Evaluated articles

Showing page 1 of 23 pages of list content

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

This article has 5 authors:
1. Fiona Teltscher
2. Petra Korlević
3. Edel Sheerin
4. Alex Makunin
5. Mara K N Lawniczak
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2026Latest activity Jul 10, 2026
Cell type transcriptomics reveal shared genetic mechanisms in Alzheimer’s and Parkinson’s disease

This article has 11 authors:
1. Anwesha Bhattacharya
2. Edward A. Fon
3. Alain Dagher
4. Yasser Iturria-Medina
5. Jo Anne Stratton
6. Chloe Savignac
7. Jack Stanley
8. Liam Hodgson
9. Badr Ait Hammou
10. David A Bennett
11. Danilo Bzdok
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Feb 19, 2025Latest activity Jul 10, 2026
4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians

This article has 37 authors:
1. Kai Han
2. Yue Chen
3. Yao Li
4. Lidong Guo
5. Yuxiaofei Wang
6. Xiawei Liu
7. Yaru Lin
8. Zhi Huang
9. Qun Liu
10. Wenjie Guo
11. Rui Zhang
12. Wandong Zhao
13. Langchao Liang
14. Xiaoyu Wei
15. Li Zhou
16. Xuebin Mao
17. Jiaqi Wang
18. Weijian Wu
19. Hongwei Pan
20. Tao Yang
21. He Zhang
22. Xiaoshan Su
23. Shanshan Liu
24. Wenwei Zhang
25. Longqi Liu
26. Søren Tvorup Christensen
27. Jifeng Fei
28. Xin Liu
29. Guangyi Fan
30. Hanbo Li
31. Ying Gu
32. Jian Wang
33. Huanming Yang
34. Gang Pei
35. Xun Xu
36. An Zeng
37. Mengyang Xu
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Feb 19, 2026Latest activity Jul 10, 2026
PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

This article has 6 authors:
1. Júlia Ortís Sunyer
2. Luis F. Delgado
3. Oskar Hickl
4. Cedric C. Laczny
5. Patrick May
6. Paul Wilmes
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Dec 11, 2024Latest activity Jul 10, 2026
FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

This article has 15 authors:
1. Jia-Yuan Zhang
2. Changjiu Miao
3. Teng Qiu
4. Junyi He
5. Wenqi Cao
6. Wei Lin
7. Xiaoshuang Xia
8. Lei He
9. Chunlei Yang
10. Yuhui Sun
11. Tao Zeng
12. Yuxiang Li
13. Xun Xu
14. Yijun Ruan
15. Yuliang Dong
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2026Latest activity Jul 10, 2026
METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions

This article has 4 authors:
1. Disha Tandon
2. Tarcisio Mendes De Farias
3. Pierre-Marie Allard
4. Emmanuel Defossez
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2026Latest activity Jul 10, 2026
HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets

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

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2026Latest activity Apr 28, 2026
MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot 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 Jan 1, 2026Latest 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 Jan 1, 2026Latest 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. María E Navarrete Rodríguez
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 Jan 1, 2026Latest activity Apr 10, 2026
Characterizing 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. Hugh 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 Jan 1, 2026Latest 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 Jan 1, 2026Latest 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 denormalization tool for integrating single-cell transcriptomics data

This article has 12 authors:
1. Yin Huang
2. Anna Vathrakokoili Pournara
3. Ying Ao
4. Ziliang Huang
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 Jan 1, 2026Latest 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 Jan 1, 2026Latest 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 1, 2026Latest activity Mar 20, 2026
Enhanced semantic classification of microbiome sample origins using large language models (LLMs)

This article has 8 authors:
1. Daniela Gaio
2. Janko Tackmann
3. Eugenio Perez-Molphe-Montoya
4. Nicolas Näpflin
5. David Patsch
6. Lukas Malfertheiner
7. Matteo Eustachio Peluso
8. Christian von Mering
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2026Latest 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 Jan 1, 2026Latest activity Feb 24, 2026

Evaluated articles

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

Cell type transcriptomics reveal shared genetic mechanisms in Alzheimer’s and Parkinson’s disease

4D Single-Cell Spatial Transcriptomics Reveals Dynamic Morphogenetic Gradients and Regenerative Domains in Planarians

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions

HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets

MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot 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

Characterizing 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 denormalization 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