Published in Biol Open on December 15, 2013
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet (2014) 1.51
Extensive copy-number variation of young genes across stickleback populations. PLoS Genet (2014) 0.92
Annual meeting of the EpiGeneSys Network of Excellence--Advancing epigenetics towards systems biology. Bioessays (2015) 0.75
Ensembl 2011. Nucleic Acids Res (2010) 14.68
NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res (2010) 14.38
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
Segmental duplications: organization and impact within the current human genome project assembly. Genome Res (2001) 11.77
The probability of duplicate gene preservation by subfunctionalization. Genetics (2000) 10.27
Mechanisms of change in gene copy number. Nat Rev Genet (2009) 9.01
Diversity of human copy number variation and multicopy genes. Science (2010) 8.97
Molecular phylogenetics and the origins of placental mammals. Nature (2001) 8.42
Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet (2009) 7.64
Mutation rates differ among regions of the mammalian genome. Nature (1989) 7.63
The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet (2010) 5.75
Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet (2006) 5.25
The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A (2007) 4.96
Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet (2002) 4.89
Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A (2009) 4.76
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res (2010) 4.67
Parallel adaptive radiations in two major clades of placental mammals. Nature (2001) 4.65
Bias of selection on human copy-number variants. PLoS Genet (2006) 4.44
The probability of preservation of a newly arisen gene duplicate. Genetics (2001) 4.42
The human phylome. Genome Biol (2007) 3.81
Human mutation rate associated with DNA replication timing. Nat Genet (2009) 3.81
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res (2009) 3.36
Is genetic evolution predictable? Science (2009) 3.10
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (2010) 3.00
Origins, evolution, and phenotypic impact of new genes. Genome Res (2010) 2.98
Duplication hotspots, rare genomic disorders, and common disease. Curr Opin Genet Dev (2009) 2.96
Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet (2011) 2.86
Inverse relationship between evolutionary rate and age of mammalian genes. Mol Biol Evol (2004) 2.79
DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat Biotechnol (2011) 2.62
The complex structure and dynamic evolution of human subtelomeres. Nat Rev Genet (2002) 2.57
Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci U S A (2007) 2.55
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
Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet (2012) 2.33
Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol (2012) 2.25
Concern Non-adaptive origins of interactome complexity. Nature (2011) 2.19
Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants. Am J Hum Genet (2009) 2.07
A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet (2007) 2.06
Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet (2010) 1.68
The life and death of gene families. Bioessays (2009) 1.66
The ATR barrier to replication-born DNA damage. DNA Repair (Amst) (2010) 1.50
A phylogenomic study of human, dog, and mouse. PLoS Comput Biol (2006) 1.49
Mutation rates across budding yeast chromosome VI are correlated with replication timing. Genome Biol Evol (2011) 1.47
Crosstalk between chromatin state and DNA damage response in cellular senescence and cancer. Nat Rev Cancer (2012) 1.45
A transcriptomic hourglass in plant embryogenesis. Nature (2012) 1.40
The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol (2008) 1.36
Dosage sensitivity shapes the evolution of copy-number varied regions. PLoS One (2010) 1.30
Studies of genomic copy number changes in human cancers reveal signatures of DNA replication stress. Mol Oncol (2011) 1.26
A time-invariant principle of genome evolution. Proc Natl Acad Sci U S A (2010) 1.24
Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age. Mol Biol Evol (2012) 1.19
Lessons from the human genome: transitions between euchromatin and heterochromatin. Hum Mol Genet (2001) 1.19
Young proteins experience more variable selection pressures than old proteins. Genome Res (2010) 1.19
Hydroxyurea induces de novo copy number variants in human cells. Proc Natl Acad Sci U S A (2011) 1.17
Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res (2011) 1.16
Stepwise evolution of essential centromere function in a Drosophila neogene. Science (2013) 1.13
Dog as an outgroup to human and mouse. PLoS Comput Biol (2007) 1.03
Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. Genome Res (2010) 1.03
Timing of replication is a determinant of neutral substitution rates but does not explain slow Y chromosome evolution in rodents. Mol Biol Evol (2009) 1.02
Drosophila duplication hotspots are associated with late-replicating regions of the genome. PLoS Genet (2011) 0.96
Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b. Mol Biol Evol (2013) 0.92
Late-replicating domains have higher divergence and diversity in Drosophila melanogaster. Mol Biol Evol (2011) 0.91
Defining the replication program through the chromatin landscape. Crit Rev Biochem Mol Biol (2011) 0.89
Divergence of mammalian higher order chromatin structure is associated with developmental loci. PLoS Comput Biol (2013) 0.89
Genetic variation and DNA replication timing, or why is there late replicating DNA? Evolution (2011) 0.86
Replication stress, a source of epigenetic aberrations in cancer? Bioessays (2010) 0.81
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
International network of cancer genome projects. Nature (2010) 20.35
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics (2005) 14.50
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18
Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet (2009) 11.73
Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet (2007) 10.38
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature (2010) 8.99
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet (2011) 6.43
A gene network for navigating the literature. Nat Genet (2004) 6.43
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics (2005) 6.02
Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A (2003) 4.88
Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol (2008) 4.36
