Published in J Comput Biol on May 01, 2007
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42
Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res (2008) 5.12
Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics (2009) 4.30
Phylo: a citizen science approach for improving multiple sequence alignment. PLoS One (2012) 2.64
PhyLAT: a phylogenetic local alignment tool. Bioinformatics (2012) 1.54
General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable? BMC Bioinformatics (2016) 1.09
General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation. BMC Bioinformatics (2016) 1.09
Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics (2010) 0.94
Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. Genome Res (2011) 0.80
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map. BMC Bioinformatics (2016) 0.80
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome. Mol Biol Evol (2013) 0.78
Evolutionary triplet models of structured RNA. PLoS Comput Biol (2009) 0.77
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. BMC Bioinformatics (2012) 0.76
Human Lineage-Specific Transcriptional Regulation through GA-Binding Protein Transcription Factor Alpha (GABPa). Mol Biol Evol (2016) 0.75
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
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res (2012) 1.97
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
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
Inferring and validating horizontal gene transfer events using bipartition dissimilarity. Syst Biol (2010) 1.15
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
Statistical analysis of systematic errors in high-throughput screening. J Biomol Screen (2005) 1.08
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
Systematic error detection in experimental high-throughput screening. BMC Bioinformatics (2011) 1.03
Evolutionary history of bacteriophages with double-stranded DNA genomes. Biol Direct (2007) 1.02
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
Two effective methods for correcting experimental high-throughput screening data. Bioinformatics (2012) 0.97
Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol Biol (2009) 0.94
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations. PLoS One (2012) 0.93
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
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
Computing chromosome conformation. Methods Mol Biol (2010) 0.90
Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res (2013) 0.90
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics (2007) 0.89
Reconstruction of biogeographic and evolutionary networks using reticulograms. Syst Biol (2002) 0.86
Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
Using clustering techniques to improve hit selection in high-throughput screening. J Biomol Screen (2006) 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
Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1. PLoS Pathog (2013) 0.84
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
Towards an accurate identification of mosaic genes and partial horizontal gene transfers. Nucleic Acids Res (2011) 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
Classifying leukemia types with chromatin conformation data. Genome Biol (2014) 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
A new effective method for estimating missing values in the sequence data prior to phylogenetic analysis. Evol Bioinform Online (2007) 0.80
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J Proteome Res (2012) 0.80
Incomplete distance matrices, supertrees and bat phylogeny. Mol Phylogenet Evol (2003) 0.80
Genetic map refinement using a comparative genomic approach. J Comput Biol (2009) 0.79
Using directed phylogenetic networks to retrace species dispersal history. Mol Phylogenet Evol (2012) 0.79
Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions. Brief Bioinform (2015) 0.78
Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77
A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. J Bioinform Comput Biol (2014) 0.77
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (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
Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index. BMC Bioinformatics (2011) 0.75
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
Using machine learning methods to predict experimental high-throughput screening data. Comb Chem High Throughput Screen (2010) 0.75