Published in PLoS Comput Biol on March 26, 2010
The evolutionary origin of orphan genes. Nat Rev Genet (2011) 2.98
Cortical evolution: judge the brain by its cover. Neuron (2013) 1.54
De novo origin of human protein-coding genes. PLoS Genet (2011) 1.48
Evolution of genetic and genomic features unique to the human lineage. Nat Rev Genet (2012) 1.44
Transposable element insertions have strongly affected human evolution. Proc Natl Acad Sci U S A (2010) 1.40
Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet (2012) 1.35
Putatively noncoding transcripts show extensive association with ribosomes. Genome Biol Evol (2011) 1.28
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics (2013) 1.23
Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol (2010) 1.19
Evolution of viral proteins originated de novo by overprinting. Mol Biol Evol (2012) 1.09
De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. PLoS Genet (2013) 1.06
CHRFAM7A, a human-specific and partially duplicated α7-nicotinic acetylcholine receptor gene with the potential to specify a human-specific inflammatory response to injury. J Leukoc Biol (2014) 1.05
CNS effects of CB2 cannabinoid receptors: beyond neuro-immuno-cannabinoid activity. J Psychopharmacol (2011) 1.02
RhesusBase: a knowledgebase for the monkey research community. Nucleic Acids Res (2012) 1.02
Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA (2011) 1.00
Evolution of prokaryotic genes by shift of stop codons. J Mol Evol (2010) 0.97
NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas. PLoS Genet (2014) 0.93
Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque. Mol Biol Evol (2014) 0.93
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution. Mol Biol Evol (2016) 0.91
Genes from scratch--the evolutionary fate of de novo genes. Trends Genet (2015) 0.91
Identification of novel GDNF isoforms and cis-antisense GDNFOS gene and their regulation in human middle temporal gyrus of Alzheimer disease. J Biol Chem (2011) 0.88
Interaction-based evolution: how natural selection and nonrandom mutation work together. Biol Direct (2013) 0.87
New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos Trans R Soc Lond B Biol Sci (2015) 0.87
De novo origins of human genes. PLoS Genet (2011) 0.86
PBOV1 is a human de novo gene with tumor-specific expression that is associated with a positive clinical outcome of cancer. PLoS One (2013) 0.84
De novo origin of protein-coding genes in murine rodents. PLoS One (2012) 0.84
Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet (2015) 0.82
The Recent De Novo Origin of Protein C-Termini. Genome Biol Evol (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
Two rapidly evolving genes contribute to male fitness in Drosophila. J Mol Evol (2013) 0.77
De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting. Genome Biol Evol (2016) 0.77
Evolution of cis-regulatory elements in yeast de novo and duplicated new genes. BMC Genomics (2012) 0.77
On the evolutionary relationship between chondrocytes and osteoblasts. Front Genet (2015) 0.77
De novo origin of VCY2 from autosome to Y-transposed amplicon. PLoS One (2015) 0.76
Analysis of in planta Expressed Orphan Genes in the Rice Blast Fungus Magnaporthe oryzae. Plant Pathol J (2014) 0.75
Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis in Both Haematological Malignancies and Solid Tumours: The Extraordinary Case of MYEOV Gene. Scientifica (Cairo) (2015) 0.75
Up-regulation of the human-specific CHRFAM7A gene in inflammatory bowel disease. BBA Clin (2016) 0.75
Cross-Species Analysis of Gene Expression and Function in Prefrontal Cortex, Hippocampus and Striatum. PLoS One (2016) 0.75
Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover. Bioessays (2016) 0.75
Reverse transcriptase and intron number evolution. Stem Cell Investig (2014) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16
Consed: a graphical tool for sequence finishing. Genome Res (1998) 59.36
DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics (2003) 32.63
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2007) 22.53
The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res (2009) 19.70
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res (1997) 13.48
Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science (1993) 4.43
Post-transcriptional regulation of the let-7 microRNA during neural cell specification. FASEB J (2006) 4.34
Molecular genetics of successful smoking cessation: convergent genome-wide association study results. Arch Gen Psychiatry (2008) 3.12
Emergence of young human genes after a burst of retroposition in primates. PLoS Biol (2005) 3.08
Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene. Trends Genet (2004) 2.87
Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci U S A (2006) 2.84
PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res (2007) 2.58
Recent de novo origin of human protein-coding genes. Genome Res (2009) 2.36
Rodent BDNF genes, novel promoters, novel splice variants, and regulation by cocaine. Brain Res (2005) 2.34
Molecular genetics of nicotine dependence and abstinence: whole genome association using 520,000 SNPs. BMC Genet (2007) 2.24
Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome Res (2005) 1.95
Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol (2008) 1.95
De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics (2008) 1.87
Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics (2007) 1.75
Genetic linkage to chromosome 22q12 for a heavy-smoking quantitative trait in two independent samples. Am J Hum Genet (2007) 1.73
Human brain derived neurotrophic factor (BDNF) genes, splicing patterns, and assessments of associations with substance abuse and Parkinson's Disease. Am J Med Genet B Neuropsychiatr Genet (2005) 1.60
The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Mol Biol Evol (2000) 1.43
Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster. PLoS Genet (2007) 1.36
Genetic basis of human brain evolution. Trends Neurosci (2008) 1.22
Cardioprotection by CaMKII-deltaB is mediated by phosphorylation of heat shock factor 1 and subsequent expression of inducible heat shock protein 70. Circ Res (2009) 1.18
Darwinian alchemy: Human genes from noncoding DNA. Genome Res (2009) 1.18
Mapping and verification of susceptibility loci for smoking quantity using permutation linkage analysis. Pharmacogenomics J (2005) 1.11
Intercenter reliability and validity of the rhesus macaque GeneChip. BMC Genomics (2007) 1.02
Transposable element fragments in protein-coding regions and their contributions to human functional proteins. Gene (2007) 0.93
Mouse brain localization of the protein kinase C-enhanced phosphatase 1 inhibitor KEPI (kinase C-enhanced PP1 inhibitor). Neuroscience (2005) 0.83
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res (2011) 16.53
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell (2008) 14.18
Bis[bis(methoxycarbimido)amine-kappa2N,N']bis(perchlorato-kappaO)copper(II) bis[bis(methoxycarbimido)amine-kappa2N,N']bis(methanol-kappaO)copper(II) bis(perchlorate) methanol disolvate. Acta Crystallogr C (2006) 14.17
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) 10.04
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res (2013) 7.63
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell (2009) 7.09
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A (2008) 6.42
Epidemiological serosurvey of hepatitis B in China--declining HBV prevalence due to hepatitis B vaccination. Vaccine (2009) 6.30
Nucleosome dynamics define transcriptional enhancers. Nat Genet (2010) 5.94
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res (2007) 5.88
Tsc tumour suppressor proteins antagonize amino-acid-TOR signalling. Nat Cell Biol (2002) 5.37
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Adjustment of systematic microarray data biases. Bioinformatics (2004) 5.22
A functional variant of SUMO4, a new I kappa B alpha modifier, is associated with type 1 diabetes. Nat Genet (2004) 4.95
Oligodendroglia metabolically support axons and contribute to neurodegeneration. Nature (2012) 4.95
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev (2008) 4.83
The growth factor progranulin binds to TNF receptors and is therapeutic against inflammatory arthritis in mice. Science (2011) 4.76
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics (2005) 4.60
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun (2011) 4.57
A mammalian organelle map by protein correlation profiling. Cell (2006) 4.54
Arsenic trioxide controls the fate of the PML-RARalpha oncoprotein by directly binding PML. Science (2010) 4.52
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res (2011) 4.44
RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res (2002) 4.35
DATF: a database of Arabidopsis transcription factors. Bioinformatics (2005) 4.34
Leaf nitrogen and phosphorus stoichiometry across 753 terrestrial plant species in China. New Phytol (2005) 4.20
Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13
Formation of ArF from LPdAr(F): catalytic conversion of aryl triflates to aryl fluorides. Science (2009) 4.13
Production of offspring from a germline stem cell line derived from neonatal ovaries. Nat Cell Biol (2009) 4.11
A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell (2010) 4.02
An emerging recombinant human enterovirus 71 responsible for the 2008 outbreak of hand foot and mouth disease in Fuyang city of China. Virol J (2010) 3.90
Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60
Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A (2013) 3.53
Antidepressant-like effects of kappa-opioid receptor antagonists in the forced swim test in rats. J Pharmacol Exp Ther (2003) 3.48
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
Reduced nicotine content cigarettes: effects on toxicant exposure, dependence and cessation. Addiction (2010) 3.26
RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention. Neuron (2013) 3.25
Human CD4+ CD25hi Foxp3+ regulatory T cells are derived by rapid turnover of memory populations in vivo. J Clin Invest (2006) 3.25
Decreased serum vitamin D levels in children with asthma are associated with increased corticosteroid use. J Allergy Clin Immunol (2010) 3.22
