotemporal Differentiation of Alpine Butterfly Parnassius glacialis (Papilionidae: Parnassiinae) in China: Evidence from Mitochondrial DNA and Nuclear Single Nucleotide Polymorphisms. PMID:32053967
Primary orthologs from local sequence context. PMID:32028880
Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection. PMID:32010166
Best match graphs and reconciliation of gene trees with species trees. PMID:32002659
Accumulation of genetic variants associated with immunity in the selective breeding of broilers. PMID:31952471
Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome. PMID:31950992
TaWAK6 encoding wall-associated kinase is involved in wheat resistance to leaf rust similar to adult plant resistance. PMID:31929605
Transcriptome-Wide Patterns of the Genetic and Expression Variations in Two Sympatric Schizothoracine Fishes in a Tibetan Plateau Glacier Lake. PMID:31917411
Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. PMID:31886458
A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa. PMID:31879283
A dispensable paralog of succinate dehydrogenase subunit C mediates standing resistance towards a subclass of SDHI fungicides in Zymoseptoria tritici. PMID:31860693
SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution. PMID:31842741
Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. PMID:31827597
Screening for mouse genes lost in mammals with long lifespans. PMID:31728160
A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization. PMID:31681395
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. PMID:31648300
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Bioinformatics Screening of Genes Specific for Well-Regenerating Vertebrates Reveals c-answer, a Regulator of Brain Development and Regeneration. PMID:31644900
OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates. PMID:31612943
Ensembl Genomes 2020-enabling non-vertebrate genomic research. PMID:31598706
The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PMID:31579570
Phylogenetic Reclassification of Vertebrate Melatonin Receptors To Include Mel1d. PMID:31416806
Episodic evolution of a eukaryotic NADK repertoire of ancient provenance. PMID:31369599
Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. PMID:31353404
Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex. PMID:31340765
Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. PMID:31276273
OMA standalone: orthology inference among public and custom genomes and transcriptomes. PMID:31235654
Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates. PMID:31234415
Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. PMID:31188086
A novel conserved family of Macro-like domains-putative new players in ADP-ribosylation signaling. PMID:31106069
Genes Encoding Teleost Fish Ligands and Associated Receptors Remained in Duplicate More Frequently than the Rest of the Genome. PMID:31087101
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
The widespread increase in inter-individual variability of gene expression in the human brain with age. PMID:31003228
Zebrafish breeding program: genetic parameters estimates for growth traits. PMID:30997663
The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system. PMID:30923320
Global DNA methylation of peripheral blood leukocytes from dogs bearing multicentric non-Hodgkin lymphomas and healthy dogs: A comparative study. PMID:30908498
Angiosperm-Wide and Family-Level Analyses of AP2/ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication. PMID:30863419
GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. PMID:30862647
Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PMID:30802244
A missense variant in the titin gene in Doberman pinscher dogs with familial dilated cardiomyopathy and sudden cardiac death. PMID:30715562
Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations. PMID:30715293
Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation. PMID:30559417
Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders. PMID:30537354
ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups with User-Selected Taxa. PMID:30517749
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? PMID:30496401
A two-level model for the role of complex and young genes in the formation of organism complexity and new insights into the relationship between evolution and development. PMID:30455862
Female Sex Development and Reproductive Duct Formation Depend on Wnt4a in Zebrafish. PMID:30446521
Comparative genomics of the major parasitic worms. PMID:30397333
Aequatus: an open-source homology browser. PMID:30395211
Whole-Genome Alignment and Comparative Annotation. PMID:30379572
A Short Indel-Lacking-Resistance Gene Triggers Silencing of the Photosynthetic Machinery Components Through TYLCSV-Associated Endogenous siRNAs in Tomato. PMID:30364213
Chromosome evolution at the origin of the ancestral vertebrate genome. PMID:30333059
Regulation of Root Angle and Gravitropism. PMID:30322904
Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird. PMID:30283495
Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. PMID:30263960
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. PMID:30184069
Time-Series Analysis of Tumorigenesis in a Murine Skin Carcinogenesis Model. PMID:30158594
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. PMID:30120140
Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. PMID:30093490
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
