Evaluated articles

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SODAR: managing multi-omics study data and metadata

This article has 7 authors:
1. Mikko Nieminen
2. Oliver Stolpe
3. Mathias Kuhring
4. January Weiner
5. Patrick Pett
6. Dieter Beule
7. Manuel Holtgrewe
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 22, 2022Latest activity Aug 21, 2023
MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction

This article has 3 authors:
1. Wenhuan Zeng
2. Anupam Gautam
3. Daniel H. Huson
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 4, 2023Latest activity Aug 21, 2023
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research

This article has 8 authors:
1. Carolina P Barros
2. Martijn F L Derks
3. Jeff Mohr
4. Benjamin J Wood
5. Richard P M A Crooijmans
6. Hendrik-Jan Megens
7. Marco C A M Bink
8. Martien A M Groenen
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity Aug 21, 2023
Training Infrastructure as a Service

This article has 14 authors:
1. Helena Rasche
2. Cameron Hyde
3. John Davis
4. Simon Gladman
5. Nate Coraor
6. Anthony Bretaudeau
7. Gianmauro Cuccuru
8. Wendi Bacon
9. Beatriz Serrano-Solano
10. Jennifer Hillman-Jackson
11. Saskia Hiltemann
12. Miaomiao Zhou
13. Björn Grüning
14. Andrew Stubbs
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity Jul 4, 2023
EraSOR: Erase Sample Overlap in polygenic score analyses

This article has 4 authors:
1. Shing Wan Choi
2. Timothy Shin Heng Mak
3. Clive J. Hoggart
4. Paul F. O’Reilly
Reviewed by GigaScience

This article has 6 evaluationsAppears in 1 listLatest version Dec 13, 2021Latest activity Jul 4, 2023
FriendlyClearMap: An optimized toolkit for mouse brain mapping and analysis

This article has 9 authors:
1. Moritz Negwer
2. Bram Bosch
3. Maren Bormann
4. Rick Hesen
5. Lukas Lütje
6. Lynn Aarts
7. Carleen Rossing
8. Nael Nadif Kasri
9. Dirk Schubert
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Feb 18, 2023Latest activity Jun 19, 2023
Strategies and techniques for quality control and semantic enrichment with multimodal data: a case study in colorectal cancer with eHDPrep

This article has 6 authors:
1. Tom M Toner
2. Rashi Pancholi
3. Paul Miller
4. Thorsten Forster
5. Helen G Coleman
6. Ian M Overton
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity Jun 19, 2023
A workflow reproducibility scale for automatic validation of biological interpretation results

This article has 4 authors:
1. Hirotaka Suetake
2. Tsukasa Fukusato
3. Takeo Igarashi
4. Tazro Ohta
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity Jun 19, 2023
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors

This article has 15 authors:
1. Markus Hoffmann
2. Nico Trummer
3. Leon Schwartz
4. Jakub Jankowski
5. Hye Kyung Lee
6. Lina-Liv Willruth
7. Olga Lazareva
8. Kevin Yuan
9. Nina Baumgarten
10. Florian Schmidt
11. Jan Baumbach
12. Marcel H Schulz
13. David B Blumenthal
14. Lothar Hennighausen
15. Markus List
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity Jun 19, 2023
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy

This article has 4 authors:
1. Anup Kumar
2. Gianmauro Cuccuru
3. Björn Grüning
4. Rolf Backofen
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity May 2, 2023
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices

This article has 6 authors:
1. Patrick König
2. Sebastian Beier
3. Martin Mascher
4. Nils Stein
5. Matthias Lange
6. Uwe Scholz
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity May 2, 2023
The Regulatory Mendelian Mutation score for GRCh38

This article has 3 authors:
1. Lusiné Nazaretyan
2. Martin Kircher
3. Max Schubach
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Mar 15, 2022Latest activity May 2, 2023
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

