Aerts Lab Publications | VIB-KU Leuven Center for Brain & Disease Research

Selected papers

Davie K*, Janssens J*, Koldere D*, De Waegeneer M, Pech U, Kreft L, Aibar Santos S, Makhzami S, Christiaens V, Bravo Gonzalez Blas M, Poovathingal S, Hulselmans G, Spanier K, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S@

Cell

982-998 e20

174

2018

SCENIC: single-cell regulatory network inference and clustering

Aibar Santos S, Bravo Gonzalez Blas M, Moerman T, Huynh-thu V, Imrichova H, Hulselmans G, Rambow F, Marine J, Geurts P, Aerts J, Van D, Kalender Z, Wouters J, Aerts S@

NAT METHODS

1083-1086

2017

All our publications

Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-like Domains.

Ravenscroft T, Janssens J, Lee P, Tepe B, Marcogliese P, Makhzami S, Holmes T, Aerts S, Bellen H

10.1523/JNEUROSCI.0142-20.2020

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

Almudi I, Vizueta J, Wyatt C, De M, Marletaz F, Firbas P, Feuda R, Masiero G, Medina P, Alcaina-caro A, Cruz F, Gomez-garrido J, Gut M, Alioto T, Vargas-chavez C, Davie K, Misof B, Gonzalez J, Aerts S, Lister R, Paps J, Rozas J, Sanchez-gracia A, Irimia M, Maeso I, Casares F

10.1038/s41467-020-16284-8

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

Bravo Gonzalez Blas M, Quan X, Duran R, Taskiran I, Koldere D, Davie K, Christiaens V, Makhzami S, Hulselmans G, De Waegeneer M, Mauduit D, Poovathingal S, Aibar Santos S, Aerts S@

10.15252/msb.20209438

Cross-species analysis of enhancer logic using deep learning.

Minnoye L*, Taskiran I*, Mauduit D, Fazio M, Van A, Hulselmans G, Christiaens V, Makhzami S, Seltenhammer M, Karras P, Primot A, Cadieu E, Van R, Marine J, Egidy G, Ghanem G, Zon L, Wouters J, Aerts S@

10.1101/gr.260844.120

LifeTime and improving European healthcare through cell-based interceptive medicine.

10.1038/s41586-020-2715-9

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

Van De Sande B*, Flerin C*, Davie K, De Waegeneer M, Hulselmans G, Aibar Santos S, Seurinck R, Saelens W, Cannoodt R, Rouchon Q, Verbeiren T, De M, Reumers J, Saeys Y, Aerts S@

10.1038/s41596-020-0336-2

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

Wouters J*, Kalender Z*, Minnoye L, Spanier K, De Waegeneer M, Bravo Gonzalez Blas M, Mauduit D, Davie K, Hulselmans G, Najem A, Dewaele M, Pedri D, Rambow F, Makhzami S, Christiaens V, Ceyssens F, Ghanem G, Marine J, Poovathingal S, Aerts S@

10.1038/s41556-020-0547-3

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

Almudi I, Martin-blanco C, Garcia-fernandez I, Lopez-catalina A, Davie K, Aerts S, Casares F

EvoDevo

2019

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

Bates A, Janssens J, Jefferis G, Aerts S@°

CURR OPIN NEUROBIOL

125-134

2019

High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease

Govaere O, Cockell S, Van H, Wouters J, Van Delm W, Van D, Bianchi A, Van E, Van S, Monbaliu D, Nevens F, Roskams T

Aerts Lab

Selected papers

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

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

SCENIC: single-cell regulatory network inference and clustering

All our publications

Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-like Domains.

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

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

Cross-species analysis of enhancer logic using deep learning.

LifeTime and improving European healthcare through cell-based interceptive medicine.

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

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

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

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

High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease

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