Loose ends: almost one in five human genes still have unresolved coding status. PMID:29982784
Adaptation and conservation insights from the koala genome. PMID:29967444
Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer. PMID:29955178
Evolutionary rates of mammalian telomere-stability genes correlate with karyotype features and female germline expression. PMID:29893967
Expanding the horizons of microRNA bioinformatics. PMID:29871895
Copper regulates rest-activity cycles through the locus coeruleus-norepinephrine system. PMID:29867144
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Role of duplicate genes in determining the tissue-selectivity of hereditary diseases. PMID:29723191
Sensing the cilium, digital capture of ciliary data for comparative genomics investigations. PMID:29713460
Alignment Modulates Ancestral Sequence Reconstruction Accuracy. PMID:29618097
Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level. PMID:29581469
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. PMID:29561359
Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes. PMID:29474932
ViCTree: an automated framework for taxonomic classification from protein sequences. PMID:29474519
The Unique Features of Proteins Depicting the Chicken Amniotic Fluid. PMID:29444982
Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the γ-toxin endonuclease. PMID:29440318
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. PMID:29440116
GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline. PMID:29425291
Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP). PMID:29391432
Evolutionary Rewiring of Human Regulatory Networks by Waves of Genome Expansion. PMID:29357977
The invasive MED/Q Bemisia tabaci genome: a tale of gene loss and gene gain. PMID:29357812
ASGDB: a specialised genomic resource for interpreting Anopheles sinensis insecticide resistance. PMID:29321052
Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility. PMID:29319911
Evidence of high-altitude adaptation in the glyptosternoid fish, Creteuchiloglanis macropterus from the Nujiang River obtained through transcriptome analysis. PMID:29169322
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study. PMID:29163570
Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives. PMID:29149296
A high-resolution mRNA expression time course of embryonic development in zebrafish. PMID:29144233
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. PMID:29136219
Faster Evolving Primate Genes Are More Likely to Duplicate. PMID:29126243
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Reading m6A in the Transcriptome: m6A-Binding Proteins. PMID:29103884
Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing. PMID:29087490
Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation. PMID:29084582
WormBase 2017: molting into a new stage. PMID:29069413
Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis. PMID:29040657
Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs. PMID:29037146
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. PMID:28981708
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. PMID:28977405
Learning causal networks with latent variables from multivariate information in genomic data. PMID:28968390
Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans. PMID:28959054
Concordant and discordant gene expression patterns in mouse strains identify best-fit animal model for human tuberculosis. PMID:28935874
A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation. PMID:28894459
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. PMID:28881964
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation. PMID:28848520
In silico prediction and characterization of secondary metabolite biosynthetic gene clusters in the wheat pathogen Zymoseptoria tritici. PMID:28818040
Zygotic Genome Activation Occurs Shortly after Fertilization in Maize. PMID:28814645
The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. PMID:28795237
The evolution of duplicate gene expression in mammalian organs. PMID:28743766
Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders. PMID:28733602
Gramene Database: Navigating Plant Comparative Genomics Resources. PMID:28713666
Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat. PMID:28698232
Identification of introns harboring functional sequence elements through positional conservation. PMID:28646210
Properties of genes essential for mouse development. PMID:28562614
Effects of arginine vasopressin on the urine proteome in rats. PMID:28560103
Spotted Gar and the Evolution of Innate Immune Receptors. PMID:28544607
MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni. PMID:28542189
Gene duplication and neo-functionalization in the evolutionary and functional divergence of the metazoan copper transporters Ctr1 and Ctr2. PMID:28507097
Selectivity determinants of GPCR-G-protein binding. PMID:28489817
Common sequence variants affect molecular function more than rare variants? PMID:28487536
Identification of MicroRNA Targets of Capsicum spp. Using MiRTrans-a Trans-Omics Approach. PMID:28443105
Ancient genes establish stress-induced mutation as a hallmark of cancer. PMID:28441401
Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity. PMID:28430951
Introgression and repeated co-option facilitated the recurrent emergence of C4 photosynthesis among close relatives. PMID:28395112
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. PMID:28365736
Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver. PMID:28360091
