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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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The Regulatory Landscape of Osteogenic Differentiation

Stem cells (Dayton, Ohio), 2014-10, Vol.32 (10), p.2780-2793

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 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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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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The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks

Human molecular genetics, 2018-04, Vol.27 (8), p.1447-1459

2018

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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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Galaxy Portal: interacting with the galaxy platform through mobile devices

Bioinformatics, 2016-06, Vol.32 (11), p.1743-1745

2016

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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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IgA subclasses have different effector functions associated with distinct glycosylation profiles

Nature communications, 2020-01, Vol.11 (1), p.120-120, Article 120

2020

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The Communication between Ocular Surface and Nasal Epithelia in 3D Cell Culture Technology for Translational Research: A Narrative Review

International journal of molecular sciences, 2021-11, Vol.22 (23), p.12994

2021

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Heat conduction in oxide glasses: Balancing diffusons and propagons by network rigidity

Applied physics letters, 2020-07, Vol.117 (3)

2020

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Results of NOPHO ALL2008 treatment for patients aged 1-45 years with acute lymphoblastic leukemia

Leukemia, 2018-03, Vol.32 (3), p.606-615

2018

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A Signature of Exaggerated Adipose Tissue Dysfunction in Type 2 Diabetes Is Linked to Low Plasma Adiponectin and Increased Transcriptional Activation of Proteasomal Degradation in Muscle

Cells (Basel, Switzerland), 2022-06, Vol.11 (13), p.2005

2022

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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

The Regulatory Landscape of Osteogenic Differentiation

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

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

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

Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis

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

The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks

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

Galaxy Portal: interacting with the galaxy platform through mobile devices

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

IgA subclasses have different effector functions associated with distinct glycosylation profiles

The Communication between Ocular Surface and Nasal Epithelia in 3D Cell Culture Technology for Translational Research: A Narrative Review

Heat conduction in oxide glasses: Balancing diffusons and propagons by network rigidity

Results of NOPHO ALL2008 treatment for patients aged 1-45 years with acute lymphoblastic leukemia

A Signature of Exaggerated Adipose Tissue Dysfunction in Type 2 Diabetes Is Linked to Low Plasma Adiponectin and Increased Transcriptional Activation of Proteasomal Degradation in Muscle

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