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GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

Bioinformatics (Oxford, England), 2019-06, Vol.35 (12), p.2159-2161

2019

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A scalable SCENIC workflow for single-cell gene regulatory network analysis

Nature protocols, 2020-07, Vol.15 (7), p.2247-2276

2020

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cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

Nature methods, 2019-05, Vol.16 (5), p.397-400

2019

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Phenotype molding of stromal cells in the lung tumor microenvironment

Nature medicine, 2018-08, Vol.24 (8), p.1277-1289

2018

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A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

Cell, 2018-08, Vol.174 (4), p.982-998.e20

2018

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Toward Minimal Residual Disease-Directed Therapy in Melanoma

Cell, 2018-08, Vol.174 (4), p.843-855.e19

2018

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Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling

PLoS genetics, 2015-02, Vol.11 (2), p.e1004994

2015

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Actuation enhances patterning in human neural tube organoids

Nature communications, 2021-05, Vol.12 (1), p.3192-3192, Article 3192

2021

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Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics

Current opinion in neurobiology, 2019-06, Vol.56, p.125-134

2019

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i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

Nucleic acids research, 2012-08, Vol.40 (15), p.e114-e114

2012

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Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

Nature cell biology, 2020-08, Vol.22 (8), p.986-998

2020

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i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Nucleic acids research, 2015-07, Vol.43 (W1), p.W57-W64

2015

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Melanoma addiction to the long non-coding RNA SAMMSON

Nature (London), 2016-03, Vol.531 (7595), p.518-522

2016

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High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

PLoS computational biology, 2012-08, Vol.8 (8), p.e1002638-e1002638

2012

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iRegulon: from a gene list to a gene regulatory network using large motif and track collections

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003731-e1003731

2014

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Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells

eLife, 2015-03, Vol.4 (Art. n°e06857)

2015

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Gitools: analysis and visualisation of genomic data using interactive heat-maps

PloS one, 2011-05, Vol.6 (5), p.e19541-e19541

2011

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Mapping gene regulatory networks from single-cell omics data

Briefings in functional genomics, 2018-07, Vol.17 (4), p.246-254

2018

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Peritumoral activation of the Hippo pathway effectors YAP and TAZ suppresses liver cancer in mice

Science (American Association for the Advancement of Science), 2019-11, Vol.366 (6468), p.1029-1034

2019

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Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

Nature communications, 2015-04, Vol.6 (1), p.6683-6683, Article 6683

2015

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An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model

Current biology, 2016-08, Vol.26 (16), p.2101-2113

2016

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Cell type diversity in a developing octopus brain

Nature communications, 2022-11, Vol.13 (1), p.7392-7392, Article 7392

2022

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ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

PloS one, 2011-01, Vol.6 (1), p.e16327-e16327

2011

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Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Genome Biology, 2022-02, Vol.23 (1), p.55-55, Article 55

2022

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Analysis of long and short enhancers in melanoma cell states

eLife, 2021-12, Vol.10

2021

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GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

A scalable SCENIC workflow for single-cell gene regulatory network analysis

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

Phenotype molding of stromal cells in the lung tumor microenvironment

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

Toward Minimal Residual Disease-Directed Therapy in Melanoma

Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling

Actuation enhances patterning in human neural tube organoids

Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Melanoma addiction to the long non-coding RNA SAMMSON

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

iRegulon: from a gene list to a gene regulatory network using large motif and track collections

Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells

Gitools: analysis and visualisation of genomic data using interactive heat-maps

Mapping gene regulatory networks from single-cell omics data

Peritumoral activation of the Hippo pathway effectors YAP and TAZ suppresses liver cancer in mice

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model

Cell type diversity in a developing octopus brain

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Analysis of long and short enhancers in melanoma cell states

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