Genome sequencing and analysis of Talaromyces pinophilus provide insights into biotechnological applications. PMID:28352091
Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework. PMID:28336965
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. PMID:28333345
Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes. PMID:28327131
Adaptive sequence convergence of the tumor suppressor ADAMTS9 between small-bodied mammals displaying exceptional longevity. PMID:28244876
Lipid droplet biology and evolution illuminated by the characterization of a novel perilipin in teleost fish. PMID:28244868
The evolution and functional diversification of the deubiquitinating enzyme superfamily. PMID:28177072
Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection. PMID:28173748
State aggregation for fast likelihood computations in molecular evolution. PMID:28172542
Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks. PMID:28155715
Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. PMID:28155655
Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. PMID:28131822
Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. PMID:28087841
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs. PMID:28030541
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. PMID:28025345
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont. PMID:27881553
The genome of Onchocerca volvulus, agent of river blindness. PMID:27869790
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Evolution of Protein Domain Repeats in Metazoa. PMID:27671125
Co-regulation of paralog genes in the three-dimensional chromatin architecture. PMID:27634932
The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. PMID:27628538
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development. PMID:27610237
Cross-species Conservation of context-specific networks. PMID:27531214
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies. PMID:27515907
Efficient Gene Tree Correction Guided by Genome Evolution. PMID:27513924
The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes. PMID:27503295
A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. PMID:27475627
The Transcriptomic Evolution of Mammalian Pregnancy: Gene Expression Innovations in Endometrial Stromal Fibroblasts. PMID:27401177
Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation. PMID:27399969
Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery. PMID:27367670
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome. PMID:27286959
Whole transcriptome data analysis of zebrafish mutants affecting muscle development. PMID:27274534
GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm. PMID:27260514
Towards Consensus Gene Ages. PMID:27259914
Analysis of tigecycline resistance development in clinical Acinetobacter baumannii isolates through a combined genomic and transcriptomic approach. PMID:27240484
The mRNA-bound proteome of the early fly embryo. PMID:27197210
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation. PMID:27190002
Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome. PMID:27135799
DNA methylation regulates hypothalamic gene expression linking parental diet during pregnancy to the offspring's risk of obesity in Psammomys obesus. PMID:27108813
The link between orthology relations and gene trees: a correction perspective. PMID:27087831
Standardized benchmarking in the quest for orthologs. PMID:27043882
Homoeologs: What Are They and How Do We Infer Them? PMID:27021699
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
ncRNA orthologies in the vertebrate lineage. PMID:26980512
Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila. PMID:26975664
Spatiotemporal variation of mammalian protein complex stoichiometries. PMID:26975353
Inferring Orthologs: Open Questions and Perspectives. PMID:26966373
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. PMID:26950095
Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods. PMID:26940047
Active DNA demethylation at enhancers during the vertebrate phylotypic period. PMID:26928226
The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. PMID:26913054
Ensembl comparative genomics resources. PMID:26896847
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform. PMID:26869702
Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution. PMID:26865329
The genomic basis of parasitism in the Strongyloides clade of nematodes. PMID:26829753
Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection. PMID:26819542
Structural and functional annotation of the MADS-box transcription factor family in grapevine. PMID:26818751
Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases. PMID:26772908
USP2-45 Is a Circadian Clock Output Effector Regulating Calcium Absorption at the Post-Translational Level. PMID:26756164
Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms. PMID:26744215
The drug target genes show higher evolutionary conservation than non-target genes. PMID:26716901
Dintor: functional annotation of genomic and proteomic data. PMID:26691694
Evidence for a common evolutionary rate in metazoan transcriptional networks. PMID:26682651
The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs. PMID:26654912
Understanding Brassicaceae evolution through ancestral genome reconstruction. PMID:26653025
Identification of Drosophila Zfh2 as a Mediator of Hypercapnic Immune Regulation by a Genome-Wide RNA Interference Screen. PMID:26643480
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins. PMID:26624019
