Published in J Comput Biol on May 01, 2007
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
Effects of blood pressure lowering on cerebral white matter hyperintensities in patients with stroke: the PROGRESS (Perindopril Protection Against Recurrent Stroke Study) Magnetic Resonance Imaging Substudy. Circulation (2005) 2.97
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
The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals. BMC Mol Biol (2008) 1.85
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
Duplication and inversion history of a tandemly repeated genes family. J Comput Biol (2007) 1.22
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
Gene family evolution by duplication, speciation, and loss. J Comput Biol (2008) 1.09
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment. Genome Biol (2013) 1.06
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics (2012) 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
Gene tree correction guided by orthology. BMC Bioinformatics (2013) 0.94
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
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
Orthology and paralogy constraints: satisfiability and consistency. BMC Genomics (2014) 0.90
Computing chromosome conformation. Methods Mol Biol (2010) 0.90
Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res (2013) 0.90
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
Ancestral genome organization: an alignment approach. J Comput Biol (2013) 0.89
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics (2007) 0.89
Inferring the evolutionary history of gene clusters from phylogenetic and gene order data. Mol Biol Evol (2009) 0.88
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics (2008) 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
Inferring ancestral gene orders for a family of tandemly arrayed genes. J Comput Biol (2008) 0.84
An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria. PLoS One (2012) 0.83
Classifying leukemia types with chromatin conformation data. Genome Biol (2014) 0.83
Gene tree correction for reconciliation and species tree inference. Algorithms Mol Biol (2012) 0.82
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
Evolution of orthologous tandemly arrayed gene clusters. BMC Bioinformatics (2011) 0.80
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
Recovering haplotype structure through recombination and gene conversion. Bioinformatics (2005) 0.78
Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
A probabilistic model for sequence alignment with context-sensitive indels. J Comput Biol (2011) 0.76
Gene trees and species trees: irreconcilable differences. BMC Bioinformatics (2012) 0.76
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res (2013) 0.76
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
Gene order alignment on trees with multiOrthoAlign. BMC Genomics (2014) 0.75
Reconstructing a SuperGeneTree minimizing reconciliation. BMC Bioinformatics (2015) 0.75
An approximation algorithm for the Noah's Ark problem with random feature loss. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.75
Gene Tree Construction and Correction using SuperTree and Reconciliation. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75
Haplotype inference constrained by plausible haplotype data. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.75
StructMiner: a tool for alignment and detection of conserved secondary structure. Genome Inform (2004) 0.75
Genome halving and double distance with losses. J Comput Biol (2011) 0.75
Simple design rules for optimal design of dielectric temperature-compensated sapphire resonators. IEEE Trans Ultrason Ferroelectr Freq Control (2003) 0.75
Locality and gaps in RNA comparison. J Comput Biol (2007) 0.75
A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error. Pac Symp Biocomput (2010) 0.75
High Q-factor Bragg-reflection sapphire-loaded cavity TE01delta mode resonators. IEEE Trans Ultrason Ferroelectr Freq Control (2002) 0.75