Published in Stat Appl Genet Mol Biol on August 25, 2003
MCOIN: a novel heuristic for determining transcription factor binding site motif width. Algorithms Mol Biol (2013) 0.78
Stochastic EM-based TFBS motif discovery with MITSU. Bioinformatics (2014) 0.75
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A (2002) 8.56
Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci U S A (2002) 6.98
Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93
Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A (2008) 6.35
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30
Rejoinder to Tan. Int J Biostat (2008) 6.21
A fine-scale linkage-disequilibrium measure based on length of haplotype sharing. Am J Hum Genet (2006) 6.02
A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell (2008) 5.63
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol (2009) 5.23
Carfilzomib, lenalidomide, and dexamethasone for relapsed multiple myeloma. N Engl J Med (2014) 5.08
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol (2005) 4.42
Noise minimization in eukaryotic gene expression. PLoS Biol (2004) 4.36
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol (2002) 4.24
GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics (2009) 4.16
Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01
Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00
GC-content normalization for RNA-Seq data. BMC Bioinformatics (2011) 3.89
Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A (2002) 3.85
Estimation of direct causal effects. Epidemiology (2006) 3.78
Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. PLoS Genet (2008) 3.69
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol (2004) 3.36
Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol (2006) 3.22
Pillbox organizers are associated with improved adherence to HIV antiretroviral therapy and viral suppression: a marginal structural model analysis. Clin Infect Dis (2007) 3.16
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol (2004) 3.15
Why PLoS became a publisher. PLoS Biol (2003) 3.09
Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A (2005) 3.04
Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet (2006) 3.01
Survival ensembles. Biostatistics (2005) 2.88
Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol (2004) 2.81
Deletion/substitution/addition algorithm in learning with applications in genomics. Stat Appl Genet Mol Biol (2004) 2.77
Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res (2006) 2.75
Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma (2007) 2.73
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol (2011) 2.68
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet (2008) 2.67
Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol (2003) 2.67
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet (2011) 2.65
Impact of chromatin structures on DNA processing for genomic analyses. PLoS One (2009) 2.63
History-adjusted marginal structural models for estimating time-varying effect modification. Am J Epidemiol (2007) 2.56
Stage II colon cancer prognosis prediction by tumor gene expression profiling. J Clin Oncol (2006) 2.49
Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43
Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol (2011) 2.43
Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol (2004) 2.34
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol (2010) 2.32
Diagnosing and responding to violations in the positivity assumption. Stat Methods Med Res (2010) 2.29
Long-term consequences of the delay between virologic failure of highly active antiretroviral therapy and regimen modification. AIDS (2008) 2.25
Multiple testing methods for ChIP-Chip high density oligonucleotide array data. J Comput Biol (2006) 2.08
Empirical efficiency maximization: improved locally efficient covariate adjustment in randomized experiments and survival analysis. Int J Biostat (2008) 2.06
Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell (2011) 2.00
Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A (2004) 1.96
Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol (2004) 1.96
Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS Genet (2011) 1.95
Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet (2010) 1.92
A targeted maximum likelihood estimator of a causal effect on a bounded continuous outcome. Int J Biostat (2010) 1.89
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) (2011) 1.86
Assessing the effectiveness of antiretroviral adherence interventions. Using marginal structural models to replicate the findings of randomized controlled trials. J Acquir Immune Defic Syndr (2006) 1.81
A method to increase the power of multiple testing procedures through sample splitting. Stat Appl Genet Mol Biol (2006) 1.81
Identification of regulatory elements using a feature selection method. Bioinformatics (2002) 1.80
Using regression models to analyze randomized trials: asymptotically valid hypothesis tests despite incorrectly specified models. Biometrics (2009) 1.77
Aging and gene expression in the primate brain. PLoS Biol (2005) 1.76
Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci U S A (2010) 1.75
GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics (2005) 1.66
Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci U S A (2005) 1.66
A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. Genes Dev (2009) 1.64
Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infection. Stat Med (2009) 1.57
Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Stat Appl Genet Mol Biol (2004) 1.55
Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell (2009) 1.52
An application of collaborative targeted maximum likelihood estimation in causal inference and genomics. Int J Biostat (2010) 1.48
A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res (2012) 1.48
Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol (2007) 1.47
Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Stat Appl Genet Mol Biol (2004) 1.47
Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus. PLoS One (2009) 1.47
Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet (2009) 1.46
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics (2006) 1.44
Collaborative targeted maximum likelihood for time to event data. Int J Biostat (2010) 1.41
Statistical methods for analyzing sequentially randomized trials. J Natl Cancer Inst (2007) 1.41
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol (2003) 1.40
Simple optimal weighting of cases and controls in case-control studies. Int J Biostat (2008) 1.40
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A (2012) 1.39
Asymptotic optimality of likelihood-based cross-validation. Stat Appl Genet Mol Biol (2004) 1.39
Targeted maximum likelihood estimation of the parameter of a marginal structural model. Int J Biostat (2010) 1.31
Supervised detection of conserved motifs in DNA sequences with cosmo. Stat Appl Genet Mol Biol (2007) 1.29
A practical illustration of the importance of realistic individualized treatment rules in causal inference. Electron J Stat (2007) 1.25
Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proc Natl Acad Sci U S A (2008) 1.25
Simple, efficient estimators of treatment effects in randomized trials using generalized linear models to leverage baseline variables. Int J Biostat (2010) 1.23
The establishment of gene silencing at single-cell resolution. Nat Genet (2009) 1.22
Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics (2006) 1.20
Individualized treatment rules: generating candidate clinical trials. Stat Med (2007) 1.19
Super learning: an application to the prediction of HIV-1 drug resistance. Stat Appl Genet Mol Biol (2007) 1.18
A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genet (2011) 1.17