Genomic Analysis of Detoxification Supergene Families in the Mosquito Anopheles sinensis. PMID:26588704
Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation. PMID:26581708
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling. PMID:26578810
Mouse genome database 2016. PMID:26578600
HGTree: database of horizontally transferred genes determined by tree reconciliation. PMID:26578597
Ensembl Genomes 2016: more genomes, more complexity. PMID:26578574
WormBase 2016: expanding to enable helminth genomic research. PMID:26578572
Gramene 2016: comparative plant genomics and pathway resources. PMID:26553803
JuncDB: an exon-exon junction database. PMID:26519469
Information Commons for Rice (IC4R). PMID:26519466
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels. PMID:26515589
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
PhytoPath: an integrative resource for plant pathogen genomics. PMID:26476449
Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish. PMID:26475317
Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes. PMID:26454018
Reconstructing a SuperGeneTree minimizing reconciliation. PMID:26451911
Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. PMID:26400176
Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals. PMID:26319403
A mouse informatics platform for phenotypic and translational discovery. PMID:26314589
Klf15 Is Critical for the Development and Differentiation of Drosophila Nephrocytes. PMID:26301956
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage. PMID:26252497
The Identification of Circulating MiRNA in Bovine Serum and Their Potential as Novel Biomarkers of Early Mycobacterium avium subsp paratuberculosis Infection. PMID:26218736
Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes. PMID:26181593
Genes conserved in bilaterians but jointly lost with Myc during nematode evolution are enriched in cell proliferation and cell migration functions. PMID:26173873
A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of the moeB Gene. PMID:26114108
Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt. PMID:26084488
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PMID:26061177
Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution. PMID:26058392
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference. PMID:26031838
Genome-wide analysis of positively selected genes in seasonal and non-seasonal breeding species. PMID:26000771
Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses. PMID:25980612
ADME SARfari: comparative genomics of drug metabolizing systems. PMID:25964657
ADHD-associated dopamine transporter, latrophilin and neurofibromin share a dopamine-related locomotor signature in Drosophila. PMID:25962619
Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PMID:25946651
Covariation Is a Poor Measure of Molecular Coevolution. PMID:25944916
The evolutionary fate of alternatively spliced homologous exons after gene duplication. PMID:25931610
Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors. PMID:25931513
Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample. PMID:25926048
Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH. PMID:25908567
The clustering of functionally related genes contributes to CNV-mediated disease. PMID:25887030
Diverse selective regimes shape genetic diversity at ADAR genes and at their coding targets. PMID:25826567
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. PMID:25806041
Evidence for widespread subfunctionalization of splice forms in vertebrate genomes. PMID:25792610
Genome-wide identification and analysis of drought-responsive genes and microRNAs in tobacco. PMID:25775154
Metabolic and chaperone gene loss marks the origin of animals: evidence for Hsp104 and Hsp78 chaperones sharing mitochondrial enzymes as clients. PMID:25710177
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. PMID:25693568
Evolution of Darwin's finches and their beaks revealed by genome sequencing. PMID:25686609
Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. PMID:25681384
The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species. PMID:25679776
STBase: one million species trees for comparative biology. PMID:25679219
PON-P2: prediction method for fast and reliable identification of harmful variants. PMID:25647319
FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize. PMID:25616871
Insights into the evolution of longevity from the bowhead whale genome. PMID:25565328
Early childhood caries is associated with genetic variants in enamel formation and immune response genes. PMID:25531160
Programmed necrosis in the cross talk of cell death and inflammation. PMID:25493335
The grapevine gene nomenclature system. PMID:25481684
Improved gene tree error correction in the presence of horizontal gene transfer. PMID:25481006
Extensive copy-number variation of young genes across stickleback populations. PMID:25474574
GenomicusPlants: a web resource to study genome evolution in flowering plants. PMID:25432975
Triticeae resources in Ensembl Plants. PMID:25432969
Neuroinformatic analyses of common and distinct genetic components associated with major neuropsychiatric disorders. PMID:25414627
Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. PMID:25413576
The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion. PMID:25413302
Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology. PMID:25405965
Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. PMID:25384563
