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Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005665-e1005665

2017

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Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

Nature genetics, 2018-02, Vol.50 (2), p.238-249

2018

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The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Molecular cell, 2011-10, Vol.44 (2), p.252-264

2011

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Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Nature communications, 2017-11, Vol.8 (1), p.1753-10, Article 1753

2017

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Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Nature communications, 2017-03, Vol.8 (1), p.14665-14665, Article 14665

2017

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

Nature reviews. Genetics, 2013-06, Vol.14 (6), p.390

2013

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Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

Nucleic acids research, 2015-04, Vol.43 (7), p.3465

2015

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Chromatin globules: a common motif of higher order chromosome structure?

Current opinion in cell biology, 2011-06, Vol.23 (3), p.325-331

2011

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Bridging the resolution gap in structural modeling of 3D genome organization

PLoS computational biology, 2011-07, Vol.7 (7), p.e1002125-e1002125

2011

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Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

Nature structural & molecular biology, 2018-06, Vol.25 (6), p.496

2018

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N‐glycosylation efficiency is determined by the distance to the C‐terminus and the amino acid preceding an Asn‐Ser‐Thr sequon

Protein science, 2011-01, Vol.20 (1), p.179-186

2011

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The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

Cell reports (Cambridge), 2015-12, Vol.13 (9), p.1855-1867

2015

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Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

Nucleic acids research, 2021-02, Vol.49 (4), p.1840

2021

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A composite score for predicting errors in protein structure models

Protein science, 2006-07, Vol.15 (7), p.1653-1666

2006

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3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?

Wiley interdisciplinary reviews. Computational molecular science, 2017-09, Vol.7 (5), p.e1308-n/a

2017

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Challenges for visualizing three‐dimensional data in genomic browsers

FEBS letters, 2017-09, Vol.591 (17), p.2505-2519

2017

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3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

Nature methods, 2020-08, Vol.17 (8), p.822

2020

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Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

Nature communications, 2020-05, Vol.11 (1), p.2564-2564, Article 2564

2020

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Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

Methods (San Diego, Calif.), 2012-11, Vol.58 (3), p.300-306

2012

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Restraint-based three-dimensional modeling of genomes and genomic domains

FEBS letters, 2015-10, Vol.589 (20), p.2987-2995

2015

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Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis

Cell reports (Cambridge), 2019-07, Vol.28 (2), p.352-367.e9

2019

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Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells

Cell reports (Cambridge), 2019-06, Vol.27 (12), p.3500-3510.e4

2019

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Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Journal of molecular biology, 2019-03, Vol.431 (6), p.1071-1087

2019

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Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

Nature communications, 2021-01, Vol.12 (1), p.651-18, Article 651

2021

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Software for predicting the 3D structure of RNA molecules

Wiley interdisciplinary reviews. Computational molecular science, 2015-01, Vol.5 (1), p.56-61

2015

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Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

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

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

Chromatin globules: a common motif of higher order chromosome structure?

Bridging the resolution gap in structural modeling of 3D genome organization

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

N‐glycosylation efficiency is determined by the distance to the C‐terminus and the amino acid preceding an Asn‐Ser‐Thr sequon

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana

A composite score for predicting errors in protein structure models

3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?

Challenges for visualizing three‐dimensional data in genomic browsers

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

Restraint-based three-dimensional modeling of genomes and genomic domains

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis

Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

Software for predicting the 3D structure of RNA molecules

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