List of works - Stein Aerts

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

article by Kristofer Davie et al published 9 August 2018 in Cell

A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing

scientific article published on 28 June 2018

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes

article

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

scientific article published on 19 June 2020

Actuation enhances patterning in human neural tube organoids

scientific article published on 27 May 2021

Adult interfollicular tumour-initiating cells are reprogrammed into an embryonic hair follicle progenitor-like fate during basal cell carcinoma initiation

scientific article

Alteration of the microRNA network during the progression of Alzheimer's disease

scientific article

Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling

scholarly article by Mariya P Dobreva published in July 2018

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

scientific article published on 26 July 2016

CD45 antigen negativity in T-lineage ALL correlates with PTPRC mutation and sensitivity to a selective JAK inhibitor.

scientific article

Cancer: Mutations close in on gene regulation

scientific article published in July 2013

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

scientific article published on 15 October 2012

Comparative oncogenomics identifies tyrosine kinase FES as a tumor suppressor in melanoma

scientific article published on 2 May 2017

Comparison and meta-analysis of microarray data: from the bench to the computer desk.

scientific article published in October 2003

Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia

scientific article

Computational Strategies for the Genome-Wide Identification of cis-Regulatory Elements and Transcriptional Targets

scientific article published on January 1, 2012

Computational detection of cis -regulatory modules.

scientific article

Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

scientific article published on June 2017

Cortical Neurogenesis Requires Bcl6-Mediated Transcriptional Repression of Multiple Self-Renewal-Promoting Extrinsic Pathways

scientific article published on 25 July 2019

Cross-species analysis of enhancer logic using deep learning

scientific article published on 30 July 2020

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

scientific article

Decoding transcriptional states in cancer

scientific article published on 24 January 2017

Defining the molecular basis of oncogenic cooperation between TAL1 expression and Pten deletion in T-ALL using a novel pro-T-cell model system.

scientific article published on 20 November 2017

Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1.

scientific article

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

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

scientific article published on 13 February 2015

ENDEAVOUR update: a web resource for gene prioritization in multiple species

scientific article

Establishment of the mayfly as a new model system to investigate insect evolution

scientific article published on 02 April 2019

Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia

scientific article

Fine-tuning enhancer models to predict transcriptional targets across multiple genomes

scientific article

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

scientific article published on 4 March 2022

Gene prioritization through genomic data fusion

scientific article

Gene profiling of hippocampal neuronal culture.

scientific article published in June 2003

Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization.

scientific article published on 23 August 2013

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

scientific article published on 26 May 2020

High accuracy mutation detection in leukemia on a selected panel of cancer genes

scientific article (publication date: 2012)

Hindsight regulates photoreceptor axon targeting through transcriptional control of jitterbug/Filamin and multiple genes involved in axon guidance in Drosophila.

scientific article

Hippo Reprograms the Transcriptional Response to Ras Signaling.

scientific article published on September 2017

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

scientific article published on 12 November 2015

Identification of IGFBP-6 as a significantly downregulated gene by beta-catenin in desmoid tumors.

scientific article published on January 2004

Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models

scientific article published on 4 May 2015

Identification of cis-regulatory modules encoding temporal dynamics during development.

scientific article

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

scientific article published on 30 August 2017

Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro.

scientific article

Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics

scientific article published on 01 May 2020

Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets

scientific article

Integrating computational biology and forward genetics in Drosophila

scientific article published on 23 January 2009

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

scientific article published on 08 April 2021

JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model

scientific article (publication date: 5 September 2014)

LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 07 September 2020

Male-specific fruitless isoforms target neurodevelopmental genes to specify a sexually dimorphic nervous system

scientific article

Mapping gene regulatory networks from single-cell omics data.

scientific article published on 12 January 2018

Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.

scientific article published on 18 December 2014

Melanoma addiction to the long non-coding RNA SAMMSON.

scientific article published in March 2016

Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

scientific article

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

scientific article published on 07 April 2008

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic

scientific article

Mutation analysis of the tyrosine phosphatase PTPN2 in Hodgkin's lymphoma and T-cell non-Hodgkin's lymphoma

scientific article published on 26 July 2011

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

scientific article published on 28 January 2019

Nuclear receptors connect progenitor transcription factors to cell cycle control.

scientific article

ORegAnno: an open-access community-driven resource for regulatory annotation

scientific article

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

scientific article published on 01 November 2019

Phenotype molding of stromal cells in the lung tumor microenvironment

scientific article published on 09 July 2018

Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus.

scientific article

Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma

scientific article

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

scientific article published on 17 March 2021

Reduced synaptic vesicle protein degradation at lysosomes curbs TBC1D24/sky-induced neurodegeneration

scientific article

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

scientific article published on 03 August 2020

Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification.

scientific article

SCENIC: single-cell regulatory network inference and clustering.

