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https://doi.org/10.12688/f1000research.22242.2
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Revised
AlignmentViewer: Sequence Analysis of Large Protein Families
[version 2; peer review: 2 approved]
Roc Reguant, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, Nicholas Paul Gauthier
Peer Reviewers Erik Larsson Lekholm; Alex Bateman
  • Funders
  • Human Frontier Science Program
  • Harvard Medical School
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 15 Oct 2020
https://doi.org/10.12688/f1000research.6348.2
Research Article metrics
Revised
A hydrophobic proclivity index for protein alignments
[version 2; peer review: 2 approved with reservations, 1 not approved]
David Cavanaugh, Krishnan Chittur
Peer Reviewers Charles Carter; Ana Jerončić ; Ruchi Lohia
LATEST VERSION PUBLISHED 15 Oct 2020
https://doi.org/10.12688/f1000research.24887.1
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The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research
[version 1; peer review: 2 approved]
David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltran, Salvador Capella-Gutierrez, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Joaquin Dopazo, Laura I. Furlong, Bo Gao, Leyla Garcia, Dietlind Gerloff, Ivo Gut, Attila Gyenesei, Nina Habermann, John M. Hancock, Marc Hanauer, Eivind Hovig, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer, Steve Laurie, Brane Leskošek, David Lloyd, Tomas Marques-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz, Ana Rath, Pubudu Samarakoon, Ferran Sanz, Gary Saunders, Daoud Sie, Morris A. Swertz, Kirill Tsukanov, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra, Christophe Béroud
Peer Reviewers Antonio Rausell; Andrew Lonie
  • Funder
  • ELIXIR Hub
PUBLISHED 13 Oct 2020
https://doi.org/10.12688/f1000research.22907.3
Software Tool Article metrics
Revised
RamaNet: Computational de novo helical protein backbone design using a long short-term memory generative neural network
[version 3; peer review: 5 not approved]
Sari Sabban, Mikhail Markovsky
Peer Reviewers Matias Valdenegro-Toro; Jan Ludwiczak and Stanislaw Dunin-Horkawicz; Anupaul Baruah; Laszlo Dobson; Hamed Khakzad
LATEST VERSION PUBLISHED 12 Oct 2020
https://doi.org/10.12688/f1000research.22954.3
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QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing
[version 3; peer review: 2 approved]
Frédéric Jarlier, Nicolas Joly, Nicolas Fedy, Thomas Magalhaes, Leonor Sirotti, Paul Paganiban, Firmin Martin, Michael McManus, Philippe Hupé
Peer Reviewers Ramon Amela Milian and Salvador Capella-Gutierrez; Yupu Liang
  • Funder
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 08 Oct 2020
https://doi.org/10.12688/f1000research.24427.1
Research Article metrics
Annotation and curation of human genomic variations: an ELIXIR Implementation Study
[version 1; peer review: 2 approved with reservations]
Alessia David, Valérie Barbié, Marcella Attimonelli, Roberto Preste, Enni Makkonen, Heidi Marjonen, Mats Lindstedt, Kati Kristiansson, Sarah E. Hunt, Fiona Cunningham, Ilkka Lappalainen, Michael J.E. Sternberg
Peer Reviewers Lina Ma; Osamu Ogasawara
  • Funders
  • ELIXIR
  • Imperial College London
  • European Molecular Biology Laboratory
PUBLISHED 08 Oct 2020
https://doi.org/10.12688/f1000research.26786.1
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VTES: a stochastic Python-based tool to simulate viral transmission
[version 1; peer review: awaiting peer review]
Danielle L. Kurtin, Daniel A.J. Parsons, Scott M. Stagg
Peer Reviewers Invited
  • Funders
  • University of Surrey
  • National Institutes of Health
PUBLISHED 05 Oct 2020
https://doi.org/10.12688/f1000research.25561.1
Research Article metrics
The challenges of theory-software translation
[version 1; peer review: 2 approved, 1 approved with reservations]
Caroline Jay, Robert Haines, Daniel S. Katz, Jeffrey C. Carver, Sandra Gesing, Steven R. Brandt, James Howison, Anshu Dubey, James C. Phillips, Hui Wan, Matthew J. Turk
Peer Reviewers Konrad Hinsen; Mike Heroux; Mozhgan Kabiri Chimeh
  • Funders
  • Engineering and Physical Sciences Research Council
  • National Science Foundation
PUBLISHED 02 Oct 2020
https://doi.org/10.12688/f1000research.15824.3
Software Tool Article metrics
Revised
sPop: Age-structured discrete-time population dynamics model in C, Python, and R
[version 3; peer review: 2 approved]
Kamil Erguler
Peer Reviewers Juliane Liepe; Matthew Silk
LATEST VERSION PUBLISHED 28 Sep 2020
https://doi.org/10.12688/f1000research.26759.1
Review metrics
How to tell time: advances in decoding circadian phase from omics snapshots
[version 1; peer review: 3 approved]
Lorenzo Talamanca, Felix Naef
Peer Reviewers Achim Kramer; Hanspeter Herzel; John B. Hogenesch
