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

por Van den Berge, Koen, Soneson, Charlotte, Robinson, Mark D., Clement, Lieven
Publicado 2017

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

por Gilis, Jeroen, Vitting-Seerup, Kristoffer, Van den Berge, Koen, Clement, Lieven
Publicado 2022

Prevalence of Fox Tapeworm in Invasive Muskrats in Flanders (North Belgium)

por Cartuyvels, Emma, Adriaens, Tim, Baert, Kristof, Huysentruyt, Frank, Van Den Berge, Koen
Publicado 2022

Altering the Sex Pheromone Cyclo(l-Pro-l-Pro) of the Diatom Seminavis robusta towards a Chemical Probe

por Bonneure, Eli, De Baets, Amber, De Decker, Sam, Van den Berge, Koen, Clement, Lieven, Vyverman, Wim, Mangelinckx, Sven
Publicado 2021

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

por Van den Berge, Koen, Chou, Hsin-Jung, Roux de Bézieux, Hector, Street, Kelly, Risso, Davide, Ngai, John, Dudoit, Sandrine
Publicado 2022

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

por Van den Berge, Koen, Roux de Bézieux, Hector, Street, Kelly, Saelens, Wouter, Cannoodt, Robrecht, Saeys, Yvan, Dudoit, Sandrine, Clement, Lieven
Publicado 2020

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

por Van den Berge, Koen, Perraudeau, Fanny, Soneson, Charlotte, Love, Michael I., Risso, Davide, Vert, Jean-Philippe, Robinson, Mark D., Dudoit, Sandrine, Clement, Lieven
Publicado 2018

Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids

por Derycke, Sofie, Kéver, Loic, Herten, Koen, Van den Berge, Koen, Van Steenberge, Maarten, Van Houdt, Jeroen, Clement, Lieven, Poncin, Pascal, Parmentier, Eric, Verheyen, Erik
Publicado 2018

Polar lake microbiomes have distinct evolutionary histories

por Tytgat, Bjorn, Verleyen, Elie, Sweetlove, Maxime, Van den Berge, Koen, Pinseel, Eveline, Hodgson, Dominic A., Chown, Steven L., Sabbe, Koen, Wilmotte, Annick, Willems, Anne, Vyverman, Wim
Publicado 2023

Distinctive Growth and Transcriptional Changes of the Diatom Seminavis robusta in Response to Quorum Sensing Related Compounds

por 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
Publicado 2020

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

por 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
Publicado 2018

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

por 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.
Publicado 2022

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

por 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
Publicado 2020

A database of threat statuses and life-history traits of Red List species in Flanders (northern Belgium)

por 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
Publicado 2019

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

por Moeys, Sara, Frenkel, Johannes, Lembke, Christine, Gillard, Jeroen T. F., Devos, Valerie, Van den Berge, Koen, Bouillon, Barbara, Huysman, Marie J. J., De Decker, Sam, Scharf, Julia, Bones, Atle, Brembu, Tore, Winge, Per, Sabbe, Koen, Vuylsteke, Marnik, Clement, Lieven, De Veylder, Lieven, Pohnert, Georg, Vyverman, Wim
Publicado 2016

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

por Yao, Zizhen, Liu, Hanqing, Xie, Fangming, Fischer, Stephan, Adkins, Ricky S., Aldridge, Andrew I., Ament, Seth A., Bartlett, Anna, Behrens, M. Margarita, Van den Berge, Koen, Bertagnolli, Darren, de Bézieux, Hector Roux, Biancalani, Tommaso, Booeshaghi, A. Sina, Bravo, Héctor Corrada, Casper, Tamara, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Crichton, Kirsten, Crow, Megan, Dee, Nick, Dougherty, Elizabeth L., Doyle, Wayne I., Dudoit, Sandrine, Fang, Rongxin, Felix, Victor, Fong, Olivia, Giglio, Michelle, Goldy, Jeff, Hawrylycz, Mike, Herb, Brian R., Hertzano, Ronna, Hou, Xiaomeng, Hu, Qiwen, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, Li, Yang Eric, Lucero, Jacinta D., Luo, Chongyuan, Mahurkar, Anup, McMillen, Delissa, Nadaf, Naeem M., Nery, Joseph R., Nguyen, Thuc Nghi, Niu, Sheng-Yong, Ntranos, Vasilis, Orvis, Joshua, Osteen, Julia K., Pham, Thanh, Pinto-Duarte, Antonio, Poirion, Olivier, Preissl, Sebastian, Purdom, Elizabeth, Rimorin, Christine, Risso, Davide, Rivkin, Angeline C., Smith, Kimberly, Street, Kelly, Sulc, Josef, Svensson, Valentine, Tieu, Michael, Torkelson, Amy, Tung, Herman, Vaishnav, Eeshit Dhaval, Vanderburg, Charles R., van Velthoven, Cindy, Wang, Xinxin, White, Owen R., Huang, Z. Josh, Kharchenko, Peter V., Pachter, Lior, Ngai, John, Regev, Aviv, Tasic, Bosiljka, Welch, Joshua D., Gillis, Jesse, Macosko, Evan Z., Ren, Bing, Ecker, Joseph R., Zeng, Hongkui, Mukamel, Eran A.
Publicado 2021