FAIRsharing.AN3lMf; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

Inparanoid
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.786607

inparanoid
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.786607

Other names: Inparanoid, inparanoid

This source may no longer be available. No known URL could be resolved successfully.

The InParanoid database provides a user interface to orthologs inferred by the InParanoid algorithm. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273 species.

Webpage:

http://inparanoid.sbc.su.se/cgi-bin/index.cgi

Publications: (6)

Publications
More detailed information about this field from each metasource.

Inparanoid: a comprehensive database of eukaryotic orthologs
PMID: 15608241
metasource: Fairsharing.org
version: FAIRsharing.org: InParanoid; InParanoid; DOI: https://doi.org/10.25504/FAIRsharing.AN3lMf; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
PMID: 19892828
metasource: Fairsharing.org
version: FAIRsharing.org: InParanoid; InParanoid; DOI: https://doi.org/10.25504/FAIRsharing.AN3lMf; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
PMID: 25429972
metasource: Fairsharing.org
version: FAIRsharing.org: InParanoid; InParanoid; DOI: https://doi.org/10.25504/FAIRsharing.AN3lMf; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

InParanoid 6: eukaryotic ortholog clusters with inparalogs
PMID: 18055500
metasource: Fairsharing.org
version: FAIRsharing.org: InParanoid; InParanoid; DOI: https://doi.org/10.25504/FAIRsharing.AN3lMf; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

http://dx.doi.org/10.1093/nar/
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/nar/gki107
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.786607

Inparanoid: a comprehensive database of eukaryotic orthologs PubMed citations: 360.

360 articles citing: Inparanoid: a comprehensive database of eukaryotic orthologs

