Trajectory-based differential expression analysis for single-cell sequencing data von Van den Berge, Koen, Roux de Bézieux, Hector, Street, Kelly, Saelens, Wouter, Cannoodt, Robrecht, Saeys, Yvan, Dudoit, Sandrine, Clement, Lieven

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

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

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

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Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications von Van den Berge, Koen, Perraudeau, Fanny, Soneson, Charlotte, Love, Michael I, Risso, Davide, Vert, Jean-Philippe, Robinson, Mark D, Dudoit, Sandrine, Clement, Lieven

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Trajectory inference across multiple conditions with condiments von Roux de Bézieux, Hector, Van den Berge, Koen, Street, Kelly, Dudoit, Sandrine

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

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

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

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Improving replicability in single-cell RNA-Seq cell type discovery with Dune von Roux de Bézieux, Hector, Street, Kelly, Fischer, Stephan, Van den Berge, Koen, Chance, Rebecca, Risso, Davide, Gillis, Jesse, Ngai, John, Purdom, Elizabeth, Dudoit, Sandrine

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RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis von Van den Berge, Koen, Hembach, Katharina M, Soneson, Charlotte, Tiberi, Simone, Clement, Lieven, Love, Michael I, Patro, Rob, Robinson, Mark D

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Altering the Sex Pheromone Cyclo(l-Pro-l-Pro) of the Diatom Seminavis robusta towards a Chemical Probe von Bonneure, Eli, De Baets, Amber, De Decker, Sam, Van den Berge, Koen, Clement, Lieven, Vyverman, Wim, Mangelinckx, Sven

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Shifting dietary habits linked with contrasting population trends of two sympatric mustelids (Martes foina and Mustela putorius) over 16 years von Eeraerts, Maxime, Verschelde, Pieter, Gouwy, Jan, Van Den Berge, Sanne, Van Den Berge, Koen

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Distinctive Growth and Transcriptional Changes of the Diatom Seminavis robusta in Response to Quorum Sensing Related Compounds von Stock, Frederike, Bilcke, Gust, De Decker, Sam, Osuna-Cruz, Cristina Maria, Van den Berge, Koen, Vancaester, Emmelien, De Veylder, Lieven, Vandepoele, Klaas, Mangelinckx, Sven, Vyverman, Wim

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Prevalence of Fox Tapeworm in Invasive Muskrats in Flanders (North Belgium) von Cartuyvels, Emma, Adriaens, Tim, Baert, Kristof, Huysentruyt, Frank, Van Den Berge, Koen

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Training of Ecological Detection Dogs for Wolf Scat (Canis lupus) von VERVAECKE, Hilde, VAN KRUNKELSVEN, Ellen, VAN DEN BERGE, Koen

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Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids von Derycke, Sofie, Kéver, Loic, Herten, Koen, Van den Berge, Koen, Van Steenberge, Maarten, Van Houdt, Jeroen, Clement, Lieven, Poncin, Pascal, Parmentier, Eric, Verheyen, Erik

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A database of threat statuses and life-history traits of Red List species in Flanders (northern Belgium) von Maes, Dirk, Brosens, Dimitri, T'jollyn, Filiep, Desmet, Peter, Piesschaert, Frederic, Van Hoey, Stijn, Adriaens, Tim, Dekoninck, Wouter, Devos, Koen, Lock, Koen, Onkelinx, Thierry, Packet, Jo, Speybroeck, Jeroen, Thomaes, Arno, Van Den Berge, Koen, Van Landuyt, Wouter, Verreycken, Hugo

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A Guide to Trajectory Inference and RNA Velocity von Weiler, Philipp, Van den Berge, Koen, Street, Kelly, Tiberi, Simone

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Hierarchical Community Detection by Recursive Partitioning von Li, Tianxi, Lei, Lihua, Bhattacharyya, Sharmodeep, Van den Berge, Koen, Sarkar, Purnamrita, Bickel, Peter J., Levina, Elizaveta

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