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res (2005) 3.16
CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15
Molecular genetics of successful smoking cessation: convergent genome-wide association study results. Arch Gen Psychiatry (2008) 3.12
Tissue Doppler imaging is superior to strain rate imaging and postsystolic shortening on the prediction of reverse remodeling in both ischemic and nonischemic heart failure after cardiac resynchronization therapy. Circulation (2004) 3.12
A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity. Science (2014) 3.11
Characterization of three H5N5 and one H5N8 highly pathogenic avian influenza viruses in China. Vet Microbiol (2013) 3.05
New approach for earthquake/tsunami monitoring using dense GPS networks. Sci Rep (2013) 3.03
New variant of porcine epidemic diarrhea virus, United States, 2014. Emerg Infect Dis (2014) 2.99
Adaptive optics parallel spectral domain optical coherence tomography for imaging the living retina. Opt Express (2005) 2.97
C-H...pi, pi-pi and C-H...Cl interactions in chloro-substituted Schiff bases and 4-chloro-N-[4-(dimethylamino)benzylidene]aniline. Acta Crystallogr C (2004) 2.97
Biosynthesis of selenocysteine on its tRNA in eukaryotes. PLoS Biol (2007) 2.96
Suppression of renin-angiotensin gene expression in the kidney by paricalcitol. Kidney Int (2008) 2.95
Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell (2013) 2.94
Brain-derived neurotrophic factor and obesity in the WAGR syndrome. N Engl J Med (2008) 2.91
CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Res (2007) 2.86
The palladium-catalyzed trifluoromethylation of aryl chlorides. Science (2010) 2.85
KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients. Proc Natl Acad Sci U S A (2009) 2.84
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84
Upconversion fluorescence imaging of cells and small animals using lanthanide doped nanocrystals. Biomaterials (2007) 2.80
The dragon strikes: lessons from the Wenchuan earthquake. Anesth Analg (2010) 2.78
Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genet (2010) 2.74
A new palladium precatalyst allows for the fast Suzuki-Miyaura coupling reactions of unstable polyfluorophenyl and 2-heteroaryl boronic acids. J Am Chem Soc (2010) 2.73
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res (2004) 2.69
Amplitude-modulated continuous arterial spin-labeling 3.0-T perfusion MR imaging with a single coil: feasibility study. Radiology (2005) 2.69
Chromatin signature of embryonic pluripotency is established during genome activation. Nature (2010) 2.64
Evaluation of the impact of hepatitis B vaccination among children born during 1992-2005 in China. J Infect Dis (2009) 2.62
Cannabinoid CB2 receptors: immunohistochemical localization in rat brain. Brain Res (2006) 2.62
KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res (2006) 2.59
Distinguishing cancer-associated missense mutations from common polymorphisms. Cancer Res (2007) 2.57
Identification and control of a poliomyelitis outbreak in Xinjiang, China. N Engl J Med (2013) 2.55
Downregulation of miR-133 and miR-590 contributes to nicotine-induced atrial remodelling in canines. Cardiovasc Res (2009) 2.54
Myocardial infarct size measurement in the mouse chronic infarction model: comparison of area- and length-based approaches. J Appl Physiol (1985) (2007) 2.52
Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet (2011) 2.52
Catena-poly[[diisothiocyanatocadmium(II)]-bis[mu-1,3-bis(1,2,4-triazol-1-ylmethyl)benzene-kappa2N4:N4']]: a double-chain coordination polymer. Acta Crystallogr C (2006) 2.50
5'-triphosphate-dependent activation of PKR by RNAs with short stem-loops. Science (2007) 2.48
Transforming growth factor-beta-regulated miR-24 promotes skeletal muscle differentiation. Nucleic Acids Res (2008) 2.44
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A (2014) 2.42
Retracted Down-regulation of miR-1/miR-133 contributes to re-expression of pacemaker channel genes HCN2 and HCN4 in hypertrophic heart. J Biol Chem (2008) 2.41
A critical role of IFNgamma in priming MSC-mediated suppression of T cell proliferation through up-regulation of B7-H1. Cell Res (2008) 2.38
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol (2011) 2.37
MG53 constitutes a primary determinant of cardiac ischemic preconditioning. Circulation (2010) 2.35
The yak genome and adaptation to life at high altitude. Nat Genet (2012) 2.34
Rodent BDNF genes, novel promoters, novel splice variants, and regulation by cocaine. Brain Res (2005) 2.34
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet (2012) 2.33
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods (2012) 2.31
Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science (2012) 2.29
Impact of a baseline polymorphism on the emergence of resistance to the hepatitis C virus nonstructural protein 5A replication complex inhibitor, BMS-790052. Hepatology (2012) 2.29
Clinical characteristics of 26 human cases of highly pathogenic avian influenza A (H5N1) virus infection in China. PLoS One (2008) 2.28
Structure-function-folding relationship in a WW domain. Proc Natl Acad Sci U S A (2006) 2.28