Zobrazeno 1 - 10
of 271
pro vyhledávání: '"Michael C. Schatz"'
Autor:
Xiangyu Yang, Xuankai Wang, Yawen Zou, Shilong Zhang, Manying Xia, Lianting Fu, Mitchell R. Vollger, Nae-Chyun Chen, Dylan J. Taylor, William T. Harvey, Glennis A. Logsdon, Dan Meng, Junfeng Shi, Rajiv C. McCoy, Michael C. Schatz, Weidong Li, Evan E. Eichler, Qing Lu, Yafei Mao
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-25 (2023)
Abstract Background The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other c
Externí odkaz:
https://doaj.org/article/be3f60bafc5d407cb3b698c836d7e9e0
Autor:
Katrien M. Devos, Peng Qi, Bochra A. Bahri, Davis M. Gimode, Katharine Jenike, Samuel J. Manthi, Dagnachew Lule, Thomas Lux, Liliam Martinez-Bello, Thomas H. Pendergast, Chris Plott, Dipnarayan Saha, Gurjot S. Sidhu, Avinash Sreedasyam, Xuewen Wang, Hao Wang, Hallie Wright, Jianxin Zhao, Santosh Deshpande, Santie de Villiers, Mathews M. Dida, Jane Grimwood, Jerry Jenkins, John Lovell, Klaus F. X. Mayer, Emmarold E. Mneney, Henry F. Ojulong, Michael C. Schatz, Jeremy Schmutz, Bo Song, Kassahun Tesfaye, Damaris A. Odeny
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-15 (2023)
Abstract Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qu
Externí odkaz:
https://doaj.org/article/ab78a9fd968d482eb132fa249a468bd2
Autor:
Aysam Guerler, Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-13 (2023)
Abstract Background Protein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a pu
Externí odkaz:
https://doaj.org/article/02770213d40246049a08d1048a98d4a6
Autor:
Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, Katie Jenike, Shujun Ou, Sergey Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz, Sebastian Soyk
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-19 (2022)
Abstract Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we establish chromosome-scale refer
Externí odkaz:
https://doaj.org/article/979ad619c3bc4354bfad9c39f34c9d5f
Autor:
Arun Das, Michael C. Schatz
Publikováno v:
BMC Bioinformatics, Vol 23, Iss 1, Pp 1-23 (2022)
Abstract Background In modern sequencing experiments, quickly and accurately identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from one of potentially many members of a community, it can be important to id
Externí odkaz:
https://doaj.org/article/4863253d5464448d8c1fc312bfd8f73d
Autor:
Martin Hunt, Brice Letcher, Kerri M. Malone, Giang Nguyen, Michael B. Hall, Rachel M. Colquhoun, Leandro Lima, Michael C. Schatz, Srividya Ramakrishnan, CRyPTIC consortium, Zamin Iqbal
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-23 (2022)
Abstract There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 sample
Externí odkaz:
https://doaj.org/article/113d5df19a8e44b995c6088b7988a543
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
Autor:
Anton Nekrutenko, Michael C. Schatz
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-4 (2020)
Externí odkaz:
https://doaj.org/article/424b1bb9f3344c4d8ad198f4677711ae
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)
Prior to genome assembly, the raw sequencing reads must be analyzed for assessment of major genome characteristics such as genome size, heterozygosity, and repetitiveness. For this purpose, the authors introduce GenomeScope 2.0, an extension of Genom
Externí odkaz:
https://doaj.org/article/bb7ec6c178e2449d9f0806ad2d30d2eb
Autor:
Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L. Grossman, Ira M. Hall, Kasper D. Hansen, Jonathan Lawson, Jeffrey T. Leek, Anne O’Donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D. O’Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J. Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet, Alexander Baumann, Andrew Rula, Anton Kovalsy, Clare Bernard, Derek Caetano-Anollés, Geraldine A. Van der Auwera, Justin Canas, Kaan Yuksel, Kate Herman, M. Morgan Taylor, Marianie Simeon, Michael Baumann, Qi Wang, Robert Title, Ruchi Munshi, Sushma Chaluvadi, Valerie Reeves, William Disman, Salin Thomas, Allie Hajian, Elizabeth Kiernan, Namrata Gupta, Trish Vosburg, Ludwig Geistlinger, Marcel Ramos, Sehyun Oh, Dave Rogers, Frances McDade, Mim Hastie, Nitesh Turaga, Alexander Ostrovsky, Alexandru Mahmoud, Dannon Baker, Dave Clements, Katherine E.L. Cox, Keith Suderman, Nataliya Kucher, Sergey Golitsynskiy, Samantha Zarate, Sarah J. Wheelan, Kai Kammers, Ana Stevens, Carolyn Hutter, Christopher Wellington, Elena M. Ghanaim, Ken L. Wiley, Jr., Shurjo K. Sen, Valentina Di Francesco, Deni s Yuen, Brian Walsh, Luke Sargent, Vahid Jalili, John Chilton, Lori Shepherd, B.J. Stubbs, Ash O’Farrell, Benton A. Vizzier, Jr., Charles Overbeck, Charles Reid, David Charles Steinberg, Elizabeth A. Sheets, Julian Lucas, Lon Blauvelt, Louise Cabansay, Noah Warren, Brian Hannafious, Tim Harris, Radhika Reddy, Eric Torstenson, M. Katie Banasiewicz, Haley J. Abel, Jason Walker
Publikováno v:
Cell Genomics, Vol 2, Iss 1, Pp 100085- (2022)
Summary: The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, managemen
Externí odkaz:
https://doaj.org/article/95ac1623e901491c821d128f529da364