System analysis of Lipomyces starkeyi during growth on various plant-based sugars. PMID:35906440
Comprehensive molecular evaluation of the histone methyltransferase gene family and their important roles in two-line hybrid wheat. PMID:35698040
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE. PMID:35524131
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Pollution induces epigenetic effects that are stably transmitted across multiple generations. PMID:35386832
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
GRAND: An Integrated Genome, Transcriptome Resources, and Gene Network Database for Gossypium. PMID:35126443
Interactomes: Experimental and In Silico Approaches. PMID:35113398
Comparative transcriptomics reveal tissue level specialization towards diet in prickleback fishes. PMID:35076747
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity. PMID:33983433
Sex-Biased Gene Expression and Evolution in the Cerebrum and Syrinx of Chinese Hwamei (Garrulax canorus). PMID:33919806
Ongoing repair of migration-coupled DNA damage allows planarian adult stem cells to reach wound sites. PMID:33890575
Identification of Genetic Modifiers of TDP-43: Inflammatory Activation of Astrocytes for Neuroinflammation. PMID:33803845
Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus. PMID:33717000
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Giant lungfish genome elucidates the conquest of land by vertebrates. PMID:33461212
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus. PMID:33096980
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways. PMID:33060198
Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi. PMID:32823730
Is Phylotranscriptomics as Reliable as Phylogenomics? PMID:32658973
Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome. PMID:32655308
Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. PMID:32427841
Yeast-Based Genetic Interaction Analysis of Human Kinome. PMID:32392905
A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae. PMID:32299836
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. PMID:32231327
A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology. PMID:32132169
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. PMID:32070255
Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. PMID:31744163
Genome-wide analysis of Homo sapiens, Arabidopsis thaliana, and Saccharomyces cerevisiae reveals novel attributes of tail-anchored membrane proteins. PMID:31711414
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Domainoid: domain-oriented orthology inference. PMID:31660857
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. PMID:31648300
Effector gene expression underlying neuron subtype-specific traits in the Motor Ganglion of Ciona. PMID:31639337
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. PMID:31293529
The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior. PMID:31282935
Comparing time series transcriptome data between plants using a network module finding algorithm. PMID:31164912
Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168
Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes). PMID:30602025
Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo. PMID:30557299
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
Development of polymorphic microsatellite markers by using de novo transcriptome assembly of Calanthe masuca and C. sinica (Orchidaceae). PMID:30400862
Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues. PMID:30382841
Genomic and functional evidence reveals molecular insights into the origin of echolocation in whales. PMID:30306134
De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. PMID:30271965
Pan-Genomic Study of Mycobacterium tuberculosis Reflecting the Primary/Secondary Genes, Generality/Individuality, and the Interconversion Through Copy Number Variations. PMID:30177918
Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus. PMID:30018396
Accurate prediction of orthologs in the presence of divergence after duplication. PMID:29950018
De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish. PMID:29793428
A brave new world of RNA-binding proteins. PMID:29339797
New Tools in Orthology Analysis: A Brief Review of Promising Perspectives. PMID:29163633
Saccharomyces genome database informs human biology. PMID:29140510
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PMID:29023445
Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. PMID:28927400
Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons. PMID:28893204
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network. PMID:28839186
Myocardial ischemic preconditioning in a porcine model leads to rapid changes in cardiac extracellular vesicle messenger RNA content. PMID:28785681
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships. PMID:28469416
Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes. PMID:28178932
Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F. PMID:28082965
The New Role for an Old Kinase: Protein Kinase CK2 Regulates Metal Ion Transport. PMID:28009816
RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection. PMID:27822542
Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host. PMID:27653464
Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics. PMID:27604225
Global Fitness Profiling Identifies Arsenic and Cadmium Tolerance Mechanisms in Fission Yeast. PMID:27558664
Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. PMID:27551064
Navigating the Phenotype Frontier: The Monarch Initiative. PMID:27516611
Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii. PMID:27487948
Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events. PMID:27303025
nana plant2 Encodes a Maize Ortholog of the Arabidopsis Brassinosteroid Biosynthesis Gene DWARF1, Identifying Developmental Interactions between Brassinosteroids and Gibberellins. PMID:27288361
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PMID:27286824
PTIR: Predicted Tomato Interactome Resource. PMID:27121261
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. PMID:27089831
Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways. PMID:26871911
Identification of Novel Pathways in Plant Lectin-Induced Cancer Cell Apoptosis. PMID:26867193
Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. PMID:26856411
The Mouse Solitary Odorant Receptor Gene Promoters as Models for the Study of Odorant Receptor Gene Choice. PMID:26794459
pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana. PMID:26792975
An integrated systems biology approach identifies positive cofactor 4 as a factor that increases reprogramming efficiency. PMID:26740582
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PMID:26587879
Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes. PMID:26581444
Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks. PMID:26572964
Changes in protein abundance are observed in bacterial isolates from a natural host. PMID:26528441
Genome comparison of Listeria monocytogenes serotype 4a strain HCC23 with selected lineage I and lineage II L. monocytogenes strains and other Listeria strains. PMID:26484097
Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum. PMID:26483033
GDSL esterase/lipase genes in Brassica rapa L.: genome-wide identification and expression analysis. PMID:26423069
Improved orthologous databases to ease protozoan targets inference. PMID:26416523
Identification of 4CL Genes in Desert Poplars and Their Changes in Expression in Response to Salt Stress. PMID:26393655
Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes). PMID:26329285
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. PMID:26243257
PlantOrDB: a genome-wide ortholog database for land plants and green algae. PMID:26112452
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. PMID:25999509
GraP: platform for functional genomics analysis of Gossypium raimondii. PMID:25982315
Saccharina genomes provide novel insight into kelp biology. PMID:25908475
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
Synergistic interactions between Drosophila orthologues of genes spanned by de novo human CNVs support multiple-hit models of autism. PMID:25816101
A meta-approach for improving the prediction and the functional annotation of ortholog groups. PMID:25573073
In vitro transcriptome analysis of two Chinese isolates of Streptococcus suis serotype 2. PMID:25526982
In silico analysis and experimental validation of active compounds from fructus Schisandrae chinensis in protection from hepatic injury. PMID:25521411
Remodeling Cildb, a popular database for cilia and links for ciliopathies. PMID:25422781
Text mining in cancer gene and pathway prioritization. PMID:25392685
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring. PMID:25096057
Identification and functional analysis of AG1-IA specific genes of Rhizoctonia solani. PMID:25070039
Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. PMID:24929830
Genome and transcriptome of the porcine whipworm Trichuris suis. PMID:24929829
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. PMID:24861622
A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae. PMID:24743507
Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. PMID:24704842
Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula. PMID:24675968
Prevalent RNA recognition motif duplication in the human genome. PMID:24667216
Molecular and cellular changes in the lumbar spinal cord following thoracic injury: regulation by treadmill locomotor training. PMID:24520355
A predicted protein interactome for rice. PMID:24279740
The basis for evolution of DNA-binding specificity of the Aft1 transcription factor in yeasts. PMID:24172132
