T
Tobias Marschall
Researcher at University of Düsseldorf
Publications - 139
Citations - 8020
Tobias Marschall is an academic researcher from University of Düsseldorf. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 30, co-authored 116 publications receiving 4722 citations. Previous affiliations of Tobias Marschall include Max Planck Society & Brown University.
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Journal ArticleDOI
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M. Wenger,Paul Peluso,William J Rowell,Pi-Chuan Chang,Richard Hall,Gregory T. Concepcion,Jana Ebler,Arkarachai Fungtammasan,Alexander Kolesnikov,Nathan D. Olson,Armin Töpfer,Michael Alonge,Medhat Mahmoud,Yufeng Qian,Chen-Shan Chin,Adam M. Phillippy,Michael C. Schatz,Gene Myers,Mark A. DePristo,Jue Ruan,Tobias Marschall,Tobias Marschall,Fritz J. Sedlazeck,Justin M. Zook,Heng Li,Sergey Koren,Andrew Carroll,David R. Rank,Michael W. Hunkapiller +28 more
TL;DR: The optimization of circular consensus sequencing (CCS) is reported to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb).
Journal ArticleDOI
Whole-genome sequence variation, population structure and demographic history of the Dutch population
Laurent C. Francioli,Androniki Menelaou,Sara L. Pulit,Freerk van Dijk,Pier Francesco Palamara,Clara C. Elbers,Pieter B. Neerincx,Kai Ye,Kai Ye,Victor Guryev,Wigard P. Kloosterman,Patrick Deelen,Abdel Abdellaoui,Elisabeth M. van Leeuwen,Mannis van Oven,Martijn Vermaat,Mingkun Li,Jeroen F. J. Laros,Lennart C. Karssen,Alexandros Kanterakis,Najaf Amin,Jouke-Jan Hottenga,Eric-Wubbo Lameijer,Mathijs Kattenberg,Martijn Dijkstra,Heorhiy Byelas,Jessica van Setten,Barbera D. C. van Schaik,Jan Bot,Isaac J. Nijman,Ivo Renkens,Tobias Marschall,Alexander Schönhuth,Jayne Y. Hehir-Kwa,Robert E. Handsaker,Robert E. Handsaker,Paz Polak,Mashaal Sohail,Mashaal Sohail,Dana Vuzman,Fereydoun Hormozdiari,David van Enckevort,Hailiang Mei,Vyacheslav Koval,Matthijs Moed,K. Joeri van der Velde,Fernando Rivadeneira,Fernando Rivadeneira,Fernando Rivadeneira,Karol Estrada,Carolina Medina-Gomez,Aaron Isaacs,Aaron Isaacs,Steven A. McCarroll,Marian Beekman,Anton J. M. de Craen,H. Eka D. Suchiman,Albert Hofman,Ben A. Oostra,André G. Uitterlinden,Gonneke Willemsen,Mathieu Platteel,Jan H. Veldink,Leonard H. van den Berg,Steven J. Pitts,Shobha Potluri,Purnima Sundar,David R. Cox,David R. Cox,Shamil R. Sunyaev,Johan T. den Dunnen,Mark Stoneking,Peter de Knijff,Manfred Kayser,Qibin Li,Yingrui Li,Yuanping Du,Ruoyan Chen,Hongzhi Cao,Ning Li,Sujie Cao,Jun Wang,Jasper A. Bovenberg,Itsik Pe'er,P. Eline Slagboom,Cornelia M. van Duijn,Dorret I. Boomsma,Gert-Jan B. van Ommen,Paul I.W. de Bakker,Paul I.W. de Bakker,Morris A. Swertz,Cisca Wijmenga +91 more
TL;DR: The Genome of the Netherlands (GoNL) Project is described, in which the whole genomes of 250 Dutch parent-offspring families were sequenced and a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions were constructed.
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
Multi-platform discovery of haplotype-resolved structural variation in human genomes
Mark Chaisson,Mark Chaisson,Ashley D. Sanders,Xuefang Zhao,Xuefang Zhao,Ankit Malhotra,David Porubsky,David Porubsky,Tobias Rausch,Eugene J. Gardner,Oscar L. Rodriguez,Li Guo,Ryan L. Collins,Xian Fan,Jia Wen,Robert E. Handsaker,Robert E. Handsaker,Susan Fairley,Zev N. Kronenberg,Xiangmeng Kong,Fereydoun Hormozdiari,Dillon Lee,Aaron M. Wenger,Alex Hastie,Danny Antaki,Thomas Anantharaman,Peter A. Audano,Harrison Brand,Stuart Cantsilieris,Han Cao,Eliza Cerveira,Chong Chen,Xintong Chen,Chen-Shan Chin,Zechen Chong,Nelson T. Chuang,Christine C. Lambert,Deanna M. Church,Laura Clarke,Andrew Farrell,Joey Flores,Timur R. Galeev,David U. Gorkin,David U. Gorkin,Madhusudan Gujral,Victor Guryev,William Haynes Heaton,Jonas Korlach,Sushant Kumar,Jee Young Kwon,Ernest T. Lam,Jong Eun Lee,Joyce V. Lee,Wan-Ping Lee,Sau Peng Lee,Shantao Li,Patrick Marks,Karine A. Viaud-Martinez,Sascha Meiers,Katherine M. Munson,Fabio C. P. Navarro,Bradley J. Nelson,Conor Nodzak,Amina Noor,Sofia Kyriazopoulou-Panagiotopoulou,Andy Wing Chun Pang,Yunjiang Qiu,Yunjiang Qiu,Gabriel Rosanio,Mallory Ryan,Adrian M. Stütz,Diana C.J. Spierings,Alistair Ward,Anne Marie E. Welch,Ming Xiao,Wei Xu,Chengsheng Zhang,Qihui Zhu,Xiangqun Zheng-Bradley,Ernesto Lowy,Sergei Yakneen,Steven A. McCarroll,Steven A. McCarroll,Goo Jun,Li Ding,Chong-Lek Koh,Bing Ren,Bing Ren,Paul Flicek,Ken Chen,Mark Gerstein,Pui-Yan Kwok,Peter M. Lansdorp,Peter M. Lansdorp,Peter M. Lansdorp,Gabor T. Marth,Jonathan Sebat,Xinghua Shi,Ali Bashir,Kai Ye,Scott E. Devine,Michael E. Talkowski,Michael E. Talkowski,Ryan E. Mills,Tobias Marschall,Jan O. Korbel,Evan E. Eichler,Charles Lee +107 more
TL;DR: A suite of long-read, short- read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms are applied to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner.
Journal ArticleDOI
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Kishwar Shafin,Trevor Pesout,Ryan Lorig-Roach,Marina Haukness,Hugh E. Olsen,Colleen M. Bosworth,Joel Armstrong,Kristof Tigyi,Nicholas Maurer,Sergey Koren,Fritz J. Sedlazeck,Tobias Marschall,Simon Mayes,Vania Costa,Justin M. Zook,Kelvin J. Liu,Duncan Kilburn,Melanie Sorensen,Katherine M. Munson,Mitchell R. Vollger,Jean Monlong,Erik Garrison,Evan E. Eichler,Evan E. Eichler,Sofie R. Salama,David Haussler,Richard E. Green,Mark Akeson,Adam M. Phillippy,Karen H. Miga,Paolo Carnevali,Miten Jain,Benedict Paten +32 more
TL;DR: High contiguity human genomes can be assembled de novo in 6 h using nanopore long-read sequences and the Shasta toolkit, and the assembly performance is compared to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed.