Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- First Published April 10, 2025
Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- First Published June 6, 2022
Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome
- First Published December 1, 2017
Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
- First Published December 13, 2016
Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site
- First Published September 1, 2015
Core promoter sequence in yeast is a major determinant of expression level
- First Published May 12, 2015
Unraveling determinants of transcription factor binding outside the core binding site
- First Published March 11, 2015
Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
- First Published October 7, 2014
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
- First Published July 16, 2014
Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
- First Published August 15, 2013
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
- First Published February 12, 2013
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
- First Published September 5, 2012
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells
- First Published September 5, 2012
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
- First Published September 5, 2012
Linking disease associations with regulatory information in the human genome
- First Published September 5, 2012
Annotation of functional variation in personal genomes using RegulomeDB
- First Published September 5, 2012
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- First Published September 5, 2012
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- First Published September 5, 2012
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters
- First Published October 18, 2011
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
- First Published February 7, 2011
C. elegans" > Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
- First Published December 22, 2010
C. elegans" > High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
- First Published December 22, 2010
C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data" > Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
- First Published December 22, 2010
p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy
- First Published August 17, 2010
Incorporating nucleosomes into thermodynamic models of transcription regulation
- First Published May 18, 2009
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
- First Published November 26, 2008
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
- First Published September 11, 2008
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- First Published February 7, 2008
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
- First Published June 13, 2007
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
- First Published June 13, 2007
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- First Published June 13, 2007
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
- First Published June 13, 2007
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
- First Published November 21, 2006
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
- First Published October 1, 2004