Zobrazeno 1 - 10
of 34
pro vyhledávání: '"Jouni Sirén"'
Autor:
Glenn Hickey, David Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak, Benedict Paten
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-17 (2020)
Abstract Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging
Externí odkaz:
https://doaj.org/article/bda69e4492de4ec38ca24a5a09d571d9
Autor:
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten
Publikováno v:
Nature. 617:312-324
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the
Autor:
Xian Chang, Jouni Sirén, Erik Garrison, Jonas Andreas Sibbesen, Jordan M. Eizenga, Benedict Paten, Adam M. Novak
Publikováno v:
Nature Methods. 20:239-247
Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were chall
Autor:
Jouni Sirén, Benedict Paten
Publikováno v:
Bioinformatics (Oxford, England). 38(22)
MotivationPangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data sp
Publikováno v:
Bioinformatics
Motivation Graph representations of genomes are capable of expressing more genetic variation and can therefore better represent a population than standard linear genomes. However, due to the greater complexity of genome graphs relative to linear geno
Autor:
Jordan M. Eizenga, Benedict Paten, Eric T. Dawson, Shilpa Garg, William J. Jones, Jouni Sirén, Adam M. Novak, Glenn Hickey, Michael F. Lin, Charles Markello, Erik Garrison, Richard Durbin
Publikováno v:
Nature Biotechnology. 36:875-879
Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references represent only one version of each locus, ignoring variation in the population. Poor representation of an individual's genome sequence impacts re
Autor:
Giovanni Manzini, Jouni Sirén, Tamer Kahveci, Christina Boucher, Marco Oliva, Massimiliano Rossi, Travis Gagie
Publikováno v:
DCC
Large sequencing projects, such as GenomeTrakr and MetaSub, are updated frequently (sometimes daily, in the case of GenomeTrakr) with new data. Therefore, it is imperative that any data structure indexing such data supports efficient updates. Toward
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::714448d1063aa4d213829998afa40293
http://hdl.handle.net/11568/1119156
http://hdl.handle.net/11568/1119156
Autor:
Andrew Carroll, Stacey Gabriel, Stephen S. Rich, Jouni Sirén, Namrata Gupta, Charles Markello, Thomas W. Blackwell, Jean Monlong, Pi-Chuan Chang, Benedict Paten, Glenn Hickey, Kent D. Taylor, Jerome I. Rotter, Jordan M. Eizenga, Adam M. Novak, Aakrosh Ratan, Erik Garrison, Xian Chang, David Haussler, Jonas Andreas Sibbesen
We introduce Giraffe, a pangenome short read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe, part of the variation graph toolkit (vg)1, maps reads to thousands of human genomes at around the s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8960ce699cb65ce924e218b33df153e7
https://doi.org/10.1101/2020.12.04.412486
https://doi.org/10.1101/2020.12.04.412486
Autor:
Jordan M. Eizenga, Adam M. Novak, Jonas A. Sibbesen, Simon Heumos, Ali Ghaffaari, Glenn Hickey, Xian Chang, Josiah D. Seaman, Robin Rounthwaite, Jana Ebler, Mikko Rautiainen, Shilpa Garg, Benedict Paten, Tobias Marschall, Jouni Sirén, Erik Garrison
Publikováno v:
Annu Rev Genomics Hum Genet
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation desc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::42dc75116426015ddeb1bfcac6d1686d
https://europepmc.org/articles/PMC8006571/
https://europepmc.org/articles/PMC8006571/
Autor:
Wayne E. Clarke, Ilia Minkin, Yassine Souilmi, Shilpa Garg, Jouni Sirén, Arkarachai Fungtammasan, Medhat Mahmoud, Giuseppe Narzisi, Peter J. Bradbury, Ben Busby, Justin Wagner, Mikko Rautiainen, Gerard R. Lazo, Rajeeva Musunuri, Fritz J. Sedlazeck, Jean Monlong, Valerie A. Schneider, Erik Garrison, Xian Chang, Justin M. Zook, Bastien Llamas, Jonas Andreas Sibbesen, Allison A. Regier, Glenn Hickey, Evan Biederstedt, Toshiyuki T. Yokoyama, Sagayamary Sagayaradj, Lon Blauvelt, Qiandong Zeng, Peter A. Audano, Charles Markello, Alan Cleary, Benedict Paten, Adam M. Novak, Chen-Shan Chin, Michael F. Lin, Tobias Marschall, Jordan M. Eizenga, Travis Wrightsman, Jana Ebler
Publikováno v:
F1000Research
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for