A scalable SCENIC workflow for single-cell gene regulatory network analysis von Van de Sande, Bram, Flerin, Christopher, Davie, Kristofer, De Waegeneer, Maxime, Hulselmans, Gert, Aibar, Sara, Seurinck, Ruth, Saelens, Wouter, Cannoodt, Robrecht, Rouchon, Quentin, Verbeiren, Toni, De Maeyer, Dries, Reumers, Joke, Saeys, Yvan, Aerts, Stein

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Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations von Lin, Yao-Cheng, Boone, Morgane, Meuris, Leander, Lemmens, Irma, Van Roy, Nadine, Soete, Arne, Reumers, Joke, Moisse, Matthieu, Plaisance, Stéphane, Drmanac, Radoje, Chen, Jason, Speleman, Frank, Lambrechts, Diether, Van de Peer, Yves, Tavernier, Jan, Callewaert, Nico

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Exploring the sequence determinants of amyloid structure using position-specific scoring matrices von Maurer-Stroh, Sebastian, Debulpaep, Maja, Kuemmerer, Nico, de la Paz, Manuela Lopez, Martins, Ivo Cristiano, Reumers, Joke, Morris, Kyle L, Copland, Alastair, Serpell, Louise, Serrano, Luis, Schymkowitz, Joost W H, Rousseau, Frederic

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Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce von Decap, Dries, Reumers, Joke, Herzeel, Charlotte, Costanza, Pascal, Fostier, Jan

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Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq von Mylka, Viacheslav, Matetovici, Irina, Poovathingal, Suresh, Aerts, Jeroen, Vandamme, Niels, Seurinck, Ruth, Verstaen, Kevin, Hulselmans, Gert, Van den Hoecke, Silvie, Scheyltjens, Isabelle, Movahedi, Kiavash, Wils, Hans, Reumers, Joke, Van Houdt, Jeroen, Aerts, Stein, Saeys, Yvan

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Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing von Reumers, Joke, De Rijk, Peter, Zhao, Hui, Liekens, Anthony, Smeets, Dominiek, Cleary, John, Van Loo, Peter, Van Den Bossche, Maarten, Catthoor, Kirsten, Sabbe, Bernard, Despierre, Evelyn, Vergote, Ignace, Hilbush, Brian, Lambrechts, Diether, Del-Favero, Jurgen

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elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling von Herzeel, Charlotte, Costanza, Pascal, Decap, Dries, Fostier, Jan, Reumers, Joke

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VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials von Lambrechts, Diether, Prof, Claes, Bart, MSc, Delmar, Paul, PhD, Reumers, Joke, PhD, Mazzone, Massimiliano, Prof, Yesilyurt, Betül T, MSc, Devlieger, Roland, Prof, Verslype, Chris, Prof, Tejpar, Sabine, Prof, Wildiers, Hans, Prof, de Haas, Sanne, PhD, Carmeliet, Peter, Prof, Scherer, Stefan J, MD, Van Cutsem, Eric, Prof

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Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks von Zhao, Hui, Thienpont, Bernard, Yesilyurt, Betül Tuba, Moisse, Matthieu, Reumers, Joke, Coenegrachts, Lieve, Sagaert, Xavier, Schrauwen, Stefanie, Smeets, Dominiek, Matthijs, Gert, Aerts, Stein, Cools, Jan, Metcalf, Alex, Spurdle, Amanda, Amant, Frederic, Lambrechts, Diether

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PepX: a structural database of non-redundant protein-peptide complexes von Vanhee, Peter, Reumers, Joke, Stricher, Francois, Baeten, Lies, Serrano, Luis, Schymkowitz, Joost, Rousseau, Frederic

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VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering von Verbist, Bie M P, Thys, Kim, Reumers, Joke, Wetzels, Yves, Van der Borght, Koen, Talloen, Willem, Aerssens, Jeroen, Clement, Lieven, Thas, Olivier

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Efficiency of whole genome amplification of single circulating tumor cells enriched by CellSearch and sorted by FACS von Swennenhuis, Joost F, Reumers, Joke, Thys, Kim, Aerssens, Jeroen, Terstappen, Leon Wmm

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Genetically Engineered iPSC-Derived FTDP-17 MAPT Neurons Display Mutation-Specific Neurodegenerative and Neurodevelopmental Phenotypes von Verheyen, An, Diels, Annick, Reumers, Joke, Van Hoorde, Kirsten, Van den Wyngaert, Ilse, van Outryve d’Ydewalle, Constantin, De Bondt, An, Kuijlaars, Jacobine, De Muynck, Louis, De Hoogt, Ronald, Bretteville, Alexis, Jaensch, Steffen, Buist, Arjan, Cabrera-Socorro, Alfredo, Wray, Selina, Ebneth, Andreas, Roevens, Peter, Royaux, Ines, Peeters, Pieter J.

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An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins von De Baets, Greet, Reumers, Joke, Delgado Blanco, Javier, Dopazo, Joaquin, Schymkowitz, Joost, Rousseau, Frederic

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Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks von Kalender Atak, Zeynep, Imrichova, Hana, Svetlichnyy, Dmitry, Hulselmans, Gert, Christiaens, Valerie, Reumers, Joke, Ceulemans, Hugo, Aerts, Stein

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A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays von Van Moerbeke, Marijke, Kasim, Adetayo, Talloen, Willem, Reumers, Joke, Göhlmann, Hinrick W H, Shkedy, Ziv

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Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations von Reumers, Joke, Schymkowitz, Joost, Rousseau, Fréderic

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Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population von Moens, Lotte N, De Rijk, Peter, Reumers, Joke, Van den Bossche, Maarten J A, Glassee, Wim, De Zutter, Sonia, Lenaerts, An-Sofie, Nordin, Annelie, Nilsson, Lars-Göran, Medina Castello, Ignacio, Norrback, Karl-Fredrik, Goossens, Dirk, Van Steen, Kristel, Adolfsson, Rolf, Del-Favero, Jurgen

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Halvade: scalable sequence analysis with MapReduce von Decap, Dries, Reumers, Joke, Herzeel, Charlotte, Costanza, Pascal, Fostier, Jan

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Reconstruction of protein backbones from the BriX collection of canonical protein fragments von Baeten, Lies, Reumers, Joke, Tur, Vicente, Stricher, François, Lenaerts, Tom, Serrano, Luis, Rousseau, Frederic, Schymkowitz, Joost

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