Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature (2013) 5.18

The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science (2013) 4.12

Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet (2014) 3.52

Mapping human epigenomes. Cell (2013) 2.44

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods (2014) 1.76

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res (2015) 1.73

The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell (2014) 1.70

Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nat Neurosci (2015) 1.60

High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol (2013) 1.53

Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling. PLoS Comput Biol (2014) 1.52

cPKC regulates interphase nuclear size during Xenopus development. J Cell Biol (2014) 1.50

Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biol (2015) 1.46

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Cell Stem Cell (2016) 1.46

Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach. Genome Biol (2015) 1.45

Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast. Nat Genet (2017) 1.44

Estrogen induces global reorganization of chromatin structure in human breast cancer cells. PLoS One (2014) 1.43

The PsychENCODE project. Nat Neurosci (2015) 1.39

The 3D Genome as Moderator of Chromosomal Communication. Cell (2016) 1.39

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res (2014) 1.32

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res (2014) 1.26

Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell (2014) 1.24

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Dev (2014) 1.20

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun (2015) 1.19

Large-scale chromatin organization: the good, the surprising, and the still perplexing. Curr Opin Cell Biol (2013) 1.16

Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat Rev Genet (2016) 1.15

Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput Biol (2014) 1.13

Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin (2014) 1.12

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps. G3 (Bethesda) (2014) 1.11

Comparison of Hi-C results using in-solution versus in-nucleus ligation. Genome Biol (2015) 1.11

An Overview of Genome Organization and How We Got There: from FISH to Hi-C. Microbiol Mol Biol Rev (2015) 1.10

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells. Cell (2015) 1.09

Analysis methods for studying the 3D architecture of the genome. Genome Biol (2015) 1.09

Protein modeling: what happened to the "protein structure gap"? Structure (2013) 1.08

Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol (2014) 1.07

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res (2014) 1.06

Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biol (2015) 1.05

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation. Nat Rev Genet (2015) 1.05

HiCdat: a fast and easy-to-use Hi-C data analysis tool. BMC Bioinformatics (2015) 1.03

Predicting expression: the complementary power of histone modification and transcription factor binding data. Epigenetics Chromatin (2014) 1.03

An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res (2014) 1.02

Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis. Expert Rev Mol Diagn (2013) 1.01

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes. Nucleic Acids Res (2013) 1.01

Predicting chromatin organization using histone marks. Genome Biol (2015) 0.99

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol (2016) 0.99

Understanding the epigenetic syntax for the genetic alphabet in the kidney. J Am Soc Nephrol (2013) 0.98

In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol (2014) 0.98

A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. PLoS Genet (2015) 0.97

The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling. Nucleic Acids Res (2013) 0.96

Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet (2014) 0.96

Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease. PLoS Genet (2015) 0.96

Cancer whole-genome sequencing: present and future. Oncogene (2015) 0.95

Transcriptional control of a whole chromosome: emerging models for dosage compensation. Nat Struct Mol Biol (2014) 0.95

A transient ischemic environment induces reversible compaction of chromatin. Genome Biol (2015) 0.94

Structural and functional diversity of Topologically Associating Domains. FEBS Lett (2015) 0.94

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus. Am J Hum Genet (2016) 0.93

Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data. Quant Biol (2013) 0.93

A simple biophysical model emulates budding yeast chromosome condensation. Elife (2015) 0.92

Spurious transcription factor binding: non-functional or genetically redundant? Bioessays (2014) 0.92

The second decade of 3C technologies: detailed insights into nuclear organization. Genes Dev (2016) 0.91

A mechanistic link between gene regulation and genome architecture in mammalian development. Curr Opin Genet Dev (2014) 0.91

Chromatin's thread to alternative splicing regulation. Chromosoma (2013) 0.91

Loss of lamin A function increases chromatin dynamics in the nuclear interior. Nat Commun (2015) 0.91

Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet (2014) 0.91

Enabling functional genomics with genome engineering. Genome Res (2015) 0.90

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics (2015) 0.90

C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol (2016) 0.90

HiCPlotter integrates genomic data with interaction matrices. Genome Biol (2015) 0.89

Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics Chromatin (2014) 0.89

TRF2 and lamin A/C interact to facilitate the functional organization of chromosome ends. Nat Commun (2014) 0.89

Genome-wide association studies of late-onset cardiovascular disease. J Mol Cell Cardiol (2015) 0.89

Variation in the Oxytocin Receptor Gene Predicts Brain Region-Specific Expression and Social Attachment. Biol Psychiatry (2015) 0.88

Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization. Genome Biol (2015) 0.87

Imaging Transcription: Past, Present, and Future. Cold Spring Harb Symp Quant Biol (2016) 0.87

Inferential modeling of 3D chromatin structure. Nucleic Acids Res (2015) 0.87

Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers. EMBO J (2016) 0.87

Imaging Specific Genomic DNA in Living Cells. Annu Rev Biophys (2016) 0.86

A predictive modeling approach for cell line-specific long-range regulatory interactions. Nucleic Acids Res (2015) 0.86

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol (2015) 0.85

DNA sense-and-respond protein modules for mammalian cells. Nat Methods (2015) 0.85

Transcriptional regulation of GAD1 GABA synthesis gene in the prefrontal cortex of subjects with schizophrenia. Schizophr Res (2014) 0.85

Computational schemes for the prediction and annotation of enhancers from epigenomic assays. Methods (2014) 0.85

Chromatin associations in Arabidopsis interphase nuclei. Front Genet (2014) 0.85

CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes Dev (2016) 0.85

A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. Nucleic Acids Res (2014) 0.84

The role of enhancers in cancer. Nat Rev Cancer (2016) 0.84

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes. Nat Commun (2015) 0.84

Neurospora chromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3. Genome Res (2016) 0.84

Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points. Exp Hematol (2014) 0.84

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains. Nucleic Acids Res (2016) 0.84

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Res (2015) 0.83

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks. Nature (2016) 0.83

Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes. Nucleic Acids Res (2015) 0.83

Exploring the emerging complexity in transcriptional regulation of energy homeostasis. Nat Rev Genet (2015) 0.83

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PLoS Comput Biol (2015) 0.83

Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Res (2016) 0.83

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol Syst Biol (2016) 0.83

Parlez-vous VUS? Genome Res (2015) 0.83

Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet (2015) 0.83

Epigenetic landscape during osteoblastogenesis defines a differentiation-dependent Runx2 promoter region. Gene (2014) 0.83

Biological techniques: Chromosomes captured one by one. Nature (2013) 0.82

An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83

Capturing chromosome conformation. Science (2002) 23.93

Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23

The accessible chromatin landscape of the human genome. Nature (2012) 16.86

CTCF: master weaver of the genome. Cell (2009) 15.09

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32

The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science (2001) 12.35

An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16

Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet (2001) 11.70

Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell (2002) 11.35

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet (2006) 11.02

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature (2008) 10.95

Architecture of the human regulatory network derived from ENCODE data. Nature (2012) 10.28

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78

Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75

Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol (2002) 9.31

The long-range interaction landscape of gene promoters. Nature (2012) 9.20

Three-dimensional folding and functional organization principles of the Drosophila genome. Cell (2012) 9.19

Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet (2006) 8.99

Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet (2004) 8.85

A map of the cis-regulatory sequences in the mouse genome. Nature (2012) 8.74

Controlling the double helix. Nature (2003) 8.61

Nuclear organization of the genome and the potential for gene regulation. Nature (2007) 8.22

A three-dimensional model of the yeast genome. Nature (2010) 7.01

CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55

Insulators: exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet (2006) 6.43

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet (2009) 6.39

Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell (2005) 5.77

The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods (2006) 5.72

Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet (2004) 5.64

The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet (2003) 5.54

Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol (2006) 5.17

Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol (1997) 5.00

A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80

Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol (2004) 4.67

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol (2011) 4.56

Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell (2011) 4.29

Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods (2012) 4.26

A decade of 3C technologies: insights into nuclear organization. Genes Dev (2012) 4.25

