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Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

Nature genetics, 2019-05, Vol.51 (5), p.835-843

2019

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Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts

Genome Biology, 2017-01, Vol.18 (1), p.21-21, Article 21

2017

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MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

Genome Biology, 2022-11, Vol.23 (1), p.247-24, Article 247

2022

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Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization

Scientific reports, 2016-10, Vol.6 (1), p.35985-35985, Article 35985

2016

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Manifold Based Optimization for Single-Cell 3D Genome Reconstruction

PLoS computational biology, 2015-08, Vol.11 (8), p.e1004396-e1004396

2015

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4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?

Genome Biology, 2016-04, Vol.17 (1), p.54-54, Article 54

2016

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TAD cliques predict key features of chromatin organization

BMC genomics, 2021-07, Vol.22 (1), p.499-499, Article 499

2021

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A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

Nucleic acids research, 2014-10, Vol.42 (18), p.e143-e143

2014

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Potentials of mean force for protein structure prediction vindicated, formalized and generalized

PloS one, 2010-11, Vol.5 (11), p.e13714-e13714

2010

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Modeling the 3D Genome Using Hi-C and Nuclear Lamin-Genome Contacts

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2301, p.337

2022

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Modeling properties of chromosome territories using polymer filaments in diverse confinement geometries

Chromosome research, 2024-08, Vol.32 (3), p.11, Article 11

2024

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Lamin A, Chromatin and FPLD2: Not Just a Peripheral Ménage-à-Trois

Frontiers in cell and developmental biology, 2018-07, Vol.6, p.73-73

2018

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Computational 3D genome modeling using Chrom3D

Nature protocols, 2018-05, Vol.13 (5), p.1137-1152

2018

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Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis

The EMBO journal, 2017-10, Vol.36 (19), p.2829-2843

2017

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Manifold Based Optimization for Single-Cell 3D Genome Reconstruction: e1004396

PLoS computational biology, 2015-08, Vol.11 (8)

2015

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Ion-pair mediated transport of small model peptides in liquid phase micro extraction under acidic conditions

Journal of separation science, 2005-02, Vol.28 (3), p.295-300

2005

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Effectiveness of new antiplatelets in the prevention of recurrent myocardial infarction

Heart (British Cardiac Society), 2018-09, Vol.104 (19), p.1583-1592

2018

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Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements

Nucleic acids research, 2013-05, Vol.41 (10), p.5164-5174

2013

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The Genomic HyperBrowser: an analysis web server for genome-scale data

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W133-W141

2013

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Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes

Nucleic acids research, 2012-11, Vol.40 (21), p.10950-10963

2012

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assessment of mitochondrial variation in Arctic gadoids

Polar biology, 2009-03, Vol.32 (3), p.471-479

2009

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Rapid Evolution of the Intergenic T-P Spacer in the mtDNA of Arctic Cod Arctogadus glacialis

Marine biotechnology (New York, N.Y.), 2008-05, Vol.10 (3), p.270-277

2008

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Physical 3D Modeling of Whole Genomes: Exploring Chromosomal Organization Properties and Principles

Modeling the 3D Conformation of Genomes, 2019, p.331-360

1, 2019

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Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction

4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?

TAD cliques predict key features of chromatin organization

A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

Potentials of mean force for protein structure prediction vindicated, formalized and generalized

Modeling the 3D Genome Using Hi-C and Nuclear Lamin-Genome Contacts

Modeling properties of chromosome territories using polymer filaments in diverse confinement geometries

Lamin A, Chromatin and FPLD2: Not Just a Peripheral Ménage-à-Trois

Computational 3D genome modeling using Chrom3D

Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction: e1004396

Ion-pair mediated transport of small model peptides in liquid phase micro extraction under acidic conditions

Effectiveness of new antiplatelets in the prevention of recurrent myocardial infarction

Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements

The Genomic HyperBrowser: an analysis web server for genome-scale data

Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes

assessment of mitochondrial variation in Arctic gadoids

Rapid Evolution of the Intergenic T-P Spacer in the mtDNA of Arctic Cod Arctogadus glacialis

The genome sequence of Atlantic cod reveals a unique immune system

Physical 3D Modeling of Whole Genomes: Exploring Chromosomal Organization Properties and Principles

Semaglutide lowers body weight in rodents via distributed neural pathways

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