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Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

Cell, 2012-03, Vol.148 (5), p.908-921

2012

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Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

Molecular cell, 2020-02, Vol.77 (4), p.688-708

2020

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Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment

PLoS computational biology, 2022-08, Vol.18 (8), p.e1010392-e1010392

2022

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MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

Science (American Association for the Advancement of Science), 2012-06, Vol.336 (6087), p.1448-1451

2012

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CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis

BMC bioinformatics, 2021-08, Vol.22 (1), p.1-397, Article 397

2021

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Diagonal integration of multimodal single-cell data: potential pitfalls and paths forward

Nature communications, 2022-06, Vol.13 (1), p.3505-3505, Article 3505

2022

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Iterative correction of Hi-C data reveals hallmarks of chromosome organization

Nature methods, 2012-10, Vol.9 (10), p.999

2012

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Inferring chromosome radial organization from Hi-C data

BMC bioinformatics, 2020-11, Vol.21 (1), p.511-511, Article 511

2020

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Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

Genome research, 2013-12, Vol.23 (12), p.2066

2013

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Radiation-induced DNA damage and repair effects on 3D genome organization

Nature communications, 2020-12, Vol.11 (1), p.6178-6178, Article 6178

2020

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Constricted migration is associated with stable 3D genome structure differences in cancer cells

EMBO reports, 2022-10, Vol.23 (10), p.e52149-n/a

2022

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Node features of chromosome structure networks and their connections to genome annotation

Computational and structural biotechnology journal, 2024-12, Vol.23, p.2240-2250

2024

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Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

The Journal of cell biology, 2022-02, Vol.221 (2), p.1

2022

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sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network

NPJ systems biology and applications, 2022-09, Vol.8 (1), p.33-33, Article 33

2022

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Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling

Scientific reports, 2022-03, Vol.12 (1), p.4721-4721, Article 4721

2022

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High-resolution DNA-binding specificity analysis of yeast transcription factors

Genome Research, 2009-04, Vol.19 (4), p.556-566

2009

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Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science

PloS one, 2023-04, Vol.18 (4), p.e0284982-e0284982

2023

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RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells

Biochimica et biophysica acta, 2016-11, Vol.1859 (11), p.1389-1397

2016

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MASI enables fast model-free standardization and integration of single-cell transcriptomics data

Communications biology, 2023-04, Vol.6 (1), p.465-465, Article 465

2023

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Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

eLife, 2022-12, Vol.11

2022

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Genome organization during the cell cycle: unity in division

Wiley interdisciplinary reviews. Mechanisms of disease, 2017-09, Vol.9 (5), p.e1389-n/a

2017

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Translocation Mapping Exposes the Risky Lifestyle of B Cells

Cell, 2011-09, Vol.147 (1), p.20-22

2011

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Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment

Stem cell reports, 2019-07, Vol.13 (1), p.193-206

2019

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SMILE: mutual information learning for integration of single-cell omics data

Bioinformatics, 2022-01, Vol.38 (2), p.476-486

2022

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How to build a cohesive genome in 3D

Nature (London), 2017-11, Vol.551 (7678), p.38-40

McCord, Rachel Patton

2017

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Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment

MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis

Diagonal integration of multimodal single-cell data: potential pitfalls and paths forward

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

Inferring chromosome radial organization from Hi-C data

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

Radiation-induced DNA damage and repair effects on 3D genome organization

Constricted migration is associated with stable 3D genome structure differences in cancer cells

Node features of chromosome structure networks and their connections to genome annotation

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network

Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling

High-resolution DNA-binding specificity analysis of yeast transcription factors

Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science

RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells

MASI enables fast model-free standardization and integration of single-cell transcriptomics data

Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

Genome organization during the cell cycle: unity in division

Translocation Mapping Exposes the Risky Lifestyle of B Cells

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment

SMILE: mutual information learning for integration of single-cell omics data

How to build a cohesive genome in 3D

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