Zobrazeno 1 - 10
of 71
pro vyhledávání: '"Erik, Garrison"'
Publikováno v:
STAR Protocols, Vol 5, Iss 2, Pp 102974- (2024)
Summary: De novo genome assemblies are common tools for examining novel biological phenomena in non-model organisms. Here, we present a protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies. We describe st
Externí odkaz:
https://doaj.org/article/10a3372f5e72476b9c9f9ee364953e9e
Autor:
Noé Cochetel, Andrea Minio, Andrea Guarracino, Jadran F. Garcia, Rosa Figueroa-Balderas, Mélanie Massonnet, Takao Kasuga, Jason P. Londo, Erik Garrison, Brandon S. Gaut, Dario Cantu
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-31 (2023)
Abstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated culti
Externí odkaz:
https://doaj.org/article/84eb690b79804b74a3c49bd82f60a7ed
Autor:
Zuyu Yang, Andrea Guarracino, Patrick J. Biggs, Michael A. Black, Nuzla Ismail, Jana Renee Wold, Tony R. Merriman, Pjotr Prins, Erik Garrison, Joep de Ligt
Publikováno v:
Frontiers in Genetics, Vol 14 (2023)
Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies
Externí odkaz:
https://doaj.org/article/ceef009a36e442af8b7829bafeada4dd
Autor:
Christof C. Smith, Kelly S. Olsen, Kaylee M. Gentry, Maria Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric Routh, Julia Kodysh, Timothy O’Donnell, Carsten Haber, Kirsten Heiss, Volker Stadler, Erik Garrison, Adam M. Sandor, Jenny P. Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark Heise, Benjamin G. Vincent, Alex Rubinsteyn
Publikováno v:
Genome Medicine, Vol 13, Iss 1, Pp 1-23 (2021)
Abstract Background Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cell
Externí odkaz:
https://doaj.org/article/1bd99e7646cd4b7097c6d90976a022a0
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 5, p e1009123 (2022)
Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies-as well as in somatic and germline mutation studies. The VCF format can represent single nu
Externí odkaz:
https://doaj.org/article/3ae05fe830ed411c84fe85dcbdd6247b
Autor:
Chen-Shan Chin, Justin Wagner, Qiandong Zeng, Erik Garrison, Shilpa Garg, Arkarachai Fungtammasan, Mikko Rautiainen, Sergey Aganezov, Melanie Kirsche, Samantha Zarate, Michael C. Schatz, Chunlin Xiao, William J. Rowell, Charles Markello, Jesse Farek, Fritz J. Sedlazeck, Vikas Bansal, Byunggil Yoo, Neil Miller, Xin Zhou, Andrew Carroll, Alvaro Martinez Barrio, Marc Salit, Tobias Marschall, Alexander T. Dilthey, Justin M. Zook
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-9 (2020)
Accurate, phased assemblies are a key tool in understanding the human genome, particularly in highly polymorphic regions like the medically important MHC. Here the authors provide an assembly-based benchmark for this difficult-to-characterize region.
Externí odkaz:
https://doaj.org/article/5e9e6d5734354b4a86ef752be8c0d26e
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-18 (2020)
Abstract Background During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutate
Externí odkaz:
https://doaj.org/article/1f23a98dfc07467784e8132bf24eb589
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
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 9, p e1009444 (2021)
Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrenc
Externí odkaz:
https://doaj.org/article/a139b8b3383047a48810a794b90b50ba
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