scientific article published on 9 October 2017

Sequencing the regulatory genome

scientific article published on 19 June 2008

Systematic benchmarking of single-cell ATAC-sequencing protocols

scientific article published in 2023

TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila

scientific article published on 17 January 2013

TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

scientific article

Text-mining assisted regulatory annotation

scientific article published on 13 February 2008

The atonal proneural transcription factor links differentiation and tumor formation in Drosophila

scientific article

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

Toucan: deciphering the cis-regulatory logic of coregulated genes.

scientific article

Toward Minimal Residual Disease-Directed Therapy in Melanoma

scientific article published on 12 July 2018

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

scientific article published on 24 March 2015

Tyrosine-Dependent Phenotype Switching Occurs Early in Many Primary Melanoma Cultures Limiting Their Translational Value

scientific article published on 11 November 2021

Using cisTargetX to predict transcriptional targets and networks in Drosophila.

scientific article published in January 2012

Variations in the exome of the LNCaP prostate cancer cell line

scientific article

Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation

scientific article published in July 2011

Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation

scientific article published on 01 April 2019

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

scientific article published on 08 April 2019

dachshund Potentiates Hedgehog Signaling during Drosophila Retinogenesis

scientific article published on 21 July 2016

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

scientific article published on 29 April 2015

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

scientific article published on June 20, 2012

iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment

scientific article published on 17 December 2015

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

scientific article

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

scientific article published on 4 July 2016

List of works by Stein Aerts

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes

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

Actuation enhances patterning in human neural tube organoids

Adult interfollicular tumour-initiating cells are reprogrammed into an embryonic hair follicle progenitor-like fate during basal cell carcinoma initiation

Alteration of the microRNA network during the progression of Alzheimer's disease

Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling

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

CD45 antigen negativity in T-lineage ALL correlates with PTPRC mutation and sensitivity to a selective JAK inhibitor.

Cancer: Mutations close in on gene regulation

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

Comparative oncogenomics identifies tyrosine kinase FES as a tumor suppressor in melanoma

Comparison and meta-analysis of microarray data: from the bench to the computer desk.

Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia

Computational Strategies for the Genome-Wide Identification of cis-Regulatory Elements and Transcriptional Targets

Computational detection of cis -regulatory modules.

Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

Cortical Neurogenesis Requires Bcl6-Mediated Transcriptional Repression of Multiple Self-Renewal-Promoting Extrinsic Pathways

Cross-species analysis of enhancer logic using deep learning

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

Decoding transcriptional states in cancer

Defining the molecular basis of oncogenic cooperation between TAL1 expression and Pten deletion in T-ALL using a novel pro-T-cell model system.

Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

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

ENDEAVOUR update: a web resource for gene prioritization in multiple species

Establishment of the mayfly as a new model system to investigate insect evolution

Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia

Fine-tuning enhancer models to predict transcriptional targets across multiple genomes

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

Gene prioritization through genomic data fusion

Gene profiling of hippocampal neuronal culture.

Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization.

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

High accuracy mutation detection in leukemia on a selected panel of cancer genes

Hindsight regulates photoreceptor axon targeting through transcriptional control of jitterbug/Filamin and multiple genes involved in axon guidance in Drosophila.

Hippo Reprograms the Transcriptional Response to Ras Signaling.

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

Identification of IGFBP-6 as a significantly downregulated gene by beta-catenin in desmoid tumors.

Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models

Identification of cis-regulatory modules encoding temporal dynamics during development.

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro.

Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics

Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets

Integrating computational biology and forward genetics in Drosophila

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model

LifeTime and improving European healthcare through cell-based interceptive medicine

Male-specific fruitless isoforms target neurodevelopmental genes to specify a sexually dimorphic nervous system

Mapping gene regulatory networks from single-cell omics data.

Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.

Melanoma addiction to the long non-coding RNA SAMMSON.

Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic

Mutation analysis of the tyrosine phosphatase PTPN2 in Hodgkin's lymphoma and T-cell non-Hodgkin's lymphoma

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

Nuclear receptors connect progenitor transcription factors to cell cycle control.

ORegAnno: an open-access community-driven resource for regulatory annotation

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

Phenotype molding of stromal cells in the lung tumor microenvironment

Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus.

Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

Reduced synaptic vesicle protein degradation at lysosomes curbs TBC1D24/sky-induced neurodegeneration

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

Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification.

SCENIC: single-cell regulatory network inference and clustering.

Sequencing the regulatory genome

Systematic benchmarking of single-cell ATAC-sequencing protocols

TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila

TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

Text-mining assisted regulatory annotation

The atonal proneural transcription factor links differentiation and tumor formation in Drosophila

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

Toucan: deciphering the cis-regulatory logic of coregulated genes.

Toward Minimal Residual Disease-Directed Therapy in Melanoma