Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data

by Nathan D. Olson, Justin M. Zook, Jayne B. Morrow, Nancy J. Lin
Published 2017-09-01

Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing.

by Justin M Zook, Daniel Samarov, Jennifer McDaniel, Shurjo K Sen, Marc Salit
Published 2012-01-01

Tools for annotation and comparison of structural variation [version 1; referees: 1 approved, 2 approved with reservations]

by Fritz J. Sedlazeck, Andi Dhroso, Dale L. Bodian, Justin Paschall, Farrah Hermes, Justin M. Zook
Published 2017-10-01

Assembly and annotation of an Ashkenazi human reference genome

by Alaina Shumate, Aleksey V. Zimin, Rachel M. Sherman, Daniela Puiu, Justin M. Wagner, Nathan D. Olson, Mihaela Pertea, Marc L. Salit, Justin M. Zook, Steven L. Salzberg
Published 2020-06-01

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

by Nathan D. Olson, Steven P. Lund, Justin M. Zook, Fabiola Rojas-Cornejo, Brian Beck, Carole Foy, Jim Huggett, Alexandra S. Whale, Zhiwei Sui, Anna Baoutina, Michael Dobeson, Lina Partis, Jayne B. Morrow
Published 2015-03-01

Best Practices for Evaluating Single Nucleotide Variant Calling Methods for Microbial Genomics

by Nathan eOlson, Steven P. Lund, Rebecca E. Colman, Jeffrey T Foster, Jason W Sahl, James M Schupp, Paul eKeim, Paul eKeim, Jayne B Morrow, Marc L Salit, Marc L Salit, Justin M Zook
Published 2015-07-01

A crowdsourced set of curated structural variants for the human genome.

by 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
Published 2020-06-01

A diploid assembly-based benchmark for variants in the major histocompatibility complex

by 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
Published 2020-09-01

A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved]

by Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, Ben Busby
Published 2021-07-01