S
Szymon M. Kielbasa
Researcher at Leiden University Medical Center
Publications - 93
Citations - 5171
Szymon M. Kielbasa is an academic researcher from Leiden University Medical Center. The author has contributed to research in topics: Gene & Promoter. The author has an hindex of 27, co-authored 84 publications receiving 3774 citations. Previous affiliations of Szymon M. Kielbasa include Humboldt University of Berlin & Loyola University Medical Center.
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Journal ArticleDOI
Adaptive seeds tame genomic sequence comparison.
TL;DR: LAST, the open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition, and guarantees that the number of matches increases linearly, instead of quadratically, with sequence length.
Journal ArticleDOI
Eleven grand challenges in single-cell data science
David Lähnemann,David Lähnemann,Johannes Köster,Johannes Köster,Ewa Szczurek,Davis J. McCarthy,Davis J. McCarthy,Stephanie C. Hicks,Mark D. Robinson,Catalina A. Vallejos,Catalina A. Vallejos,Kieran R Campbell,Kieran R Campbell,Niko Beerenwinkel,Niko Beerenwinkel,Ahmed Mahfouz,Ahmed Mahfouz,Luca Pinello,Luca Pinello,Pavel Skums,Alexandros Stamatakis,Alexandros Stamatakis,Camille Stephan Otto Attolini,Samuel Aparicio,Samuel Aparicio,Jasmijn A. Baaijens,Marleen Balvert,Marleen Balvert,Buys de Barbanson,Antonio Cappuccio,Giacomo Corleone,Bas E. Dutilh,Bas E. Dutilh,Maria Florescu,Victor Guryev,Rens Holmer,Katharina Jahn,Katharina Jahn,Thamar Jessurun Lobo,Emma M. Keizer,Indu Khatri,Szymon M. Kielbasa,Jan O. Korbel,Alexey M. Kozlov,Tzu Hao Kuo,Boudewijn P. F. Lelieveldt,Boudewijn P. F. Lelieveldt,Ion I. Mandoiu,John C. Marioni,John C. Marioni,John C. Marioni,Tobias Marschall,Tobias Marschall,Felix Mölder,Amir Niknejad,Lukasz Raczkowski,Marcel J. T. Reinders,Marcel J. T. Reinders,Jeroen de Ridder,Antoine-Emmanuel Saliba,Antonios Somarakis,Oliver Stegle,Oliver Stegle,Fabian J. Theis,Huan Yang,Alexander Zelikovsky,Alexander Zelikovsky,Alice C. McHardy,Benjamin J. Raphael,Sohrab P. Shah,Alexander Schönhuth,Alexander Schönhuth +71 more
TL;DR: This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years in single-cell data science.
Journal ArticleDOI
Disease variants alter transcription factor levels and methylation of their binding sites.
Marc Jan Bonder,René Luijk,Daria V. Zhernakova,Matthijs Moed,Patrick Deelen,Martijn Vermaat,Maarten van Iterson,Freerk van Dijk,Michiel van Galen,Jan Bot,Roderick C. Slieker,P. Mila Jhamai,Michael Verbiest,H. Eka D. Suchiman,Marijn Verkerk,Ruud van der Breggen,Jeroen van Rooij,Nico Lakenberg,Wibowo Arindrarto,Szymon M. Kielbasa,Iris Jonkers,Peter van ‘t Hof,Irene Nooren,Marian Beekman,Joris Deelen,Diana van Heemst,Alexandra Zhernakova,Ettje F. Tigchelaar,Morris A. Swertz,Albert Hofman,André G. Uitterlinden,René Pool,Jenny van Dongen,Jouke J. Hottenga,Coen D.A. Stehouwer,Carla J.H. van der Kallen,Casper G. Schalkwijk,Leonard H. van den Berg,Erik W. van Zwet,Hailiang Mei,Yang Li,Mathieu Lemire,Thomas J. Hudson,Thomas J. Hudson,P. Eline Slagboom,Cisca Wijmenga,Jan H. Veldink,Marleen M.J. van Greevenbroek,Cornelia M. van Duijn,Dorret I. Boomsma,Aaron Isaacs,Aaron Isaacs,Rick Jansen,Joyce B. J. van Meurs,Peter A C 't Hoen,Lude Franke,Bastiaan T. Heijmans +56 more
TL;DR: It is shown that disease-associated variants have widespread effects on DNA methylation in trans that likely reflect differential occupancy of trans binding sites by cis-regulated transcription factors.
Journal ArticleDOI
Identification of context-dependent expression quantitative trait loci in whole blood
Daria V. Zhernakova,Patrick Deelen,Martijn Vermaat,Maarten van Iterson,Michiel van Galen,Wibowo Arindrarto,Peter van ‘t Hof,Hailiang Mei,Freerk van Dijk,Harm-Jan Westra,Harm-Jan Westra,Marc Jan Bonder,Jeroen van Rooij,Marijn Verkerk,P. Mila Jhamai,Matthijs Moed,Szymon M. Kielbasa,Jan Bot,Irene Nooren,René Pool,Jenny van Dongen,Jouke J. Hottenga,Coen D.A. Stehouwer,Carla J.H. van der Kallen,Casper G. Schalkwijk,Alexandra Zhernakova,Yang I. Li,Ettje F. Tigchelaar,Niek de Klein,Marian Beekman,Joris Deelen,Diana van Heemst,Leonard H. van den Berg,Albert Hofman,André G. Uitterlinden,Marleen M.J. van Greevenbroek,Jan H. Veldink,Dorret I. Boomsma,Cornelia M. van Duijn,Cisca Wijmenga,P. Eline Slagboom,Morris A. Swertz,Aaron Isaacs,Aaron Isaacs,Joyce B. J. van Meurs,Rick Jansen,Bastiaan T. Heijmans,Peter A C 't Hoen,Lude Franke +48 more
TL;DR: This work generated peripheral blood RNA–seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers.
Journal ArticleDOI
Regulation of Clock-Controlled Genes in Mammals.
Katarzyna Bozek,Angela Relógio,Szymon M. Kielbasa,Markus Heine,Christof Dame,Achim Kramer,Hanspeter Herzel +6 more
TL;DR: A large scale analysis of the CCG promoters reveals the complexity and extensiveness of the circadian regulation in mammals and points to connections of the calendar clock to other functional systems including metabolism, endocrine regulation and pharmacokinetics.