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. PMID:24104479
Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees. PMID:24079845
The REIL1 and REIL2 proteins of Arabidopsis thaliana are required for leaf growth in the cold. PMID:24038679
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. PMID:23986771
De novo assembly and characterization of two transcriptomes reveal multiple light-mediated functions in the scallop eye (Bivalvia: Pectinidae). PMID:23922823
Common and pathogen-specific virulence factors are different in function and structure. PMID:23863604
Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. PMID:23851338
A guide to best practices for Gene Ontology (GO) manual annotation. PMID:23842463
Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions. PMID:23829473
Evolution of protein indels in plants, animals and fungi. PMID:23826714
The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PMID:23818858
FSRD: fungal stress response database. PMID:23757396
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. PMID:23749301
The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium. PMID:23725226
Flagellated algae protein evolution suggests the prevalence of lineage-specific rules governing evolutionary rates of eukaryotic proteins. PMID:23563973
Transcriptome Profiling Following Neuronal and Glial Expression of ALS-Linked SOD1 in Drosophila. PMID:23550139
Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae. PMID:23531409
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. PMID:23481403
Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti. PMID:23431003
High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes. PMID:23363624
Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. PMID:23292137
Large-scale reverse docking profiles and their applications. PMID:23282219
large-scale screening for targeted knockouts in the Caenorhabditis elegans genome. PMID:23173093
The ac53, ac78, ac101, and ac103 genes are newly discovered core genes in the family Baculoviridae. PMID:22933288
Mulet (mlt) encodes a tubulin-binding cofactor E-like homolog required for spermatid individualization in Drosophila melanogaster. PMID:22885996
Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. PMID:22862991
A methodology for detecting the orthology signal in a PPI network at a functional complex level. PMID:22759423
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
AlignNemo: a local network alignment method to integrate homology and topology. PMID:22719866
Origin and evolution of carnivorism in the Ascomycota (fungi). PMID:22715289
Essential gene profiles in breast, pancreatic, and ovarian cancer cells. PMID:22585861
Morphine produces immunosuppressive effects in nonhuman primates at the proteomic and cellular levels. PMID:22580588
Exploring the yeast acetylome using functional genomics. PMID:22579291
Fast skeletal muscle transcriptome of the gilthead sea bream (Sparus aurata) determined by next generation sequencing. PMID:22577894
Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome. PMID:22536428
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
A Resource of Quantitative Functional Annotation for Homo sapiens Genes. PMID:22384401
Interrogation of alternative splicing events in duplicated genes during evolution. PMID:22369477
Identification of gene-oriented exon orthology between human and mouse. PMID:22369432
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase. PMID:22356826
Computational identification of protein-protein interactions in rice based on the predicted rice interactome network. PMID:22196356
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PMID:22174796
A phenome-based functional analysis of transcription factors in the cereal head blight fungus, Fusarium graminearum. PMID:22028654
Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. PMID:22026465
Profiling the Trypanosoma cruzi phosphoproteome. PMID:21966514
Comparative genomics study of multi-drug-resistance mechanisms in the antibiotic-resistant Streptococcus suis R61 strain. PMID:21966396
Network-based prediction and analysis of HIV dependency factors. PMID:21966263
Phylogenomics reveals deep molluscan relationships. PMID:21892190
An integrative approach to ortholog prediction for disease-focused and other functional studies. PMID:21880147
Biological interaction networks are conserved at the module level. PMID:21861884
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
Comparative genomic analysis of Drosophila melanogaster and vector mosquito developmental genes. PMID:21754989
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins. PMID:21695268
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling. PMID:21694719
Computational methods for Gene Orthology inference. PMID:21690100
Minimal regulatory spaces in yeast genomes. PMID:21679449
A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae. PMID:21649883
GiSAO.db: a database for ageing research. PMID:21609420
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. PMID:21595981
Evolutionary plasticity determination by orthologous groups distribution. PMID:21586164
PRIN: a predicted rice interactome network. PMID:21575196
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PMID:21559529
Evaluating ortholog prediction algorithms in a yeast model clade. PMID:21533202
Unexpected complexity of the reef-building coral Acropora millepora transcription factor network. PMID:21526989
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. PMID:21470961
Haploinsufficiency and the sex chromosomes from yeasts to humans. PMID:21356089
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. PMID:21342548
Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network. PMID:21297957
PNAC: a protein nucleolar association classifier. PMID:21272300
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. PMID:21257609
Measuring the evolutionary rewiring of biological networks. PMID:21253555
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. PMID:21179023
IsoBase: a database of functionally related proteins across PPI networks. PMID:21177658
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. PMID:21092245
Functional genomics complements quantitative genetics in identifying disease-gene associations. PMID:21085640
At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1. PMID:21059957
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. PMID:21047383
Understanding kidney disease: toward the integration of regulatory networks across species. PMID:21044762
A network approach to predict pathogenic genes for Fusarium graminearum. PMID:20957229
ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. PMID:20952411
Gene annotation and drug target discovery in Candida albicans with a tagged transposon mutant collection. PMID:20949076
Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera. PMID:20942950
ChemProt: a disease chemical biology database. PMID:20935044
The FLIGHT Drosophila RNAi database: 2010 update. PMID:20855970
Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections. PMID:20844032
Comparing peripheral glial cell differentiation in Drosophila and vertebrates. PMID:20820850
Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response. PMID:20736407
Widespread protein aggregation as an inherent part of aging in C. elegans. PMID:20711477
Dynamic switch of negative feedback regulation in Drosophila Akt-TOR signaling. PMID:20585550
Dissecting spatio-temporal protein networks driving human heart development and related disorders. PMID:20571530
Scaffold filling, contig fusion and comparative gene order inference. PMID:20525342
Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode. PMID:20515465
Searching for signaling balance through the identification of genetic interactors of the Rab guanine-nucleotide dissociation inhibitor gdi-1. PMID:20498707
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. PMID:20439257
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
Cildb: a knowledgebase for centrosomes and cilia. PMID:20428338
Gene-oriented ortholog database: a functional comparison platform for orthologous loci. PMID:20428317
MRE11 and COM1/SAE2 are required for double-strand break repair and efficient chromosome pairing during meiosis of the protist Tetrahymena. PMID:20422424
Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. PMID:20333200
An atlas of combinatorial transcriptional regulation in mouse and man. PMID:20211142
Evolutionary dynamics of U12-type spliceosomal introns. PMID:20163699
Integrative approaches to the prediction of protein functions based on the feature selection. PMID:20043848
The maize root stem cell niche: a partnership between two sister cell populations. PMID:20041334
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. PMID:20003425
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. PMID:19783819
Phase Coupled Meta-analysis: sensitive detection of oscillations in cell cycle gene expression, as applied to fission yeast. PMID:19761608
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. PMID:19706486
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. PMID:19698106
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. PMID:19607672
Computational identification of potential molecular interactions in Arabidopsis. PMID:19592425
Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. PMID:19577928
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. PMID:19563678
Comparative transcriptomics in the Triticeae. PMID:19558723
A systems biology view of cancer. PMID:19505535
Global alignment of protein-protein interaction networks by graph matching methods. PMID:19477997
