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https://doi.org/10.12688/f1000research.20233.1
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A Sequence Distance Graph framework for genome assembly and analysis
[version 1; peer review: 2 approved, 1 approved with reservations]
Luis Yanes, Gonzalo Garcia Accinelli, Jonathan Wright, Ben J. Ward, Bernardo J. Clavijo
Peer Reviewers Erik Garrison; Eric T. Dawson; Max Alekseyev and Pavel Avdeyev
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 23 Aug 2019
https://doi.org/10.12688/f1000research.18491.1
Review metrics
Polygenic risk scores in psychiatry: Will they be useful for clinicians?
[version 1; peer review: 4 approved]
Janice M. Fullerton, John I. Nurnberger
Peer Reviewers Joanna M. Biernacka; Jeremy Hall; Ingrid Melle; Cathryn M. Lewis
  • Funders
  • National Institute of Mental Health
  • Janette Mary O'Neil Research Fellowship
  • Australian National Health and Medical Research Council
PUBLISHED 31 Jul 2019
https://doi.org/10.12688/f1000research.19320.1
Opinion Article metrics
Introduction to Genomic Analysis Workshop: A catalyst for engaging life-science researchers in high throughput analysis
[version 1; peer review: 2 approved]
Phillip A. Richmond, Wyeth W. Wasserman
Peer Reviewers Richard Fitzpatrick and Melanie I. Stefan; Michael Springer
  • Funders
  • Natural Sciences and Engineering Research Council
  • BC Children’s Hospital Research Institute
PUBLISHED 30 Jul 2019
https://doi.org/10.12688/f1000research.19140.1
Software Tool Article metrics
Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich’s ataxia, and other rare iron-related diseases
[version 1; peer review: 2 approved]
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
Peer Reviewers Karl E Anderson; Robert J. Desnick
  • Funders
  • American Cancer Society
  • WHC
  • U.S. National Library of Medicine
  • University of South Florida
  • National Science Foundation
PUBLISHED 19 Jul 2019
https://doi.org/10.12688/f1000research.18674.2
Software Tool Article metrics
Revised
CGAT-core: a python framework for building scalable, reproducible computational biology workflows
[version 2; peer review: 1 approved, 1 approved with reservations]
Adam P. Cribbs, Sebastian Luna-Valero, Charlotte George, Ian M. Sudbery, Antonio J. Berlanga-Taylor, Stephen N. Sansom, Tom Smith, Nicholas E. Ilott, Jethro Johnson, Jakub Scaber, Katherine Brown, David Sims, Andreas Heger
Peer Reviewers Devon P. Ryan; Alexander Peltzer
  • Funder
  • Medical Research Council
LATEST VERSION PUBLISHED 16 Jul 2019
https://doi.org/10.12688/f1000research.19592.1
Software Tool Article metrics
Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz
[version 1; peer review: 3 approved]
Aurora S. Blucher, Shannon K. McWeeney, Lincoln Stein, Guanming Wu
Peer Reviewers Fuhai Li; Aritro Nath; Tero Aittokallio and Ziaurrehman Tanoli
  • Funder
  • National Institutes of Health
PUBLISHED 20 Jun 2019
https://doi.org/10.12688/f1000research.18214.2
Software Tool Article metrics
Revised
Assessing drug target suitability using TargetMine
[version 2; peer review: 2 approved]
Yi-An Chen, Erika Yogo, Naoko Kurihara, Tomoshige Ohno, Chihiro Higuchi, Masatomo Rokushima, Kenji Mizuguchi
Peer Reviewers Rachel Lyne; Anne Hersey
  • Funder
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 28 May 2019
https://doi.org/10.12688/f1000research.19221.1
Editorial metrics NOT PEER REVIEWED
2019 ISCB Innovator Award recognizes William Stafford Noble
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19220.1
Editorial metrics NOT PEER REVIEWED
2019 ISCB Overton Prize: Christophe Dessimoz
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19219.1
Editorial metrics NOT PEER REVIEWED
Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.19218.1
Editorial metrics NOT PEER REVIEWED
2019 Outstanding Contributions to ISCB awarded to Barb Bryant
