Bioinformatics

Bioinformatics

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161-180 of 378 ARTICLES
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https://doi.org/10.12688/f1000research.54418.1
Software Tool Article metrics
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality
[version 1; peer review: 2 approved]
Davide Albanese, Claudio Donati
Peer Reviewers Thomas S. B. Schmidt, Anthony Fullam and Askarbek Orakov; Denis Baurain
  • Funder
  • Autonomous Province of Trento (Accordo di Programma)
PUBLISHED 17 Aug 2021
https://doi.org/10.12688/f1000research.54071.1
Data Note metrics
Organizing knowledge to enable faster data interpretation in COVID-19 research
[version 1; peer review: 2 approved with reservations]
Joseph Hearnshaw, Marco Brandizi, Ajit Singh, Chris Rawlings, Keywan Hassani-Pak
Peer Reviewers Justin Reese; Keith Hall
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 30 Jul 2021
https://doi.org/10.12688/f1000research.19630.2
Software Tool Article metrics
Revised
A strategy for building and using a human reference pangenome
[version 2; peer review: 2 approved]
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
Peer Reviewers Anna Kuosmanen; Robert A. Beagrie
  • Funders
  • Simons Foundation
  • Carlsbergfondet
  • U.S. National Library of Medicine
  • W. M. Keck Foundation
  • National Institutes of Health
  • Australian Research Council
LATEST VERSION PUBLISHED 29 Jul 2021
https://doi.org/10.12688/f1000research.27868.3
Method Article metrics
Revised
WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
[version 3; peer review: 2 approved]
Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Peer Reviewers Juan Pablo Tosar; Wen Yao
  • Funders
  • Italian Association for Cancer Research
  • Ministero dell’Istruzione, dell’Università e della Ricerca
  • Horizon 2020
  • Regione Campania
LATEST VERSION PUBLISHED 12 Jul 2021
https://doi.org/10.12688/f1000research.27214.2
Software Tool Article metrics
Revised
iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing
[version 2; peer review: 2 approved]
Ahmad Rajeh, Kyle Wolf, Courtney Schiebout, Nabeel Sait, Tim Kosfeld, Richard J. DiPaolo, Tae-Hyuk Ahn
Peer Reviewers Shuo-Wang Qiao and Ying Yao; Se-Ran Jun
  • Funder
  • Federal Bureau of Investigations
LATEST VERSION PUBLISHED 29 Jun 2021
https://doi.org/10.12688/f1000research.24345.2
Software Tool Article metrics
Update
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
[version 2; peer review: 3 approved]
Justin Wagner, Jayaram Kancherla, Domenick Braccia, James Matsumara, Victor Felix, Jonathan Crabtree, Anup Mahurkar, Héctor Corrada Bravo
Peer Reviewers Ekaterina Smirnova; Edoardo Pasolli; Levi Waldron
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 21 Jun 2021
https://doi.org/10.12688/f1000research.27395.2
Software Tool Article metrics
Revised
GeNePy3D: a quantitative geometry python toolbox for bioimaging
[version 2; peer review: 2 approved]
Minh-Son Phan, Anatole Chessel
Peer Reviewers Virginie Uhlmann; Yizhi Wang
  • Funder
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 17 Jun 2021
https://doi.org/10.12688/f1000research.51613.2
Data Note metrics
Revised
A draft reference assembly of the Psilocybe cubensis genome
[version 2; peer review: 2 approved]
Kevin McKernan, Liam T. Kane, Seth Crawford, Chen-Shan Chin, Aaron Trippe, Stephen McLaughlin
Peer Reviewers Jason C. Slot; Anders Goncalves da Silva and Philippe Henry
LATEST VERSION PUBLISHED 15 Jun 2021
https://doi.org/10.12688/f1000research.28022.2
Software Tool Article metrics
Revised
BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS
[version 2; peer review: 3 approved]
Caroline Gaud, Bebiana C. Sousa, An Nguyen, Maria Fedorova, Zhixu Ni, Valerie B. O’Donnell, Michael J.O. Wakelam, Simon Andrews, Andrea F. Lopez-Clavijo
Peer Reviewers Amaury Cazenave Gassiot; Phillip Whitfield; Ginger Milne
  • Funders
  • German Federal Ministry of Education and Research
  • Wellcome Trust
LATEST VERSION PUBLISHED 09 Jun 2021
https://doi.org/10.12688/f1000research.52460.1
Software Tool Article metrics
scNetViz: from single cells to networks using Cytoscape
[version 1; peer review: 2 approved]
Krishna Choudhary, Elaine C. Meng, J. Javier Diaz-Mejia, Gary D. Bader, Alexander R. Pico, John H. Morris
Peer Reviewers Luca Pinello; Kenji Kamimoto
  • Funders
  • National Resource for Network Biology
  • Chan Zuckerberg Initiative
PUBLISHED 07 Jun 2021
https://doi.org/10.12688/f1000research.53408.1
Editorial metrics NOT PEER REVIEWED
Highlights from the 16th International Society for Computational Biology Student Council Symposium 2020
[version 1; peer review: not peer reviewed]
Wim L. Cuypers, Handan Melike Dönertaş, Jasleen K. Grewal, Nazeefa Fatima, Chase Donnelly, Arvind Singh Mer, Spencer Krieger, Bart Cuypers, Farzana Rahman
PUBLISHED 04 Jun 2021
https://doi.org/10.12688/f1000research.50857.2
Brief Report metrics
Revised
Interactive SARS-CoV-2 mutation timemaps