This article has 16 authors:
1. Luc Cornet
2. Benoit Durieu
3. Frederik Baert
4. Elizabet D'hooge
5. David Colignon
6. Loic Meunier
7. Valérian Lupo
8. Ilse Cleenwerck
9. Heide-Marie Daniel
10. Leen Rigouts
11. Damien Sirjacobs
12. Stéphane Declerck
13. Peter Vandamme
14. Annick Wilmotte
15. Denis Baurain
16. Pierre Becker
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity May 2, 2023
Contamination detection and microbiome exploration with GRIMER

This article has 2 authors:
1. Vitor C Piro
2. Bernhard Y Renard
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity Apr 10, 2023
The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

This article has 16 authors:
1. J. William O. Ballard
2. Matt A. Field
3. Richard J. Edwards
4. Laura A.B. Wilson
5. Loukas G. Koungoulos
6. Benjamin D. Rosen
7. Barry Chernoff
8. Olga Dudchenko
9. Arina Omer
10. Jens Keilwagen
11. Ksenia Skvortsova
12. Ozren Bogdanovic
13. Eva Chan
14. Robert Zammit
15. Vanessa Hayes
16. Erez Lieberman Aiden
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Jan 27, 2023Latest activity Apr 10, 2023
Cell type–specific interpretation of noncoding variants using deep learning–based methods

This article has 9 authors:
1. Maria Sindeeva
2. Nikolay Chekanov
3. Manvel Avetisian
4. Tatiana I Shashkova
5. Nikita Baranov
6. Elian Malkin
7. Alexander Lapin
8. Olga Kardymon
9. Veniamin Fishman
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2023Latest activity Apr 10, 2023
ViReMa : a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids

This article has 7 authors:
1. Stephanea Sotcheff
2. Yiyang Zhou
3. Jason Yeung
4. Yan Sun
5. John E Johnson
6. Bruce E Torbett
7. Andrew L Routh
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2023Latest activity Apr 10, 2023
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

This article has 6 authors:
1. Chen Yang
2. Theodora Lo
3. Ka Ming Nip
4. Saber Hafezqorani
5. René L Warren
6. Inanc Birol
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2023Latest activity Apr 10, 2023
FAIR data station for lightweight metadata management and validation of omics studies

This article has 3 authors:
1. Bart Nijsse
2. Peter J Schaap
3. Jasper J Koehorst
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 28, 2022Latest activity Apr 10, 2023
3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

This article has 32 authors:
1. Mihaly Varadi
2. Sreenath Nair
3. Ian Sillitoe
4. Gerardo Tauriello
5. Stephen Anyango
6. Stefan Bienert
7. Clemente Borges
8. Mandar Deshpande
9. Tim Green
10. Demis Hassabis
11. Andras Hatos
12. Tamas Hegedus
13. Maarten L Hekkelman
14. Robbie Joosten
15. John Jumper
16. Agata Laydon
17. Dmitry Molodenskiy
18. Damiano Piovesan
19. Edoardo Salladini
20. Steven L. Salzberg
21. Markus J Sommer
22. Martin Steinegger
23. Erzsebet Suhajda
24. Dmitri Svergun
25. Luiggi Tenorio-Ku
26. Silvio Tosatto
27. Kathryn Tunyasuvunakool
28. Andrew Mark Waterhouse
29. Augustin Žídek
30. Torsten Schwede
31. Christine Orengo
32. Sameer Velankar
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Aug 3, 2022Latest activity Mar 24, 2023

Evaluated articles

SODAR: managing multi-omics study data and metadata

MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction

A new haplotype-resolved turkey genome to enable turkey genetics and genomics research

Training Infrastructure as a Service

EraSOR: Erase Sample Overlap in polygenic score analyses

FriendlyClearMap: An optimized toolkit for mouse brain mapping and analysis

Strategies and techniques for quality control and semantic enrichment with multimodal data: a case study in colorectal cancer with eHDPrep

A workflow reproducibility scale for automatic validation of biological interpretation results

TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors

An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy

DivBrowse—interactive visualization and exploratory data analysis of variant call matrices

The Regulatory Mendelian Mutation score for GRCh38

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

Contamination detection and microbiome exploration with GRIMER

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Cell type–specific interpretation of noncoding variants using deep learning–based methods

ViReMa : a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

FAIR data station for lightweight metadata management and validation of omics studies

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources