Bioinformatics

Bioinformatics

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41-60 of 389 ARTICLES
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 in 
https://doi.org/10.12688/f1000research.126734.2
Opinion Article metrics
Revised
Systems Biology in ELIXIR: modelling in the spotlight
[version 2; peer review: 2 approved, 1 approved with reservations]
Vitor Martins dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja Arts, Rui Benfeitas, Victoria Dominguez Del Angel, Elena Domínguez-Romero, Polonca Ferk, Dirk Fey, Carole Goble, Martin Golebiewski, Kristina Gruden, Katharina F. Heil, Henning Hermjakob, Pascal Kahlem, Maria I. Klapa, Jasper Koehorst, Alexey Kolodkin, Martina Kutmon, Brane Leskošek, Sébastien Moretti, Wolfgang Müller, Marco Pagni, Tadeja Rezen, Miguel Rocha, Damjana Rozman, David Šafránek, William T. Scott, Rahuman S. Malik Sheriff, Maria Suarez Diez, Kristel Van Steen, Hans V Westerhoff, Ulrike Wittig, Katherine Wolstencroft, Anze Zupanic, Chris T. Evelo, John M. Hancock
Peer Reviewers Yoram Vodovotz; Herbert Sauro; Ioannis Androulakis
  • Funder
  • EPAnEk-NSRF
LATEST VERSION PUBLISHED 31 May 2024
https://doi.org/10.12688/f1000research.135164.2
Method Article metrics
Revised
On the limits of inferring biophysical parameters of RBP-RNA interactions from in vitro RNA Bind’n Seq data
[version 2; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Niels Schlusser, Mihaela Zavolan
Peer Reviewers Johannes Söding; Jun Zhang; Junbai Wang; Andreas Schlundt
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 29 May 2024
https://doi.org/10.12688/f1000research.134798.2
Software Tool Article metrics
Revised
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
[version 2; peer review: 1 approved, 3 approved with reservations]
Maxime Borry, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, Andrea Quagliariello, Anna E. White, Arthur Kocher, Åshild J. Vågene‬, Bjørn Peare Bartholdy, Diāna Spurīte, Gabriel Yaxal Ponce-Soto, Gunnar Neumann, I-Ting Huang, Ian Light, Irina M. Velsko, Iseult Jackson, Jasmin Frangenberg, Javier G. Serrano, Julien Fumey, Kadir T. Özdoğan, Kelly E. Blevins, Kevin G. Daly, Maria Lopopolo, Markella Moraitou, Megan Michel, Meriam van Os, Miriam J. Bravo-Lopez, Mohamed S. Sarhan, Nihan D. Dagtas, Nikolay Oskolkov, Olivia S. Smith, Ophélie Lebrasseur, Piotr Rozwalak, Raphael Eisenhofer, Sally Wasef, Shreya L. Ramachandran, Valentina Vanghi, Christina Warinner, James A. Fellows Yates
Peer Reviewers Timothy Read and Robert Petit III; Jonas Coelho Kasmanas; Intikhab Alam; Emma Griffiths
  • Funders
  • Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
  • Carlsbergfondet
  • H2020 European Research Council
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
  • Knut och Alice Wallenbergs Stiftelse
  • National Institutes of Health
  • Carl Tryggers Stiftelse för Vetenskaplig Forskning
  • Deutsche Forschungsgemeinschaft
  • Friedrich-Schiller-Universität Jena
  • Science for Life Laboratory National Sequencing Projects
  • Werner Siemens-Stiftung
  • Max-Planck-Gesellschaft
  • National Science Foundation
  • Leverhulme Trust
  • Svenska Forskningsrådet Formas
  • Science Foundation Ireland-Irish Research Council
  • Science Foundation Ireland Centre for Research Training in Genomics Data Science
  • Università degli Studi di Padova
  • Institut Pasteur
  • H2020 Marie Skłodowska-Curie Actions
LATEST VERSION PUBLISHED 28 May 2024
https://doi.org/10.12688/f1000research.149237.1
Software Tool Article metrics
ZARP: A user-friendly and versatile RNA-seq analysis workflow
[version 1; peer review: 2 approved with reservations]
