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K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells

International journal of molecular sciences, 2021-08, Vol.22 (15), p.8067

2021

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Automated inference of gene regulatory networks using explicit regulatory modules

Journal of theoretical biology, 2020-02, Vol.486, p.110091-110091, Article 110091

2020

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Distributed Bayesian networks reconstruction on the whole genome scale

PeerJ (San Francisco, CA), 2018-10, Vol.6, p.e5692-e5692, Article e5692

2018

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Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Nature communications, 2021-06, Vol.12 (1), p.3621-3621, Article 3621

2021

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BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations

Journal of computational biology, 2019-04, Vol.26 (4), p.305-314

2019

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BNFinder: exact and efficient method for learning Bayesian networks

Bioinformatics, 2009-01, Vol.25 (2), p.286-287

2009

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Author Correction: The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

Scientific reports, 2021-09, Vol.11 (1), p.19628-4, Article 19628

2021

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QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models

Methods (San Diego, Calif.), 2020-10, Vol.181-182, p.80-85

2020

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Author Correction: Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Nature communications, 2021-12, Vol.12 (1), p.7218-7218, Article 7218

2021

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Applying dynamic Bayesian networks to perturbed gene expression data

BMC bioinformatics, 2006-05, Vol.7 (1), p.249-249, Article 249

2006

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BNFinder2: Faster Bayesian network learning and Bayesian classification

Bioinformatics, 2013-08, Vol.29 (16), p.2068-2070

2013

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Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Nature genetics, 2012-02, Vol.44 (2), p.148-156

2012

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Dynamic CRM occupancy reflects a temporal map of developmental progression

Molecular systems biology, 2010-06, Vol.6 (1), p.383-n/a

2010

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Supervised learning method for predicting chromatin boundary associated insulator elements

Journal of bioinformatics and computational biology, 2014-12, Vol.12 (6), p.1442006

2014

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The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

Scientific reports, 2021-08, Vol.11 (1), p.15668-15, Article 15668

2021

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Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data

BMC systems biology, 2013-12, Vol.7 Suppl 6 (S6), p.S16-S16, Article S16

2013

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HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data

International journal of molecular sciences, 2021-08, Vol.22 (15), p.8123

2021

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Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis

G3 : genes - genomes - genetics, 2015-05, Vol.5 (7), p.1503-1515

2015

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Biopython: freely available Python tools for computational molecular biology and bioinformatics

Bioinformatics, 2009-06, Vol.25 (11), p.1422-1423

2009

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Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis

Development (Cambridge), 2014-07, Vol.141 (13), p.2633-2643

2014

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Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression

Nucleic acids research, 2017-04, Vol.45 (6), p.3116

2017

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HiCEnterprise: identifying long range chromosomal contacts in Hi-C data

PeerJ (San Francisco, CA), 2021-04, Vol.9, p.e10558-e10558, Article e10558

2021

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Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers

BMC cancer, 2018-01, Vol.18 (1), p.23-23, Article 23

2018

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Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers

BMC medical genomics, 2017-05, Vol.10 (Suppl 1), p.34-34, Article 34

2017

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Regulatory Network Reconstruction Using Stochastic Logical Networks

Computational Methods in Systems Biology, 2006, p.142-154

2006

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K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells

Automated inference of gene regulatory networks using explicit regulatory modules

Distributed Bayesian networks reconstruction on the whole genome scale

Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations

BNFinder: exact and efficient method for learning Bayesian networks

Author Correction: The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

QChromosomeVisualizer: A new tool for 3D visualization of long simulations of polymer-like chromosome models

Author Correction: Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Applying dynamic Bayesian networks to perturbed gene expression data

BNFinder2: Faster Bayesian network learning and Bayesian classification

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Dynamic CRM occupancy reflects a temporal map of developmental progression

Supervised learning method for predicting chromatin boundary associated insulator elements

The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data

HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data

Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis

Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression

HiCEnterprise: identifying long range chromosomal contacts in Hi-C data

Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers

Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers

Regulatory Network Reconstruction Using Stochastic Logical Networks

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