Evaluated articles

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A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

This article has 18 authors:
1. Hardip R. Patel
2. Kirat Alreja
3. Andre L.M. Reis
4. J King Chang
5. Zahra A. Chew
6. Hyungtaek Jung
7. Jillian M. Hammond
8. Ira W. Deveson
9. Aurora Ruiz-Herrera
10. Laia Marin-Gual
11. Clare E. Holleley
12. Xiuwen Zhang
13. Nicholas C. Lister
14. Sarah Whiteley
15. Lei Xiong
16. Duminda S.B. Dissanayake
17. Paul D. Waters
18. Arthur Georges
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version May 2, 2025Latest activity Aug 26, 2025
Telomere-to-telomere African wild rice ( Oryza longistaminata ) reference genome reveals segmental and structural variation

This article has 23 authors:
1. Xuanmin Guang
2. Jingnan Yang
3. Shilai Zhang
4. Fei Guo
5. Linzhou Li
6. Xiaoping Lian
7. Tao Zeng
8. Chongyang Cai
9. Fushu Liu
10. Zhihao Li
11. Yangzi Hu
12. Dongming Fang
13. Weiming He
14. Sunil Kumar Sahu
15. Wangsheng Li
16. Haorong Lu
17. Yuxiang Li
18. Huan Liu
19. Xun Xu
20. Ying Gu
21. Fengyi Hu
22. Yuliang Dong
23. Tong Wei
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Sep 7, 2024Latest activity Aug 26, 2025
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

This article has 24 authors:
1. Qunfei Guo
2. Youliang Pan
3. Wei Dai
4. Fei Guo
5. Tao Zeng
6. Wanyi Chen
7. Yaping Mi
8. Yanshu Zhang
9. Shuaizhen Shi
10. Wei Jiang
11. Huimin Cai
12. Beiying Wu
13. Yang Zhou
14. Ying Wang
15. Chentao Yang
16. Xiao Shi
17. Xu Yan
18. Junyi Chen
19. Chongyang Cai
20. Jingnan Yang
21. Xun Xu
22. Ying Gu
23. Yuliang Dong
24. Qiye Li
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Sep 10, 2024Latest activity Aug 26, 2025
SeuratExtend: Streamlining Single-Cell RNA-Seq Analysis Through an Integrated and Intuitive Framework

This article has 4 authors:
1. Yichao Hua
2. Linqian Weng
3. Fang Zhao
4. Florian Rambow
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 4, 2024Latest activity Aug 4, 2025
Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

This article has 11 authors:
1. Oscar Aramburu
2. Belén Gómez-Pardo
3. Paula Rodríguez-Villamayor
4. Andrés Blanco-Hortas
5. Jesús Lamas
6. Pooran Dewari
7. Diego Perojil-Morata
8. Pierre Boudinot
9. Daniel J. Macqueen
10. Carmen Bouza
11. Paulino Martínez
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Feb 15, 2024Latest activity Aug 4, 2025
CellBinDB: A Large-Scale Multimodal Annotated Dataset for Cell Segmentation with Benchmarking of Universal Models

This article has 13 authors:
1. Can Shi
2. Jinghong Fan
3. Zhonghan Deng
4. Huanlin Liu
5. Qiang Kang
6. Yumei Li
7. Jing Guo
8. Jingwen Wang
9. Jinjiang Gong
10. Sha Liao
11. Ao Chen
12. Ying Zhang
13. Mei Li
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Nov 21, 2024Latest activity Jul 8, 2025
Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database

This article has 8 authors:
1. Shuya Ikeda
2. Zhaonan Zou
3. Hidemasa Bono
4. Yuki Moriya
5. Shuichi Kawashima
6. Toshiaki Katayama
7. Shinya Oki
8. Tazro Ohta
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Feb 22, 2025Latest activity Jul 8, 2025
The FIP 1.0 Data Set: Highly Resolved Annotated Image Time Series of 4,000 Wheat Plots Grown in Six Years

This article has 28 authors:
1. Lukas Roth
2. Mike Boss
3. Norbert Kirchgessner
4. Helge Aasen
5. Brenda Patricia Aguirre-Cuellar
6. Price Pius Atuah Akiina
7. Jonas Anderegg
8. Joaquin Gajardo Castillo
9. Xiaoran Chen
10. Simon Corrado
11. Krzysztof Cybulski
12. Beat Keller
13. Stefan Göbel Kortstee
14. Lukas Kronenberg
15. Frank Liebisch
16. Paraskevi Nousi
17. Corina Oppliger
18. Gregor Perich
19. Johannes Pfeifer
20. Kang Yu
21. Nicola Storni
22. Flavian Tschurr
23. Simon Treier
24. Michele Volpi
25. Hansueli Zellweger
26. Olivia Zumsteg
27. Andreas Hund
28. Achim Walter
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Oct 5, 2024Latest activity Jul 8, 2025
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome

This article has 5 authors:
1. Murilo Caminotto Barbosa
2. João Fernando Marques da Silva
3. Leonardo Cardoso Alves
4. Robert D Finn
5. Alexandre Rossi Paschoal
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Jul 19, 2024Latest activity Jul 8, 2025
Chromosome-level genome assembly and methylome profile enables insights for the conservation of endangered loggerhead sea turtles

This article has 10 authors:
1. Eugenie C. Yen
2. James D. Gilbert
3. Alice Balard
4. Albert Taxonera
5. Kirsten Fairweather
6. Heather L. Ford
7. Doko-Miles J. Thorburn
8. Stephen J. Rossiter
9. José M. Martín-Durán
10. Christophe Eizaguirre
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Aug 28, 2024Latest activity Jul 8, 2025
Health Data Nexus: an open data platform for AI research and education in medicine

