Evaluated articles

Showing page 1 of 23 pages of list content

HVRLocator: A Computationally Efficient Tool for Identifying Hypervariable Regions in 16S rRNA Big Datasets

This article has 7 authors:
1. Clara Arboleda-Baena
2. Felipe Borim Correa
3. Joao Pedro Saraiva
4. Santiago Castillo
5. Jonas Coelho Kasmanas
6. Antonis Chatzinotas
7. Stephanie D. Jurburg
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 29, 2025Latest activity Apr 28, 2026
MicroFinder: Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes

This article has 4 authors:
1. Thomas C. Mathers
2. Michael Paulini
3. Cibele G. Sotero-Caio
4. Jonathan M. D. Wood
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version May 14, 2025Latest activity Apr 28, 2026
GEfetch2R : fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools

This article has 3 authors:
1. Yabing Song
2. Jianbin Wang
3. Jiaxin Gao
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Nov 20, 2023Latest activity Apr 28, 2026
Patterns of aDNA Damage Through Time and Environments – lessons from herbarium specimens

This article has 12 authors:
1. Stefano Porrelli
2. Alice Fornasiero
3. Hong Phuong Le
4. Wenzhe Yin
5. Maria Navarrete Rodriguez
6. Nahed Mohammed
7. Axel Himmelbach
8. Andrew C. Clarke
9. Nils Stein
10. Paul J. Kersey
11. Rod A. Wing
12. Rafal M. Gutaker
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Oct 26, 2025Latest activity Apr 10, 2026
Characterising a species-rich and understudied tropical insect fauna using DNA barcoding

This article has 11 authors:
1. David R. Hemprich-Bennett
2. Ezekiel Donkor
3. Bernard Adams
4. Naana Afua Acquaah
5. Eva D. Ofori
6. Samuel Anie-Amoah
7. Abigail Bailey
8. H. Charles J. Godfray
9. Owen T. Lewis
10. Fred Aboagye-Antwi
11. Talya D. Hackett
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Oct 1, 2025Latest activity Apr 10, 2026
MADRe: Strain-Level Metagenomic Classification Through Assembly-Driven Database Reduction

This article has 4 authors:
1. Josipa Lipovac
2. Mile Šikić
3. Riccardo Vicedomini
4. Krešimir Križanović
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version May 15, 2025Latest activity Apr 10, 2026
Sex Chromosome Turnover and Structural Interspecific Genome Divergence Shapes Meiotic Outcomes in Hybridizing Cobitis

This article has 23 authors:
1. S. A. Schlebusch
2. V. Trifonov
3. Z. Halenková
4. M. Klianitskaya
5. D. Dedukh
6. A. Ruiz Herrera
7. L. Álvarez González
8. G. Pujol Infantes
9. E. Hřibová
10. L. Andjel
11. O. Bartoš
12. P. Pajer
13. T. Tichopád
14. D. Kulik
15. J. Kotusz
16. M. Kaštánková Doležálková
17. A. Bohne
18. A. Marta
19. P. Horna
20. R. Reifová
21. Y. Guiguen
22. J. Pačes
23. K. Janko
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Apr 6, 2025Latest activity Apr 10, 2026
scDenorm: a denormalisation tool for integrating single-cell transcriptomics data

This article has 12 authors:
1. Yin Huang
2. Anna Vathrakokili Pournara
3. Ying Ao
4. Lirong Yang
5. Hui Zhang
6. Yongjian Zhang
7. Sheng Liu
8. Alvis Brazma
9. Irene Papatheodorou
10. Xinlu Yang
11. Ming Shi
12. Zhichao Miao
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version May 15, 2025Latest activity Apr 9, 2026
Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination

This article has 4 authors:
1. Aitor Zabala
2. Alex M. Ascensión
3. Iñigo Prada-Luengo
4. David Otaegui
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 18, 2025Latest activity Mar 20, 2026
MIReVTD, a Minimum Information Standard for Reporting Vector Trait Data

This article has 7 authors:
1. Sadie J. Ryan
2. Paul J. Huxley
3. Catherine A. Lippi
4. Samraat Pawar
5. Lauren Cator
6. Samuel S.C. Rund
7. Leah R. Johnson
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 28, 2025Latest activity Mar 20, 2026
Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs)

This article has 7 authors:
1. Daniela Gaio
2. Janko Tackmann
3. Eugenio Perez-Molphe-Montoya
4. Nicolas Näpflin
5. David Patsch
6. Lukas Malfertheiner
7. Christian von Mering
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Apr 27, 2025Latest activity Feb 24, 2026
Improved genome assembly of whale shark, the world’s biggest fish: revealing “chromocline” in intragenomic heterogeneity

