Evaluated articles

Showing page 1 of 21 pages of list content

EssSubgraph improves performance and generalizability of mammalian essential gene prediction with large networks

This article has 6 authors:
1. Haimei Wen
2. Susan Carpenter
3. Karen McGinnis
4. Andrew Nelson
5. Keriayn Smith
6. Tian Hong
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 25, 2025Latest activity Oct 30, 2025
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes

This article has 6 authors:
1. Caner Bağcı
2. Timo Negri
3. Elena Buena Atienza
4. Caspar Gross
5. Stephan Ossowski
6. Nadine Ziemert
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version May 28, 2025Latest activity Oct 30, 2025
TinkerHap - A Novel Read-Based Phasing Algorithm with Integrated Multi-Method Support for Enhanced Accuracy

This article has 5 authors:
1. Uri Hartmann
2. Eran Shaham
3. Dafna Nathan
4. Ilana Blech
5. Danny Zeevi
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Feb 20, 2025Latest activity Oct 30, 2025
GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction

This article has 3 authors:
1. Baohua Chen
2. Dongya Wu
3. Guojie Zhang
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 12, 2025Latest activity Oct 30, 2025
On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

This article has 18 authors:
1. Caroline Howard
2. Amy Denton
3. Benjamin Jackson
4. Adam Bates
5. Jessie Jay
6. Halyna Yatsenko
7. Priyanka Sethu Raman
8. Abitha Thomas
9. Graeme Oatley
10. Raquel Vionette do Amaral
11. Zeynep Ene Göktan
12. Juan Pablo Narváez Gómez
13. Isabelle Clayton Lucey
14. Elizabeth Sinclair
15. Michael A. Quail
16. Mark Blaxter
17. Kerstin Howe
18. Mara K. N. Lawniczak
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Apr 11, 2025Latest activity Oct 30, 2025
Improving the Reliability and Quality of Nextflow Pipelines with nf-test

This article has 2 authors:
1. Lukas Forer
2. Sebastian Schoenherr
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version May 30, 2024Latest activity Oct 30, 2025
CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology

This article has 8 authors:
1. Qibo Xu
2. Leon Wu
3. Michael Rebelo
4. Shi Feng
5. Xinye Yu
6. Farhanaz Farheen
7. Daisuke Kihara
8. Z. Hong Zhou
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Sep 10, 2025Latest activity Oct 30, 2025
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data

This article has 5 authors:
1. Hasindu Gamaarachchi
2. Sasha Jenner
3. Hiruna Samarakoon
4. James M. Ferguson
5. Ira W. Deveson
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 4, 2025Latest activity Oct 30, 2025
Reproducible processing of TCGA regulatory networks

This article has 10 authors:
1. Viola Fanfani
2. Katherine H. Shutta
3. Panagiotis Mandros
4. Jonas Fischer
5. Enakshi Saha
6. Soel Micheletti
7. Chen Chen
8. Marouen Ben Guebila
9. Camila M. Lopes-Ramos
10. John Quackenbush
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Nov 7, 2024Latest activity Oct 30, 2025
GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator

This article has 3 authors:
1. Martin Fahrenberger
2. Christopher Esk
3. Arndt von Haeseler
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 3, 2024Latest activity Oct 30, 2025
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

Evaluated articles

EssSubgraph improves performance and generalizability of mammalian essential gene prediction with large networks

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes

TinkerHap - A Novel Read-Based Phasing Algorithm with Integrated Multi-Method Support for Enhanced Accuracy

GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Improving the Reliability and Quality of Nextflow Pipelines with nf-test

CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology

The enduring advantages of the SLOW5 file format for raw nanopore sequencing data

Reproducible processing of TCGA regulatory networks

GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator

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