The GOA database: gene Ontology annotation updates for 2015. PMID:25378336
Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics. PMID:25378326
Analysis of micro-rearrangements in 25 eukaryotic species pairs by SyntenyMapper. PMID:25375783
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
A census of human RNA-binding proteins. PMID:25365966
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PMID:25320677
Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. PMID:25309574
Evolutionary dynamics of coding and non-coding transcriptomes. PMID:25297727
Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals. PMID:25281000
The early expansion and evolutionary dynamics of POU class genes. PMID:25261405
Structural divergence in vertebrate phylogeny of a duplicated prototype galectin. PMID:25260584
Polytomy refinement for the correction of dubious duplications in gene trees. PMID:25161242
Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations. PMID:25158795
The G protein α subunit Gαs is a tumor suppressor in Sonic hedgehog-driven medulloblastoma. PMID:25150496
Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid. PMID:25116687
A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. PMID:25111899
PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees. PMID:25103980
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring. PMID:25096057
The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species. PMID:25085202
Human dominant disease genes are enriched in paralogs originating from whole genome duplication. PMID:25080083
The inference of gene trees with species trees. PMID:25070970
Long-term asymmetrical acceleration of protein evolution after gene duplication. PMID:25070510
Expanded identification and characterization of mammalian circular RNAs. PMID:25070500
iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PMID:25058159
Sequence, structural and expression divergence of duplicate genes in the bovine genome. PMID:25054921
Uncovering adaptive evolution in the human lineage. PMID:25030307
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PMID:25013894
A universal genomic coordinate translator for comparative genomics. PMID:24976580
Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats. PMID:24945355
Representing kidney development using the gene ontology. PMID:24941002
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. PMID:24927599
A bioinformatic and computational study of myosin phosphatase subunit diversity. PMID:24898838
High-throughput capturing and characterization of mutations in essential genes of Caenorhabditis elegans. PMID:24884423
Protein flexibility facilitates quaternary structure assembly and evolution. PMID:24866000
Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. PMID:24833233
A Proteome-wide Domain-centric Perspective on Protein Phosphorylation. PMID:24830415
Reconciliation of gene and species trees. PMID:24800245
SwissTargetPrediction: a web server for target prediction of bioactive small molecules. PMID:24792161
Patterns of positive selection in seven ant genomes. PMID:24782441
Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication. PMID:24760277
Genome-wide transcriptional profiling of skin and dorsal root ganglia after ultraviolet-B-induced inflammation. PMID:24732968
Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses. PMID:24718597
Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula. PMID:24675968
An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection. PMID:24675550
The functional consequences of variation in transcription factor binding. PMID:24603674
Accumulation of CTCF-binding sites drives expression divergence between tandemly duplicated genes in humans. PMID:24564680
Gene tree correction guided by orthology. PMID:24564227
TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets. PMID:24558259
The R-spondin/Lgr5/Rnf43 module: regulator of Wnt signal strength. PMID:24532711
Functionally enigmatic genes: a case study of the brain ignorome. PMID:24523945
Deep conservation of human protein tandem repeats within the eukaryotes. PMID:24497029
On the origin and evolutionary history of NANOG. PMID:24465486
The evolution of lncRNA repertoires and expression patterns in tetrapods. PMID:24463510
NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo. PMID:24454279
Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites. PMID:24438588
Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing. PMID:24383959
Rapid diversification of FoxP2 in teleosts through gene duplication in the teleost-specific whole genome duplication event. PMID:24349554
POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants. PMID:24340041
Novel protein interactions with endoglin and activin receptor-like kinase 1: potential role in vascular networks. PMID:24319055
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. PMID:24310000
The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. PMID:24297902
NECTAR: a database of codon-centric missense variant annotations. PMID:24297257
Late-replicating CNVs as a source of new genes. PMID:24285712
Parallel evolution of chordate cis-regulatory code for development. PMID:24282393
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. PMID:24275491
Protein subcellular relocalization increases the retention of eukaryotic duplicate genes. PMID:24265504
Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. PMID:24259317
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PMID:24244129
