Evaluated articles

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A high-quality reference genome for the Ural Owl ( Strix uralensis ) enables investigations of cell cultures as a genomic resource for endangered species

This article has 10 authors:
1. Ioannis Chrysostomakis
2. Annika Mozer
3. Camilla Bruno Di-Nizo
4. Dominik Fischer
5. Nafiseh Sargheini
6. Laura von der Mark
7. Bruno Huettel
8. Jonas J. Astrin
9. Till Töpfer
10. Astrid Böhne
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 24, 2025Latest activity Sep 30, 2025
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

This article has 5 authors:
1. Engy Nasr
2. Anna Henger
3. Björn Grüning
4. Paul Zierep
5. Bérénice Batut
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jun 30, 2024Latest activity Sep 30, 2025
First chromosome-level genome assembly of the colonial tunicate Botryllus schlosseri

This article has 10 authors:
1. Olivier De Thier
2. Mohammed M.Tawfeeq
3. Roland Faure
4. Marie Lebel
5. Philippe Dru
6. Simon Blanchoud
7. Alexandre Alié
8. Federico D. Brown
9. Jean-François Flot
10. Stefano Tiozzo
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jun 2, 2024Latest activity Sep 30, 2025
Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

This article has 20 authors:
1. Larissa S. Arantes
2. Tom Brown
3. Diego De Panis
4. Scott D. Whiting
5. Erin L. LaCasella
6. Gabriella A. Carvajal
7. Adam Kennedy
8. Deana Edmunds
9. Blair P. Bentley
10. Jennifer Balacco
11. Conor Whelan
12. Nivesh Jain
13. Tatiana Tilley
14. Brian O’Toole
15. Patrick Traore
16. Erich D. Jarvis
17. Oliver Berry
18. Peter H. Dutton
19. Lisa M. Komoroske
20. Camila J. Mazzoni
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Mar 28, 2025Latest activity Sep 30, 2025
CNSistent integration and feature extraction from somatic copy number profiles

This article has 2 authors:
1. Adam Streck
2. Roland F. Schwarz
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Dec 23, 2024Latest activity Sep 30, 2025
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing

This article has 8 authors:
1. Jessie J -Y Chang
2. Xuan Yang
3. Haotian Teng
4. Jianshu Zhang
5. Benjamin Reames
6. Shuxin Zhang
7. Vincent Corbin
8. Lachlan J M Coin
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Sep 30, 2025
The Open Pediatric Cancer Project

This article has 49 authors:
1. Zhuangzhuang Geng
2. Eric Wafula
3. Ryan J Corbett
4. Yuanchao Zhang
5. Run Jin
6. Krutika S Gaonkar
7. Sangeeta Shukla
8. Komal S Rathi
9. Dave Hill
10. Aditya Lahiri
11. Daniel P Miller
12. Alex Sickler
13. Kelsey Keith
14. Christopher Blackden
15. Antonia Chroni
16. Miguel A Brown
17. Adam A Kraya
18. Kaylyn L Clark
19. Brian R Rood
20. Adam C Resnick
21. Nicholas Van Kuren
22. John M Maris
23. Alvin Farrel
24. Mateusz P Koptyra
25. Gerri R Trooskin
26. Noel Coleman
27. Yuankun Zhu
28. Stephanie Stefankiewicz
29. Zied Abdullaev
30. Asif T Chinwalla
31. Mariarita Santi
32. Ammar S Naqvi
33. Jennifer L Mason
34. Carl J Koschmann
35. Xiaoyan Huang
36. Sharon J Diskin
37. Kenneth Aldape
38. Bailey K Farrow
39. Weiping Ma
40. Bo Zhang
41. Brian M Ennis
42. Sarah Tasian
43. Saksham Phul
44. Matthew R Lueder
45. Chuwei Zhong
46. Joseph M Dybas
47. Pei Wang
48. Deanne Taylor
49. Jo Lynne Rokita
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Sep 30, 2025
Nanopore- and AI-empowered microbial viability inference

This article has 19 authors:
1. Harika Ürel
2. Sabrina Benassou
3. Hanna Marti
4. Tim Reska
5. Ela Sauerborn
6. Yuri Pinheiro Alves De Souza
7. Albert Perlas
8. Enrique Rayo
9. Michael Biggel
10. Stefan Kesselheim
11. Nicole Borel
12. Edward J Martin
13. Constanza B Venegas
14. Michael Schloter
15. Kathrin Schröder
16. Jana Mittelstrass
17. Simone Prospero
18. James M Ferguson
19. Lara Urban
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Sep 30, 2025
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population specific signatures of selection

This article has 8 authors:
1. Fazeela Arshad
2. Siddharth Jayaraman
3. Andrea Talenti
4. Rachel Owen
5. Muhammad Mohsin
6. Shahid Mansoor
7. Muhammad Asif
8. James Prendergast
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version May 9, 2025Latest activity Sep 30, 2025
SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis

This article has 23 authors:
1. Xiao Li
2. Ximo Pechuan-Jorge
3. Tyler Risom
4. Conrad Foo
5. Alexander Prilipko
6. Artem Zubkov
7. Caleb Chan
8. Patrick Chang
9. Frank Peale
10. James Ziai
11. Sandra Rost
12. Derrek Hibar
13. Lisa McGinnis
14. Evgeniy Tabatsky
15. Xin Ye
16. Hector Corrada Bravo
17. Zhen Shi
18. Malgorzata Nowicka
19. Jon Scherdin
20. James Cowan
21. Jennifer Giltnane
22. Darya Orlova
23. Rajiv Jesudason
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Sep 30, 2025
Comparing Linear and Nonlinear Finite Element Models of Vertebral Strength Across the Thoracolumbar Spine: A Benchmark from Density-Calibrated Computed Tomography

This article has 3 authors:
1. Matthias Walle
2. Bryn E. Matheson
3. Steven K. Boyd
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Apr 23, 2025Latest activity Sep 30, 2025
WaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning

This article has 9 authors:
1. Hoang-Hai Nguyen
2. Josip Rudar
3. Nathaniel Lesperance
4. Oksana Vernygora
5. Graham W. Taylor
6. Chad Laing
7. David Lapen
8. Carson K. Leung
9. Oliver Lung
Reviewed by GigaScience

This article has 6 evaluationsAppears in 1 listLatest version Feb 28, 2025Latest activity Sep 30, 2025
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 Jan 1, 2025Latest 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 Jan 1, 2025Latest 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 6 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 Jan 1, 2025Latest activity Jul 8, 2025

Evaluated articles

A high-quality reference genome for the Ural Owl ( Strix uralensis ) enables investigations of cell cultures as a genomic resource for endangered species

PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

First chromosome-level genome assembly of the colonial tunicate Botryllus schlosseri

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

CNSistent integration and feature extraction from somatic copy number profiles

Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing

The Open Pediatric Cancer Project

Nanopore- and AI-empowered microbial viability inference

A comprehensive water buffalo pangenome reveals extensive structural variation linked to population specific signatures of selection

SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis

Comparing Linear and Nonlinear Finite Element Models of Vertebral Strength Across the Thoracolumbar Spine: A Benchmark from Density-Calibrated Computed Tomography

WaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning

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 6 years