Zobrazeno 1 - 10
of 20
pro vyhledávání: '"MARC SALIT"'
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:
Lesley M Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M Watson, Christos Proukakis, Wayne E Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza E Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M Wenger, Marc Salit, Justin M Zook
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 6, p e1007933 (2020)
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more c
Externí odkaz:
https://doaj.org/article/b08f9ccca37e4727afc897d6fa521024
Autor:
P. Scott Pine, Steven P. Lund, Sanford A. Stass, Debra Kukuruga, Feng Jiang, Lynn Sorbara, Sudhir Srivastava, Marc Salit
Publikováno v:
BMC Biotechnology, Vol 18, Iss 1, Pp 1-14 (2018)
Abstract Background We demonstrate the feasibility of creating a pair of reference samples to be used as surrogates for clinical samples measured in either a research or clinical laboratory setting. The reference sample paradigm presented and evaluat
Externí odkaz:
https://doaj.org/article/c1985298d13648b2a7a1a095e1ca1f0f
Publikováno v:
PLoS ONE, Vol 7, Iss 7, p e41356 (2012)
While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cau
Externí odkaz:
https://doaj.org/article/a35ecb62c8ca4ec2a8ace6b4145a01de
Autor:
Tim Mercer, Neil Almond, Michael A. Crone, Patrick S. G. Chain, Alina Deshpande, Deepa Eveleigh, Paul Freemont, Sebastien Fuchs, Russell Garlick, Jim Huggett, Martin Kammel, Po-E Li, Mojca Milavec, Elizabeth M. Marlowe, Denise M. O’Sullivan, Mark Page, Gary A. Pestano, Sara Suliman, Birgitte Simen, John J. Sninsky, Lynne Sopchak, Cristina M. Tato, Peter M. Vallone, Jo Vandesompele, Thomas J. White, Heinz Zeichhardt, Marc Salit
Publikováno v:
Nature Biotechnology. 40:1563-1568
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::45540898bec3110a9f817bedc03ed3bd
https://doi.org/10.1038/s41587-022-01538-1
https://doi.org/10.1038/s41587-022-01538-1
Autor:
Nathan D. Olson, Justin Wagner, Nathan Dwarshuis, Karen H. Miga, Fritz J. Sedlazeck, Marc Salit, Justin M. Zook
Publikováno v:
Nature Reviews Genetics.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7130432b526559086e82fdc89e04629a
https://doi.org/10.1038/s41576-023-00590-0
https://doi.org/10.1038/s41576-023-00590-0
Autor:
Justin Wagner, Nathan D. Olson, Lindsay Harris, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stankovic, Vladimir Kovacevic, Byunggil Yoo, Neil Miller, Jeffrey A. Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael C. Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne Clarke, Uday S. Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Peter Ebert, Tobias Marschall, Peter Lansdorp, Vincent Hanlon, Carl-Adam Mattsson, Alvaro Martinez Barrio, Ian T. Fiddes, Chunlin Xiao, Arkarachai Fungtammasan, Chen-Shan Chin, Aaron M. Wenger, William J. Rowell, Fritz J. Sedlazeck, Andrew Carroll, Marc Salit, Justin M. Zook
Publikováno v:
Cell genomics. 2(5)
Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04ccc6f93198a30cb4549290f5d6b5bf
https://pubmed.ncbi.nlm.nih.gov/36452119
https://pubmed.ncbi.nlm.nih.gov/36452119
Autor:
Tori Tonn, Hakan Ozadam, Crystal Han, Alia Segura, Duc Tran, David Catoe, Marc Salit, Can Cenik
Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP),
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::daf9ea17d325b890b007c50df8ddca45
https://doi.org/10.1101/2021.12.07.471408
https://doi.org/10.1101/2021.12.07.471408
Autor:
Marc, Salit, Janet, Woodcock
Publikováno v:
Nature biotechnology. 39(9)
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::8f8adbccb23693e66687fd3d54891b40
https://pubmed.ncbi.nlm.nih.gov/34504343
https://pubmed.ncbi.nlm.nih.gov/34504343
Autor:
Rebecca Abergel, Parul Adams, Dion Antonopoulos, Gyorgy Babnigg, Scott Baker, Daniel Bedinger, Monica Borucki, Steven Bradfute, Thomas Bunt, Chris Daum, Joseph Fitch, Vince Gerbasi, Paul Gilna, David Graham, Michael Guarnieri, Sally Hall, Nathan Hillson, Elizabeth Hong-Geller, Greg Hura, Crystal Jaing, Ramesh Jha, Andrzej Joachimiak, Bishoy Kamel, Jeff Kimbrel, Antonietta Lillo, Betty Mangadu, Robert Meagher, Joseph Moon, Nigel Mouncey, Michael Morrison, Nisha Mulakken, Hau Nguyen, Marit Nilsen-Hamilton, Kristin Omberg, Hugh O'Neal, Jerry Parks, Lili Pasa-Tolic, Christa Pennacchio, Dave Rakestraw, Scott Retterer, Marc Salit, Blake Simmons, Anup Singh, Jess Sustarich, James Thissen, Nileena Velappan, Geoffrey Waldo, Kelly Williams, Jesse Wilson, Chunyan Ye, Malin Young, Yuko Yoshinaga, Mowei Zhou
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b557fb404565249c2b2d9a6c10e3c577
https://doi.org/10.2172/1807806
https://doi.org/10.2172/1807806