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https://doi.org/10.12688/f1000research.18238.1
Opinion Article metrics
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
[version 1; peer review: 2 approved with reservations]
Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul J. P. Bonnal, Hidemasa Bono, Jesualdo T. Fernández-Breis, Robert Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin B. Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla Garcia, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Perez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi
Peer Reviewers Todd J. Vision; João Moreira
  • Funder
  • National Bioscience Database Center, the Japan Science and Technology Agency (JST)
PUBLISHED 23 Sep 2019
https://doi.org/10.12688/f1000research.19029.2
Software Tool Article metrics
Revised
Network-based Observability and Controllability Analysis of Dynamical Systems: the NOCAD toolbox
[version 2; peer review: 2 approved]
Dániel Leitold, Ágnes Vathy-Fogarassy, János Abonyi
Peer Reviewers Gilles Didier; Arthur Montanari, Ercílio Moreira and Luis A. Aguirre
  • Funders
  • Emberi Eroforrások Minisztériuma
  • Országos Tudományos Kutatási Alapprogramok
LATEST VERSION PUBLISHED 18 Sep 2019
https://doi.org/10.12688/f1000research.19427.1
Research Article metrics
Understanding life sciences data curation practices via user research
[version 1; peer review: 1 approved, 1 approved with reservations]
Aravind Venkatesan, Nikiforos Karamanis, Michele Ide-Smith, Jonathan Hickford, Johanna McEntyre
Peer Reviewers Lynette Hirschman; Cecilia N. Arighi
  • Funder
  • European Commission
PUBLISHED 11 Sep 2019
https://doi.org/10.12688/f1000research.20421.1
Research Article metrics
Optimal price-based control of heterogeneous thermostatically controlled loads under uncertainty using LSTM networks and genetic algorithms
[version 1; peer review: 2 approved with reservations, 1 not approved]
Taha Abdelhalim Nakabi, Pekka Toivanen
Peer Reviewers Matsukawa Shun; Chiou-Jye Huang; Shanti Swarup
  • Funder
  • Jenny ja Antti Wihurin Rahasto
PUBLISHED 10 Sep 2019
https://doi.org/10.12688/f1000research.17204.3
Data Note metrics
Revised
Pan-cancer repository of validated natural and cryptic mRNA splicing mutations
[version 3; peer review: 2 approved, 1 approved with reservations]
Ben C. Shirley, Eliseos J. Mucaki, Peter K. Rogan
Peer Reviewers Emanuele Buratti; Francesca D. Ciccarelli; W.W.M. Pim Pijnappel
  • Funders
  • Natural Sciences and Engineering Research Council of Canada
  • CytoGnomix Inc.
  • Compute Canada
  • Canadian Foundation for Innovation
  • Canada Research Chairs
  • Shared Hierarchical Academic Research Computing Network
LATEST VERSION PUBLISHED 06 Sep 2019
https://doi.org/10.12688/f1000research.20408.1
Editorial metrics NOT PEER REVIEWED
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers
[version 1; peer review: not peer reviewed]
Sayane Shome, R. Gonzalo Parra, Nazeefa Fatima, Alexander Miguel Monzon, Bart Cuypers, Yumna Moosa, Nilson Da Rocha Coimbra, Juliana Assis, Carla Giner-Delgado, Handan Melike Dönertaş, Yesid Cuesta-Astroz, Geetha Saarunya, Imane Allali, Shruti Gupta, Ambuj Srivastava, Manisha Kalsan, Catalina Valdivia, Gabriel J. Olguin-Orellana, Sofia Papadimitriou, Daniele Parisi, Nikolaj Pagh Kristensen, Leonor Rib, Marouen Ben Guebila, Eugen Bauer, Gaia Zaffaroni, Amel Bekkar, Efejiro Ashano, Lisanna Paladin, Marco Necci, Nicolás N. Moreyra, Martin Rydén, Jordan Villalobos-Solís, Nikolaos Papadopoulos, Candice Rafael, Tülay Karakulak, Yasin Kaya, Yvonne Gladbach, Sandeep Kumar Dhanda, Nikolina Šoštarić, Aishwarya Alex, Dan DeBlasio, Farzana Rahman
  • Funder
  • International Society for Computational Biology
PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.18705.2
Research Article metrics
Revised
Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models
[version 2; peer review: 1 approved, 2 approved with reservations]
Katharina Baum, Jagath C. Rajapakse, Francisco Azuaje
Peer Reviewers Lei Xie and Yue Qiu; Silvia Pineda San Juan; Ana Conesa and Manuel Ugidos
  • Funders
  • Fonds National de la Recherche Luxembourg
  • Joachim Herz Stiftung
LATEST VERSION PUBLISHED 27 Aug 2019
https://doi.org/10.12688/f1000research.20193.1
Data Note metrics
Curation of an intensive care research dataset from routinely collected patient data in an NHS trust.