This article has 3 authors:
1. Yawako W. Kawaguchi
2. Rui Matsumoto
3. Shigehiro Kuraku
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Sep 10, 2025Latest activity Feb 24, 2026
Single-nucleus multiple-organ chromatin accessibility mapping in the rat

This article has 9 authors:
1. Ronghai Li
2. Yue Yuan
3. Shanshan Duan
4. Qiuting Deng
5. Wen Ma
6. Chang Liu
7. Peng Gao
8. Li Lu
9. Chuanyu Liu
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Nov 11, 2024Latest activity Feb 24, 2026
An Interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis

This article has 7 authors:
1. Zexuan Wang
2. Qipeng Zhan
3. Shu Yang
4. Zhuoping Zhou
5. Mengyuan Kan
6. Tianhuan Zhai
7. Li Shen
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Nov 2, 2024Latest activity Feb 24, 2026
Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine

This article has 9 authors:
1. Abdulkadir Elmas
2. Hillary M. Layden
3. Jacob D. Ellis
4. Luke N. Bartlett
5. Xian Zhao
6. Reika Kawabata-Iwakawa
7. Hideru Obinata
8. Scott W. Hiebert
9. Kuan-lin Huang
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Oct 21, 2024Latest activity Jan 30, 2026
Federated Knowledge Retrieval Elevates Large Language Model Performance on Biomedical Benchmarks

This article has 2 authors:
1. Janet Joy
2. Andrew I. Su
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 2, 2025Latest activity Jan 29, 2026
SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

This article has 2 authors:
1. Souvik Seal
2. Brian Neelon
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Apr 3, 2025Latest activity Jan 29, 2026
nf-core/proteinfamilies: A scalable pipeline for the generation of protein families

This article has 13 authors:
1. Evangelos Karatzas
2. Martin Beracochea
3. Fotis A. Baltoumas
4. Eleni Aplakidou
5. Lorna Richardson
6. James A. Fellows Yates
7. Daniel Lundin
8. nf-core community
9. Aydin Buluç
10. Nikos C. Kyrpides
11. Ilias Georgakopoulos-Soares
12. Georgios A. Pavlopoulos
13. Robert D. Finn
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 16, 2025Latest activity Jan 29, 2026
Comparative evaluation of computational methods for reconstruction of human viral genomes

This article has 7 authors:
1. Maria J. P. Sousa
2. Mari Toppinen
3. Lari Pyöriä
4. Klaus Hedman
5. Antti Sajantila
6. Maria F. Perdomo
7. Diogo Pratas
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 22, 2025Latest activity Jan 5, 2026
Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

This article has 12 authors:
1. Sarah L.F. Martin
2. Renato La Torre
3. Bram Danneels
4. Ave Tooming-Klunderud
5. Morten Skage
6. Spyridon Kollias
7. Ole Kristian Tørresen
8. Mohsen Falahati Anbaran
9. Elisabeth Stur
10. Kjetill S. Jakobsen
11. Michael D. Martin
12. Torbjørn Ekrem
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 1, 2025Latest activity Jan 5, 2026

Evaluated articles

HVRLocator: A Computationally Efficient Tool for Identifying Hypervariable Regions in 16S rRNA Big Datasets

MicroFinder: Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes

GEfetch2R : fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools

Patterns of aDNA Damage Through Time and Environments – lessons from herbarium specimens

Characterising a species-rich and understudied tropical insect fauna using DNA barcoding

MADRe: Strain-Level Metagenomic Classification Through Assembly-Driven Database Reduction

Sex Chromosome Turnover and Structural Interspecific Genome Divergence Shapes Meiotic Outcomes in Hybridizing Cobitis

scDenorm: a denormalisation tool for integrating single-cell transcriptomics data

Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination

MIReVTD, a Minimum Information Standard for Reporting Vector Trait Data

Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs)

Improved genome assembly of whale shark, the world’s biggest fish: revealing “chromocline” in intragenomic heterogeneity

Single-nucleus multiple-organ chromatin accessibility mapping in the rat

An Interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis

Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine

Federated Knowledge Retrieval Elevates Large Language Model Performance on Biomedical Benchmarks

SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

nf-core/proteinfamilies: A scalable pipeline for the generation of protein families

Comparative evaluation of computational methods for reconstruction of human viral genomes

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids