DangerTrack: A scoring system to detect difficult-to-assess regions [version 1; referees: 2 approved, 1 approved with reservations]

by Igor Dolgalev, Fritz Sedlazeck, Ben Busby
Published 2017-04-01

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes.

by Moamen M Elmassry, Sunghwan Kim, Ben Busby
Published 2021-01-01

Matchmaking in Bioinformatics [version 1; referees: 2 approved]

by Ewy Mathé, Ben Busby, Helen Piontkivska, Team of Developers
Published 2018-02-01

Viewing RNA-seq data on the entire human genome [version 1; referees: 3 approved]

by Eric M. Weitz, Lorena Pantano, Jingzhi Zhu, Bennett Upton, Ben Busby
Published 2017-04-01

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive [version 2; peer review: 2 approved]

by Matthew N. Bernstein, Ariella Gladstein, Khun Zaw Latt, Emily Clough, Ben Busby, Allissa Dillman
Published 2020-08-01

Magic-BLAST, an accurate RNA-seq aligner for long and short reads

by Grzegorz M. Boratyn, Jean Thierry-Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas L. Madden
Published 2019-07-01

PubRunner: A light-weight framework for updating text mining results [version 2; referees: 1 approved, 2 approved with reservations]

by Kishore R. Anekalla, J.P. Courneya, Nicolas Fiorini, Jake Lever, Michael Muchow, Ben Busby
Published 2017-10-01

Extending TCGA queries to automatically identify analogous genomic data from dbGaP [version 1; referees: 2 approved, 1 approved with reservations]

by Erin K. Wagner, Satyajeet Raje, Liz Amos, Jessica Kurata, Abhijit S. Badve, Yingquan Li, Ben Busby
Published 2017-03-01

MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis [version 1; referees: 3 approved]

by Eric Moyer, Megan Hagenauer, Matthew Lesko, Felix Francis, Oscar Rodriguez, Vijayaraj Nagarajan, Vojtech Huser, Ben Busby
Published 2016-04-01

geneHummus: an R package to define gene families and their expression in legumes and beyond

by Jose V. Die, Moamen M. Elmassry, Kimberly H. LeBlanc, Olaitan I. Awe, Allissa Dillman, Ben Busby
Published 2019-07-01

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis [version 4; peer review: 2 approved, 1 not approved]

by Syed Hussain Ather, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby
Published 2020-09-01

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies [version 2; referees: 2 approved]

by Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan Dunn, Andrew Olson, Ben Busby, Alexander T. Dilthey
Published 2018-12-01

dbVar structural variant cluster set for data analysis and variant comparison [version 2; referees: 2 approved]

by Lon Phan, Jeffrey Hsu, Le Quang Minh Tri, Michaela Willi, Tamer Mansour, Yan Kai, John Garner, John Lopez, Ben Busby
Published 2017-02-01

Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich’s ataxia, and other rare iron-related diseases [version 1; peer review: 2 approved]

by Gloria C. Ferreira, Jenna Oberstaller, Renée Fonseca, Thomas E. Keller, Swamy Rakesh Adapa, Justin Gibbons, Chengqi Wang, Xiaoming Liu, Chang Li, Minh Pham, Guy W. Dayhoff II, Linh M. Duong, Luis Tañón Reyes, Luciano Enrique Laratelli, Douglas Franz, Segun Fatumo, ATM Golam Bari, Audrey Freischel, Lindsey Fiedler, Omkar Dokur, Krishna Sharma, Deborah Cragun, Ben Busby, Rays H.Y. Jiang
Published 2019-07-01

NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements

by Ryan Connor, Rodney Brister, Jan P. Buchmann, Ward Deboutte, Rob Edwards, Joan Martí-Carreras, Mike Tisza, Vadim Zalunin, Juan Andrade-Martínez, Adrian Cantu, Michael D’Amour, Alexandre Efremov, Lydia Fleischmann, Laura Forero-Junco, Sanzhima Garmaeva, Melissa Giluso, Cody Glickman, Margaret Henderson, Benjamin Kellman, David Kristensen, Carl Leubsdorf, Kyle Levi, Shane Levi, Suman Pakala, Vikas Peddu, Alise Ponsero, Eldred Ribeiro, Farrah Roy, Lindsay Rutter, Surya Saha, Migun Shakya, Ryan Shean, Matthew Miller, Benjamin Tully, Christopher Turkington, Ken Youens-Clark, Bert Vanmechelen, Ben Busby
Published 2019-09-01

NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index

by Joan Martí-Carreras, Alejandro Rafael Gener, Sierra D. Miller, Anderson F. Brito, Christiam E. Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David M. Kristensen, Wynn K. Meyer, Sejal Modha, Alexis L. Norris, Surya Saha, Anna K. Belford, Evan Biederstedt, James Rodney Brister, Jan P. Buchmann, Nicholas P. Cooley, Robert A. Edwards, Kiran Javkar, Michael Muchow, Harihara Subrahmaniam Muralidharan, Charles Pepe-Ranney, Nidhi Shah, Migun Shakya, Michael J. Tisza, Benjamin J. Tully, Bert Vanmechelen, Valerie C. Virta, Jake L. Weissman, Vadim Zalunin, Alexandre Efremov, Ben Busby
Published 2020-12-01

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

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates [version 2; peer review: 1 approv...

by Ann M. Mc Cartney, Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel L Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M Khayat, Maximillian Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jingwen Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Soylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J Sedlazeck
Published 2021-09-01