Published in Bioinformatics on November 26, 2013
Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science (2014) 2.99
Transcriptional diversity during lineage commitment of human blood progenitors. Science (2014) 1.93
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol (2015) 1.17
The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape. Cell Death Dis (2015) 0.93
Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells. Nat Commun (2015) 0.88
Distinct Genetic Networks Orchestrate the Emergence of Specific Waves of Fetal and Adult B-1 and B-2 Development. Immunity (2016) 0.87
Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription. Sci Rep (2015) 0.83
Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain. Elife (2015) 0.81
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. Cell Rep (2017) 0.79
MetaDiff: differential isoform expression analysis using random-effects meta-regression. BMC Bioinformatics (2015) 0.78
The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data. Nucleic Acids Res (2016) 0.78
The genetic basis and fitness consequences of sperm midpiece size in deer mice. Nat Commun (2016) 0.77
Hybrid mice reveal parent-of-origin and Cis- and trans-regulatory effects in the retina. PLoS One (2014) 0.77
Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate. BMC Bioinformatics (2015) 0.77
Bayesian identification of bacterial strains from sequencing data. Microb Genom (2016) 0.75
Modeling Exon-Specific Bias Distribution Improves the Analysis of RNA-Seq Data. PLoS One (2015) 0.75
Platelet function is modified by common sequence variation in megakaryocyte super enhancers. Nat Commun (2017) 0.75
Population genomics of human gene expression. Nat Genet (2007) 24.49
Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (2007) 23.38
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature (2012) 20.47
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
Autophagy mediates the mitotic senescence transition. Genes Dev (2009) 6.80
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol (2007) 6.41
beadarray: R classes and methods for Illumina bead-based data. Bioinformatics (2007) 6.08
Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci U S A (2013) 5.68
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol (2007) 4.70
Linkage disequilibrium: what history has to tell us. Trends Genet (2002) 4.33
Species-specific transcription in mice carrying human chromosome 21. Science (2008) 4.03
Statistical issues in the analysis of Illumina data. BMC Bioinformatics (2008) 3.66
Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol (2007) 3.54
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res (2009) 3.50
Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell (2008) 3.37
Defining stem cell dynamics in models of intestinal tumor initiation. Science (2013) 3.26
Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc Natl Acad Sci U S A (2004) 2.94
Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science (2011) 2.58
BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics (2009) 2.47
Modern computational approaches for analysing molecular genetic variation data. Nat Rev Genet (2006) 2.24
Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes. Genome Biol (2007) 2.12
Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell (2012) 2.02
Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci U S A (2009) 1.98
Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States. J Bacteriol (2004) 1.94
Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85
Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics (2006) 1.83
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (2009) 1.83
Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev (2009) 1.78
Population genetic inference from resequencing data. Genetics (2008) 1.77
CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics (2010) 1.74
Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell (2012) 1.70
Counting divisions in a human somatic cell tree: how, what and why? Cell Cycle (2006) 1.62
Pretumor progression: clonal evolution of human stem cell populations. Am J Pathol (2004) 1.57
Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas. Cell Stem Cell (2013) 1.56
The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics (2009) 1.55
Enhanced stem cell survival in familial adenomatous polyposis. Am J Pathol (2004) 1.51
A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers. Mol Biol Evol (2006) 1.51
O fly, where art thou? J R Soc Interface (2008) 1.50
Sequential DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic progression. Gut (2010) 1.44
Modifier effects between regulatory and protein-coding variation. PLoS Genet (2008) 1.42
Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics (2005) 1.41
The stem cell population of the human colon crypt: analysis via methylation patterns. PLoS Comput Biol (2007) 1.38
Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Res Notes (2008) 1.28
Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization. Cancer Res (2012) 1.28
Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proc Natl Acad Sci U S A (2005) 1.24
BayesPeak--an R package for analysing ChIP-seq data. Bioinformatics (2011) 1.23
The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res (2010) 1.22
Inferring relative numbers of human leucocyte genome replications. Br J Haematol (2008) 1.22
Characterisation of microRNA expression in post-natal mouse mammary gland development. BMC Genomics (2009) 1.21
Non-linear analysis of GeneChip arrays. Nucleic Acids Res (2006) 1.21
Drosophila melanogaster p53 has developmental stage-specific and sex-specific effects on adult life span indicative of sexual antagonistic pleiotropy. Aging (Albany NY) (2009) 1.19
Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae. Genes Dev (2008) 1.19
Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors. PLoS Comput Biol (2011) 1.18
High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genet (2010) 1.18
Explaining differences in saturation levels for Affymetrix GeneChip arrays. Nucleic Acids Res (2007) 1.16
Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression. Nucleic Acids Res (2009) 1.15
Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes. Microbes Infect (2006) 1.15
Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster. PLoS One (2009) 1.15
Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Mol Biol Evol (2005) 1.14
A screen of apoptosis and senescence regulatory genes for life span effects when over-expressed in Drosophila. Aging (Albany NY) (2009) 1.14
Many colorectal cancers are "flat" clonal expansions. Cell Cycle (2009) 1.10
Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS One (2007) 1.07
Age-related human small intestine methylation: evidence for stem cell niches. BMC Med (2005) 1.06
Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging. BMC Med Genet (2007) 1.04
Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes. PLoS Genet (2013) 1.03
Pediatric malignant germ cell tumors show characteristic transcriptome profiles. Cancer Res (2008) 1.03
Three-dimensional tracking and behaviour monitoring of multiple fruit flies. J R Soc Interface (2012) 1.02
Simultaneous tracking of fly movement and gene expression using GFP. BMC Biotechnol (2008) 1.02
Endometrial-peritoneal interactions during endometriotic lesion establishment. Am J Pathol (2008) 1.01
MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res (2006) 1.00
The level of origin firing inversely affects the rate of replication fork progression. J Cell Biol (2013) 1.00
High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers. PLoS One (2011) 0.98
Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists. BMC Cancer (2014) 0.98
Colorectal pretumor progression before and after loss of DNA mismatch repair. Am J Pathol (2004) 0.97
Inferring population parameters from single-feature polymorphism data. Genetics (2006) 0.92
Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. BMC Bioinformatics (2010) 0.92
Stem cell chronicles: autobiographies within genomes. Stem Cell Rev (2007) 0.91
Human hair genealogies and stem cell latency. BMC Biol (2006) 0.89
The importance of platform annotation in interpreting microarray data. Lancet Oncol (2010) 0.88
Older individuals appear to acquire mitotically older colorectal cancers. J Pathol (2009) 0.88
Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes. BMC Res Notes (2009) 0.88
Primate origins: implications of a cretaceous ancestry. Folia Primatol (Basel) (2007) 0.88
Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments. Am J Hum Genet (2007) 0.87
Using expression arrays for copy number detection: an example from E. coli. BMC Bioinformatics (2007) 0.86
Hidden copy number variation in the HapMap population. Proc Natl Acad Sci U S A (2008) 0.85
The relative timing of mutations in a breast cancer genome. PLoS One (2013) 0.84
Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel. Anal Chem (2009) 0.84
Estimating primate divergence times by using conditioned birth-and-death processes. Theor Popul Biol (2009) 0.83
Calling sample mix-ups in cancer population studies. PLoS One (2012) 0.83
Strategies for analyzing highly enriched IP-chip datasets. BMC Bioinformatics (2009) 0.82
Testing the mean matrix in high-dimensional transposable data. Biometrics (2015) 0.81
Numbers of mutations to different types of colorectal cancer. BMC Cancer (2005) 0.81
CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data. Bioinformatics (2010) 0.81
The cost of reducing starting RNA quantity for Illumina BeadArrays: a bead-level dilution experiment. BMC Genomics (2010) 0.80
Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. BMC Bioinformatics (2010) 0.79
Using GFP video to track 3D movement and conditional gene expression in free-moving flies. PLoS One (2012) 0.78
Assessing senescence in Drosophila using video tracking. Methods Mol Biol (2013) 0.78
A Bayesian approach to phylogeographic clustering. Interface Focus (2011) 0.76