Evaluated articles

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Context-aware simulation enables systematic optimization of long-read mapping parameters

This article has 4 authors:
1. Jiang Hu
2. Dongming Fang
3. Xin Jin
4. Chentao Yang
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 8, 2025Latest activity Aug 7, 2026
NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing

This article has 15 authors:
1. Yuqian Liu
2. Zidong Su
3. Wenzhen Yang
4. Denghui Li
5. Jiawen Zhang
6. Yuning Zhang
7. Tao Zeng
8. Yong Zhang
9. Yuxiang Li
10. Guangyi Fan
11. Kailong Ma
12. Shanshan Liu
13. Xun Xu
14. Yuliang Dong
15. Zongan Wang
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Nov 28, 2025Latest activity Aug 7, 2026
Extending Protein Language Models to a Viral Genomic Scale Using Biologically Induced Sparse Attention

This article has 8 authors:
1. Thibaut Dejean
2. Barbra D. Ferrell
3. William Harrigan
4. Zachary D. Schreiber
5. Rajan Sawhney
6. K. Eric Wommack
7. Shawn W. Polson
8. Mahdi Belcaid
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jun 1, 2025Latest activity Aug 7, 2026
KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences

This article has 9 authors:
1. Brook E. Santangelo
2. Harshad Hegde
3. J. Harry Caufield
4. Justin Reese
5. Tomas Kliegr
6. Lawrence E. Hunter
7. Catherine A. Lozupone
8. Christopher J. Mungall
9. Marcin P. Joachimiak
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Feb 28, 2025Latest activity Aug 7, 2026
ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data

This article has 12 authors:
1. Danni Luo
2. Sophie Robertson
3. Yuanchun Zhan
4. Ruichen Rong
5. Shidan Wang
6. Xi Jiang
7. Sen Yang
8. Suzette Palmer
9. Liwei Jia
10. Qiwei Li
11. Guanghua Xiao
12. Xiaowei Zhan
Reviewed by GigaScience

This article has 5 evaluationsAppears in 1 listLatest version Jul 25, 2023Latest activity Aug 7, 2026
Comparison of Deep Learning Approaches for Extreme Low-SNR Image Restoration

This article has 6 authors:
1. Nasreen Elizabeth Buhn
2. Sriya Reddy Adunur
3. Joseph Hamilton
4. Summer Levis
5. Guy M. Hagen
6. Jonathan D. Ventura
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 20, 2026Latest activity Aug 7, 2026
ChatMDV: Democratising Bioinformatics Analysis Using Large Language Models

This article has 9 authors:
1. Maria Kiourlappou
2. Peter Todd
3. Yaxuan Kong
4. Jayesh Hire
5. Sibgathullah Furquan Nawab Mohammed
6. Martin Sergeant
7. Stefan Zohren
8. Jim Hughes
9. Stephen Taylor
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 27, 2025Latest activity Aug 7, 2026
CPSM: R-package of an Automated Machine Learning Pipeline for Predicting the Survival Probability of Single Cancer Patient

This article has 4 authors:
1. Harpreet Kaur
2. Pijush Das
3. Kevin Camphausen
4. Uma Shankavaram
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Nov 15, 2024Latest activity Aug 7, 2026
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