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics (2005) 3.85
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Text-mining and information-retrieval services for molecular biology. Genome Biol (2005) 3.54
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol (2008) 3.54
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet (2012) 3.08
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics (2011) 3.03
An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform (2010) 3.01
Great ape genetic diversity and population history. Nature (2013) 2.95
Increased telomere fragility and fusions resulting from TRF1 deficiency lead to degenerative pathologies and increased cancer in mice. Genes Dev (2009) 2.91
Substrate fate in activated macrophages: a comparison between innate, classic, and alternative activation. J Immunol (2010) 2.88
Introducing meta-services for biomedical information extraction. Genome Biol (2008) 2.78
Emerging methods in protein co-evolution. Nat Rev Genet (2013) 2.72
BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford) (2013) 2.69
Copy number variation and evolution in humans and chimpanzees. Genome Res (2008) 2.69
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66
iHOP web services. Nucleic Acids Res (2007) 2.65
A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nat Genet (2010) 2.57
EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res (2003) 2.50
The bonobo genome compared with the chimpanzee and human genomes. Nature (2012) 2.49
Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat Genet (2013) 2.44
Predicting reliable regions in protein alignments from sequence profiles. J Mol Biol (2003) 2.42
Automatic methods for predicting functionally important residues. J Mol Biol (2003) 2.39
Text mining for the biocuration workflow. Database (Oxford) (2012) 2.37
Overview of the BioCreative III Workshop. BMC Bioinformatics (2011) 2.31
On the organization of bioinformatics core services in biology-based research institutes. Bioinformatics (2011) 2.29
Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins (2005) 2.27
The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A (2012) 2.24
The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol (2010) 2.18
A text-mining perspective on the requirements for electronically annotated abstracts. FEBS Lett (2008) 2.10
Identification of amino acid residues crucial for chemokine receptor dimerization. Nat Immunol (2004) 2.09
In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins (2002) 2.05
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res (2012) 2.04
POTRA: a conserved domain in the FtsQ family and a class of beta-barrel outer membrane proteins. Trends Biochem Sci (2003) 2.02
Characterization of six human disease-associated inversion polymorphisms. Hum Mol Genet (2009) 2.00
Assessment of predictions submitted for the CASP7 function prediction category. Proteins (2007) 1.98
Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. Am J Hum Genet (2010) 1.97
EnrichNet: network-based gene set enrichment analysis. Bioinformatics (2012) 1.92
Text mining for biology--the way forward: opinions from leading scientists. Genome Biol (2008) 1.91
firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res (2007) 1.91
Text-mining approaches in molecular biology and biomedicine. Drug Discov Today (2005) 1.91
Clustering of proximal sequence space for the identification of protein families. Bioinformatics (2002) 1.87
The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Res (2009) 1.87
Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform (2008) 1.80
Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem (2002) 1.74
Death and resurrection of the human IRGM gene. PLoS Genet (2009) 1.72
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci U S A (2008) 1.72
MARVEL: a conserved domain involved in membrane apposition events. Trends Biochem Sci (2002) 1.71
Text mining for metabolic pathways, signaling cascades, and protein networks. Sci STKE (2005) 1.71
Cohesin organizes chromatin loops at DNA replication factories. Genes Dev (2010) 1.71
Filamin-A regulates actin-dependent clustering of HIV receptors. Nat Cell Biol (2007) 1.71
Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A (2010) 1.71
Analysis of biological processes and diseases using text mining approaches. Methods Mol Biol (2010) 1.70
p23 and HSP20/alpha-crystallin proteins define a conserved sequence domain present in other eukaryotic protein families. FEBS Lett (2002) 1.66
BRICHOS: a conserved domain in proteins associated with dementia, respiratory distress and cancer. Trends Biochem Sci (2002) 1.66
DNA methylation contributes to natural human variation. Genome Res (2013) 1.66
Protein co-evolution, co-adaptation and interactions. EMBO J (2008) 1.65
Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods (2013) 1.64
Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery. J Mol Biol (2005) 1.63
Life cycles of successful genes. Trends Genet (2003) 1.61
A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinformatics (2005) 1.59
Information extraction in molecular biology. Brief Bioinform (2002) 1.57
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome Res (2013) 1.51
The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol (2012) 1.50
Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res (2011) 1.47
Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform (2009) 1.44
firestar--advances in the prediction of functionally important residues. Nucleic Acids Res (2011) 1.43
The small GTP-binding protein, Rhes, regulates signal transduction from G protein-coupled receptors. Oncogene (2004) 1.42
Assessment of intramolecular contact predictions for CASP7. Proteins (2007) 1.40
CASP6 assessment of contact prediction. Proteins (2005) 1.39
The success (or not) of HUGO nomenclature. Genome Biol (2006) 1.37
Defining functional distances over gene ontology. BMC Bioinformatics (2008) 1.33
Cyclin-dependent kinase inhibitor p21 controls adult neural stem cell expansion by regulating Sox2 gene expression. Cell Stem Cell (2012) 1.33
The three-dimensional structure of an eukaryotic glutamine synthetase: functional implications of its oligomeric structure. J Struct Biol (2006) 1.31
No paradox, no progress: inverse cancer comorbidity in people with other complex diseases. Lancet Oncol (2011) 1.30
Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol (2011) 1.30