[version 1; peer review: 2 approved]
Chris McWilliams, Joshua Inoue, Philip Wadey, Graeme Palmer, Raul Santos-Rodriguez, Christopher Bourdeaux
Peer Reviewers J Duncan Young; Min Ji Lee and Steve Harris
  • Funders
  • Above and Beyond
  • Engineering and Physical Sciences Research Council
PUBLISHED 19 Aug 2019
https://doi.org/10.12688/f1000research.14613.2
Software Tool Article metrics
Revised
CyTargetLinker app update: A flexible solution for network extension in Cytoscape
[version 2; peer review: 2 approved]
Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. Coort
Peer Reviewers Alex Gutteridge; John H. Morris
  • Funders
  • ELIXIR
  • Dutch Province of Limburg
LATEST VERSION PUBLISHED 13 Aug 2019
https://doi.org/10.12688/f1000research.16083.2
Software Tool Article metrics
Revised
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data
[version 2; peer review: 1 approved, 1 not approved]
Erik Fasterius, Cristina Al-Khalili Szigyarto
Peer Reviewers Matej Lexa; Jean Fan
  • Funder
  • European Community 7th Framework Program
LATEST VERSION PUBLISHED 12 Aug 2019
https://doi.org/10.12688/f1000research.16817.2
Research Article metrics
Revised
Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon
[version 2; peer review: 2 approved, 3 approved with reservations]
Anna Cuscó, Carlotta Catozzi, Joaquim Viñes, Armand Sanchez, Olga Francino
Peer Reviewers Alfonso Benítez-Páez; Rasmus H. Kirkegaard; Amanda Warr; Kon Chu; Lee J. Kerkhof
  • Funder
  • Agència de Gestió d’Ajuts Universitaris i de Recerca
LATEST VERSION PUBLISHED 01 Aug 2019
https://doi.org/10.12688/f1000research.20027.1
Software Tool Article metrics
ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data
[version 1; peer review: 3 approved with reservations]
Ruben Esse
Peer Reviewers Tao Liu; Hinrich Gronemeyer and Marco Antonio Mendoza-Parra; Thomas Carroll
  • Funder
  • National Institutes of Health
PUBLISHED 31 Jul 2019
https://doi.org/10.12688/f1000research.16356.1
Review metrics
Recent advances in surgical management of urinary incontinence
[version 1; peer review: 2 approved]
Alison Downey, Richard D. Inman
Peer Reviewers Wayne J. G. Hellstrom and Pete Tsambarlis; David Waltregny
PUBLISHED 31 Jul 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.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.17824.2
Method Article metrics
Revised
Enhancing gene set enrichment using networks
[version 2; peer review: 2 approved, 2 approved with reservations]
Michael Prummer
Peer Reviewers Kimberly Glass; Monther Alhamdoosh; Jill P. Mesirov and Alexander Wenzel; Rita Casadio
LATEST VERSION PUBLISHED 16 Jul 2019
https://doi.org/10.12688/f1000research.19238.1
Research Article metrics
Screening of terpenoids as potential therapeutics against Zaire ebolavirus infection through pharmacophore-based drug design
[version 1; peer review: 1 approved with reservations, 1 not approved]
Ade Hanna Natalia, Usman Sumo Friend Tambunan
Peer Reviewers Ndumiso N. Mhlongo; Daryono Hadi Tjahjono
  • Funder
  • Universitas Indonesia
PUBLISHED 10 Jul 2019
https://doi.org/10.12688/f1000research.19675.1
Software Tool Article metrics
Large-scale sequence comparisons with sourmash
[version 1; peer review: 2 approved]
N. Tessa Pierce, Luiz Irber, Taylor Reiter, Phillip Brooks, C. Titus Brown
Peer Reviewers Brad Solomon; Rayan Chikhi
  • Funders
  • Gordon and Betty Moore Foundation
  • National Science Foundation
PUBLISHED 04 Jul 2019
https://doi.org/10.12688/f1000research.18480.1
Review metrics
A theoretical model of temperate phages as mediators of gut microbiome dysbiosis
[version 1; peer review: 2 approved]
Derek M. Lin, Henry C. Lin
Peer Reviewers Hariom Yadav; Deanna L Gibson
  • Funder
  • Winkler Bacterial Overgrowth Research Fund
PUBLISHED 01 Jul 2019
261-280 of 630 ARTICLES
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