Zobrazeno 1 - 10
of 24
pro vyhledávání: '"Maria Nattestad"'
Autor:
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John Gorzynski, Sneha Goenka, Euan A. Ashley, Miten Jain, Karen H. Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)
Abstract Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences
Externí odkaz:
https://doaj.org/article/9736ff93823742a28239875aa6195f95
Publikováno v:
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-8 (2020)
Abstract Background Genome-wide association studies (GWAS) are typically visualized using a two-dimensional Manhattan plot, displaying chromosomal location of SNPs along the x-axis and the negative log-10 of their p-value on the y-axis. This traditio
Externí odkaz:
https://doaj.org/article/8ee2dfd804554d94baa5edc263806b85
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:
Sneha D. Goenka, John E. Gorzynski, Kishwar Shafin, Dianna G. Fisk, Trevor Pesout, Tanner D. Jensen, Jean Monlong, Pi-Chuan Chang, Gunjan Baid, Jonathan A. Bernstein, Jeffrey W. Christle, Karen P. Dalton, Daniel R. Garalde, Megan E. Grove, Joseph Guillory, Alexey Kolesnikov, Maria Nattestad, Maura R. Z. Ruzhnikov, Mehrzad Samadi, Ankit Sethia, Elizabeth Spiteri, Christopher J. Wright, Katherine Xiong, Tong Zhu, Miten Jain, Fritz J. Sedlazeck, Andrew Carroll, Benedict Paten, Euan A. Ashley
Publikováno v:
Nature Biotechnology. 40:1035-1041
Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nano
Autor:
Gunjan Baid, Daniel E. Cook, Kishwar Shafin, Taedong Yun, Felipe Llinares-López, Quentin Berthet, Anastasiya Belyaeva, Armin Töpfer, Aaron M. Wenger, William J. Rowell, Howard Yang, Alexey Kolesnikov, Waleed Ammar, Jean-Philippe Vert, Ashish Vaswani, Cory Y. McLean, Maria Nattestad, Pi-Chuan Chang, Andrew Carroll
Publikováno v:
Nature Biotechnology.
Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10-25 kilobases), accurate 'HiFi' reads by combining serial observations of a DNA molecule into a consensus sequence. The standard approach to consensus genera
Autor:
Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily Boja, Ezekiel J. Maier, Omar Serang, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz-Barrera, Luis A. Rubio-Rodríguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, ChouXian Ma, LinQi Tang, YuanPing Du, ShaoWei Zhang, Jordi Morata, Raúl Tonda, Genís Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Gungor Budak, Kübra Narcı, Elif Arslan, Richard Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Mian Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, Justin M. Zook
Publikováno v:
Cell genomics. 2(5)
The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for
Autor:
John E. Gorzynski, Sneha D. Goenka, Kishwar Shafin, Tanner D. Jensen, Dianna G. Fisk, Megan E. Grove, Elizabeth Spiteri, Trevor Pesout, Jean Monlong, Gunjan Baid, Jonathan A. Bernstein, Scott Ceresnak, Pi-Chuan Chang, Jeffrey W. Christle, Henry Chubb, Karen P. Dalton, Kyla Dunn, Daniel R. Garalde, Joseph Guillory, Joshua W. Knowles, Alexey Kolesnikov, Michael Ma, Tia Moscarello, Maria Nattestad, Marco Perez, Maura R.Z. Ruzhnikov, Mehrzad Samadi, Ankit Setia, Chris Wright, Courtney J. Wusthoff, Katherine Xiong, Tong Zhu, Miten Jain, Fritz J. Sedlazeck, Andrew Carroll, Benedict Paten, Euan A. Ashley
Publikováno v:
New England Journal of Medicine. 386:700-702
Publikováno v:
Mathematics Magazine. 94:83-98
Disclaimer This article was written prior to the COVID-19 pandemic, and it is in no way meant to replace or supersede the advice of expert epidemiologists. We are grateful to those in the scientifi...
Autor:
Andrew Carroll, Pi-Chuan Chang, Sidharth Goel, Howard Yang, Taedong Yun, Alexey Kolesnikov, Gunjan Baid, Maria Nattestad, Cory Y. McLean
Every human inherits one copy of the genome from their mother and another from their father. Parental inheritance helps us understand the transmission of traits and genetic diseases, which often involve de novo variants and rare recessive alleles. He
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0f2bf16c653dfd975a3fe1a8686554e4
https://doi.org/10.1101/2021.04.05.438434
https://doi.org/10.1101/2021.04.05.438434
Autor:
Maria Nattestad, Kishwar Shafin, Pi-Chuan Chang, Miten Jain, Gunjan Baid, Andrew Carroll, Jordan M. Eizenga, Mikhail Kolmogorov, Benedict Paten, Paolo Carnevali, Trevor Pesout, Karen H. Miga, Sidharth Goel, Alexey Kolesnikov
Publikováno v:
Nature methods, vol 18, iss 11
Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read-based phasing. Third-generation nanopore sequence data have demonst