Published in Genome Res on January 13, 2012
Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest. Cell (2015) 2.31
Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet (2012) 1.68
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev (2012) 1.53
Zygotic genome activation during the maternal-to-zygotic transition. Annu Rev Cell Dev Biol (2014) 1.30
Zelda potentiates morphogen activity by increasing chromatin accessibility. Curr Biol (2014) 1.09
Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proc Natl Acad Sci U S A (2014) 1.00
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genet (2013) 0.97
From egg to gastrula: how the cell cycle is remodeled during the Drosophila mid-blastula transition. Annu Rev Genet (2014) 0.94
Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila. Genes Dev (2014) 0.91
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Res (2015) 0.91
Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics (2013) 0.89
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo. Genome Res (2015) 0.85
HOT DNAs: a novel class of developmental enhancers. Genes Dev (2012) 0.80
Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster. Brief Funct Genomics (2012) 0.79
Comparing mRNA levels using in situ hybridization of a target gene and co-stain. Methods (2014) 0.79
Evolution of the sex-lethal gene in insects and origin of the sex-determination system in Drosophila. J Mol Evol (2013) 0.78
Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis. BMC Genomics (2013) 0.78
BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms. PLoS Genet (2014) 0.77
Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster. F1000Res (2017) 0.75
Regulation of DNA Replication in Early Embryonic Cleavages. Genes (Basel) (2017) 0.75
A sequence level model of an intact locus predicts the location and function of nonadditive enhancers. PLoS One (2017) 0.75
Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (1999) 14.36
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res (2008) 12.15
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
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
Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci U S A (2001) 6.39
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30
Fast statistical alignment. PLoS Comput Biol (2009) 5.92
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
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
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev (2007) 4.59
Non-transcriptional control of DNA replication by c-Myc. Nature (2007) 4.55
Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature (2009) 3.85
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.06
The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature (2008) 3.04
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A (2009) 2.96
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol (2011) 2.68
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res (2009) 2.66
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet (2011) 2.65
Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. Nature (2002) 2.61
Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol (2011) 2.43
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol (2010) 2.32
DNA replication control through interaction of E2F-RB and the origin recognition complex. Nat Cell Biol (2001) 2.24
The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription. Development (2006) 2.19
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet (2011) 1.94
A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr Biol (2010) 1.93
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res (2010) 1.88
Chromatin. Ga-ga over GAGA factor. Curr Biol (1995) 1.77
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol (2011) 1.61
Chromatin remodeling by GAGA factor and heat shock factor at the hypersensitive Drosophila hsp26 promoter in vitro. EMBO J (1995) 1.57
Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence. Dev Biol (2008) 1.45
Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol (2010) 1.40
Chromatin remodeling mediated by Drosophila GAGA factor and ISWI activates fushi tarazu gene transcription in vitro. Mol Cell Biol (1998) 1.18
Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes. Dev Biol (2010) 1.11
Mutations of the Drosophila zinc finger-encoding gene vielfältig impair mitotic cell divisions and cause improper chromosome segregation. Mol Biol Cell (2006) 1.06
Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. Development (2011) 1.04
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucleic Acids Res (2011) 0.87
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell (2013) 3.35
Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. Genes Dev (2013) 1.31
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol (2008) 1.30
XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics (2006) 1.29
Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics (2007) 1.15
Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics (2012) 1.14
Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet (2013) 1.12
Erratum: Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins. Nat Med (2016) 0.76
Integrative Clinical Genomics of Advanced Prostate Cancer. Cell (2015) 0.75