An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15

The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev (2004) 4.04

Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell (2012) 4.02

Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol (2002) 3.99

The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Cell (2008) 3.92

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell (2011) 3.61

The hierarchy of the 3D genome. Mol Cell (2013) 3.54

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol (2010) 3.39

8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A (2010) 3.37

Spatially confined folding of chromatin in the interphase nucleus. Proc Natl Acad Sci U S A (2009) 3.19

Active RNA polymerases are localized within discrete transcription "factories' in human nuclei. J Cell Sci (1996) 3.16

A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell (2008) 3.15

Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol (2008) 3.13

Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol Cell (2012) 3.08

A self-associating protein critical for chromosome attachment, division, and polar organization in caulobacter. Cell (2008) 3.02

Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J (2007) 2.99

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res (2010) 2.96

My5C: web tools for chromosome conformation capture studies. Nat Methods (2009) 2.96

Conformational and thermodynamic properties of supercoiled DNA. J Mol Biol (1992) 2.94

Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell (2012) 2.87

Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol (2010) 2.80

Making contacts on a nucleic acid polymer. Trends Biochem Sci (2001) 2.70

Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science (1992) 2.69

Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell (2012) 2.67

A random-walk/giant-loop model for interphase chromosomes. Proc Natl Acad Sci U S A (1995) 2.66

Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J Cell Biol (2006) 2.63

Genomics tools for unraveling chromosome architecture. Nat Biotechnol (2010) 2.63

Long-range chromosomal interactions and gene regulation. Mol Biosyst (2008) 2.56

The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions. J Exp Med (2008) 2.50

The fractal globule as a model of chromatin architecture in the cell. Chromosome Res (2011) 2.48

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol (2012) 2.37

Centromere clustering is a major determinant of yeast interphase nuclear organization. J Cell Sci (2000) 2.25

Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res (2006) 2.13

Structure and dynamics of interphase chromosomes. PLoS Comput Biol (2008) 2.07

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res (2012) 1.95

Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev (2011) 1.88

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res (2011) 1.80

Interactions among Polycomb domains are guided by chromosome architecture. PLoS Genet (2011) 1.76

Complexity of chromatin folding is captured by the strings and binders switch model. Proc Natl Acad Sci U S A (2012) 1.73

Initial genomics of the human nucleolus. PLoS Genet (2010) 1.71

Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68

Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol (2013) 1.66

Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev (2012) 1.60

Polymer models of meiotic and mitotic chromosomes. Mol Biol Cell (1997) 1.57

High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol Biol Cell (2010) 1.56

Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS One (2010) 1.51

Polymer models for interphase chromosomes. Proc Natl Acad Sci U S A (1993) 1.49

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosome Res (2011) 1.46

Entropic organization of interphase chromosomes. J Cell Biol (2009) 1.40

Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput Biol (2011) 1.39

Structure and function in the budding yeast nucleus. Genetics (2012) 1.37

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res (2010) 1.36

Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet (2009) 1.36

A view of nuclear Polycomb bodies. Curr Opin Genet Dev (2011) 1.31

Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc Natl Acad Sci U S A (2009) 1.29

Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model. Biophys J (1994) 1.27

Looping probabilities in model interphase chromosomes. Biophys J (2010) 1.26

Statistics of polymer rings in the melt: a numerical simulation study. Phys Biol (2009) 1.22

Stable morphology, but dynamic internal reorganisation, of interphase human chromosomes in living cells. PLoS One (2010) 1.17

The physics behind the larger scale organization of DNA in eukaryotes. Phys Biol (2009) 1.14

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83

Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A (2003) 9.03

Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci (2007) 5.81

MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2004) 4.54

Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods (2012) 4.26

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys J (2004) 3.93

Tools for comparative protein structure modeling and analysis. Nucleic Acids Res (2003) 3.68

