Academic Bibliography

Search 200 years of publications by Ghent University researchers.

Koen Van den Berge

No current affiliation with UGent

ORCID iD: 0000-0002-1833-8478

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- Journal Article
- A1
- open access
Differential detection workflows for multi-sample single-cell RNA-seq data

Jeroen Gilis, Laura Perin, Milan Malfait, Helena L. Crowell, Koen Van den Berge (UGent) , Alemu Takele Assefa, Bie Verbist, Davide Risso and Lieven Clement (UGent)

(2025) BMC GENOMICS. 26(1).
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- Journal Article
- A1
- open access
Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean

Gust Bilcke (UGent) , Lucia Campese, Rossella Annunziata, Luz Amadei Martínez (UGent) , Camilla Borgonuovo, Nadine Rijsdijk (UGent) , Peter Chaerle (UGent) , Koen Van den Berge (UGent) , Sofie D'hondt (UGent) , Daniele Iudicone, et al.

(2025) NATURE COMMUNICATIONS. 16(1).
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- Journal Article
- A1
- open access
Trajectory inference across multiple conditions with condiments

Hector Roux de Bézieux, Koen Van den Berge (UGent) , Kelly Street and Sandrine Dudoit

(2024) NATURE COMMUNICATIONS. 15(1).
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- Journal Article
- A1
- open access
Structure learning for zero-inflated counts with an application to single-cell RNA sequencing data

Thi Kim Hue Nguyen, Koen Van den Berge (UGent) , Monica Chiogna and Davide Risso

(2023) ANNALS OF APPLIED STATISTICS. 17(3). p.2555-2573
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- Journal Article
- A1
- open access
Polar lake microbiomes have distinct evolutionary histories

Bjorn Tytgat (UGent) , Elie Verleyen (UGent) , Maxime Sweetlove (UGent) , Koen Van den Berge (UGent) , Eveline Pinseel (UGent) , Dominic A. Hodgson, Steven L. Chown, Koen Sabbe (UGent) , Annick Wilmotte, Anne Willems (UGent) , et al.

(2023) SCIENCE ADVANCES. 9(46).
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- Journal Article
- A1
- open access
Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline

Eveline Pinseel (UGent) , Teofil Nakov, Koen Van den Berge (UGent) , Kala M. Downey, Kathryn J. Judy, Olga Kourtchenko, Anke Kremp, Elizabeth C. Ruck, Conny Sjoqvist, Mats Topel, et al.

(2022) ISME JOURNAL. 16(7). p.1776-1787
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- Book Chapter
A guide to trajectory inference and RNA velocity

Philipp Weiler, Koen Van den Berge (UGent) , Kelly Street and Simone Tiberi

(2022) Single cell transcriptomics : methods and protocols. In Methods in molecular biology (MIMB) 2584. p.269-292
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- Journal Article
- A2
- open access
Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Koen Van den Berge (UGent) , Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street, Davide Risso, John Ngai and Sandrine Dudoit

(2022) CELL REPORTS METHODS. 2(11).
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- Conference Paper
- C3
Transcriptional response of the marine diatom Skeletonema Marinoi during acclimation along a salinity gradient

Eveline Pinseel (UGent) , Teofil Nakov, Koen Van den Berge (UGent) , Kala Downey, Kathryn Judy, Elizabeth Ruck and Andrew J. Alverson

(2021) PHYCOLOGIA. In Phycologia 60(Supplement 1). p.112-112
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- Journal Article
- A1
- open access
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S. Adkins, Andrew I. Aldridge, Seth A. Ament, Anna Bartlett, M. Margarita Behrens, Koen Van den Berge (UGent) , et al.

(2021) NATURE. 598(7879). p.103-110

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