Research Explorer

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Project

High-resolution differential expression analysis for single-cell RNA-seq data

Outputs and Outcomes

Publications

Trajectory inference across multiple conditions with condiments

Hector Roux de BézieuxKoen Van den BergeKelly StreetSandrine Dudoit

A1 Journal Article in NATURE COMMUNICATIONS

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

Polar lake microbiomes have distinct evolutionary histories

Bjorn TytgatElie VerleyenMaxime SweetloveKoen Van den BergeEveline PinseelDominic A. HodgsonSteven L. ChownKoen SabbeAnnick WilmotteAnne WillemsWim Vyverman[missing] on behalf of The Polar Lake Sampling Consortium et al.

A1 Journal Article in SCIENCE ADVANCES

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 TopelAnna GodheAndrew J. Alverson et al.

A1 Journal Article in ISME JOURNAL

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

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. FletcherDiya DasKelly StreetHector Roux de BezieuxYoon-Gi ChoiDavide RissoSandrine DudoitElizabeth PurdomJonathan MillRalph Abi HachemHiroaki MatsunamiDarren W. LoganBradley J. GoldsteinMatthew S. GrubbJohn NgaiSandeep Robert Datta et al.

A1 Journal Article in SCIENCE ADVANCES