Published in Nucleic Acids Res on June 08, 2013
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Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
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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
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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
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
A method for probing the mutational landscape of amyloid structure. Bioinformatics (2011) 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
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure. J Comput Biol (2011) 0.97
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
Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. PLoS Comput Biol (2013) 0.93
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
Using the fast fourier transform to accelerate the computational search for RNA conformational switches. PLoS One (2012) 0.91
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. Bioinformatics (2013) 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
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
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics (2012) 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
Expected distance between terminal nucleotides of RNA secondary structures. J Math Biol (2011) 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
Computational assembly of polymorphic amyloid fibrils reveals stable aggregates. Biophys J (2013) 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
A global sampling approach to designing and reengineering RNA secondary structures. Nucleic Acids Res (2012) 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
Whole mount RNA fluorescent in situ hybridization of Drosophila embryos. J Vis Exp (2013) 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
corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs. Nucleic Acids Res (2011) 0.81
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics (2015) 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
The many functions of mRNA localization during normal development and disease: from pillar to post. Wiley Interdiscip Rev Dev Biol (2013) 0.79
Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. J Comput Biol (2013) 0.78
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
Efficient traversal of beta-sheet protein folding pathways using ensemble models. J Comput Biol (2011) 0.77
Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77
The functions and regulatory principles of mRNA intracellular trafficking. Adv Exp Med Biol (2014) 0.76
Introduction to RNA secondary structure comparison. Methods Mol Biol (2014) 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
A probabilistic model for sequence alignment with context-sensitive indels. J Comput Biol (2011) 0.76
Preface. J Comput Biol (2015) 0.75
The BRaliBase dent-a tale of benchmark design and interpretation. Brief Bioinform (2017) 0.75
An approximation algorithm for the Noah's Ark problem with random feature loss. 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
A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error. Pac Symp Biocomput (2010) 0.75
Gene maps linearization using genomic rearrangement distances. J Comput Biol (2007) 0.75
Design of RNAs: comparing programs for inverse RNA folding. Brief Bioinform (2017) 0.75