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

Van den Berge, Koen ; Roux de Bézieux, Hector ; Street, Kelly ; Saelens, Wouter ; Cannoodt, Robrecht ; Saeys, Yvan ; Dudoit, Sandrine ; Clement, Lieven

Nature communications, 2020-03, Vol.11 (1), p.1201-1201, Article 1201 [Periódico revisado por pares]

England: Nature Publishing Group

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2
satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications [version 2; peer review: 2 approved]
satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications [version 2; peer review: 2 approved]
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satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications [version 2; peer review: 2 approved]

Gilis, Jeroen ; Vitting-Seerup, Kristoffer ; Van den Berge, Koen ; Clement, Lieven

F1000 research, 2022, Vol.10, p.374-374 [Periódico revisado por pares]

London: Faculty of 1000 Ltd

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3
Role of mustelids in the life-cycle of ixodid ticks and transmission cycles of four tick-borne pathogens
Role of mustelids in the life-cycle of ixodid ticks and transmission cycles of four tick-borne pathogens
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Role of mustelids in the life-cycle of ixodid ticks and transmission cycles of four tick-borne pathogens

Hofmeester, Tim R ; Krawczyk, Aleksandra I ; van Leeuwen, Arieke Docters ; Fonville, Manoj ; Montizaan, Margriet G E ; van den Berge, Koen ; Gouwy, Jan ; Ruyts, Sanne C ; Verheyen, Kris ; Sprong, Hein

Parasites & vectors, 2018-11, Vol.11 (1), p.600-600, Article 600 [Periódico revisado por pares]

England: BioMed Central

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4
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
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Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Van den Berge, Koen ; Perraudeau, Fanny ; Soneson, Charlotte ; Love, Michael I ; Risso, Davide ; Vert, Jean-Philippe ; Robinson, Mark D ; Dudoit, Sandrine ; Clement, Lieven

Genome Biology, 2018-02, Vol.19 (1), p.24-24, Article 24 [Periódico revisado por pares]

England: BioMed Central

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5
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
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stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Van den Berge, Koen ; Soneson, Charlotte ; Robinson, Mark D ; Clement, Lieven

Genome Biology, 2017-08, Vol.18 (1), p.151-151, Article 151 [Periódico revisado por pares]

England: BioMed Central

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6
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
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Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

Brann, David H ; Tsukahara, Tatsuya ; Weinreb, Caleb ; Lipovsek, Marcela ; Van den Berge, Koen ; Gong, Boying ; Chance, Rebecca ; Macaulay, Iain C ; Chou, Hsin-Jung ; Fletcher, Russell B ; Das, Diya ; Street, Kelly ; de Bezieux, Hector Roux ; Choi, Yoon-Gi ; Risso, Davide ; Dudoit, Sandrine ; Purdom, Elizabeth ; Mill, Jonathan ; Hachem, Ralph Abi ; Matsunami, Hiroaki ; Logan, Darren W ; Goldstein, Bradley J ; Grubb, Matthew S ; Ngai, John ; Datta, Sandeep Robert

Science advances, 2020-07, Vol.6 (31) [Periódico revisado por pares]

United States: American Association for the Advancement of Science

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7
Trajectory inference across multiple conditions with condiments
Trajectory inference across multiple conditions with condiments
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Trajectory inference across multiple conditions with condiments

Roux de Bézieux, Hector ; Van den Berge, Koen ; Street, Kelly ; Dudoit, Sandrine

Nature communications, 2024-01, Vol.15 (1), p.833-833, Article 833 [Periódico revisado por pares]

England: Nature Publishing Group

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8
Improving replicability in single-cell RNA-Seq cell type discovery with Dune
Improving replicability in single-cell RNA-Seq cell type discovery with Dune
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Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Roux de Bézieux, Hector ; Street, Kelly ; Fischer, Stephan ; Van den Berge, Koen ; Chance, Rebecca ; Risso, Davide ; Gillis, Jesse ; Ngai, John ; Purdom, Elizabeth ; Dudoit, Sandrine

BMC bioinformatics, 2024-05, Vol.25 (1), p.198-198, Article 198 [Periódico revisado por pares]

England: BioMed Central Ltd

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9
Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
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Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

Bilcke, Gust ; Van den Berge, Koen ; De Decker, Sam ; Bonneure, Eli ; Poulsen, Nicole ; Bulankova, Petra ; Osuna-Cruz, Cristina Maria ; Dickenson, Jack ; Sabbe, Koen ; Pohnert, Georg ; Vandepoele, Klaas ; Mangelinckx, Sven ; Clement, Lieven ; De Veylder, Lieven ; Vyverman, Wim

The ISME Journal, 2021-02, Vol.15 (2), p.562-576 [Periódico revisado por pares]

England: Nature Publishing Group

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10
Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
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Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline

Pinseel, Eveline ; Nakov, Teofil ; Van den Berge, Koen ; Downey, Kala M ; Judy, Kathryn J ; Kourtchenko, Olga ; Kremp, Anke ; Ruck, Elizabeth C ; Sjöqvist, Conny ; Töpel, Mats ; Godhe, Anna ; Alverson, Andrew J

The ISME Journal, 2022-07, Vol.16 (7), p.1776-1787 [Periódico revisado por pares]

England: Nature Publishing Group

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