  • Funders
  • Ecole Polytechnique Fédérale de Lausann
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
PUBLISHED 17 Sep 2020
https://doi.org/10.12688/f1000research.25902.1
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BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations
[version 1; peer review: 2 approved]
Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis Dean
Peer Reviewers Ezekiel Maier; Yuriy Gusev
  • Funders
  • National Cancer Institute
  • National Institutes of Health
PUBLISHED 16 Sep 2020
https://doi.org/10.12688/f1000research.24544.1
Research Article metrics
A new virtue of phantom MRI data: explaining variance in human participant data
[version 1; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Christopher P. Cheng, Yaroslav O. Halchenko
Peer Reviewers Xiangrui Li; Blaise Frederick; Simon Duchesne; Jens Sommer
  • Funders
  • Dartmouth College
  • National Institutes of Health
  • National Institute of Biomedical Imaging and Bioengineering
  • Department of Psychological and Brain Sciences, Dartmouth College
  • National Science Foundation
PUBLISHED 14 Sep 2020
https://doi.org/10.12688/f1000research.26228.1
Method Article metrics
Extraction of CPRD additional clinical data using R
[version 1; peer review: 2 approved with reservations]
Anthony Nash, M. Zameel Cader
Peer Reviewers Zhi Yang; Jessica Pinaire
  • Funder
  • National Institute for Health Research Oxford Health Biomedical Research Centre
PUBLISHED 11 Sep 2020
https://doi.org/10.12688/f1000research.20244.2
Opinion Article metrics
Revised
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
[version 2; peer review: 2 approved]
Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher
Peer Reviewers Roland Krause; Loredana Le Pera and Allegra Via
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen
LATEST VERSION PUBLISHED 11 Sep 2020
https://doi.org/10.12688/f1000research.25501.1
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MSclassifier: median-supplement model-based classification tool for automated knowledge discovery
[version 1; peer review: 2 approved]
Emmanuel S. Adabor, George K. Acquaah-Mensah, Gaston K. Mazandu
Peer Reviewers Gregory Hart; Alper Uzun
  • Funders
  • Ghana Institute of Management and Public Administration
  • National Institutes of Health
  • African Institute for Mathematical Sciences
  • Massachusetts College of Pharmacy and Health Sciences
PUBLISHED 10 Sep 2020
https://doi.org/10.12688/f1000research.16665.2
Software Tool Article metrics
Revised
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
[version 2; peer review: 2 approved]
Maxime Garcia, Szilveszter Juhos, Malin Larsson, Pall I. Olason, Marcel Martin, Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Díaz De Ståhl, Philip Ewels, Valtteri Wirta, Monica Nistér, Max Käller, Björn Nystedt
Peer Reviewers Tony Håndstad; Esa Pitkänen
  • Funders
  • Vetenskapsrådet
  • Barncancerfonden
  • Knut och Alice Wallenbergs Stiftelse
LATEST VERSION PUBLISHED 04 Sep 2020
https://doi.org/10.12688/f1000research.20419.1
Review metrics
Pediatric SJS-TEN: Where are we now?
[version 1; peer review: 2 approved]
Michele Ramien, Jennifer L. Goldman
Peer Reviewers Teresa Bellón; Sayan Basu
PUBLISHED 13 Aug 2020
https://doi.org/10.12688/f1000research.25144.1
Software Tool Article metrics
Dictionary of disease ontologies (DODO): a graph database to facilitate access and interaction with disease and phenotype ontologies
[version 1; peer review: 1 approved, 1 approved with reservations]
Liesbeth François, Jonathan van Eyll, Patrice Godard
Peer Reviewers Nicole Vasilevsky; Jeremy G. Frey and Samantha Pearman-Kanza
  • Funder
  • UCB Pharma
PUBLISHED 07 Aug 2020
https://doi.org/10.12688/f1000research.24494.2
Research Article metrics
Revised
An inexpensive and easy-to-implement approach to a Quality Management System for an academic research lab
[version 2; peer review: 2 approved, 1 approved with reservations]
Michael Hewera, Ann-Christin Nickel, Nina Knipprath, Sajjad Muhammad, Xiaolong Fan, Hans-Jakob Steiger, Daniel Hänggi, Ulf Dietrich Kahlert
Peer Reviewers Jan Vollert; Judith J. de Haan and Frank Miedema; Clarissa Carneiro and Olavo B. Amaral
  • Funder
  • Bundesministerium für Bildung und Forschung
LATEST VERSION PUBLISHED 06 Aug 2020
https://doi.org/10.12688/f1000research.23180.2
Software Tool Article metrics
Revised
Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive
[version 2; peer review: 2 approved]
Matthew N. Bernstein, Ariella Gladstein, Khun Zaw Latt, Emily Clough, Ben Busby, Allissa Dillman
Peer Reviewers Zichen Wang; Shannon Ellis
  • Funders
  • National Library of Medicine, National Institutes of Health
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 04 Aug 2020
381-400 of 1,016 ARTICLES
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