K. Davie

发表

Extracellular matrix flow guides in-vitro epithelial morphogenesis

S. Poovathingal, A. Ranga, K. Vints, 2022, bioRxiv.

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

Daniel A. Sutton, Stephen L. Holtz, A. M. Allen, 2022, Science.

Mitochondria metabolism sets the species-specific tempo of neuronal development

S. Aerts, P. Vanderhaeghen, S. Poovathingal, 2023, Science.

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

Yvan Saeys, Robrecht Cannoodt, Wouter Saelens, 2020, Nature Protocols.

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

P. Verstreken, S. Aerts, T. Voet, 2018, Cell.

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

S. Aerts, G. Halder, Kristofer Davie, 2018, Nature Genetics.

Xenotransplanted Human Cortical Neurons Reveal Species-Specific Development and Functional Integration into Mouse Visual Circuits

K. Conzelmann, P. Vanderhaeghen, V. Bonin, 2019, Neuron.

Cis-topic modelling of single-cell epigenomes

Stein Aerts, Carmen Bravo González-Blas, Liesbeth Minnoye, 2018, bioRxiv.

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

Stein Aerts, Liesbeth Minnoye, Dafni Papasokrati, 2019, Nature Methods.

Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

A. M. Allen, Robert C. Jones, J. Leskovec, 2021, bioRxiv.

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

S. Aerts, Kristofer Davie, Duygu Koldere, 2019, bioRxiv.

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

S. Aerts, G. Halder, Duygu Koldere, 2018, Nature Genetics.

Species-specific mitochondria dynamics and metabolism regulate the timing of neuronal development

S. Aerts, P. Vanderhaeghen, S. Poovathingal, 2021, bioRxiv.

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

Y. Saeys, S. Aerts, R. Seurinck, 2020, Nature Protocols.

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

S. Aerts, G. Halder, Kristofer Davie, 2015, PLoS genetics.

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

S. Aerts, Kristofer Davie, Duygu Koldere, 2020, Molecular systems biology.

Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching

S. Aerts, J. Marine, Kristofer Davie, 2019, bioRxiv.

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

S. Aerts, J. Marine, Kristofer Davie, 2020, Nature Cell Biology.

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

S. Aerts, F. Casares, I. Almudi, 2018, bioRxiv.

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

T. Alioto, M. Gut, S. Aerts, 2020, Nature Communications.

Hexanucleotide repeat expansions in C9orf72 alter microglial responses and prevent a coordinated glial reaction in ALS

P. van Damme, R. Mancuso, Kristofer Davie, 2022, bioRxiv.

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic

S. Aerts, Kristofer Davie, V. Christiaens, 2016, Genome research.

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

T. Alioto, M. Gut, S. Aerts, 2019, bioRxiv.

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

S. Aerts, F. Casares, I. Almudi, 2018, EvoDevo.

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

T. Alioto, M. Gut, S. Aerts, 2020, Nature Communications.

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

Pierre Geurts, Stein Aerts, Gert Hulselmans, 2014, Cell reports.

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

S. Aerts, S. Aibar, V. Christiaens, 2019, Nature Methods.

Single-cell transcriptomics reveals that glial cells integrate homeostatic and circadian processes to drive sleep-wake cycles

S. Poovathingal, Sha Liu, J. Dopp, 2023, bioRxiv.

Actuation enhances patterning in human neural tube organoids

Peter Dedecker, Adrian Ranga, Kristofer Davie, 2020, Nature Communications.

microRNA-132 regulates gene expression programs involved in microglial homeostasis

B. de Strooper, R. Mancuso, M. Fiers, 2023, iScience.

Early alterations in the MCH system link aberrant neuronal activity and sleep disturbances in a mouse model of Alzheimer’s disease

I. Slutsky, A. Adamantidis, B. de Strooper, 2023, Nature Neuroscience.

A single-cell catalogue of regulatory states in the ageing Drosophila brain

P. Verstreken, S. Aerts, J. Lammertyn, 2017, bioRxiv.

Melanin Concentrating Hormone- and sleep-dependent synaptic downscaling is impaired in Alzheimer’s Disease

B. de Strooper, S. Poovathingal, M. Fiers, 2021, bioRxiv.

Theme 04 - In Vivo Experimetal Models

P. Carmeliet, M. Mongillo, S. Poovathingal, 2022, Amyotrophic lateral sclerosis & frontotemporal degeneration.

Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics

S. Poovathingal, A. Verfaillie, Nikky Corthout, 2024, bioRxiv.