Bioinformatics

Bioinformatics

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21-40 of 377 ARTICLES
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https://doi.org/10.12688/f1000research.140344.2
Research Article metrics
Revised
NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling
[version 2; peer review: 2 approved]
Friederike Hanssen, Gisela Gabernet, Famke Bäuerle, Bianca Stöcker, Felix Wiegand, Nicholas H. Smith, Christian Mertes, Avirup Guha Neogi, Leon Brandhoff, Anna Ossowski, Janine Altmueller, Kerstin Becker, Andreas Petzold, Marc Sturm, Tyll Stöcker, Sugirthan Sivalingam, Fabian Brand, Axel Schmidt, Andreas Buness, Alexander J. Probst, Susanne Motameny, Johannes Köster
Peer Reviewers Justin M. Zook; Kez Cleal
  • Funders
  • German Federal Ministry for Education and Research
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 12 Sep 2024
https://doi.org/10.12688/f1000research.153895.1
Opinion Article metrics
From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure
[version 1; peer review: 3 approved with reservations]
Bogdan Mirăuță, Cătălina Zenoaga-Barbăroșie, Monica Abrudan, Marius Mihășan, Mădălina Giurgiu, Daria Mihalachi, Michalis-Daniel Lazăr, RSBI Members, Horia L. Banciu
Peer Reviewers Francis Ouellette; Federico Zambelli; Carol Goble
  • Funder
  • EEA Grants/Norway Grants (Bioinformatics Capacity Building Human Genomics, an RSBI and ELIXIR Norway bilateral project)
PUBLISHED 03 Sep 2024
https://doi.org/10.12688/f1000research.131134.2
Research Article metrics
Revised
Improving genomic prediction of rhizomania resistance in sugar beet (Beta vulgaris L.) by implementing epistatic effects and feature selection
[version 2; peer review: 1 approved with reservations, 3 not approved]
Thomas Martin Lange, Felix Heinrich, Friedrich Kopisch-Obuch, Harald Keunecke, Mehmet Gültas, Armin O. Schmitt
Peer Reviewers J Mitchell McGrath; Muhammad Massub Tehseen; Daniela Holtgräwe; Chenggen Chu
LATEST VERSION PUBLISHED 28 Aug 2024
https://doi.org/10.12688/f1000research.150115.1
Research Article metrics
Unraveling the Interplay of Autophagy Genes and KLF3/KLF8 in Colorectal Cancer Metastasis: A Bioinformatics and cellular Exploration
[version 1; peer review: 1 approved with reservations, 1 not approved]
Eglal Mahgoub, Jalal Taneera, Samrein B. Ahmed, shirin hafezi, Thenmozhi Venkatachalam, Mahmood Hachim, Nabil Sulaiman, Rifat Hamoudi, Maha Saber-Ayad
Peer Reviewers Aamir Ahmed; Mohammad Azhar Aziz
  • Funders
  • University of Sharjah
  • Mohammed Bin Rashid University of Medicine and Health Sciences
PUBLISHED 30 Jul 2024
https://doi.org/10.12688/f1000research.139356.2
Research Article metrics
Revised
Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric
[version 2; peer review: 3 approved]
James Fleming, Pia Merete Eriksen, Torsten Hugo Struck
Peer Reviewers Paul Zaharias; Xianzhao Kan; Anthony K. Redmond
  • Funders
  • Norges Forskningsråd
  • Norwegian Metacenter for Computational Science
LATEST VERSION PUBLISHED 10 Jul 2024
https://doi.org/10.12688/f1000research.134956.2
Research Article metrics
Revised
In silico screening for potential inhibitors from the phytocompounds of Carica papaya against Zika virus NS5 protein
[version 2; peer review: 3 approved]
Kishore Krishna Kumaree, Naga Venkata Anusha Anthikapalli, Anchalee Prasansuklab
Peer Reviewers Arumugam Vijaya Anand; Luis Marquez-Dominguez; Tiratha Raj Singh
  • Funder
  • Second Century Fund (C2F) Postdoctoral Fellowship, Chulalongkorn University
LATEST VERSION PUBLISHED 25 Jun 2024
https://doi.org/10.12688/f1000research.122924.2
Software Tool Article metrics
Revised
Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics
[version 2; peer review: 2 approved, 2 approved with reservations]
Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita, Takeshi Fujino, Tsuyoshi Hachiya, Yuichi Kodama, Takatomo Fujisawa, Osamu Ogasawara, Atsushi Shimizu, Masanori Arita, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta
Peer Reviewers Justin M. Wozniak; Iacopo Colonnelli; Denis Yuen; Stephen R. Piccolo
  • Funders
  • JSPS KAKENHI
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan
  • Japan Science and Technology Agency
LATEST VERSION PUBLISHED 24 Jun 2024
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
21-40 of 377 ARTICLES
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