Evaluated articles

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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
Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spider

This article has 4 authors:
1. Guoqing Zhang
2. Yiru Wang
3. Hongcen Jiang
4. Yi Wang
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 31, 2024Latest activity Apr 3, 2025
Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage

This article has 18 authors:
1. Gang Wang
2. Liping Ban
3. Xinye Zhang
4. Xiurong Zhao
5. Xufang Ren
6. Anqi Chen
7. Li Zhang
8. Yan Lu
9. Zhihua Jiang
10. Xiaoyu Zhao
11. Junhui Wen
12. Yalan Zhang
13. Xue Cheng
14. Huie Wang
15. Wenting Dai
16. Yong Liu
17. Zhonghua Ning
18. Lujiang Qu
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 27, 2023Latest activity Mar 3, 2025
xRead: a coverage-guided approach for scalable construction of read overlapping graph

This article has 3 authors:
1. Tangchao Kong
2. Yadong Wang
3. Bo Liu
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Mar 3, 2025
TransHLA: A Hybrid Transformer Model for HLA-Presented Epitope Detection

This article has 5 authors:
1. Tianchi Lu
2. Xueying Wang
3. Wan Nie
4. Miaozhe Huo
5. Shuaicheng Li
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 24, 2025Latest activity Mar 3, 2025
A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus ) provide evidence of haplotype diversity

This article has 9 authors:
1. Temitope Opeyemi Oriowo
2. Ioannis Chrysostomakis
3. Sebastian Martin
4. Sandra Kukowka
5. Thomas Brown
6. Sylke Winkler
7. Eugene W Myers
8. Astrid Böhne
9. Madlen Stange
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Feb 10, 2025
Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering

This article has 6 authors:
1. Yichun Feng
2. Lu Zhou
3. Chao Ma
4. Yikai Zheng
5. Ruikun He
6. Yixue Li
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2025Latest activity Feb 4, 2025
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure

This article has 7 authors:
1. Yongxin Ji
2. Jiayu Shang
3. Jiaojiao Guan
4. Wei Zou
5. Herui Liao
6. Xubo Tang
7. Yanni Sun
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Jul 6, 2024Latest activity Jan 5, 2025
demuxSNP: supervised demultiplexing scRNAseq using cell hashing and SNPs

This article has 4 authors:
1. Michael P. Lynch
2. Yufei Wang
3. Laurent Gatto
4. Aedin C. Culhane
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Apr 26, 2024Latest activity Dec 5, 2024
stMMR: accurate and robust spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation

This article has 10 authors:
1. Daoliang Zhang
2. Na Yu
3. Wenrui Li
4. Xue Sun
5. Qi Zou
6. Xiangyu Li
7. Zhiping Liu
8. Zhiyuan Yuan
9. Wei Zhang
10. Rui Gao
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Feb 29, 2024Latest activity Dec 5, 2024
De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

This article has 19 authors:
1. Carolina Heloisa de Souza Borges
2. Ricardo Utsunomia
3. Alessandro Varani
4. Marcela Uliano-Silva
5. Lieschen Valeria G. Lira
6. Arno J. Butzge
7. John F. Gomez Agudelo
8. Shisley Manso
9. Milena V. Freitas
10. Raquel B. Ariede
11. Vito A. Mastrochirico-Filho
12. Carolina Penaloza
13. Agustín Barria
14. Fábio Porto-Foresti
15. Fausto Foresti
16. Ricardo Hattori
17. Yann Guiguen
18. Ross D. Houston
19. Diogo Teruo Hashimoto
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Mar 12, 2024Latest activity Dec 5, 2024
CAT Bridge: An Efficient Toolkit for Gene-Metabolite Association Mining from Multi-Omics Data

This article has 11 authors:
1. Bowen Yang
2. Tan Meng
3. Xinrui Wang
4. Jun Li
5. Shuang Zhao
6. Yingheng Wang
7. Shu Yi
8. Yi Zhou
9. Yi Zhang
10. Liang Li
11. Li Guo
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Oct 22, 2024Latest activity Dec 5, 2024
Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

This article has 5 authors:
1. Seth A. Frazer
2. Mahdi Baghbanzadeh
3. Ali Rahnavard
4. Keith A. Crandall
5. Todd H. Oakley
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Feb 14, 2024Latest activity Nov 23, 2024
CoCoPyE: feature engineering for learning and prediction of genome quality indices

This article has 7 authors:
1. Niklas Birth
2. Nicolina Leppich
3. Julia Schirmacher
4. Nina Andreae
5. Rasmus Steinkamp
6. Matthias Blanke
7. Peter Meinicke
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Sep 9, 2024Latest activity Nov 23, 2024

Evaluated articles

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

Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spider

Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage

xRead: a coverage-guided approach for scalable construction of read overlapping graph

TransHLA: A Hybrid Transformer Model for HLA-Presented Epitope Detection

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus ) provide evidence of haplotype diversity

Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering

PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure

demuxSNP: supervised demultiplexing scRNAseq using cell hashing and SNPs

stMMR: accurate and robust spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

CAT Bridge: An Efficient Toolkit for Gene-Metabolite Association Mining from Multi-Omics Data

Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

CoCoPyE: feature engineering for learning and prediction of genome quality indices