[version 2; peer review: 3 approved]
René L. Warren, Inanc Birol
Peer Reviewers Ingo Ebersberger and Ruben Iruegas; Takahiko Koyama; Jale Moradi
  • Funders
  • National Institute for Health Research
  • Genome Canada
LATEST VERSION PUBLISHED 03 Jun 2021
https://doi.org/10.12688/f1000research.25148.2
Research Article metrics
Revised
First draft genome assembly of the desert locust, Schistocerca gregaria
[version 2; peer review: 3 approved]
Heleen Verlinden, Lieven Sterck, Jia Li, Zhen Li, Anna Yssel, Yannick Gansemans, Rik Verdonck, Michiel Holtof, Hojun Song, Spencer T. Behmer, Gregory A. Sword, Tom Matheson, Swidbert R. Ott, Dieter Deforce, Filip Van Nieuwerburgh, Yves Van de Peer, Jozef Vanden Broeck
Peer Reviewers Uwe Homberg; Surya Saha; Joshua B. Benoit
  • Funders
  • U.S. Department of Agriculture
  • University of Pretoria
  • KU Leuven
  • Fonds Wetenschappelijk Onderzoek
  • Universiteit Gent
  • Biotechnology and Biological Sciences Research Council
  • National Science Foundation
LATEST VERSION PUBLISHED 21 May 2021
https://doi.org/10.12688/f1000research.50850.3
Research Article metrics
Revised
Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches
[version 3; peer review: 3 approved]
Gurudeeban Selvaraj, Satyavani Kaliamurthi, Gilles H. Peslherbe, Dong-Qing Wei
Peer Reviewers Sugunadevi Sakkiah; Dhurvas C. Dinesh; Turanli Beste
  • Funders
  • Natural Sciences and Engineering Research Council of Canada
  • Ministry of Science and Technology of the People's Republic of China
  • Concordia University
  • National Natural Science Foundation of China
  • MITACS Global Research
LATEST VERSION PUBLISHED 17 May 2021
https://doi.org/10.12688/f1000research.27500.2
Opinion Article metrics
Revised
The need for standardisation in life science research - an approach to excellence and trust.
[version 2; peer review: 3 approved]
Susanne Hollmann, Andreas Kremer, Špela Baebler, Christophe Trefois, Kristina Gruden, Witold R. Rudnicki, Weida Tong, Aleksandra Gruca, Erik Bongcam-Rudloff, Chris T. Evelo, Alina Nechyporenko, Marcus Frohme, David Šafránek, Babette Regierer, Domenica D'Elia
Peer Reviewers David Nickerson; Laurent Falquet; Antonella Lanati
  • Funder
  • Horizon 2020
LATEST VERSION PUBLISHED 10 May 2021
https://doi.org/10.12688/f1000research.52141.1
Software Tool Article metrics AWAITING PEER REVIEW
Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design
[version 1; peer review: awaiting peer review]
Kristianne Arielle Gabriel, Maria Rejane Nepacina, Francis Tablizo, Carlo Lapid, Mark Lenczner Mendoza, Daniella Jean Pamulaklakin, Jobeth Domingo, Marc Jermaine Pontiveros, Hannah Mae Magno, Joshua Gregor Dizon, El King Morado, Jan Michael Yap
Peer Reviewers Invited
  • Funder
  • Philippine Council for Industry, Energy and Emerging Technology Research and Development of the Department of Science and Technology
PUBLISHED 07 May 2021
https://doi.org/10.12688/f1000research.25485.1
Opinion Article metrics
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists
[version 1; peer review: 2 approved]
Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura
Peer Reviewers Thorsten Wohland; Kevin Eliceiri
  • Funders
  • Swedish Foundation for Strategic Research
  • Fundação para a Ciência e a Tecnologia
  • COST
  • Luxembourg National Research Fund
  • Cancer Research UK
  • Deutsche Forschungsgemeinschaft
  • Swedish National Microscopy infrastructure
  • UK Medical Research Council
  • France BioImaging national infrastructure
  • Wellcome Trust
PUBLISHED 30 Apr 2021
https://doi.org/10.12688/f1000research.52531.1
Opinion Article metrics
Developing open-source software for bioimage analysis: opportunities and challenges
[version 1; peer review: 2 approved]
Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Peer Reviewers Loïc A. Royer; Nico Stuurman
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Institut National de la Santé et de la Recherche Médicale
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.29032.2
Method Article metrics
Revised
Sustainable data analysis with Snakemake
[version 2; peer review: 2 approved]
Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
Peer Reviewers Michael Reich; Caroline C. Friedel
  • Funders
  • Netherlands Organisation for Scientific Research (NWO)
  • Deutsche Stiftung für Herzforschung
  • United States National Science Foundation Graduate Research Fellowship Program (NSF-GRFP)
  • Google LLC
LATEST VERSION PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.28608.2
Method Article metrics
Revised
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
[version 2; peer review: 2 approved]
Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap
Peer Reviewers Caitlin Simopoulos; Won Kyong Cho
  • Funders
  • National Cancer Institute
  • University of Minnesota
  • National Science Foundation
LATEST VERSION PUBLISHED 19 Apr 2021
161-180 of 378 ARTICLES
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