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The role of transcription in shaping the spatial organization of the genome

Nature reviews. Molecular cell biology, 2019-06, Vol.20 (6), p.327

2019

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The road ahead in genetics and genomics

Nature reviews. Genetics, 2020-10, Vol.21 (10), p.581

2020

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Combinatorial binding predicts spatio-temporal cis -regulatory activity

Nature (London), 2009-11, Vol.462 (7269), p.65-70

2009

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A Versatile, Low-Cost, Multiway Microfluidic Sorter for Droplets, Cells, and Embryos

Analytical chemistry (Washington), 2018-05, Vol.90 (10), p.5982-5988

2018

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Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

eLife, 2015-03, Vol.4

2015

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Enhancer loops appear stable during development and are associated with paused polymerase

Nature (London), 2014-08, Vol.512 (7512), p.96-100

2014

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Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

Nature genetics, 2019-08, Vol.51 (8), p.1272-1282

2019

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Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

Nature protocols, 2012-05, Vol.7 (5), p.978-994

2012

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Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state

PLoS computational biology, 2012-12, Vol.8 (12), p.e1002798-e1002798

2012

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Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development

PLoS genetics, 2019-09, Vol.15 (9), p.e1008382-e1008382

2019

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Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

PLoS computational biology, 2016-09, Vol.12 (9), p.e1005073-e1005073

2016

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Model-based method for transcription factor target identification with limited data

Proceedings of the National Academy of Sciences - PNAS, 2010-04, Vol.107 (17), p.7793-7798

2010

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Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis

Development (Cambridge), 2014-07, Vol.141 (13), p.2633-2643

2014

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Promoter shape varies across populations and affects promoter evolution and expression noise

Nature genetics, 2017-04, Vol.49 (4), p.550-558

2017

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Predictive features of gene expression variation reveal mechanistic link with differential expression

Molecular systems biology, 2020-08, Vol.16 (8), p.e9539-n/a

2020

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Regulating specificity in enhancer–promoter communication

Current opinion in cell biology, 2022-04, Vol.75, p.102065-102065, Article 102065

2022

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Expanding the mesodermal transcriptional network by genome‐wide identification of Zinc finger homeodomain 1 (Zfh1) targets

FEBS letters, 2019-07, Vol.593 (14), p.1698-1710

2019

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Myofilin, a protein in the thick filaments of insect muscle

Journal of cell science, 2005-04, Vol.118 (7), p.1527-1536

2005

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Enhancers have more cofactor specificity than we think: A potential new way to classify enhancers based on their functional cofactor requirements

Molecular cell, 2022-08, Vol.82 (16), p.2922-2924

2022

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Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

Nature (London), 2024-02, Vol.626 (7997), p.207-211

2024

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Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network

Development (Cambridge), 2016-12, Vol.143 (23), p.4533-4542

2016

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Fragmentation of DNA in a sub-microliter microfluidic sonication device

Lab on a chip, 2012-11, Vol.12 (22), p.4677-4682

2012

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Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

Genes & development, 2007-10, Vol.21 (19), p.2448-2460

2007

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The continuum of Drosophila embryonic development at single-cell resolution

Science (American Association for the Advancement of Science), 2022-08, Vol.377 (6606), p.eabn5800-eabn5800

2022

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To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?

Current opinion in genetics & development, 2021-04, Vol.67, p.119-129

2021

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The role of transcription in shaping the spatial organization of the genome

The road ahead in genetics and genomics

Combinatorial binding predicts spatio-temporal cis -regulatory activity

A Versatile, Low-Cost, Multiway Microfluidic Sorter for Droplets, Cells, and Embryos

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

Enhancer loops appear stable during development and are associated with paused polymerase

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

Model-based method for transcription factor target identification with limited data

Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis

Promoter shape varies across populations and affects promoter evolution and expression noise

Predictive features of gene expression variation reveal mechanistic link with differential expression

Regulating specificity in enhancer–promoter communication

Expanding the mesodermal transcriptional network by genome‐wide identification of Zinc finger homeodomain 1 (Zfh1) targets

Myofilin, a protein in the thick filaments of insect muscle

Enhancers have more cofactor specificity than we think: A potential new way to classify enhancers based on their functional cofactor requirements

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network

Fragmentation of DNA in a sub-microliter microfluidic sonication device

Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

The continuum of Drosophila embryonic development at single-cell resolution

To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?

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