Selectome update: quality control and computational improvements to a database of positive selection. PMID:24225318
Gramene 2013: comparative plant genomics resources. PMID:24217918
Human testis-specific genes are under relaxed negative selection. PMID:24202551
TreeFam v9: a new website, more species and orthology-on-the-fly. PMID:24194607
The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications. PMID:24180662
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family. PMID:24158625
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. PMID:24092820
Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints. PMID:24072814
Lineage-specific duplications of Muroidea Faim and Spag6 genes and atypical accelerated evolution of the parental Spag6 gene. PMID:24071998
WormBase: Annotating many nematode genomes. PMID:24058818
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss. PMID:24033262
The relationship between gene isoform multiplicity, number of exons and protein divergence. PMID:24023641
Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes? PMID:23995460
ArkMAP: integrating genomic maps across species and data sources. PMID:23941167
BlackOPs: increasing confidence in variant detection through mappability filtering. PMID:23935067
Analysis of unannotated equine transcripts identified by mRNA sequencing. PMID:23922931
Screening for candidate genes involved in the production of mouse subventricular zone proliferative cells and an estimation of their changes in evolutionary pressure during primate evolution. PMID:23914158
Time-dependent gene expression analysis of the developing superior olivary complex. PMID:23893414
Genomics analysis of potassium channel genes in songbirds reveals molecular specializations of brain circuits for the maintenance and production of learned vocalizations. PMID:23845108
A guide to best practices for Gene Ontology (GO) manual annotation. PMID:23842463
Using an isolated rat kidney model to identify kidney origin proteins in urine. PMID:23825584
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements. PMID:23815359
Getting to the roots of it: Genetic and hormonal control of root architecture. PMID:23785372
Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay. PMID:23766421
Evolutionarily conserved structural changes in phosphatidylinositol 5-phosphate 4-kinase (PI5P4K) isoforms are responsible for differences in enzyme activity and localization. PMID:23758345
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. PMID:23749191
Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method. PMID:23741529
Structural and functional annotation of the porcine immunome. PMID:23676093
Draft genome sequence of the Tibetan antelope. PMID:23673643
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. PMID:23668630
The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates. PMID:23637639
Distinct types of disorder in the human proteome: functional implications for alternative splicing. PMID:23633940
Identification of transcriptional regulators in the mouse immune system. PMID:23624555
A protein prioritization approach tailored for the FA/BRCA pathway. PMID:23620800
Computational identification of functional introns: high positional conservation of introns that harbor RNA genes. PMID:23605046
The zebrafish reference genome sequence and its relationship to the human genome. PMID:23594743
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. PMID:23537068
The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels. PMID:23496936
A Drosophila functional evaluation of candidates from human genome-wide association studies of type 2 diabetes and related metabolic traits identifies tissue-specific roles for dHHEX. PMID:23445342
Predicting physical interactions between protein complexes. PMID:23438732
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. PMID:23435085
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. PMID:23433480
A system-level, molecular evolutionary analysis of mammalian phototransduction. PMID:23433342
Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. PMID:23432897
Epigenetic epistatic interactions constrain the evolution of gene expression. PMID:23423319
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. PMID:23402223
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
Improving genome-wide scans of positive selection by using protein isoforms of similar length. PMID:23377868
Genome-wide analysis of human hotspot intersected genes highlights the roles of meiotic recombination in evolution and disease. PMID:23368819
Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. PMID:23368094
Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors. PMID:23355009
Inferring hierarchical orthologous groups from orthologous gene pairs. PMID:23342000
Mendelian and non-Mendelian regulation of gene expression in maize. PMID:23341782
Kerfuffle: a web tool for multi-species gene colocalization analysis. PMID:23327649
Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins. PMID:23246795
Seventy-five genetic loci influencing the human red blood cell. PMID:23222517
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PMID:23209799
Ensembl 2013. PMID:23203987
Genome evolution in the cold: Antarctic icefish muscle transcriptome reveals selective duplications increasing mitochondrial function. PMID:23196969
Genomicus: five genome browsers for comparative genomics in eukaryota. PMID:23193262