[version 1; peer review: not peer reviewed]
Diane Kovats, Ron Shamir, Christiana Fogg
  • Funder
  • International Society for Computational Biology
PUBLISHED 23 May 2019
https://doi.org/10.12688/f1000research.18424.1
Review metrics
Recent advances in the characterization of plant transcriptomes in response to drought, salinity, heat, and cold stress
[version 1; peer review: 2 approved]
Khurram Bashir, Akihiro Matsui, Sultana Rasheed, Motoaki Seki
Peer Reviewers Byeong-ha Lee; Hikmet Budak
  • Funders
  • Japan Science and Technology Agency (CREST)
  • Ministry of Education, Culture, Sports, Science and Technology, Japan
PUBLISHED 14 May 2019
https://doi.org/10.12688/f1000research.14012.3
Software Tool Article metrics
Revised
Gene Annotation Easy Viewer (GAEV): Integrating KEGG’s Gene Function Annotations and Associated Molecular Pathways
[version 3; peer review: 3 approved]
Trung Huynh, Sen Xu
Peer Reviewers Fragiskos N Kolisis and Efthymios Ladoukakis; Tonia S. Schwartz; Simo V. Zhang
  • Funder
  • University of Texas at Arlington
LATEST VERSION PUBLISHED 09 May 2019
https://doi.org/10.12688/f1000research.13204.3
Method Article metrics
Revised
META-pipe cloud setup and execution
[version 3; peer review: 2 approved, 1 approved with reservations]
Aleksandr Agafonov, Kimmo Mattila, Cuong Duong Tuan, Lars Tiede, Inge Alexander Raknes, Lars Ailo Bongo
Peer Reviewers Olivier Collin; Kang Ning; Chunlei Wu
  • Funders
  • Norges Forskningsråd
  • UiT The Arctic University of Norway
  • EGI-Engage
  • Horizon 2020
LATEST VERSION PUBLISHED 02 May 2019
https://doi.org/10.12688/f1000research.17956.1
Review metrics
Detection and analysis of RNA methylation
[version 1; peer review: 2 approved]
Nigel P. Mongan, Richard D. Emes, Nathan Archer
Peer Reviewers Thomas Preiss; Marco Biggiogera
  • Funder
  • University of Nottingham
PUBLISHED 26 Apr 2019
https://doi.org/10.12688/f1000research.18676.1
Software Tool Article metrics
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
[version 1; peer review: 2 approved]
Saket Choudhary
Peer Reviewers Simon Andrews; Ryan K. Dale
PUBLISHED 23 Apr 2019
https://doi.org/10.12688/f1000research.15091.2
Research Note metrics
Revised
Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach
[version 2; peer review: 2 approved with reservations]
Pedro Morell Miranda, Francesca Bertolini, Haja N. Kadarmideen
Peer Reviewers Yasir Suhail; Manikandan Narayanan
  • Funders
  • Technical University of Denmark, DTU Bioinformatics
  • The Danish Independent Research Council
LATEST VERSION PUBLISHED 17 Apr 2019
https://doi.org/10.12688/f1000research.16005.3
Software Tool Article metrics
Revised
MSF: Modulated Sub-graph Finder
[version 3; peer review: 3 approved]
Mariam R. Farman, Ivo L. Hofacker, Fabian Amman
Peer Reviewers Guanming Wu; Stefanie Widder; Haibo Liu
  • Funder
  • Austrian Science Fund
LATEST VERSION PUBLISHED 14 Apr 2019
https://doi.org/10.12688/f1000research.17548.2
Software Tool Article metrics
Revised
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
[version 2; peer review: 2 approved]
Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Peer Reviewers Bastian Greshake Tzovaras and Ngoc-Vinh Tran; Laurent Gatto
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • University College London
  • Swiss State Secretariat for Education
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 29 Mar 2019
https://doi.org/10.12688/f1000research.16252.3
Method Article metrics
Revised
Improved inference of chromosome conformation from images of labeled loci
[version 3; peer review: 2 approved]
Brian C. Ross, James C. Costello
Peer Reviewers Ewan Birney and Carl Barton; Marco Cosentino Lagomarsino and Vittore Scolari
  • Funders
  • Boettcher Foundation
  • Cancer League of Colorado
  • National Institutes of Health
LATEST VERSION PUBLISHED 28 Mar 2019
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