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Transcription factors: from enhancer binding to developmental control

Nature reviews. Genetics, 2012-09, Vol.13 (9), p.613-626

2012

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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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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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Developmental enhancers and chromosome topology

Science (American Association for the Advancement of Science), 2018-09, Vol.361 (6409), p.1341-1345

2018

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Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Nature genetics, 2012-02, Vol.44 (2), p.148-156

2012

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The cis-regulatory dynamics of embryonic development at single-cell resolution

Nature (London), 2018-03, Vol.555 (7697), p.538-542

2018

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A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

Cell, 2012-02, Vol.148 (3), p.473-486

2012

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Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

Development (Cambridge), 2019-09, Vol.146 (19)

2019

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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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Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

Current biology, 2016-01, Vol.26 (1), p.38-51

2016

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The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

Genes & development, 2018-01, Vol.32 (1), p.42-57

2018

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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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Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements

Genes & development, 2017-03, Vol.31 (6), p.590-602

2017

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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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FourCSeq: analysis of 4C sequencing data

Bioinformatics, 2015-10, Vol.31 (19), p.3085-3091

2015

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Ultrasensitive proteome analysis using paramagnetic bead technology

Molecular systems biology, 2014-10, Vol.10 (10), p.757-n/a

2014

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A core transcriptional network for early mesoderm development in Drosophila melanogaster

Genes & development, 2007-02, Vol.21 (4), p.436-449

2007

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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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Dynamic Regulation by Polycomb Group Protein Complexes Controls Pattern Formation and the Cell Cycle in Drosophila

Developmental cell, 2008-12, Vol.15 (6), p.877-889

2008

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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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A conserved role for Snail as a potentiator of active transcription

Genes & development, 2014-01, Vol.28 (2), p.167-181

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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A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

Developmental cell, 2006-06, Vol.10 (6), p.797-807

2006

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easyRNASeq: a bioconductor package for processing RNA-Seq data

Bioinformatics (Oxford, England), 2012-10, Vol.28 (19), p.2532-2533

2012

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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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Transcription factors: from enhancer binding to developmental control

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

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

Developmental enhancers and chromosome topology

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

The cis-regulatory dynamics of embryonic development at single-cell resolution

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

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

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

Combinatorial binding predicts spatio-temporal cis -regulatory activity

Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements

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

FourCSeq: analysis of 4C sequencing data

Ultrasensitive proteome analysis using paramagnetic bead technology

A core transcriptional network for early mesoderm development in Drosophila melanogaster

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

Dynamic Regulation by Polycomb Group Protein Complexes Controls Pattern Formation and the Cell Cycle in Drosophila

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

A conserved role for Snail as a potentiator of active transcription

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

A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

easyRNASeq: a bioconductor package for processing RNA-Seq data

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

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