Maria Katsantoni, Foivos Gypas, Christina J Herrmann, Dominik Burri, Maciej Bąk, Paula Iborra, Krish Agarwal, Meriç Ataman, Máté Balajti, Noè Pozzan, Niels Schlusser, Youngbin Moon, Aleksei Mironov, Anastasiya Börsch, Mihaela Zavolan, Alexander Kanitz
Peer Reviewers Silvia Liu; Bo Li
  • Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • National Center of Competence in Research RNA & Disease
PUBLISHED 24 May 2024
https://doi.org/10.12688/f1000research.133724.2
Opinion Article metrics
Revised
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity
[version 2; peer review: 3 approved]
Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Bachir Balech, Endre Barta, Physilia Ying Shi Chua, Valeria Di Cola, Katharina F. Heil, Graham M. Hughes, Lars S. Jermiin, Matúš Kalaš, Jerry Lanfear, Evangelos Pafilis, Patricia M. Palagi, Aristotelis C. Papageorgiou, Joana Paupério, Fotis Psomopoulos, Niels Raes, Josephine Burgin, Toni Gabaldón
Peer Reviewers Patrick Comer; Abigail Benson and Stephen Formel; Cher FY Chow
  • Funders
  • Swiss State Secretariat for Education, Research and Innovation (SERI)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 22 May 2024
https://doi.org/10.12688/f1000research.150049.1
Research Article metrics
Design of SARS-CoV-2 protein S peptides recognized by the most frequent HLA alleles in the Moroccan population using an immunoinformatics approach
[version 1; peer review: 1 not approved]
Meryem Fakhkhari, Bouabid Badaoui, Hicham Oumzil, Khalid Sadki
Peer Reviewers Gustavo Fioravanti Vieira
PUBLISHED 20 May 2024
https://doi.org/10.12688/f1000research.145486.1
Research Article metrics
Negligible effects of read trimming on the accuracy of germline short variant calling in the human genome
[version 1; peer review: 2 approved with reservations]
Yury Barbitoff, Alexander Predeus
Peer Reviewers Dharma Varapula; Xihao Li and Muqing Zhou
PUBLISHED 17 May 2024
https://doi.org/10.12688/f1000research.134465.2
Research Article metrics
Revised
Spatiotemporal structure and composition of the microbial communities in hypersaline Lake Magadi, Kenya
[version 2; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Alex Kipnyargis, Eucharia Kenya, Fathiya Khamis, Romano Mwirichia
Peer Reviewers Marianne Haines; Srijak Bhatnagar; Cristiano Pedroso-Roussado; Addis Simachew
  • Funder
  • National Research Fund, Kenya
LATEST VERSION PUBLISHED 17 May 2024
https://doi.org/10.12688/f1000research.74416.2
Software Tool Article metrics
Revised
BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data
[version 2; peer review: 1 approved, 2 approved with reservations]
Alan O'Callaghan, Nils Eling, John C. Marioni, Catalina A. Vallejos
Peer Reviewers Oliver M. Crook; Andrew McDavid; Michel S Naslavsky
  • Funders
  • Cancer Research UK
  • University of Edinburgh
  • European Molecular Biology Laboratory
LATEST VERSION PUBLISHED 07 May 2024
https://doi.org/10.12688/f1000research.127348.2
Software Tool Article metrics
Revised
CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes
[version 2; peer review: 1 approved, 2 approved with reservations]
Jianqiang Sun, Xi Fu, Wei Cao
Peer Reviewers Eric Soler and Mohammad Salma; Xueyi Dong; Alexander Zelikovsky and Bikram Sahoo
  • Funder
  • Japan Society for the Promotion of Science
LATEST VERSION PUBLISHED 30 Apr 2024
https://doi.org/10.12688/f1000research.124059.2
Software Tool Article metrics
Revised
LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies
[version 2; peer review: 2 approved]
Alaina Shumate, Steven Salzberg
Peer Reviewers Adam Frankish; Mark Borodovsky
  • Funder
  • National Institutes of Health
LATEST VERSION PUBLISHED 29 Apr 2024
https://doi.org/10.12688/f1000research.140624.3
Opinion Article metrics
Revised
Creating cloud platforms for supporting FAIR data management in biomedical research projects.
