Published in PLoS Comput Biol on June 28, 2012
"Out of pollen" hypothesis for origin of new genes in flowering plants: study from Arabidopsis thaliana. Genome Biol Evol (2014) 1.44
Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. Mol Biol Evol (2014) 0.92
How old is my gene? Trends Genet (2013) 0.91
Exploring fold space preferences of new-born and ancient protein superfamilies. PLoS Comput Biol (2013) 0.84
Emergence of novel domains in proteins. BMC Evol Biol (2013) 0.83
A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun (2015) 0.81
Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. BMC Evol Biol (2015) 0.80
Integrative analysis of young genes, positively selected genes and lncRNAs in the development of Drosophila melanogaster. BMC Evol Biol (2014) 0.80
Emergence and evolutionary analysis of the human DDR network: implications in comparative genomics and downstream analyses. Mol Biol Evol (2014) 0.78
Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. Am J Hum Genet (2016) 0.77
Systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution. PLoS Comput Biol (2013) 0.77
Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PLoS Comput Biol (2016) 0.77
Computational assessment of feature combinations for pathogenic variant prediction. Mol Genet Genomic Med (2016) 0.76
Physicochemical properties that control protein aggregation also determine whether a protein is retained or released from necrotic cells. Open Biol (2016) 0.75
Computational Identification of Novel Genes: Current and Future Perspectives. Bioinform Biol Insights (2016) 0.75
High GC content causes orphan proteins to be intrinsically disordered. PLoS Comput Biol (2017) 0.75
Expression of evolutionarily novel genes in tumors. Infect Agent Cancer (2016) 0.75
Systematic Analyses and Prediction of Human Drug Side Effect Associated Proteins from the Perspective of Protein Evolution. Genome Biol Evol (2017) 0.75
Distinct distributions of genomic features of the 5' and 3' partners of coding somatic cancer gene fusions: arising mechanisms and functional implications. Oncotarget (2016) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80
PANTHER: a library of protein families and subfamilies indexed by function. Genome Res (2003) 21.64
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2008) 21.36
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
Broad phylogenomic sampling improves resolution of the animal tree of life. Nature (2008) 11.84
TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006) 10.24
Transcription regulation and animal diversity. Nature (2003) 9.22
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol (2009) 7.95
Natural history and evolutionary principles of gene duplication in fungi. Nature (2007) 7.26
The Gene Ontology: enhancements for 2011. Nucleic Acids Res (2011) 5.82
DendroPy: a Python library for phylogenetic computing. Bioinformatics (2010) 5.09
Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics (2006) 3.98
QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics (2009) 3.36
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (2010) 3.00
Inverse relationship between evolutionary rate and age of mammalian genes. Mol Biol Evol (2004) 2.79
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A (2009) 2.50
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics (2010) 1.98
Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol (2010) 1.87
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS One (2007) 1.83
An ancient evolutionary origin of genes associated with human genetic diseases. Mol Biol Evol (2008) 1.73
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol (2010) 1.40
Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol (2006) 1.33
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PLoS Comput Biol (2008) 1.23
Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol (2010) 1.19
Young proteins experience more variable selection pressures than old proteins. Genome Res (2010) 1.19
GLOOME: gain loss mapping engine. Bioinformatics (2010) 1.08
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol (2009) 1.07
SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Aging (Albany NY) (2011) 1.01
The accumulation of gene regulation through time. Genome Biol Evol (2011) 0.87
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. Nucleic Acids Res (2008) 0.83
PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya. Bioinformatics (2011) 0.80
When the pie is too small. Genome Biol (2010) 0.77
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell (2012) 4.22
The UCSC Archaeal Genome Browser. Nucleic Acids Res (2006) 2.65
Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science (2013) 2.62
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol (2011) 2.54
PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform (2010) 2.36
Novel bacterial taxa in the human microbiome. PLoS One (2012) 2.35
Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol (2004) 2.34
Hotspots of biased nucleotide substitutions in human genes. PLoS Biol (2009) 1.89
The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol (2009) 1.77
Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res (2007) 1.72
Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nat Commun (2011) 1.69
Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet (2011) 1.58
Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Stat Appl Genet Mol Biol (2004) 1.55
Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Stat Appl Genet Mol Biol (2004) 1.47
Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell (2013) 1.40
Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol (2011) 1.36
Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics (2003) 1.34
Identifying genetic networks underlying myometrial transition to labor. Genome Biol (2005) 1.28
Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. BMC Genomics (2008) 1.24
Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol (2007) 1.23
The phylogenetic diversity of metagenomes. PLoS One (2011) 1.21
Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol (2010) 1.19
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol (2015) 1.13
Global marine bacterial diversity peaks at high latitudes in winter. ISME J (2013) 1.10
The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol Biol Evol (2010) 1.08
Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J Bacteriol (2008) 1.06
Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci (2013) 1.03
SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Aging (Albany NY) (2011) 1.01
Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol (2011) 0.99
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res (2008) 0.99
Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS One (2011) 0.99
The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol (2011) 0.98
A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet (2013) 0.97
How old is my gene? Trends Genet (2013) 0.91
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics (2012) 0.90
GC-biased evolution near human accelerated regions. PLoS Genet (2010) 0.89
Noncoding sequences near duplicated genes evolve rapidly. Genome Biol Evol (2010) 0.88
Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One (2012) 0.87
Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics (2014) 0.86
Evaluation of two methods to estimate and monitor bird populations. PLoS One (2008) 0.85
Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. BMC Neurosci (2007) 0.82
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics (2012) 0.82
A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol (2013) 0.81
From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One (2013) 0.79
Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis. BMC Genomics (2013) 0.77
Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform (2016) 0.76
The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae. Mol Biosyst (2011) 0.76
Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes. Genet Res (Camb) (2010) 0.75