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PMID:23144785
Genome-wide scan for bats and dolphin to detect their genetic basis for new locomotive styles. PMID:23139738
Genome-scale coestimation of species and gene trees. PMID:23132911
Insights into the evolutionary features of human neurodegenerative diseases. PMID:23118989
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. PMID:23088596
Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions. PMID:23070853
Predicting the functional effect of amino acid substitutions and indels. PMID:23056405
A calibrated human Y-chromosomal phylogeny based on resequencing. PMID:23038768
Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene. PMID:23029450
Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PMID:23028352
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. PMID:22978381
Evolution of gene neighborhoods within reconciled phylogenies. PMID:22962456
Whole-genome duplication and the functional diversification of teleost fish hemoglobins. PMID:22949522
TreeFix: statistically informed gene tree error correction using species trees. PMID:22949484
Dissecting the role of low-complexity regions in the evolution of vertebrate proteins. PMID:22920595
Extensive compensatory cis-trans regulation in the evolution of mouse gene expression. PMID:22919075
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). PMID:22839781
Functional divergence of gene duplicates - a domain-centric view. PMID:22839301
Quality of computationally inferred gene ontology annotations. PMID:22693439
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. PMID:22689773
The iPlant Collaborative: Cyberinfrastructure for Plant Biology. PMID:22645531
Identification of novel human damage response proteins targeted through yeast orthology. PMID:22615993
Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PMID:22615540
Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity. PMID:22595969
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny. PMID:22568790
Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species. PMID:22563380
Identification and characterization of lineage-specific highly conserved noncoding sequences in Mammalian genomes. PMID:22505575
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. PMID:22454131
Interrogation of alternative splicing events in duplicated genes during evolution. PMID:22369477
Fast computation and applications of genome mappability. PMID:22276185
Unified modeling of gene duplication, loss, and coalescence using a locus tree. PMID:22271778
Adrenal androgen production in catarrhine primates and the evolution of adrenarche. PMID:22271526
Global analysis of small molecule binding to related protein targets. PMID:22253582
Measuring passive myocardial stiffness in Drosophila melanogaster to investigate diastolic dysfunction. PMID:22225769
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PMID:22174796
The impact of focused Gene Ontology curation of specific mammalian systems. PMID:22174742
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. PMID:22135296
The UniProt-GO Annotation database in 2011. PMID:22123736
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
Ensembl 2012. PMID:22086963
CADRE: the Central Aspergillus Data REpository 2012. PMID:22080563
Developing a community-based genetic nomenclature for anole lizards. PMID:22077994
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. PMID:22067447
No excess gene movement is detected off the avian or lepidopteran Z chromosome. PMID:22024813
The evolution of gene expression levels in mammalian organs. PMID:22012392
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. PMID:21970648
Whole-genome duplications spurred the functional diversification of the globin gene superfamily in vertebrates. PMID:21965344
Molecular characterization of the translocation breakpoints in the Down syndrome mouse model Ts65Dn. PMID:21953412
Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny. PMID:21900599
Role of testis-specific gene expression in sex-chromosome evolution of Anopheles gambiae. PMID:21890740
An integrative approach to ortholog prediction for disease-focused and other functional studies. PMID:21880147
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. PMID:21873635
Diversification and molecular evolution of ATOH8, a gene encoding a bHLH transcription factor. PMID:21857980
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
A limited role for gene duplications in the evolution of platypus venom. PMID:21816864
Ensembl BioMarts: a hub for data retrieval across taxonomic space. PMID:21785142
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. PMID:21737420
MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes. PMID:21712981
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
On the origins of Mendelian disease genes in man: the impact of gene duplication. PMID:21705381
Differential loss and retention of cytoglobin, myoglobin, and globin-E during the radiation of vertebrates. PMID:21697098
Testing the ortholog conjecture with comparative functional genomic data from mammals. PMID:21695233
Computational methods for Gene Orthology inference. PMID:21690100
Structural and functional relationships between photoreceptor tetraspanins and other superfamily members. PMID:21655915
OrthoList: a compendium of C. elegans genes with human orthologs. PMID:21647448
A gene-phenotype network for the laboratory mouse and its implications for systematic phenotyping. PMID:21625554