EDGAR: a software framework for the comparative analysis of prokaryotic genomes. PMID:19457249
Positional homology in bacterial genomes. PMID:19455203
Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. PMID:19403727
Rich can get poor: conversion of hub to non-hub proteins. PMID:19399641
Perturbation of interaction networks for application to cancer therapy. PMID:19390668
Conservation of core gene expression in vertebrate tissues. PMID:19371447
Genomic regions with distinct genomic distance conservation in vertebrate genomes. PMID:19323843
Protein-protein interaction as a predictor of subcellular location. PMID:19243629
Phylogenetic diversity of stress signalling pathways in fungi. PMID:19232129
Enumeration of condition-dependent dense modules in protein interaction networks. PMID:19213739
Multiple whole-genome alignments without a reference organism. PMID:19176791
Functional organization of the yeast proteome by a yeast interactome map. PMID:19164585
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. PMID:19151087
Detailed transcriptome atlas of the pancreatic beta cell. PMID:19146692
Association rate constants of ras-effector interactions are evolutionarily conserved. PMID:19096503
COPI complex is a regulator of lipid homeostasis. PMID:19067489
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. PMID:19025642
Traumatic brain injury alters expression of hippocampal microRNAs: potential regulators of multiple pathophysiological processes. PMID:19021292
Combining multiple positive training sets to generate confidence scores for protein-protein interactions. PMID:19010802
Structural relationships between highly conserved elements and genes in vertebrate genomes. PMID:19008958
MoKCa database--mutations of kinases in cancer. PMID:18986996
The Human Ageing Genomic Resources: online databases and tools for biogerontologists. PMID:18986374
Large-scale assignment of orthology: back to phylogenetics? PMID:18983710
Rapid changes of mRNA-binding protein levels following glucose and 3-isobutyl-1-methylxanthine stimulation of insulinoma INS-1 cells. PMID:18854578
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. PMID:18840285
Automatically extracting functionally equivalent proteins from SwissProt. PMID:18838004
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. PMID:18832442
Evolutionary origins of human apoptosis and genome-stability gene networks. PMID:18832373
Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions. PMID:18831792
A genomewide functional network for the laboratory mouse. PMID:18818725
Employing conservation of co-expression to improve functional inference. PMID:18808668
Interspecies data mining to predict novel ING-protein interactions in human. PMID:18801192
Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution. PMID:18752680
Global alignment of multiple protein interaction networks with application to functional orthology detection. PMID:18725631
SynBlast: assisting the analysis of conserved synteny information. PMID:18721485
An approach of orthology detection from homologous sequences under minimum evolution. PMID:18676448
An en masse phenotype and function prediction system for Mus musculus. PMID:18613952
Predicting gene function in a hierarchical context with an ensemble of classifiers. PMID:18613947
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. PMID:18613946
Exploring the structure and function paradigm. PMID:18554899
Designating eukaryotic orthology via processed transcription units. PMID:18445630
Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. PMID:18426584
Overlapping genes in the human and mouse genomes. PMID:18410680
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PMID:18389064
Walking the interactome for prioritization of candidate disease genes. PMID:18371930
LocateP: genome-scale subcellular-location predictor for bacterial proteins. PMID:18371216
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. PMID:18321373
Reductive genome evolution in chemoautotrophic intracellular symbionts of deep-sea Calyptogena clams. PMID:18305898
Protein function assignment through mining cross-species protein-protein interactions. PMID:18253506
Analysis of the codon use frequency of AMPK family genes from different species. PMID:18188681
AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips. PMID:18065560
TreeFam: 2008 Update. PMID:18056084
InParanoid 6: eukaryotic ortholog clusters with inparalogs. PMID:18055500
OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. PMID:18053139
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. PMID:18045462
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. PMID:18039369
Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. PMID:18024567
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. PMID:18021451
WormBase 2007. PMID:17991679
Analysis of feedback loops and robustness in network evolution based on Boolean models. PMID:17988389
GreenPhylDB: a database for plant comparative genomics. PMID:17986457
The HGNC Database in 2008: a resource for the human genome. PMID:17984084
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. PMID:17984073
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. PMID:17982176
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. PMID:17962307
OrthoDB: the hierarchical catalog of eukaryotic orthologs. PMID:17947323
eggNOG: automated construction and annotation of orthologous groups of genes. PMID:17942413
Systematic analysis of alternative first exons in plant genomes. PMID:17941993
OPTIC: orthologous and paralogous transcripts in clades. PMID:17933761
A genome-wide survey and systematic RNAi-based characterization of helicase-like genes in Caenorhabditis elegans. PMID:17921522
High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PMID:17850180
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PMID:17712414
Distinct functions of the Drosophila Nup153 and Nup214 FG domains in nuclear protein transport. PMID:17682050
A predicted interactome for Arabidopsis. PMID:17675552
Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains. PMID:17641976
Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD. PMID:17623072
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
Dating the early evolution of plants: detection and molecular clock analyses of orthologs. PMID:17593393
oPOSSUM: integrated tools for analysis of regulatory motif over-representation. PMID:17576675
The Release 5.1 annotation of Drosophila melanogaster heterochromatin. PMID:17569856
The human phylome. PMID:17567924
Assessing performance of orthology detection strategies applied to eukaryotic genomes. PMID:17440619
BranchClust: a phylogenetic algorithm for selecting gene families. PMID:17425803
Towards complete sets of farnesylated and geranylgeranylated proteins. PMID:17411337
Large-scale mapping of human protein-protein interactions by mass spectrometry. PMID:17353931
Orthology prediction at scalable resolution by phylogenetic tree analysis. PMID:17346331
The (in)dependence of alternative splicing and gene duplication. PMID:17335345
Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach. PMID:17327921
Specificity and evolvability in eukaryotic protein interaction networks. PMID:17305419
PlnTFDB: an integrative plant transcription factor database. PMID:17286856
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. PMID:17274809
Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. PMID:17244357
GenomeBlast: a web tool for small genome comparison. PMID:17217510
DiscoverySpace: an interactive data analysis application. PMID:17210078
T1DBase: integration and presentation of complex data for type 1 diabetes research. PMID:17169983
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. PMID:17142475
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. PMID:17112386
Combining expression and comparative evolutionary analysis. The COBRA gene family. PMID:17098858
U12DB: a database of orthologous U12-type spliceosomal introns. PMID:17082203
Comparison of protein interaction networks reveals species conservation and divergence. PMID:17044912
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. PMID:17029626
Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PMID:17009864
Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. PMID:16951058
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. PMID:16845020
ESTimating plant phylogeny: lessons from partitioning. PMID:16776834
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
Improving the specificity of high-throughput ortholog prediction. PMID:16729895
Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. PMID:16649112
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. PMID:16608522
Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. PMID:16606698
Stable evolutionary signal in a yeast protein interaction network. PMID:16441898
cisRED: a database system for genome-scale computational discovery of regulatory elements. PMID:16381958
BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. PMID:16381946
TreeFam: a curated database of phylogenetic trees of animal gene families. PMID:16381935
FlyBase: anatomical data, images and queries. PMID:16381917
FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. PMID:16381916
SIMAP: the similarity matrix of proteins. PMID:16381858
Evolution of alternative splicing after gene duplication. PMID:16365379
Ulysses - an application for the projection of molecular interactions across species. PMID:16356269
HCOP: the HGNC comparison of orthology predictions search tool. PMID:16284797
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis PubMed citations: 341.

