Published in Methods Mol Biol on January 01, 2010
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics (2011) 1.78
Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev (2014) 1.76
Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet (2013) 1.35
An Overview of Genome Organization and How We Got There: from FISH to Hi-C. Microbiol Mol Biol Rev (2015) 1.10
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proc Natl Acad Sci U S A (2016) 0.93
Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res (2013) 0.90
From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods (2012) 0.89
Shh and ZRS enhancer colocalisation is specific to the zone of polarising activity. Development (2016) 0.78
Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements. Nucleic Acids Res (2015) 0.77
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Res (2017) 0.75
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24
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
Gene expression during acute and prolonged hypoxia is regulated by distinct mechanisms of translational control. EMBO J (2006) 2.41
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
Mapping chromatin interactions by chromosome conformation capture. Curr Protoc Mol Biol (2006) 1.95
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics (2011) 1.78
Complexity of chromatin folding is captured by the strings and binders switch model. Proc Natl Acad Sci U S A (2012) 1.73
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
The Gemin6-Gemin7 heterodimer from the survival of motor neurons complex has an Sm protein-like structure. Structure (2005) 1.64
BH3-ligand regulates access of MCL-1 to its E3 ligase. FEBS Lett (2005) 1.49
Gemins modulate the expression and activity of the SMN complex. Hum Mol Genet (2005) 1.42
Repurposing CRISPR/Cas9 for in situ functional assays. Genes Dev (2013) 1.41
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
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet (2009) 1.32
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
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
Discovering genome regulation with 3C and 3C-related technologies. Biochim Biophys Acta (2011) 0.93
Chromatin conformation signatures: ideal human disease biomarkers? Biomark Med (2010) 0.92
FootPrinter3: phylogenetic footprinting in partially alignable sequences. Nucleic Acids Res (2006) 0.92
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
Shaping the Genome with Non-Coding RNAs. Curr Genomics (2011) 0.90
From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods (2012) 0.89
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. BMC Bioinformatics (2007) 0.89
p53 inhibits angiogenesis by inducing the production of Arresten. Cancer Res (2012) 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
A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing. Methods Enzymol (2012) 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
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
A polymer model explains the complexity of large-scale chromatin folding. Nucleus (2013) 0.82
Diagnostic accuracy and utility of intraoperative microscopic margin analysis of gastric and esophageal adenocarcinoma. Ann Surg Oncol (2014) 0.81
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
A model of the large-scale organization of chromatin. Biochem Soc Trans (2013) 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
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
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
A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error. Pac Symp Biocomput (2010) 0.75
An approximation algorithm for the Noah's Ark problem with random feature loss. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.75