PhyleasProg: a user-oriented web server for wide evolutionary analyses. PMID:21531699
Ultra-fast sequence clustering from similarity networks with SiLiX. PMID:21513511
Identification and characterization of KCASH2 and KCASH3, 2 novel Cullin3 adaptors suppressing histone deacetylase and Hedgehog activity in medulloblastoma. PMID:21472142
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. PMID:21457909
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. PMID:21320298
Large scale comparison of global gene expression patterns in human and mouse. PMID:21182765
Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. PMID:21173032
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. PMID:21149260
2R and remodeling of vertebrate signal transduction engine. PMID:21144020
Refining orthologue groups at the transcript level. PMID:21143794
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
Gramene database in 2010: updates and extensions. PMID:21076153
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. PMID:21075798
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
Ensembl 2011. PMID:21045057
Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. PMID:21036921
Genome-wide comparative gene family classification. PMID:20976221
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
The impact of gene expression regulation on evolution of extracellular signaling pathways. PMID:20935258
A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals. PMID:20931201
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PMID:20838655
Digital gene expression signatures for maize development. PMID:20833728
Protein connectivity and protein complexity promotes human gene duplicability in a mutually exclusive manner. PMID:20829394
Sequencing and analysis of an Irish human genome. PMID:20822512
Non-homologous sex chromosomes of birds and snakes share repetitive sequences. PMID:20734128
A Bayesian approach for fast and accurate gene tree reconstruction. PMID:20660489
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. PMID:20624743
Segmental duplications in the human genome reveal details of pseudogene formation. PMID:20615899
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. PMID:20534164
eHive: an artificial intelligence workflow system for genomic analysis. PMID:20459813
Touring Ensembl: a practical guide to genome browsing. PMID:20459808
Consistent annotation of gene expression arrays. PMID:20459806
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. PMID:20439257
Gene-oriented ortholog database: a functional comparison platform for orthologous loci. PMID:20428317
Adaptive evolution of energy metabolism genes and the origin of flight in bats. PMID:20421465
Getting started in gene orthology and functional analysis. PMID:20361041
Building and analyzing protein interactome networks by cross-species comparisons. PMID:20353594
Natural selection drives the accumulation of amino acid tandem repeats in human proteins. PMID:20335526
Historical constraints on vertebrate genome evolution. PMID:20333219
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. PMID:20333184
Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttata. PMID:20237222
Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility. PMID:20208995
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. PMID:20185404
2x genomes--depth does matter. PMID:20144222
Translog, a web browser for studying the expression divergence of homologous genes. PMID:20122234
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. PMID:20122162
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. PMID:20053291
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. PMID:20040540
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. PMID:20003425
A genome-wide characterization of microRNA genes in maize. PMID:19936050
Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication. PMID:19930686
Ensembl's 10th year. PMID:19906699
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
Ensembl Genomes: extending Ensembl across the taxonomic space. PMID:19884133
Nme protein family evolutionary history, a vertebrate perspective. PMID:19852809
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. PMID:19698106
Identification of deleterious mutations within three human genomes. PMID:19602639
Does the human X contain a third evolutionary block? Origin of genes on human Xp11 and Xq28. PMID:19439513
Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes. PMID:19211788
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phylogenetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:36.128941
sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:36.128941
bioinformatics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:36.128941
comparative genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:36.128941
phylogenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:36.128941
Tags
More detailed information about this field from each metasource.
phylogenetics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:36.128941
sequence analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:36.128941
bioinformatics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:36.128941
comparative genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:36.128941
phylogenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:36.128941
phylogenetics sequence analysis bioinformatics comparative genomics phylogenomics
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