341 articles citing: InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae. PMID:35664330
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. PMID:35561192
An Iterative Method for Predicting Essential Proteins Based on Multifeature Fusion and Linear Neighborhood Similarity. PMID:35140599
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. PMID:34953462
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms. PMID:34791383
A Novel Collaborative Filtering Model-Based Method for Identifying Essential Proteins. PMID:34745230
Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. PMID:34603269
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. PMID:34496745
A Novel Method for Identifying Essential Proteins Based on Non-negative Matrix Tri-Factorization. PMID:34422014
Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data. PMID:34407772
A Novel Model for Identifying Essential Proteins Based on Key Target Convergence Sets. PMID:34394201
A nomenclature for echinoderm genes. PMID:34386815
Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding. PMID:34341383
Method for Identifying Essential Proteins by Key Features of Proteins in a Novel Protein-Domain Network. PMID:34267785
The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts. PMID:34253727
The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses. PMID:34194450
Integration of 1:1 orthology maps and updated datasets into Echinobase. PMID:34010390
Identification and Regulation of Tomato Serine/Arginine-Rich Proteins Under High Temperatures. PMID:33854522
Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network. PMID:33815480
Prevention and Control of Pathogens Based on Big-Data Mining and Visualization Analysis. PMID:33718431
Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley (Hordeum vulgare L.). PMID:33414683
Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling. PMID:33007944
A large accessory protein interactome is rewired across environments. PMID:32924934
The differential expression patterns of paralogs in response to stresses indicate expression and sequence divergences. PMID:32546126
Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei. PMID:32520929
GATA-type transcription factor MrNsdD regulates dimorphic transition, conidiation, virulence and microsclerotium formation in the entomopathogenic fungus Metarhizium rileyi. PMID:32395911
A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks. PMID:32373163
Noncoding regions underpin avian bill shape diversification at macroevolutionary scales. PMID:32269134
A novel method to predict essential proteins based on tensor and HITS algorithm. PMID:32252824
New molecular target for the phylogenetic identification of Leptospira species directly from clinical samples: an alternative gene to 16S rRNA. PMID:32187337
Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera). PMID:32134461
Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study. PMID:32108239
Analogous and Diverse Functions of APSES-Type Transcription Factors in the Morphogenesis of the Entomopathogenic Fungus Metarhizium rileyi. PMID:32005738
Comparative Genomics Reveals Accelerated Evolution of Fright Reaction Genes in Ostariophysan Fishes. PMID:31921316
JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants. PMID:31874631
The water lily genome and the early evolution of flowering plants. PMID:31853069
Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). PMID:31816089
OrthoFinder: phylogenetic orthology inference for comparative genomics. PMID:31727128
Comparative Analysis of Intra- and Inter-Specific Genomic Variability in the Peach Potato Aphid, Myzus persicae. PMID:31652640
Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges. PMID:31602614
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PMID:31471988
Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code. PMID:31356126
Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet. PMID:31312428
Membrane protein-regulated networks across human cancers. PMID:31311925
An iteration method for identifying yeast essential proteins from heterogeneous network. PMID:31234779
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism. PMID:31159924
The Evolutionary Traceability of a Protein. PMID:30649284
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. PMID:30365026
Genomic data integration systematically biases interactome mapping. PMID:30332399
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. PMID:30299502
PGAweb: A Web Server for Bacterial Pan-Genome Analysis. PMID:30186253
Genome-wide analysis of root hair-preferential genes in rice. PMID:30159808
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. PMID:30143032
The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans. PMID:29988559
Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications. PMID:29925317
Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes. PMID:29898652
Using the Candida Genome Database. PMID:29761455
The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. PMID:29666630
The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). PMID:29659812
Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. PMID:29634727
Time-consistent reconciliation maps and forbidden time travel. PMID:29441122
A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley. PMID:29202692
Global landscape of cell envelope protein complexes in Escherichia coli. PMID:29176613
Alternative transcription start site selection in Mr-OPY2 controls lifestyle transitions in the fungus Metarhizium robertsii. PMID:29146899
Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization. PMID:29017458
Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges. PMID:28947760
The Apostasia genome and the evolution of orchids. PMID:28902843
Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling. PMID:28887381
Pyruvate Accumulation Is the First Line of Cell Defense against Heat Stress in a Fungus. PMID:28874474
Biologically feasible gene trees, reconciliation maps and informative triples. PMID:28861118
A new computational strategy for identifying essential proteins based on network topological properties and biological information. PMID:28753682
Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction. PMID:28646875
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement. PMID:28633662
Genomics insights into different cellobiose hydrolysis activities in two Trichoderma hamatum strains. PMID:28420406
Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions. PMID:28385878
Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes. PMID:28379977
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. PMID:28327943
A STRIPAK complex mediates axonal transport of autophagosomes and dense core vesicles through PP2A regulation. PMID:28100687
Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids. PMID:28031797
Fused Regression for Multi-source Gene Regulatory Network Inference. PMID:27923054
A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. PMID:27883890
Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species. PMID:27795388
Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species. PMID:27790228
The role of PHD2 mutations in the pathogenesis of erythrocytosis. PMID:27774468
Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes. PMID:27742722
A global genetic interaction network maps a wiring diagram of cellular function. PMID:27708008
Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research. PMID:27677461
Evolutionary analyses of mitochondrial carrier family of dictyostelids. PMID:27652040
Predicting essential proteins based on subcellular localization, orthology and PPI networks. PMID:27586883
DDRprot: a database of DNA damage response-related proteins. PMID:27577567
Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing. PMID:27561673
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. PMID:27502555
An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. PMID:27447865
Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. PMID:27436282
Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PMID:27359102
Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. PMID:27289096
Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein. PMID:27272207
Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus. PMID:27267057
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. PMID:27249958
Comparative genomics explains the evolutionary success of reef-forming corals. PMID:27218454
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans. PMID:27027346
Inside the Pan-genome - Methods and Software Overview. PMID:27006628
A Protein Complex Map of Trypanosoma brucei. PMID:26991453
An extended set of yeast-based functional assays accurately identifies human disease mutations. PMID:26975778
Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes. PMID:26956888
Overlapping cell population expression profiling and regulatory inference in C. elegans. PMID:26926147
Genomic and phenotypic characterization of the species Acinetobacter venetianus. PMID:26902269
A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks. PMID:26881892
Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides. PMID:26801645
Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. PMID:26782935
Genome-wide analysis of excretory/secretory proteins in Echinococcus multilocularis: insights into functional characteristics of the tapeworm secretome. PMID:26715441
Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress. PMID:26704366
Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PMID:26698123
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. PMID:26694192
A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans. PMID:26676933
The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids. PMID:26643275
The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. PMID:26632259
Conserved mRNA-binding proteomes in eukaryotic organisms. PMID:26595419
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PMID:26587879
Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks. PMID:26572964
SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. PMID:26560340
Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis. PMID:26556047
Information Commons for Rice (IC4R). PMID:26519466
How to Use the Candida Genome Database. PMID:26519061
Insights from the genome of Ophiocordyceps polyrhachis-furcata to pathogenicity and host specificity in insect fungi. PMID:26511477
A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging. PMID:26456335
Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. PMID:26442085
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. PMID:26420834
Dissecting Germ Cell Metabolism through Network Modeling. PMID:26367011
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Phylogenetic analysis of methionine synthesis genes from Thalassiosira pseudonana. PMID:26251775
The roots of future rice harvests. PMID:26224558
Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach. PMID:26198337
GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks. PMID:26165520
Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks. PMID:26115027
PlantOrDB: a genome-wide ortholog database for land plants and green algae. PMID:26112452
Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation. PMID:26099751
Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park. PMID:26092468
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum. PMID:26002871
Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. PMID:25887590
The composition of the global and feature specific cyanobacterial core-genomes. PMID:25852675
RiceNet v2: an improved network prioritization server for rice genes. PMID:25813048
Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae. PMID:25708804
Techniques for transferring host-pathogen protein interactions knowledge to new tasks. PMID:25699028
Gene expression defines natural changes in mammalian lifespan. PMID:25677554
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
Identifying gene clusters by discovering common intervals in indeterminate strings. PMID:25571793
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. PMID:25532137
In vivo assessment of protease dynamics in cutaneous wound healing by degradomics analysis of porcine wound exudates. PMID:25516628
Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor HET-s/HET-s. PMID:25500536
The evolution of sex ratio distorter suppression affects a 25 cM genomic region in the butterfly Hypolimnas bolina. PMID:25474676
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. PMID:25429972
ModuleBlast: identifying activated sub-networks within and across species. PMID:25428368
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda. PMID:25397810
Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes. PMID:25393533
Genome-wide analyses and functional classification of proline repeat-rich proteins: potential role of eIF5A in eukaryotic evolution. PMID:25364902
Genenames.org: the HGNC resources in 2015. PMID:25361968
The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach. PMID:25341656
Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. PMID:25332401
Comparative analyses of C₄ and C₃ photosynthesis in developing leaves of maize and rice. PMID:25306245
Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae. PMID:25301375
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. PMID:25261295
Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora. PMID:25255320
Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. PMID:25173756
Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems. PMID:25150862
Hepatic transcriptomic profiling reveals early toxicological mechanisms of uranium in Atlantic salmon (Salmo salar). PMID:25145280
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring. PMID:25096057
