Bioinformatics
Bioinformatics
Software Tool Article
metrics
scRICA: An R package for multiple-sample single-cell RNA-seq data integrative comparative analysis
[version 1; peer review: 1 approved with reservations, 1 not approved]
Peer Reviewers
Pedro L Baldoni;
Sebastiaan Valkiers
- Funders
- University of Chicago
- National Institutes of Health
- Institute for Translational Medicine
Research Article
metrics
Revised
In silico molecular docking and molecular dynamic simulation of agarwood compounds with molecular targets of Alzheimer’s disease
[version 2; peer review: 3 approved, 1 not approved]
Peer Reviewers
Sailu Sarvagalla;
Yassir Boulaamane and Iman Touati;
Abdul Rajjak Shaikh;
James Adams
- Funder
- Thailand Science Research and Innovation Fund Chulalongkorn University
Software Tool Article
metrics
Revised
RBP-Tar – a searchable database for experimental RBP binding sites
[version 3; peer review: 2 approved, 4 approved with reservations]
Peer Reviewers
Xiaoyong Pan;
Clifford A Meyer;
Michiel Stock;
Eric Van Nostrand;
M. J. Nishanth;
Zhi-Ping Liu
- Funders
- ELIXIR-CZ
- Ministry of Education, Youth and Sports of the Czech Republic
- MEYS
- Horizon europe
Software Tool Article
metrics
BEpipeR: a user-friendly, flexible, and scalable data synthesis pipeline for the Biodiversity Exploratories and other research consortia
[version 1; peer review: 1 approved with reservations, 1 not approved]
Peer Reviewers
Elliot Gould;
Matthias Grenié
- Funder
- Deutsche Forschungsgemeinschaft
Research Article
metrics
Revised
A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.
[version 3; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Thi Thanh Binh Nguyen;
Rituraj Purohit;
Behrooz sadeghi kalani
- Funder
- Ministry of Science and Technology, Government of the People’s Republic of Bangladesh
Software Tool Article
metrics
Revised
Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG
[version 2; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Abraham Gihawi;
Fotis Baltoumas;
Juliette Hayer
- Funders
- Centenary Research Fund of the University of Fribourg
- Fondation de Recherche en Biochimie, Epalinges, Switzerland
Research Article
metrics
Revised
In silico analysis of molecular mimicry between human aquaporin 3, Aspergillus fumigatus aquaporin and aquaporins from allergic sources
[version 2; peer review: 2 approved]
Peer Reviewers
Celso Eduardo Olivier;
Elizabeth Garcia
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]
Peer Reviewers
Justin M. Zook;
Kez Cleal
- Funders
- German Federal Ministry for Education and Research
- Deutsche Forschungsgemeinschaft
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]
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)
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]
Peer Reviewers
J Mitchell McGrath;
Muhammad Massub Tehseen;
Daniela Holtgräwe;
Chenggen Chu
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]
Peer Reviewers
Aamir Ahmed;
Mohammad Azhar Aziz
- Funders
- University of Sharjah
- Mohammed Bin Rashid University of Medicine and Health Sciences
Research Article
metrics
Revised
Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric
[version 2; peer review: 3 approved]
Peer Reviewers
Paul Zaharias;
Xianzhao Kan;
Anthony K. Redmond
- Funders
- Norges Forskningsråd
- Norwegian Metacenter for Computational Science
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]
Peer Reviewers
Arumugam Vijaya Anand;
Luis Marquez-Dominguez;
Tiratha Raj Singh
- Funder
- Second Century Fund (C2F) Postdoctoral Fellowship, Chulalongkorn University
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]
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
Opinion Article
metrics
Revised
Systems Biology in ELIXIR: modelling in the spotlight
[version 2; peer review: 2 approved, 1 approved with reservations]
Peer Reviewers
Yoram Vodovotz;
Herbert Sauro;
Ioannis Androulakis
- Funder
- EPAnEk-NSRF
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]
Peer Reviewers
Johannes Söding;
Jun Zhang;
Junbai Wang;
Andreas Schlundt
- Funder
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
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]
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
Software Tool Article
metrics
ZARP: A user-friendly and versatile RNA-seq analysis workflow
[version 1; peer review: 2 approved with reservations]
Peer Reviewers
Silvia Liu;
Bo Li
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- National Center of Competence in Research RNA & Disease
Opinion Article
metrics
Revised
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity
[version 2; peer review: 3 approved]
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
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]
Peer Reviewers
Gustavo Fioravanti Vieira
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