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Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/bies.080085openalex-snapshot
The life and death of gene families
inferredcites →https://doi.org/10.1002/pro.143openalex-snapshot
Evolutionary constraints on structural similarity in orthologs and paralogs
inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot
Evolution by Gene Duplication
inferredcites →https://doi.org/10.1016/j.tig.2004.09.001openalex-snapshot
The altered evolutionary trajectories of gene duplicates
inferredcites →https://doi.org/10.1016/j.tig.2008.08.009openalex-snapshot
The quest for orthologs: finding the corresponding gene across genomes
inferredcites →https://doi.org/10.1038/nature06340openalex-snapshot
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
inferredcites →https://doi.org/10.1038/nature06341openalex-snapshot
Evolution of genes and genomes on the Drosophila phylogeny
inferredcites →https://doi.org/10.1038/nature13668openalex-snapshot
Comparative analysis of regulatory information and circuits across distant species
inferredcites →https://doi.org/10.1073/pnas.0403094101openalex-snapshot
Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss
inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot
Amino acid substitution matrices from protein blocks.
inferredcites →https://doi.org/10.1093/bib/bbr030openalex-snapshot
Computational methods for Gene Orthology inference
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.301openalex-snapshot
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
inferredcites →https://doi.org/10.1093/bioinformatics/bti325openalex-snapshot
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
inferredcites →https://doi.org/10.1093/bioinformatics/btl213openalex-snapshot
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/molbev/msg236openalex-snapshot
Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks
inferredcites →https://doi.org/10.1093/molbev/msi111openalex-snapshot
Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
inferredcites →https://doi.org/10.1093/molbev/msm105openalex-snapshot
Rare Coding Sequence Changes are Consistent with Ecdysozoa, not Coelomata
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/30.7.1575openalex-snapshot
An efficient algorithm for large-scale detection of protein families
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkj118openalex-snapshot
TreeFam: a curated database of phylogenetic trees of animal gene families
inferredcites →https://doi.org/10.1093/nar/gkl091openalex-snapshot
M-Coffee: combining multiple sequence alignment methods with T-Coffee
inferredcites →https://doi.org/10.1093/nar/gkp373openalex-snapshot
Berkeley PHOG: PhyloFacts orthology group prediction web server
inferredcites →https://doi.org/10.1093/nar/gkq1238openalex-snapshot
OMA 2011: orthology inference among 1000 complete genomes
inferredcites →https://doi.org/10.1093/sysbio/28.2.132openalex-snapshot
Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences
inferredcites →https://doi.org/10.1093/sysbio/43.1.58openalex-snapshot
Maps Between Trees and Cladistic Analysis of Historical Associations among Genes,Organisms, and Areas
inferredcites →https://doi.org/10.1093/sysbio/sys076openalex-snapshot
TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
inferredcites →https://doi.org/10.1101/gr.073585.107openalex-snapshot
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1101/gr.123901.111openalex-snapshot
Unified modeling of gene duplication, loss, and coalescence using a locus tree
inferredcites →https://doi.org/10.1126/science.278.5338.631openalex-snapshot
A Genomic Perspective on Protein Families
inferredcites →https://doi.org/10.1126/science.287.5461.2204openalex-snapshot
Comparative Genomics of the Eukaryotes
inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.114725openalex-snapshot
Orthologs, Paralogs, and Evolutionary Genomics
inferredcites →https://doi.org/10.1186/1471-2105-8-294openalex-snapshot
Quantitative sequence-function relationships in proteins based on gene ontology
inferredcites →https://doi.org/10.1186/1471-2105-8-83openalex-snapshot
Orthology prediction at scalable resolution by phylogenetic tree analysis
inferredcites →https://doi.org/10.1186/1471-2164-8-222openalex-snapshot
Quantitative assessment of relationship between sequence similarity and function similarity
inferredcites →https://doi.org/10.1186/gb-2007-8-7-r141openalex-snapshot
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
inferredcites →https://doi.org/10.1371/journal.pbio.0050008openalex-snapshot
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
inferredcites →https://doi.org/10.1371/journal.pcbi.1002073openalex-snapshot
Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals
inferredcites →https://doi.org/10.1371/journal.pcbi.1002386openalex-snapshot
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report
inferredcites →https://doi.org/10.1371/journal.pcbi.1002514openalex-snapshot
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs
inferredcites →https://doi.org/10.1371/journal.pcbi.1002784openalex-snapshot
The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pgen.0020173openalex-snapshot
Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1371/journal.pgen.0030007openalex-snapshot
Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model
inferredcites →https://doi.org/10.1371/journal.pone.0012776openalex-snapshot
Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
inferredcites →https://doi.org/10.2307/2412448openalex-snapshot
Distinguishing Homologous from Analogous Proteins
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-3-030-20242-2_7openalex-snapshot
Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model
inferred← citeshttps://doi.org/10.1038/nature13992openalex-snapshot
A comparative encyclopedia of DNA elements in the mouse genome
inferred← citeshttps://doi.org/10.1093/nar/gky018openalex-snapshot
Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse
inferred← citeshttps://doi.org/10.1101/gr.170100.113openalex-snapshot
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data
inferred← citeshttps://doi.org/10.1109/tcbb.2018.2846253openalex-snapshot
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution
inferred← citeshttps://doi.org/10.1145/3233547.3233603openalex-snapshot
An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem
inferred← citeshttps://doi.org/10.1159/000514180openalex-snapshot
The Deep Roots of Addiction: A Comparative Perspective
inferred← citeshttps://doi.org/10.12688/f1000research.6536.1openalex-snapshot
A reanalysis of mouse ENCODE comparative gene expression data
inferred← citeshttps://doi.org/10.12794/metadc1752394openalex-snapshot
Analysis of the Cytochrome P450 and UDP-Glucuronosyltransferase Families and Vitamin D3- Supplementation in Anoxia Survival in Caenorhabditis elegans
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005274openalex-snapshot
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
inferred← citeshttps://doi.org/10.29245/2578-2959/2018/3.1135openalex-snapshot
The Deep Evolutionary Roots of 'Addiction'
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