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
Highly variable recombinational landscape modulates efficacy of natural selection in birds. PMID:25062920
Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the Smut Fungus Melanopsichium pennsylvanicum. PMID:25062916
Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus. PMID:25056288
SFannotation: A Simple and Fast Protein Function Annotation System. PMID:25031571
Genome-wide analysis of trans-splicing in the nematode Pristionchus pacificus unravels conserved gene functions for germline and dauer development in divergent operons. PMID:25015138
The genome of Eucalyptus grandis. PMID:24919147
Integrating the interactome and the transcriptome of Drosophila. PMID:24913703
Secretome analysis reveals effector candidates associated with broad host range necrotrophy in the fungal plant pathogen Sclerotinia sclerotiorum. PMID:24886033
Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass. PMID:24885077
High-throughput capturing and characterization of mutations in essential genes of Caenorhabditis elegans. PMID:24884423
Protein-protein interaction network of the marine microalga Tetraselmis subcordiformis: prediction and application for starch metabolism analysis. PMID:24879479
The transcriptomes of the crucian carp complex (Carassius auratus) provide insights into the distinction between unisexual triploids and sexual diploids. PMID:24871367
Network analyses reveal pervasive functional regulation between proteases in the human protease web. PMID:24865846
The complex hybrid origins of the root knot nematodes revealed through comparative genomics. PMID:24860695
Worm variation made accessible: Take your shopping cart to store, link, and investigate! PMID:24843834
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. PMID:24835588
Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. PMID:24833233
CMT-associated mutations in glycyl- and tyrosyl-tRNA synthetases exhibit similar pattern of toxicity and share common genetic modifiers in Drosophila. PMID:24807208
Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infections. PMID:24757665
Building a phylogenomic pipeline for the eukaryotic tree of life - addressing deep phylogenies with genome-scale data. PMID:24707447
Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula. PMID:24675968
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
in silico identification of protein-protein interactions in Silkworm, Bombyx mori. PMID:24616555
In silico prediction of antimalarial drug target candidates. PMID:24533280
Predicting the dynamics of protein abundance. PMID:24532840
ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome. PMID:24501395
Evolutionary rate covariation identifies new members of a protein network required for Drosophila melanogaster female post-mating responses. PMID:24453993
Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota). PMID:24438332
gsGator: an integrated web platform for cross-species gene set analysis. PMID:24423189
Ancient signals: comparative genomics of green plant CDPKs. PMID:24342084
Novel protein interactions with endoglin and activin receptor-like kinase 1: potential role in vascular networks. PMID:24319055
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. PMID:24280312
Prediction of essential proteins based on gene expression programming. PMID:24267033
PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics. PMID:24250218
Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. PMID:24249833
Profiling of Parkin-binding partners using tandem affinity purification. PMID:24244333
The evolution of the ribosome biogenesis pathway from a yeast perspective. PMID:24234440
NeuroGeM, a knowledgebase of genetic modifiers in neurodegenerative diseases. PMID:24229347
WormQTLHD--a web database for linking human disease to natural variation data in C. elegans. PMID:24217915
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. PMID:24147765
How unique is the low oxygen response? An analysis of the anaerobic response during germination and comparison with abiotic stress in rice and Arabidopsis. PMID:24101922
ExpressionBlast: mining large, unstructured expression databases. PMID:24076985
A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells. PMID:24068970
Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. PMID:24068555
Punctuated emergences of genetic and phenotypic innovations in eumetazoan, bilaterian, euteleostome, and hominidae ancestors. PMID:24065732
WormBase: Annotating many nematode genomes. PMID:24058818
Transimulation - protein biosynthesis web service. PMID:24040122
The REIL1 and REIL2 proteins of Arabidopsis thaliana are required for leaf growth in the cold. PMID:24038679
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
Phylogenies of central element proteins reveal the dynamic evolutionary history of the mammalian synaptonemal complex: ancient and recent components. PMID:24026100
The relationship between gene isoform multiplicity, number of exons and protein divergence. PMID:24023641
Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals. PMID:24013106
A comparative genomic approach for identifying synthetic lethal interactions in human cancer. PMID:23980094
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study. PMID:23947337
Cell- and subunit-specific mechanisms of CNG channel ciliary trafficking and localization in C. elegans. PMID:23886944
TCW: transcriptome computational workbench. PMID:23874959
Structural disorder provides increased adaptability for vesicle trafficking pathways. PMID:23874186
Mapping the functional yeast ABC transporter interactome. PMID:23831759
Using an isolated rat kidney model to identify kidney origin proteins in urine. PMID:23825584
A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations. PMID:23819456
Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era. PMID:23805917
Consensus and conflict cards for metabolic pathway databases. PMID:23803311
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. PMID:23800157
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
Genetic circuitry of Survival motor neuron, the gene underlying spinal muscular atrophy. PMID:23757500
FSRD: fungal stress response database. PMID:23757396
Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula. PMID:23735511
Fungal genes in context: genome architecture reflects regulatory complexity and function. PMID:23699226
The signatures of selection for translational accuracy in plant genes. PMID:23695187
Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis. PMID:23688303
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. PMID:23685612
Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. PMID:23674305
Networks of bZIP protein-protein interactions diversified over a billion years of evolution. PMID:23661758
Comparative proteomic analysis of supportive and unsupportive extracellular matrix substrates for human embryonic stem cell maintenance. PMID:23658023
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
Towards systems biology of mycotoxin regulation. PMID:23598563
Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins. PMID:23555228
OrthoRBH: A streamlined pipeline for mining large gene family sequences in related species. PMID:23515897
Sequencing and annotation of the Ophiostoma ulmi genome. PMID:23496816
One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012. PMID:23494302
Flying saucer1 is a transmembrane RING E3 ubiquitin ligase that regulates the degree of pectin methylesterification in Arabidopsis seed mucilage. PMID:23482858
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. PMID:23418180
The Eimeria transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria. PMID:23411718
Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation. PMID:23408995
Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity. PMID:23360999
Inferring hierarchical orthologous groups from orthologous gene pairs. PMID:23342000
Network analysis of functional genomics data: application to avian sex-biased gene expression. PMID:23319882
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
Large-scale reverse docking profiles and their applications. PMID:23282219
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
The evolution of ultraconserved elements with different phylogenetic origins. PMID:23217155
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing. PMID:23193293
CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. PMID:23193288
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. PMID:23193286
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. PMID:23193276
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology. PMID:23148687
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. PMID:23110901
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
"Orphan" retrogenes in the human genome. PMID:23066043
Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network. PMID:23056995
GenoSets: visual analytic methods for comparative genomics. PMID:23056299
BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity. PMID:23046607
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. PMID:22978381
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. PMID:22940862
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. PMID:22889830
Towards biological characters of interactions between transcription factors and their DNA targets in mammals. PMID:22888987
Protein phosphorylation changes reveal new candidates in the regulation of egg activation and early embryogenesis in D. melanogaster. PMID:22884528
A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome. PMID:22823938
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. PMID:22808943
Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. PMID:22799003
Conserved rules govern genetic interaction degree across species. PMID:22747640
Duplicate gene enrichment and expression pattern diversification in multicellularity. PMID:22645319
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
Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa. PMID:22465851
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. PMID:22454131
Deletion of Siah-interacting protein gene in Drosophila causes cardiomyopathy. PMID:22398840
Analysis of high accuracy, quantitative proteomics data in the MaxQB database. PMID:22301388
The Ras protein superfamily: evolutionary tree and role of conserved amino acids. PMID:22270915
A dynamic view of domain-motif interactions. PMID:22253583
Roundup 2.0: enabling comparative genomics for over 1800 genomes. PMID:22247275
A vector space model approach to identify genetically related diseases. PMID:22227640
Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes. PMID:22195734
Molecular links between cellular senescence, longevity and age-related diseases - a systems biology perspective. PMID:22184282
Comparative interactomics with Funcoup 2.0. PMID:22110034
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
WormBase 2012: more genomes, more data, new website. PMID:22067452
EcoliWiki: a wiki-based community resource for Escherichia coli. PMID:22064863
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. PMID:22058225
Gadd45 proteins: relevance to aging, longevity and age-related pathologies. PMID:21986581
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. PMID:21970648
SILAC compatible strain of Pichia pastoris for expression of isotopically labeled protein standards and quantitative proteomics. PMID:21942632
Computational approaches to selecting and optimising targets for structural biology. PMID:21906678
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Domain architecture conservation in orthologs. PMID:21819573
Functional integrative levels in the human interactome recapitulate organ organization. PMID:21799769
Identification and characterization of NF-Y transcription factor families in the monocot model plant Brachypodium distachyon. PMID:21738795
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. PMID:21737420
Computational methods for Gene Orthology inference. PMID:21690100
OrthoList: a compendium of C. elegans genes with human orthologs. PMID:21647448
Non-adaptive origins of interactome complexity. PMID:21593762
PRIN: a predicted rice interactome network. PMID:21575196
Unexpected complexity of the reef-building coral Acropora millepora transcription factor network. PMID:21526989
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. PMID:21367939
RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum. PMID:21332983
Gene set enrichment analysis of microarray data from Pimephales promelas (Rafinesque), a non-mammalian model organism. PMID:21269471
Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PMID:21253567
Human cardiomyopathy mutations induce myocyte hyperplasia and activate hypertrophic pathways during cardiogenesis in zebrafish. PMID:21245263
OrthoInspector: comprehensive orthology analysis and visual exploration. PMID:21219603
OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. PMID:21186175
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. PMID:21124763
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection. PMID:21106128
InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. PMID:21106116
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. PMID:21047383
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
genenames.org: the HGNC resources in 2011. PMID:20929869
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis. PMID:20833631
FACT: functional annotation transfer between proteins with similar feature architectures. PMID:20696036
CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. PMID:20126624
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic PubMed citations: 235.

235 articles citing: InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

The Potential Anti-remodeling Effect of Paroxetine After Myocardial Infarction May Be Blunted by Beta-Blockers. PMID:35898267
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment. PMID:35859153
Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. PMID:35812973
Humanized yeast to model human biology, disease and evolution. PMID:35661208
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins. PMID:35610035
GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis. PMID:35495163
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. PMID:35451481
An interolog-based barley interactome as an integration framework for immune signaling. PMID:35435213
Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. PMID:35351103
Cardiac protection by pirfenidone after myocardial infarction: a bioinformatic analysis. PMID:35304529
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery. PMID:35173350
Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment. PMID:35120462
Interactomes: Experimental and In Silico Approaches. PMID:35113398
Deep Learning Analyses to Delineate the Molecular Remodeling Process after Myocardial Infarction. PMID:34943776
Small molecules for cell reprogramming: a systems biology analysis. PMID:34919532
Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets. PMID:34764269
An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. PMID:34745452
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
ConVarT: a search engine for matching human genetic variants with variants from non-human species. PMID:34718716
Aspergillus fumigatus versus Genus Aspergillus: Conservation, Adaptive Evolution and Specific Virulence Genes. PMID:34683335
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. PMID:34669962
Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19. PMID:34667255
Label-Free Liquid Chromatography-Mass Spectrometry Proteomic Analysis of the Urinary Proteome for Measuring the Escitalopram Treatment Response From Major Depressive Disorder. PMID:34658947
Employing Cross-Species Approaches to Construct Humanized Genetic Interaction Networks. PMID:34590273
Systems biology analysis of lung fibrosis-related genes in the bleomycin mouse model. PMID:34588506
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species. PMID:34328525
Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics. PMID:34227830
The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses. PMID:34194450
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence. PMID:34082735
Network-based analysis of key regulatory genes implicated in Type 2 Diabetes Mellitus and Recurrent Miscarriages in Turner Syndrome. PMID:34021221
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. PMID:33973408
Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species. PMID:33968592
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Blood Pressure Regulation Evolved from Basic Homeostatic Components. PMID:33923023
Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing. PMID:33919312
Aging features of the migratory locust at physiological and transcriptional levels. PMID:33838645
Ten Years of Collaborative Progress in the Quest for Orthologs. PMID:33822172
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. PMID:33787851
Multimerization variants as potential drivers of neofunctionalization. PMID:33771868
Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes. PMID:33767674
SVEP1 is a human coronary artery disease locus that promotes atherosclerosis. PMID:33762433
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. PMID:33606106
Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis. PMID:33372598
Comparison of the central human and mouse platelet signaling cascade by systems biological analysis. PMID:33353544
The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of Swordtails. PMID:33275891
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
GelFAP: Gene Functional Analysis Platform for Gastrodia elata. PMID:33193491
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. PMID:33179748
Comparative Genome Analysis Reveals Natural Variations in the Genomes of Erwinia pyrifoliae, a Black Shoot Blight Pathogen in Apple and Pear. PMID:33082727
Evolutionary Study of Disorder in Protein Sequences. PMID:33036302
A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. PMID:33020633
Ginsenoside Re Treatment Attenuates Myocardial Hypoxia/Reoxygenation Injury by Inhibiting HIF-1α Ubiquitination. PMID:33013381
Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. PMID:32956445
Systematic analysis of bypass suppression of essential genes. PMID:32939983
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration. PMID:32791514
Building the vertebrate codex using the gene breaking protein trap library. PMID:32779569
Genomic Dissection of a Wild Region in a Superior Solanum pennellii Introgression Sub-Line with High Ascorbic Acid Accumulation in Tomato Fruit. PMID:32722275
Characterization of glutathione proteome in CHO cells and its relationship with productivity and cholesterol synthesis. PMID:32662871
A Yeast-Based Model for Hereditary Motor and Sensory Neuropathies: A Simple System for Complex, Heterogeneous Diseases. PMID:32560077
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes. PMID:32522745
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. PMID:32325033
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Genome sequence of the potential probiotic eukaryote Saccharomyces cerevisiae KCCM 51299. PMID:32257741
MaveQuest: a web resource for planning experimental tests of human variant effects. PMID:32251504
Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b. PMID:32244934
Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations. PMID:32181804
Comprehensive phylogenomic analysis of ERF genes in sorghum provides clues to the evolution of gene functions and redundancy among gene family members. PMID:32158635
A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology. PMID:32132169
Frameshifting preserves key physicochemical properties of proteins. PMID:32127487
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components. PMID:32039234
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Genomic characterization of Parengyodontium americanum sp. nov. PMID:32028048
Prevalence and Molecular Characteristics of Extended-Spectrum and AmpC β-Lactamase Producing Escherichia coli in Grazing Beef Cattle. PMID:31998282
Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain. PMID:31980617
Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. PMID:31822585
ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology. PMID:31733062
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
Domainoid: domain-oriented orthology inference. PMID:31660857
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. PMID:31648300
PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation. PMID:31642469
Evolutionary flexibility in flooding response circuitry in angiosperms. PMID:31604238
Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects. PMID:31527046
Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species. PMID:31501870
Reconciling event-labeled gene trees with MUL-trees and species networks. PMID:31410552
Link clustering explains non-central and contextually essential genes in protein interaction networks. PMID:31406201
Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer. PMID:31351478
Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes. PMID:31346350
EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550
Aging Increases Hippocampal DUSP2 by a Membrane Cholesterol Loss-Mediated RTK/p38MAPK Activation Mechanism. PMID:31293510
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. PMID:31278252
Advances and Applications in the Quest for Orthologs. PMID:31241141
OMA standalone: orthology inference among public and custom genomes and transcriptomes. PMID:31235654
Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass. PMID:31194847
A web-based tool for the prediction of rice transcription factor function. PMID:31169887
Alternative characterizations of Fitch's xenology relation. PMID:31111195
LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species. PMID:31106360
Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168
A universal transcriptomic signature of age reveals the temporal scaling of Caenorhabditis elegans aging trajectories. PMID:31089188
Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms. PMID:30975080
Gcorn Plant: A Database for Retrieving Functional and Evolutionary Traits of Plant Genes. PMID:30971448
croFGD: Catharanthus roseus Functional Genomics Database. PMID:30967897
Defining the RNA interactome by total RNA-associated protein purification. PMID:30962360
Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata. PMID:30949663
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Exploring integument transcriptomes, cuticle ultrastructure, and cuticular hydrocarbons profiles in eusocial and solitary bee species displaying heterochronic adult cuticle maturation. PMID:30870522
Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. PMID:30814064
A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. PMID:30759970
A comparative transcriptome analysis of the novel obligate methanotroph Methylomonas sp. DH-1 reveals key differences in transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol. PMID:30755173
Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata. PMID:30680121
Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora. PMID:30665399
Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PMID:30650107
Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. PMID:30576513
PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. PMID:30555515
Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. PMID:30550790
An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus. PMID:30514240
SynerClust: a highly scalable, synteny-aware orthologue clustering tool. PMID:30418868
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
CRM Discovery Beyond Model Insects. PMID:30414115
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. PMID:30395283
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection. PMID:30341719
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. PMID:30299502
Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. PMID:30277459
Convergent evolution of the ladder-like ventral nerve cord in Annelida. PMID:30275868
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses. PMID:30248119
Target of Rapamycin Inhibition in Chlamydomonas reinhardtii Triggers de Novo Amino Acid Synthesis by Enhancing Nitrogen Assimilation. PMID:30228127
Short term optical defocus perturbs normal developmental shifts in retina/RPE protein abundance. PMID:30157773
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. PMID:30120140
JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. PMID:30084941
SonicParanoid: fast, accurate and easy orthology inference. PMID:30032301
A mosaic monoploid reference sequence for the highly complex genome of sugarcane. PMID:29980662
Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach. PMID:29973620
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
PrimAlign: PageRank-inspired Markovian alignment for large biological networks. PMID:29949962
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Genetic Network Complexity Shapes Background-Dependent Phenotypic Expression. PMID:29903533
Evaluation of functionality for serine and threonine phosphorylation with different evolutionary ages in human and mouse. PMID:29866046
A Multi-Omics Database for Parasitic Nematodes and Trematodes. PMID:29761465
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota. PMID:29690866
Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs). PMID:29659815
DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. PMID:29656893
Oenococcus oeni in Chilean Red Wines: Technological and Genomic Characterization. PMID:29491847
Systematic Functional Characterization of Human 21st Chromosome Orthologs in Caenorhabditis elegans. PMID:29367452
A brave new world of RNA-binding proteins. PMID:29339797
Muscle molecular adaptations to endurance exercise training are conditioned by glycogen availability: a proteomics-based analysis in the McArdle mouse model. PMID:29315579
The retina/RPE proteome in chick myopia and hyperopia models: Commonalities with inherited and age-related ocular pathologies. PMID:29259393
Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways. PMID:29257953
Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. PMID:29242500
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
FunCoup 4: new species, data, and visualization. PMID:29165593
Synima: a Synteny imaging tool for annotated genome assemblies. PMID:29162056
ECOdrug: a database connecting drugs and conservation of their targets across species. PMID:29140522
OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation. PMID:29133277
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Systems Study on the Antirheumatic Mechanism of Tibetan Medicated-Bath Therapy Using Wuwei-Ganlu-Yaoyu-Keli. PMID:29090217
Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins. PMID:29083303
Structural complexity and functional diversity of plant NADPH oxidases. PMID:29071531
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis. PMID:29040657
Microbial genome analysis: the COG approach. PMID:28968633
Wide-scale comparative analysis of longevity genes and interventions. PMID:28836369
Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I. PMID:28817247
Differentially expressed genes in PPARγ-deficient MSCs. PMID:28774780
Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. PMID:28764653
Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. PMID:28746735
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Mechanisms of action of sacubitril/valsartan on cardiac remodeling: a systems biology approach. PMID:28649439
Identifying pathogenicity of human variants via paralog-based yeast complementation. PMID:28542158
Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection. PMID:28494245
Co-occurring protein phosphorylation are functionally associated. PMID:28459814
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs. PMID:28344339
Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor. PMID:28335716
FcRav2, a gene with a ROGDI domain involved in Fusarium head blight and crown rot on durum wheat caused by Fusarium culmorum. PMID:28322011
Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics' and structural biology's lenses. PMID:28256589
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. PMID:28209129
Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development. PMID:28207760
Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks. PMID:28155715
Protein Bioinformatics Databases and Resources. PMID:28150231
Genomic and transcriptomic comparison between Staphylococcus aureus strains associated with high and low within herd prevalence of intra-mammary infection. PMID:28103794
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
Functional constraints on adaptive evolution of protein ubiquitination sites. PMID:28054638
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Xenopus Piwi proteins interact with a broad proportion of the oocyte transcriptome. PMID:28031481
Genome-wide Analysis of WD40 Protein Family in Human. PMID:27991561
Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome. PMID:27934892
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
A comprehensive map of molecular drug targets. PMID:27910877
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts. PMID:27822292
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PMID:27812085
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
A computational interactome and functional annotation for the human proteome. PMID:27770567
HieranoiDB: a database of orthologs inferred by Hieranoid. PMID:27742821
In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings. PMID:27729395
Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum. PMID:27695302
CardioTF, a database of deconstructing transcriptional circuits in the heart system. PMID:27635320
A full-body transcriptome and proteome resource for the European common carp. PMID:27590662
Genome Sequence of a Lactococcus lactis Strain Isolated from Salmonid Intestinal Microbiota. PMID:27563049
PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants. PMID:27515999
SoyNet: a database of co-functional networks for soybean Glycine max. PMID:27492285
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PMID:27286824
Towards Consensus Gene Ages. PMID:27259914
Independent Evolution of Winner Traits without Whole Genome Duplication in Dekkera Yeasts. PMID:27152421
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny. PMID:27103098
Tissue repair genes: the TiRe database and its implication for skin wound healing. PMID:27049721
Standardized benchmarking in the quest for orthologs. PMID:27043882
dbPAF: an integrative database of protein phosphorylation in animals and fungi. PMID:27010073
Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana. PMID:26980300
Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains. PMID:26954687
Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast. PMID:26896331
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28. PMID:26375680
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Phylogenomics databases for facilitating functional genomics in rice. PMID:26223238
Suppression of ASKβ (AtSK32), a Clade III Arabidopsis GSK3, Leads to the Pollen Defect during Late Pollen Development. PMID:25997736
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. PMID:25964301
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
Leveraging DNA damage response signaling to identify yeast genes controlling genome stability. PMID:25721128
Systematic characterization and prediction of post-translational modification cross-talk. PMID:25605461
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347
InParanoid 6: eukaryotic ortholog clusters with inparalogs PubMed citations: 127.