[version 3; peer review: 2 approved]
Marcel Jentsch, Valentin Schneider-Lunitz, Ulrike Taron, Martin Braun, Naveed Ishaque, Harald Wagener, Christian Conrad, Sven Twardziok
Peer Reviewers Anna Bernasconi; Joseph Bonello
  • Funders
  • Bundesministerium für Bildung und Forschung
  • HORIZON EUROPE European Research Council
LATEST VERSION PUBLISHED 29 Apr 2024
https://doi.org/10.12688/f1000research.136683.2
Software Tool Article metrics
Revised
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
[version 2; peer review: 2 approved]
Marie Lataretu, Oliver Drechsel, René Kmiecinski, Kathrin Trappe, Martin Hölzer, Stephan Fuchs
Peer Reviewers Wolfgang Maier; Sondes Haddad-Boubaker
  • Funder
  • European Centre for Disease Prevention and Control
LATEST VERSION PUBLISHED 16 Apr 2024
https://doi.org/10.12688/f1000research.140403.2
Brief Report metrics
Revised
Methylation risk score in peripheral blood predictive of conversion from mild cognitive impairment to Alzheimer's Disease
[version 2; peer review: 2 approved with reservations, 1 not approved]
Jarrett D. Morrow
Peer Reviewers Adam Smith; Rachel Cavill; Lily Wang and Wei Zhang
  • Funder
  • National Heart, Lung, and Blood Institute
LATEST VERSION PUBLISHED 15 Mar 2024
https://doi.org/10.12688/f1000research.126215.2
Method Article metrics
Revised
Bayesian Multi-View Clustering given complex inter-view structure
[version 2; peer review: 2 approved]
Benjamin D. Shapiro, Alexis Battle
Peer Reviewers Sara Mostafavi; Max Moldovan
  • Funders
  • Microsoft
  • National Institute of General Medical Sciences
LATEST VERSION PUBLISHED 29 Feb 2024
https://doi.org/10.12688/f1000research.141786.2
Review metrics
Revised
Models for the retention of duplicate genes and their biological underpinnings
[version 2; peer review: 2 approved]
Raquel Assis, Gavin Conant, Barbara Holland, David A. Liberles, Malgorzata M. O'Reilly, Amanda E. Wilson
Peer Reviewers Nadia El-Mabrouk; Arturo Becerra
LATEST VERSION PUBLISHED 12 Feb 2024
https://doi.org/10.12688/f1000research.127061.2
Research Article metrics
Revised
Understanding the high electronic quantum similarity of a series of ligands used as inhibitors of the SARS-CoV-2 virus by molecular mechanics and density functional theory approaches
[version 2; peer review: 1 approved, 1 approved with reservations, 3 not approved]
Alejandro Morales-Bayuelo, Jesús Sánchez-Márquez
Peer Reviewers Ahmed Metwaly; Ramon Carbó-Dorca; Kiran Bharat Lokhande; Vikram Dalal; Mohnad Abdalla
  • Funder
  • Fundación Universitaria Tecnológico Comfenalco
LATEST VERSION PUBLISHED 06 Feb 2024
https://doi.org/10.12688/f1000research.125325.2
Software Tool Article metrics
Revised
Librarian: A quality control tool to analyse sequencing library compositions
[version 2; peer review: 2 approved, 1 approved with reservations]
Kartavya Vashishtha, Caroline Gaud, Simon Andrews, Christel Krueger
Peer Reviewers Andrew Keniry; Konstantin Okonechnikov; Karim Gharbi
  • Funder
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 24 Jan 2024
https://doi.org/10.12688/f1000research.135250.2
Software Tool Article metrics
Revised
DrosOMA: the Drosophila Orthologous Matrix browser
[version 2; peer review: 4 approved]
Antonin Thiébaut, Adrian M. Altenhoff, Giulia Campli, Natasha Glover, Christophe Dessimoz, Robert M. Waterhouse
Peer Reviewers Berend Snel; Daofeng Li; Jung-Wan Mok; Elise Parey
  • Funder
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 16 Jan 2024
https://doi.org/10.12688/f1000research.138059.1
Method Article metrics
A tutorial hub for realising the potential of tools within the SPARC ecosystem
[version 1; peer review: 2 approved with reservations]
Niloofar Shahidi, Omkar Athavale, Yuda Munarko, Mathias Roesler, Kenneth Tran
Peer Reviewers Bhavesh Patel; Andrey Andreev
PUBLISHED 08 Jan 2024
41-60 of 389 ARTICLES
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