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ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Molecular biology and evolution, 2016-06, Vol.33 (6), p.1635-1638

2016

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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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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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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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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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Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

Genes & development, 2014-10, Vol.28 (19), p.2151-2162

2014

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The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer

Nature communications, 2023-12, Vol.14 (1), p.8084-8084, Article 8084

2023

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Role of tomato BRANCHED1‐like genes in the control of shoot branching

The Plant journal : for cell and molecular biology, 2011-08, Vol.67 (4), p.701-714

2011

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p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response

Nature communications, 2024-04, Vol.15 (1), p.2821-2821, Article 2821

2024

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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.3465-3477

2015

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Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

Nature communications, 2023-01, Vol.14 (1), p.268-268, Article 268

2023

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STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

Nucleic acids research, 2021-11, Vol.49 (19), p.11005-11021

2021

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Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Nucleic acids research, 2011-07, Vol.39 (Web Server issue), p.W470-W474

2011

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Identification of chromatin loops from Hi-C interaction matrices by CTCF–CTCF topology classification

NAR genomics and bioinformatics, 2022-03, Vol.4 (1)

2022

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Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments

Methods in molecular biology (Clifton, N.J.), 2021, Vol.2157, p.35

2021

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Neutral theory predicts the relative abundance and diversity of genetic elements in a broad array of eukaryotic genomes

PloS one, 2013-06, Vol.8 (6), p.e63915-e63915

2013

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S109: P53 ORCHESTRATES SPATIO‐TEMPORAL EPIGENOME REWIRING TO TRANSCRIPTIONALLY PREVENT MALIGNANT TRANSFORMATION

HemaSphere, 2023-08, Vol.7 (S3), p.e67884fc-n/a

2023

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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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Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments

Environmental microbiology, 2012-03, Vol.14 (3), p.691-701

2012

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Recent human evolution has shaped geographical differences in susceptibility to disease

BMC genomics, 2011-01, Vol.12 (1), p.55-55, Article 55

2011

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Natural selection on functional modules, a genome-wide analysis

PLoS computational biology, 2011-03, Vol.7 (3), p.e1001093-e1001093

2011

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Parallel sequencing lives, or what makes large sequencing projects successful

Gigascience, 2017-11, Vol.6 (11), p.1-6

2017

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Positive selection in nucleoporins challenges constraints on early expressed genes in Drosophila development

Genome biology and evolution, 2013-01, Vol.5 (11), p.2231-2241

2013

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Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group

Evolutionary Bioinformatics, 2012-01, Vol.2012 (2012), p.89-104

2012

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Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements

Genome biology and evolution, 2015-06, Vol.7 (6), p.1490-1505

2015

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ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

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

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

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

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

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer

Role of tomato BRANCHED1‐like genes in the control of shoot branching

p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response

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

Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Identification of chromatin loops from Hi-C interaction matrices by CTCF–CTCF topology classification

Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments

Neutral theory predicts the relative abundance and diversity of genetic elements in a broad array of eukaryotic genomes

S109: P53 ORCHESTRATES SPATIO‐TEMPORAL EPIGENOME REWIRING TO TRANSCRIPTIONALLY PREVENT MALIGNANT TRANSFORMATION

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

Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments

Recent human evolution has shaped geographical differences in susceptibility to disease

Natural selection on functional modules, a genome-wide analysis

Parallel sequencing lives, or what makes large sequencing projects successful

Positive selection in nucleoporins challenges constraints on early expressed genes in Drosophila development

Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group

Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements

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