Published in Trends Genet on March 26, 2007
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
Proto-genes and de novo gene birth. Nature (2012) 3.43
Retrocopy contributions to the evolution of the human genome. BMC Genomics (2008) 1.95
The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference. BMC Genomics (2008) 1.31
New gene evolution: little did we know. Annu Rev Genet (2013) 1.22
Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol (2009) 1.18
Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris. Plant Cell (2010) 1.09
Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs. Genome Biol (2012) 1.07
Principles of glomerular organization in the human olfactory bulb--implications for odor processing. PLoS One (2008) 1.06
Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol (2009) 1.05
Toward a general model for the evolutionary dynamics of gene duplicates. Genome Biol Evol (2011) 1.02
RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics (2014) 1.01
The case for junk DNA. PLoS Genet (2014) 1.00
Molecular identification of NAT8 as the enzyme that acetylates cysteine S-conjugates to mercapturic acids. J Biol Chem (2010) 0.99
Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics. BMC Genomics (2010) 0.97
Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics (2011) 0.95
Comparative analysis of pseudogenes across three phyla. Proc Natl Acad Sci U S A (2014) 0.88
Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains. BMC Evol Biol (2009) 0.88
Pseudogenes as an alternative source of natural antisense transcripts. BMC Evol Biol (2010) 0.87
Characterization of human pseudogene-derived non-coding RNAs for functional potential. PLoS One (2014) 0.87
Geographic and molecular variation in a natural plant transgene. Genetica (2010) 0.86
Evolution of gene regulatory networks by fluctuating selection and intrinsic constraints. PLoS Comput Biol (2010) 0.86
A copy number variation in human NCF1 and its pseudogenes. BMC Genet (2010) 0.86
Functional pseudogenes inhibit the superoxide production. Precis Med (2015) 0.85
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE. BMC Genomics (2007) 0.84
Segmental duplication, microinversion, and gene loss associated with a complex inversion breakpoint region in Drosophila. Mol Biol Evol (2012) 0.83
Genome-wide computational prediction of tandem gene arrays: application in yeasts. BMC Genomics (2010) 0.83
Inferring bacterial genome flux while considering truncated genes. Genetics (2010) 0.80
Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6. BMC Genomics (2009) 0.80
Arxes: retrotransposed genes required for adipogenesis. Nucleic Acids Res (2010) 0.80
Evolutionary and functional novelty of pancreatic ribonuclease: a study of Musteloidea (order Carnivora). Sci Rep (2014) 0.79
Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes. BMC Evol Biol (2013) 0.78
Comparative genomics of the anopheline glutathione S-transferase epsilon cluster. PLoS One (2011) 0.78
Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. PLoS One (2012) 0.78
Why rodent pseudogenes refuse to retire. Genome Biol (2012) 0.77
Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics. BMC Evol Biol (2015) 0.77
Distinct evolutionary strategies in the GGPPS family from plants. Front Plant Sci (2014) 0.77
Pseudogenes. Comp Funct Genomics (2012) 0.77
Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes. J Mol Evol (2015) 0.76
A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease. Mem Inst Oswaldo Cruz (2015) 0.75
Pseudogenes and Their Genome-Wide Prediction in Plants. Int J Mol Sci (2016) 0.75
Novel Role of 3'UTR-Embedded Alu Elements as Facilitators of Processed Pseudogene Genesis and Host Gene Capture by Viral Genomes. PLoS One (2016) 0.75
Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum (cv. Heinz 1706). G3 (Bethesda) (2016) 0.75
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Unlocking the secrets of the genome. Nature (2009) 11.80
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Variation in transcription factor binding among humans. Science (2010) 9.33
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Relating three-dimensional structures to protein networks provides evolutionary insights. Science (2006) 5.50
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A (2006) 4.84
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics (2006) 4.55
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18
An integrated approach for finding overlooked genes in yeast. Nat Biotechnol (2002) 3.88
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov (2011) 3.43
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A (2007) 3.35
Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer (2009) 3.03
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal (2010) 2.95
Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A (2009) 2.89
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics (2007) 2.55
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
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res (2010) 2.50
Molecular sampling of prostate cancer: a dilemma for predicting disease progression. BMC Med Genomics (2010) 2.40
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res (2007) 2.39
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A (2009) 2.36
The real cost of sequencing: higher than you think! Genome Biol (2011) 2.22
A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood (2009) 2.18
Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res (2008) 2.17
Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics (2007) 2.08
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res (2007) 2.03
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res (2006) 1.95
Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol (2010) 1.92
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res (2007) 1.82
Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma. Sci Transl Med (2011) 1.79
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78
A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biol (2006) 1.74
Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol (2012) 1.72
N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Neoplasia (2009) 1.68
High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet (2008) 1.60
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Res (2012) 1.57
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56
Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics (2008) 1.54
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res (2011) 1.43
Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev (2009) 1.43
Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer Res (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
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res (2010) 1.35
Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators. Sci Signal (2010) 1.35
Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol (2011) 1.35
Robust-linear-model normalization to reduce technical variability in functional protein microarrays. J Proteome Res (2009) 1.29
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci U S A (2010) 1.24
Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci (2007) 1.23
Understanding modularity in molecular networks requires dynamics. Sci Signal (2009) 1.22
Integrated assessment of genomic correlates of protein evolutionary rate. PLoS Comput Biol (2009) 1.20
Getting started in gene orthology and functional analysis. PLoS Comput Biol (2010) 1.20
Computational analysis of membrane proteins: the largest class of drug targets. Drug Discov Today (2009) 1.19
Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput Biol (2009) 1.18
Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. Genome Res (2010) 1.13
HingeMaster: normal mode hinge prediction approach and integration of complementary predictors. Proteins (2008) 1.13
Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res (2004) 1.11
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics (2009) 1.10
Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinformatics (2007) 1.06
Pseudofam: the pseudogene families database. Nucleic Acids Res (2008) 1.06
StoneHinge: hinge prediction by network analysis of individual protein structures. Protein Sci (2009) 1.06
Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol (2009) 1.05
FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinformatics (2007) 1.02
Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J (2014) 1.02
An efficient pseudomedian filter for tiling microrrays. BMC Bioinformatics (2007) 1.00
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods Enzymol (2006) 0.99
Getting started in text mining: part two. PLoS Comput Biol (2009) 0.97
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Sci (2011) 0.96
Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res (2010) 0.95
MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics (2010) 0.93
Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol (2010) 0.92
Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PLoS Genet (2012) 0.91
Structured digital tables on the Semantic Web: toward a structured digital literature. Mol Syst Biol (2010) 0.88
Sixty years of genome biology. Genome Biol (2013) 0.85
Novel insights through the integration of structural and functional genomics data with protein networks. J Struct Biol (2012) 0.84
Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. Genome Biol (2011) 0.83
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. BMC Bioinformatics (2010) 0.83
Uncovering trends in gene naming. Genome Biol (2008) 0.82
Predicting protein ligand binding motions with the conformation explorer. BMC Bioinformatics (2011) 0.80
Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun (2015) 0.78
The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. Genome Biol (2011) 0.75