This article has 12 authors:
1. January Adams
2. Rafal Cymerys
3. Karol Szuster
4. Daniel Hekman
5. Zoryana Salo
6. Rutvik Solanki
7. Muhammad Mamdani
8. Alistair Johnson
9. Katarzyna Ryniak
10. Tom Pollard
11. David Rotenberg
12. Benjamin Haibe-Kains
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Jan 1, 2025Latest activity Jul 8, 2025
Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )

This article has 15 authors:
1. Gabriel Mochales-Riaño
2. Samuel R. Hirst
3. Adrián Talavera
4. Bernat Burriel-Carranza
5. Viviana Pagone
6. Maria Estarellas
7. Theo Busschau
8. Stéphane Boissinot
9. Michael P. Hogan
10. Jordi Tena-Garcés
11. Davinia Pla
12. Juan J. Calvete
13. Johannes Els
14. Mark J. Margres
15. Salvador Carranza
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jul 29, 2024Latest activity Jul 8, 2025
Analysis-ready VCF at Biobank scale using Zarr

This article has 16 authors:
1. Eric Czech
2. Timothy R. Millar
3. Will Tyler
4. Tom White
5. Benjamin Elsworth
6. Jérémy Guez
7. Jonny Hancox
8. Ben Jeffery
9. Konrad J. Karczewski
10. Alistair Miles
11. Sam Tallman
12. Per Unneberg
13. Rafal Wojdyla
14. Shadi Zabad
15. Jeff Hammerbacher
16. Jerome Kelleher
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jun 12, 2024Latest activity Jul 8, 2025
The first near-complete genome assembly of pig: enabling more accurate genetic research

This article has 13 authors:
1. Caiyun Cao
2. Jian Miao
3. Qinqin Xie
4. Jiabao Sun
5. Hong Cheng
6. Zhenyang Zhang
7. Fen Wu
8. Shuang Liu
9. Xiaowei Ye
10. Zhe Zhang
11. Qishan Wang
12. Yuchun Pan
13. Zhen Wang
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Oct 15, 2024Latest activity Jun 3, 2025
Spatial Integration of Multi-Omics Data using the novel Multi-Omics Imaging Integration Toolset

This article has 9 authors:
1. Maximillian Wess
2. Maria K. Andersen
3. Elise Midtbust
4. Juan Carlos Cabellos Guillem
5. Trond Viset
6. Øystein Størkersen
7. Sebastian Krossa
8. Morten Beck Rye
9. May-Britt Tessem
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jun 12, 2024Latest activity Jun 3, 2025
External validation of machine learning models—registered models and adaptive sample splitting

This article has 8 authors:
1. Giuseppe Gallitto
2. Robert Englert
3. Balint Kincses
4. Raviteja Kotikalapudi
5. Jialin Li
6. Kevin Hoffschlag
7. Ulrike Bingel
8. Tamas Spisak
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Jun 3, 2025
Defining the limits of plant chemical space: challenges and estimations

This article has 10 authors:
1. Chloe Engler Hart
2. Yojana Gadiya
3. Tobias Kind
4. Christoph A. Krettler
5. Matthew Gaetz
6. Biswapriya B. Misra
7. David Healey
8. August Allen
9. Viswa Colluru
10. Daniel Domingo-Fernández
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 13, 2025Latest activity May 6, 2025
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species

This article has 23 authors:
1. David Kainer
2. Matthew Lane
3. Kyle A Sullivan
4. J Izaak Miller
5. Mikaela Cashman
6. Mallory Morgan
7. Ashley Cliff
8. Jonathon Romero
9. Angelica Walker
10. D Dakota Blair
11. Hari Chhetri
12. Yongqin Wang
13. Mirko Pavicic
14. Anna Furches
15. Jaclyn Noshay
16. Meghan Drake
17. A J Ireland
18. Ali Missaoui
19. Yun Kang
20. John C Sedbrook
21. Paramvir Dehal
22. Shane Canon
23. Daniel Jacobson
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Jan 1, 2025Latest activity May 6, 2025
Network-based anomaly detection algorithm reveals proteins with major roles in human tissues

This article has 4 authors:
1. Dima Kagan
2. Juman Jubran
3. Esti Yeger-Lotem
4. Michael Fire
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Apr 28, 2025
Healthy microbiome—moving towards functional interpretation

This article has 5 authors:
1. Kinga Zielińska
2. Klas I Udekwu
3. Witold Rudnicki
4. Alina Frolova
5. Paweł P Łabaj
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Apr 3, 2025

Evaluated articles

A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

Telomere-to-telomere African wild rice ( Oryza longistaminata ) reference genome reveals segmental and structural variation

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

SeuratExtend: Streamlining Single-Cell RNA-Seq Analysis Through an Integrated and Intuitive Framework

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

CellBinDB: A Large-Scale Multimodal Annotated Dataset for Cell Segmentation with Benchmarking of Universal Models

Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database

The FIP 1.0 Data Set: Highly Resolved Annotated Image Time Series of 4,000 Wheat Plots Grown in Six Years

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome

Chromosome-level genome assembly and methylome profile enables insights for the conservation of endangered loggerhead sea turtles

Health Data Nexus: an open data platform for AI research and education in medicine

Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )

Analysis-ready VCF at Biobank scale using Zarr

The first near-complete genome assembly of pig: enabling more accurate genetic research

Spatial Integration of Multi-Omics Data using the novel Multi-Omics Imaging Integration Toolset

External validation of machine learning models—registered models and adaptive sample splitting

Defining the limits of plant chemical space: challenges and estimations

RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species

Network-based anomaly detection algorithm reveals proteins with major roles in human tissues

Healthy microbiome—moving towards functional interpretation