Research Explorer

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Researcher

Koen Van den Berge

Awards & Distinctions

24 Results

2024

Methods for differential expression analysis in single-cell transcriptomics at the gene- and subgene level

Jeroen GilisLieven ClementYvan SaeysKoen Van den Berge

Trajectory inference across multiple conditions with condiments

Hector Roux de BézieuxKoen Van den BergeKelly StreetSandrine Dudoit

A1 Journal Article in NATURE COMMUNICATIONS

2023

Polar lake microbiomes have distinct evolutionary histories

Bjorn TytgatElie VerleyenMaxime SweetloveKoen Van den BergeEveline PinseelDominic A. HodgsonSteven L. ChownKoen SabbeAnnick WilmotteAnne Willems et al.

A1 Journal Article in SCIENCE ADVANCES

Structure learning for zero-inflated counts with an application to single-cell RNA sequencing data

Thi Kim Hue NguyenKoen Van den BergeMonica ChiognaDavide Risso

A1 Journal Article in ANNALS OF APPLIED STATISTICS

2022

A guide to trajectory inference and RNA velocity

Philipp WeilerKoen Van den BergeKelly StreetSimone Tiberi

Bookchapter in Single cell transcriptomics : methods and protocols

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Koen Van den BergeHsin-Jung ChouHector Roux de BézieuxKelly StreetDavide RissoJohn NgaiSandrine Dudoit

A2 Journal Article in CELL REPORTS METHODS

Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline

Eveline PinseelTeofil NakovKoen Van den BergeKala M. DowneyKathryn J. JudyOlga KourtchenkoAnke KrempElizabeth C. RuckConny SjoqvistMats Topel et al.

A1 Journal Article in ISME JOURNAL

2021

A multimodal cell census and atlas of the mammalian primary motor cortex

Edward M. CallawayHong-Wei DongJoseph R. EckerMichael J. HawrylyczZ. Josh HuangEd S. LeinJohn NgaiPavel OstenBing RenAndreas Savas Tolias et al.

A1 Journal Article in NATURE

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Zizhen YaoHanqing LiuFangming XieStephan FischerRicky S. AdkinsAndrew I. AldridgeSeth A. AmentAnna BartlettM. Margarita BehrensKoen Van den Berge et al.

A1 Journal Article in NATURE

Altering the sex pheromone cyclo(L-Pro-L-Pro) of the diatom Seminavis robusta towards a chemical probe

Eli BonneureAmber De BaetsSam De DeckerKoen Van den BergeLieven ClementWim VyvermanSven Mangelinckx

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

Gust BilckeKoen Van den BergeSam De DeckerEli BonneureNicole PoulsenPetra BulánkováCristina OsunaJack DickensonKoen SabbeGeorg Pohnert et al.

A1 Journal Article in ISME JOURNAL

satuRn : Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications

Jeroen GilisKristoffer Vitting-SeerupKoen Van den BergeLieven Clement

satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications

Jeroen GilisKristoffer Vitting-SeerupKoen Van den BergeLieven Clement

A2 Journal Article in F1000RESEARCH

2020

Distinctive growth and transcriptional changes of the diatom Seminavis robusta in response to quorum sensing related compounds

Frederike Stock genannt SchroerGust BilckeSam De DeckerCristina OsunaKoen Van den BergeEmmelien VancaesterLieven De VeylderKlaas VandepoeleSven MangelinckxWim Vyverman

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

David H. BrannTatsuya TsukaharaCaleb WeinrebMarcela LipovsekKoen Van den BergeBoying GongRebecca ChanceIain C. MacaulayHsin-Jung ChouRussell B. Fletcher et al.

A1 Journal Article in SCIENCE ADVANCES

Trajectory-based differential expression analysis for single-cell sequencing data

Koen Van den BergeHector Roux de BézieuxKelly StreetWouter SaelensRobrecht CannoodtYvan SaeysSandrine DudoitLieven Clement

A1 Journal Article in NATURE COMMUNICATIONS

2019

RNA sequencing data : hitchhiker's guide to expression analysis

Koen Van den BergeKatharina M HembachCharlotte SonesonSimone TiberiLieven ClementMichael I LoveRob PatroMark D Robinson

A2 Journal Article in ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE

Statistical methods for differential expression analysis in bulk and single-cell RNA-sequencing applications

Koen Van den BergeLieven Clement

2018

Effect of management and age of ploughed out grass-clover on forage maize yield and residual soil nitrogen

Mathias CougnonKoen Van den BergeTommy D'HoseLieven ClementDirk Reheul

A1 Journal Article in JOURNAL OF AGRICULTURAL SCIENCE

Neurogenomic profiling reveals distinct gene expression profiles between brain parts that are consistent in ophthalmotilapia cichlids

Sofie DeryckeLoic KéverKoen HertenKoen Van den BergeMaarten Van SteenbergeJeroen Van HoudtLieven ClementPascal PoncinEric ParmentierErik Verheyen

A1 Journal Article in FRONTIERS IN NEUROSCIENCE

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Koen Van den BergeFanny PerraudeauCharlotte SonesonMichael I LoveDavide RissoJean-Philippe VertMark D RobinsonSandrine DudoitLieven Clement

A1 Journal Article in GENOME BIOLOGY

2017

stageR : a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Koen Van den BergeCharlotte SonesonMark D RobinsonLieven Clement

A1 Journal Article in GENOME BIOLOGY

2016

A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta

Sara MoeysJohannes FrenkelChristine LembkeJeroen GillardValerie DevosKoen Van den BergeBarbara BouillonMarie HuysmanSam De DeckerJulia Scharf et al.

A1 Journal Article in SCIENTIFIC REPORTS

2015

Quantifying expression divergence of duplicated genes with microarrays

Koen Van den BergeRiet De SmetYves Van de PeerLieven Clement