Evaluated articles

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Comparative evaluation of computational methods for reconstruction of human viral genomes

This article has 7 authors:
1. Maria J. P. Sousa
2. Mari Toppinen
3. Lari Pyöriä
4. Klaus Hedman
5. Antti Sajantila
6. Maria F. Perdomo
7. Diogo Pratas
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 22, 2025Latest activity Jan 5, 2026
Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

This article has 12 authors:
1. Sarah L.F. Martin
2. Renato La Torre
3. Bram Danneels
4. Ave Tooming-Klunderud
5. Morten Skage
6. Spyridon Kollias
7. Ole Kristian Tørresen
8. Mohsen Falahati Anbaran
9. Elisabeth Stur
10. Kjetill S. Jakobsen
11. Michael D. Martin
12. Torbjørn Ekrem
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Aug 1, 2025Latest activity Jan 5, 2026
Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using AI: A Case Study on Almonds

This article has 4 authors:
1. Mas-Gómez Jorge
2. Rubio Manuel
3. Dicenta Federico
4. Martínez-García Pedro José
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version May 6, 2025Latest activity Jan 5, 2026
A sulfatide-centered ultra-high resolution magnetic resonance MALDI imaging benchmark dataset for MS1-based lipid annotation tools

This article has 4 authors:
1. Lars Gruber
2. Stefan Schmidt
3. Thomas Enzlein
4. Carsten Hopf
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Oct 20, 2025Latest activity Jan 5, 2026
An Integrative Multi-Omics Random Forest Framework for Robust Biomarker Discovery

This article has 5 authors:
1. Wei Zhang
2. Hanchen Huang
3. Lily Wang
4. Brian D. Lehmann
5. Steven X. Chen
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Mar 6, 2025Latest activity Jan 5, 2026
The Good, the Bad, and the Ugly: Segmentation-Based Quality Control of Structural Magnetic Resonance Images

This article has 5 authors:
1. Robert Dahnke
2. Polona Kalc
3. Gabriel Ziegler
4. Julian Grosskreutz
5. Christian Gaser
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Mar 1, 2025Latest activity Jan 5, 2026
pyRootHair: Machine Learning Accelerated Software for High-Throughput Phenotyping of Plant Root Hair Traits

This article has 6 authors:
1. Ian Tsang
2. Lawrence Percival-Alwyn
3. Stephen Rawsthorne
4. James Cockram
5. Fiona Leigh
6. Jonathan A. Atkinson
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 18, 2025Latest activity Nov 28, 2025
RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

This article has 4 authors:
1. Cenny Taslim
2. Yuan Zhang
3. Genevieve C. Kendall
4. Emily R. Theisen
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 23, 2024Latest activity Nov 28, 2025
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

Evaluated articles

Comparative evaluation of computational methods for reconstruction of human viral genomes

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using AI: A Case Study on Almonds

A sulfatide-centered ultra-high resolution magnetic resonance MALDI imaging benchmark dataset for MS1-based lipid annotation tools

An Integrative Multi-Omics Random Forest Framework for Robust Biomarker Discovery

The Good, the Bad, and the Ugly: Segmentation-Based Quality Control of Structural Magnetic Resonance Images

pyRootHair: Machine Learning Accelerated Software for High-Throughput Phenotyping of Plant Root Hair Traits

RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

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