Published in Genome Res on July 14, 2008
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Tetraploidy and chromosomal instability are early events during cervical carcinogenesis. Carcinogenesis (2005) 1.85
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Murine segmental duplications are hot spots for chromosome and gene evolution. Genomics (2005) 1.07
Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii. Mol Phylogenet Evol (2004) 1.05
Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution. BMC Genomics (2006) 1.04
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A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (2002) 20.59
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A human protein-protein interaction network: a resource for annotating the proteome. Cell (2005) 18.97
A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
Microarray data representation, annotation and storage. Adv Biochem Eng Biotechnol (2002) 11.13
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (2012) 9.68
Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol Biol Evol (2002) 7.03
The DNA sequence of the human X chromosome. Nature (2005) 6.97
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
The genome of a songbird. Nature (2010) 5.90
A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84
Dissecting the genomic complexity underlying medulloblastoma. Nature (2012) 4.77
Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics (2008) 4.74
Mutations in DNAH5 cause primary ciliary dyskinesia and randomization of left-right asymmetry. Nat Genet (2002) 4.64
Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics (2007) 4.32
Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database. PLoS Genet (2012) 4.27
Histone modification levels are predictive for gene expression. Proc Natl Acad Sci U S A (2010) 4.00
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res (2010) 3.36
A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell (2004) 3.26
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
The senescence-related mitochondrial/oxidative stress pathway is repressed in human induced pluripotent stem cells. Stem Cells (2010) 3.17
Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell (2013) 3.08
Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature (2011) 3.06
Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Res (2003) 3.02
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
GOblet: a platform for Gene Ontology annotation of anonymous sequence data. Nucleic Acids Res (2004) 2.99
The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res (2012) 2.94
A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature (2010) 2.88
Construction and analysis of a human-chimpanzee comparative clone map. Science (2002) 2.83
ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res (2010) 2.79
ConsensusPathDB--a database for integrating human functional interaction networks. Nucleic Acids Res (2008) 2.77
A gene expression map of human chromosome 21 orthologues in the mouse. Nature (2002) 2.76
Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing. BMC Genomics (2004) 2.74
Mapping translocation breakpoints by next-generation sequencing. Genome Res (2008) 2.73
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. J Biol (2007) 2.70
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res (2010) 2.61
Increase of functional diversity by alternative splicing. Trends Genet (2003) 2.59
Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature (2004) 2.54
On the power of profiles for transcription factor binding site detection. Stat Appl Genet Mol Biol (2003) 2.52
A bile acid-like steroid modulates Caenorhabditis elegans lifespan through nuclear receptor signaling. Proc Natl Acad Sci U S A (2007) 2.50
T cells become licensed in the lung to enter the central nervous system. Nature (2012) 2.45
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet (2013) 2.42
Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules. Mol Biol Cell (2007) 2.30
Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of down syndrome. Genome Res (2004) 2.29
Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics (2011) 2.24
A comparison of oligonucleotide and cDNA-based microarray systems. Physiol Genomics (2004) 2.21
The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF. Mol Cell (2004) 2.19
On the origin of the chordate central nervous system: expression of onecut in the sea urchin embryo. Evol Dev (2004) 2.19
Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells. Stem Cells (2006) 2.18
Plant nitric oxide synthase: a never-ending story? Trends Plant Sci (2006) 2.12
MicroRNA profiling of clear cell renal cell cancer identifies a robust signature to define renal malignancy. J Cell Mol Med (2009) 2.12
Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis. PLoS One (2010) 2.10
Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics (2008) 2.09
Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics (2006) 2.06
Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS One (2009) 2.04
Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev (2008) 1.96
T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Res (2005) 1.93
Fibroblast growth factor 2 modulates transforming growth factor beta signaling in mouse embryonic fibroblasts and human ESCs (hESCs) to support hESC self-renewal. Stem Cells (2006) 1.88
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88
Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis. Trends Genet (2005) 1.87
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science (2010) 1.86
TLR2 has a detrimental role in mouse transient focal cerebral ischemia. Biochem Biophys Res Commun (2007) 1.84
PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics (2008) 1.82
An efficient and economic enhancer mix for PCR. Biochem Biophys Res Commun (2006) 1.82
A centrosome-independent role for gamma-TuRC proteins in the spindle assembly checkpoint. Science (2006) 1.76
High throughput identification of potential Arabidopsis mitogen-activated protein kinases substrates. Mol Cell Proteomics (2005) 1.75
Genetic analysis of the mouse brain proteome. Nat Genet (2002) 1.73
Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase. J Theor Biol (2005) 1.71
Parameter estimation for the calibration and variance stabilization of microarray data. Stat Appl Genet Mol Biol (2003) 1.70
Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells. Stem Cells (2005) 1.68
No evidence for a shift in pyruvate kinase PKM1 to PKM2 expression during tumorigenesis. Oncotarget (2011) 1.68
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res (2003) 1.65
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein. Nucleic Acids Res (2002) 1.65
Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics (2011) 1.63
Modeling read counts for CNV detection in exome sequencing data. Stat Appl Genet Mol Biol (2011) 1.55
A catabolic block does not sufficiently explain how 2-deoxy-D-glucose inhibits cell growth. Proc Natl Acad Sci U S A (2008) 1.54
Detection of angiotensin II in supernatants of stimulated mononuclear leukocytes by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass analysis. Hypertension (2005) 1.52
The effect of micrococcal nuclease digestion on nucleosome positioning data. PLoS One (2010) 1.51
The SYSTERS Protein Family Database in 2005. Nucleic Acids Res (2005) 1.49
Natural similarity measures between position frequency matrices with an application to clustering. Bioinformatics (2008) 1.48
Normalization and quantification of differential expression in gene expression microarrays. Brief Bioinform (2006) 1.47
Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. J Biol Chem (2001) 1.45