Published in Nucleic Acids Res on July 01, 2006
The value of position-specific priors in motif discovery using MEME. BMC Bioinformatics (2010) 1.60
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. Nucleic Acids Res (2008) 1.22
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. Adv Genet (2008) 0.96
Phylogenetic footprinting: a boost for microbial regulatory genomics. Protoplasma (2011) 0.82
Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Evol Bioinform Online (2008) 0.81
Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis. Sci Rep (2014) 0.80
Context specific transcription factor prediction. Ann Biomed Eng (2007) 0.78
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature (2004) 21.40
Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet (2004) 9.96
ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res (2004) 4.99
rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res (2004) 4.93
Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res (2002) 4.25
FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res (2003) 2.82
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics (2004) 1.97
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet (2009) 4.72
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol (2005) 4.48
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics (2004) 3.63
Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. Cell Metab (2007) 3.00
Phylo: a citizen science approach for improving multiple sequence alignment. PLoS One (2012) 2.64
A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res (2009) 2.55
Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (2004) 2.50
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27
Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells. Proc Natl Acad Sci U S A (2004) 2.21
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol (2014) 2.01
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics (2011) 1.78
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68
BH3-ligand regulates access of MCL-1 to its E3 ligase. FEBS Lett (2005) 1.49
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet (2013) 1.37
The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res (2010) 1.36
Exact and heuristic algorithms for the Indel Maximum Likelihood Problem. J Comput Biol (2007) 1.35
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods (2009) 1.24
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics (2010) 1.23
On the inference of parsimonious indel evolutionary scenarios. J Bioinform Comput Biol (2006) 1.14
Seeder: discriminative seeding DNA motif discovery. Bioinformatics (2008) 1.10
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment. Genome Biol (2013) 1.06
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics (2012) 1.03
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics (2009) 1.01
Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol (2010) 0.99
Detecting non-coding selective pressure in coding regions. BMC Evol Biol (2007) 0.98
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol Biol (2009) 0.94
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PLoS One (2011) 0.90
Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res (2013) 0.90
Computing chromosome conformation. Methods Mol Biol (2010) 0.90
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics (2007) 0.89
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics (2008) 0.85
Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2. Nucleic Acids Res (2013) 0.84
Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1. PLoS Pathog (2013) 0.84
Classifying leukemia types with chromatin conformation data. Genome Biol (2014) 0.83
An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria. PLoS One (2012) 0.83
A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses. J Comput Biol (2009) 0.82
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). Biochem Cell Biol (2008) 0.81
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J Proteome Res (2012) 0.80
Genetic map refinement using a comparative genomic approach. J Comput Biol (2009) 0.79
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77
Positional mapping and candidate gene analysis of the mouse Ccs3 locus that regulates differential susceptibility to carcinogen-induced colorectal cancer. PLoS One (2013) 0.76
A probabilistic model for sequence alignment with context-sensitive indels. J Comput Biol (2011) 0.76
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res (2013) 0.76
An approximation algorithm for the Noah's Ark problem with random feature loss. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.75
A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error. Pac Symp Biocomput (2010) 0.75
StructMiner: a tool for alignment and detection of conserved secondary structure. Genome Inform (2004) 0.75
Gene maps linearization using genomic rearrangement distances. J Comput Biol (2007) 0.75