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell (2011) 3.61

Organization of the mitotic chromosome. Science (2013) 3.50

Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell (2007) 3.41

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol (2010) 3.39

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med (2013) 2.63

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat Biotechnol (2011) 2.63

EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res (2003) 2.50

Impact of deleterious passenger mutations on cancer progression. Proc Natl Acad Sci U S A (2013) 2.23

High-resolution mapping of the spatial organization of a bacterial chromosome. Science (2013) 2.17

Protein knot server: detection of knots in protein structures. Nucleic Acids Res (2007) 2.15

The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol (2005) 2.13

Intricate knots in proteins: Function and evolution. PLoS Comput Biol (2006) 2.07

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol (2006) 2.06

MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2008) 2.02

ModView, visualization of multiple protein sequences and structures. Bioinformatics (2003) 1.99

Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet (2009) 1.95

A composite score for predicting errors in protein structure models. Protein Sci (2006) 1.92

Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res (2004) 1.84

Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys J (2008) 1.70

Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci U S A (2003) 1.67

Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp (2010) 1.67

How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci U S A (2007) 1.64

Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev (2012) 1.60

A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A (2006) 1.59

Operating regimes of signaling cycles: statics, dynamics, and noise filtering. PLoS Comput Biol (2007) 1.51

Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Res (2008) 1.48

A single-molecule characterization of p53 search on DNA. Proc Natl Acad Sci U S A (2010) 1.43

A Stevedore's protein knot. PLoS Comput Biol (2010) 1.43

Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel (2009) 1.43

Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput Biol (2011) 1.39

Variable gap penalty for protein sequence-structure alignment. Protein Eng Des Sel (2006) 1.34

Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem (2011) 1.30

RNA structure alignment by a unit-vector approach. Bioinformatics (2008) 1.27

SARA: a server for function annotation of RNA structures. Nucleic Acids Res (2009) 1.25

Using the topology of metabolic networks to predict viability of mutant strains. Biophys J (2006) 1.24

Diffusion in correlated random potentials, with applications to DNA. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 1.17

Sequence-dependent sliding kinetics of p53. Proc Natl Acad Sci U S A (2012) 1.13

Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res (2011) 1.11

Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans. Hum Mutat (2008) 1.11

Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol (2002) 1.08

Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease. PLoS One (2012) 1.08

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets. Proteins (2006) 1.05

Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol (2007) 1.01

Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PLoS Comput Biol (2013) 1.01

All-atom knowledge-based potential for RNA structure prediction and assessment. Bioinformatics (2011) 1.00

A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis (2009) 1.00

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform. Methods (2012) 0.99

Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A (2005) 0.93

Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res (2009) 0.92

Impact of Fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824. Antimicrob Agents Chemother (2011) 0.91

Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics (2008) 0.90

N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon. Protein Sci (2011) 0.90

Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci (2006) 0.89

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC Bioinformatics (2010) 0.89

Protein translocation into peroxisomes by ring-shaped import receptors. FEBS Lett (2007) 0.88

Structure-based statistical analysis of transmembrane helices. Eur Biophys J (2012) 0.88

A kernel for the Tropical Disease Initiative. Nat Biotechnol (2009) 0.87

Predicting transcription factor specificity with all-atom models. Nucleic Acids Res (2008) 0.86

A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases. J Biol Chem (2013) 0.86

Polar/Ionizable residues in transmembrane segments: effects on helix-helix packing. PLoS One (2012) 0.85

Membrane protein integration into the endoplasmic reticulum. FEBS J (2011) 0.83

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Bioinformatics (2013) 0.82

Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Biol (2009) 0.81

Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs. Genome Biol (2008) 0.81

Effects of topological constraints on globular polymers. Soft Matter (2014) 0.80

CoC: a database of universally conserved residues in protein folds. Bioinformatics (2005) 0.79

ModLink+: improving fold recognition by using protein-protein interactions. Bioinformatics (2009) 0.78