127 articles citing: InParanoid 6: eukaryotic ortholog clusters with inparalogs

A Pan-Cancer Analysis of the Oncogenic Role of WD Repeat Domain 74 in Multiple Tumors. PMID:35559034
Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis. PMID:35053577
SBSA: an online service for somatic binding sequence annotation. PMID:34606615
RNA editing affects cis-regulatory elements and predicts adverse cancer survival. PMID:34319007
Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. PMID:34069857
Integrative omics analysis reveals relationships of genes with synthetic lethal interactions through a pan-cancer analysis. PMID:33240468
SMDB: pivotal somatic sequence alterations reprogramming regulatory cascades. PMID:33094288
Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses. PMID:31346329
RRMdb-an evolutionary-oriented database of RNA recognition motif sequences. PMID:30649297
RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics. PMID:30558267
Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei. PMID:30097472
Adaptation of Arabidopsis thaliana to the Yangtze River basin. PMID:29284515
Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives. PMID:29141655
Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. PMID:28927400
Approximating the correction of weighted and unweighted orthology and paralogy relations. PMID:28293276
DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues. PMID:28132027
The link between orthology relations and gene trees: a correction perspective. PMID:27087831
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PMID:26587879
Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes. PMID:26581444
Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. PMID:26538579
Reconstructing a SuperGeneTree minimizing reconciliation. PMID:26451911
Molecular dynamics study of naturally existing cavity couplings in proteins. PMID:25816327
Systems-based analysis of the Sarcocystis neurona genome identifies pathways that contribute to a heteroxenous life cycle. PMID:25670772
Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection. PMID:25603810
Orthology and paralogy constraints: satisfiability and consistency. PMID:25572629
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. PMID:25429972
New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. PMID:25323955
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. PMID:25218058
Orthology detection combining clustering and synteny for very large datasets. PMID:25137074
The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration. PMID:24879305
Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors. PMID:24710207
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. PMID:24684742
NADH binds and stabilizes the 26S proteasomes independent of ATP. PMID:24596095
Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of developmental system drift on gene function. PMID:24516395
De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda. PMID:24475219
Mating type gene homologues and putative sex pheromone-sensing pathway in arbuscular mycorrhizal fungi, a presumably asexual plant root symbiont. PMID:24260466
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
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
Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees. PMID:24079845
Ultrasonic incisions produce less inflammatory mediator response during early healing than electrosurgical incisions. PMID:24058457
Circadian rhythms of sense and antisense transcription in sugarcane, a highly polyploid crop. PMID:23936527
The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PMID:23818858
FSRD: fungal stress response database. PMID:23757396
The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees. PMID:23620730
SH3 interactome conserves general function over specific form. PMID:23549480
Spatial and functional organization of mitochondrial protein network. PMID:23466738
A novel method for cross-species gene expression analysis. PMID:23444967
A role for more axillary growth1 (MAX1) in evolutionary diversity in strigolactone signaling upstream of MAX2. PMID:23424248
Prediction of C. elegans longevity genes by human and worm longevity networks. PMID:23144747
Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder. PMID:23055912
Transcriptome response to nitrogen starvation in rice. PMID:22922198
Towards biological characters of interactions between transcription factors and their DNA targets in mammals. PMID:22888987
A methodology for detecting the orthology signal in a PPI network at a functional complex level. PMID:22759423
Conserved rules govern genetic interaction degree across species. PMID:22747640
Morphine produces immunosuppressive effects in nonhuman primates at the proteomic and cellular levels. PMID:22580588
Treatment of SIV-infected sooty mangabeys with a type-I IFN agonist results in decreased virus replication without inducing hyperimmune activation. PMID:22550346
Orthology relations, symbolic ultrametrics, and cographs. PMID:22456957
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. PMID:22403033
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Broad phylogenomic sampling and the sister lineage of land plants. PMID:22253761
Functional analysis of the kinome of the wheat scab fungus Fusarium graminearum. PMID:22216007
The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. PMID:22194470
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PMID:22174796
Developing a community-based genetic nomenclature for anole lizards. PMID:22077994
CCR5 blockade is well tolerated and induces changes in the tissue distribution of CCR5+ and CD25+ T cells in healthy, SIV-uninfected rhesus macaques. PMID:22077380
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. PMID:21970648
Domain architecture conservation in orthologs. PMID:21819573
Wdr74 is required for blastocyst formation in the mouse. PMID:21799883
Necroptosis: biochemical, physiological and pathological aspects. PMID:21773880
MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes. PMID:21712981
SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. PMID:21701047
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling. PMID:21694719
Predicting selective drug targets in cancer through metabolic networks. PMID:21694718
Evolutionary plasticity of segmentation clock networks. PMID:21652651
PRIN: a predicted rice interactome network. PMID:21575196
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
Proteinortho: detection of (co-)orthologs in large-scale analysis. PMID:21526987
Mapping protein interactions between Dengue virus and its human and insect hosts. PMID:21358811
Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination. PMID:21307298
Identification of genes required for neural-specific glycosylation using functional genomics. PMID:21203496
A scalable approach for discovering conserved active subnetworks across species. PMID:21170309
Refining orthologue groups at the transcript level. PMID:21143794
dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. PMID:21087999
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. PMID:21047383
RBPDB: a database of RNA-binding specificities. PMID:21036867
Molecular characterization of the evolution of phagosomes. PMID:20959821
Modifiers of notch transcriptional activity identified by genome-wide RNAi. PMID:20959007
Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. PMID:20943681
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections. PMID:20844032
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. PMID:20823322
Comparing peripheral glial cell differentiation in Drosophila and vertebrates. PMID:20820850
A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase. PMID:20819218
Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response. PMID:20736407
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. PMID:20624743
Molecular evolution of genes in avian genomes. PMID:20573239
Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture. PMID:20497561
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. PMID:20463971
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. PMID:20210993
Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. PMID:20102611
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. PMID:20053291
Identification of mammalian orthologs using local synteny. PMID:20030836
The phylogenetic distribution of non-CTCF insulator proteins is limited to insects and reveals that BEAF-32 is Drosophila lineage specific. PMID:20024537
WormBase: a comprehensive resource for nematode research. PMID:19910365
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. PMID:19892828
Divergence of exonic splicing elements after gene duplication and the impact on gene structures. PMID:19883501
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
Functional characterization of the Arabidopsis bHLH92 transcription factor in abiotic stress. PMID:19760256
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. PMID:19698106
The Chicken Gene Nomenclature Committee report. PMID:19607656
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PMID:19578431
Databases of homologous gene families for comparative genomics. PMID:19534752
Identifying the topology of protein complexes from affinity purification assays. PMID:19505940
GoGene: gene annotation in the fast lane. PMID:19465383
COFECO: composite function annotation enriched by protein complex data. PMID:19429688
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PMID:19260763
Global networks of functional coupling in eukaryotes from comprehensive data integration. PMID:19246318
Revisiting the missing protein-coding gene catalog of the domestic dog. PMID:19193219
Phylogenetic and functional assessment of orthologs inference projects and methods. PMID:19148271
Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. PMID:19053807
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. PMID:19043069
PIPs: human protein-protein interaction prediction database. PMID:18988626
ERGR: An ethanol-related gene resource. PMID:18978021
SynBlast: assisting the analysis of conserved synteny information. PMID:18721485
Wormnet: a crystal ball for Caenorhabditis elegans. PMID:18533047
Analysis of the codon use frequency of AMPK family genes from different species. PMID:18188681
http://dx.doi.org/10.1093/nar/

http://dx.doi.org/10.1093/nar/gki107

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orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: InParanoid; InParanoid; DOI: https://doi.org/10.25504/FAIRsharing.AN3lMf; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

proteome
metasource: Fairsharing.org
version: FAIRsharing.org: InParanoid; InParanoid; DOI: https://doi.org/10.25504/FAIRsharing.AN3lMf; Last edited: Jan. 8, 2019, 1:26 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

evolutionary biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.786607

function analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:15.786607

orthology proteome protein sequence protein domains and classification evolutionary biology function analysis

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HieranoiDB

Networks of Functional Coupling of proteins

Orthodisease

iPfam

LenVarDB

InterDom

Database of Orthologous Groups

Protein Clusters

OPTIC

siRNAdb

OrtholugeDB

Orthologous MAtrix

FunShift

ADDA - A Domain Database

Acytostelium Gene Database

UniProt Knowledgebase

PALI

Stockholm Multiple Alignment Format

TIGRFAMs

ProDom