Evaluated articles

Showing page 5 of 19 pages of list content

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

This article has 4 authors:
1. Hirotaka Suetake
2. Tsukasa Fukusato
3. Takeo Igarashi
4. Tazro Ohta
Reviewed by Arcadia Science, GigaScience

This article has 22 evaluationsAppears in 2 listsLatest version Dec 28, 2022Latest activity Apr 14, 2023
Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

This article has 3 authors:
1. Jeremiah Miller
2. Aleksey V Zimin
3. Andrew Gordus
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Dec 28, 2022Latest activity Mar 4, 2023
A molecular phenotypic map of malignant pleural mesothelioma

This article has 7 authors:
1. Alex Di Genova
2. Lise Mangiante
3. Alexandra Sexton-Oates
4. Catherine Voegele
5. Lynnette Fernandez-Cuesta
6. Nicolas Alcala
7. Matthieu Foll
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Dec 28, 2022Latest activity Mar 4, 2023
scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

This article has 4 authors:
1. Malindrie Dharmaratne
2. Ameya S Kulkarni
3. Atefeh Taherian Fard
4. Jessica C Mar
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Dec 28, 2022Latest activity Mar 4, 2023
xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments

This article has 13 authors:
1. Jesse Farek
2. Daniel Hughes
3. Adam Mansfield
4. Olga Krasheninina
5. Waleed Nasser
6. Fritz J Sedlazeck
7. Ziad Khan
8. Eric Venner
9. Ginger Metcalf
10. Eric Boerwinkle
11. Donna M Muzny
12. Richard A Gibbs
13. William Salerno
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Apr 5, 2018Latest activity Mar 4, 2023
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation

This article has 15 authors:
1. Harsh Shukla
2. Kushal Suryamohan
3. Anubhab Khan
4. Krishna Mohan
5. Rajadurai C Perumal
6. Oommen K Mathew
7. Ramesh Menon
8. Mandumpala Davis Dixon
9. Megha Muraleedharan
10. Boney Kuriakose
11. Saju Michael
12. Sajesh P Krishnankutty
13. Arun Zachariah
14. Somasekar Seshagiri
15. Uma Ramakrishnan
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Dec 28, 2022Latest activity Mar 4, 2023
Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation

This article has 5 authors:
1. Jorge Avila Cartes
2. Santosh Anand
3. Simone Ciccolella
4. Paola Bonizzoni
5. Gianluca Della Vedova
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Jun 13, 2022Latest activity Mar 4, 2023
A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization

This article has 13 authors:
1. Hongbo Wang
2. Hin Ting Wan
3. Bin Wu
4. Jianbo Jian
5. Alice HM Ng
6. Claire Yik-Lok Chung
7. Eugene Yui-Ching Chow
8. Jizhou Zhang
9. Anderson OL Wong
10. Keng Po Lai
11. Ting Fung Chan
12. Eric Lu Zhang
13. Chris Kong-Chu Wong
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jul 1, 2022Latest activity Mar 4, 2023
DeePVP: Identification and classification of phage virion proteins using deep learning

This article has 4 authors:
1. Zhencheng Fang
2. Tao Feng
3. Hongwei Zhou
4. Muxuan Chen
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Mar 1, 2023
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

This article has 22 authors:
1. Hollis A Dahn
2. Jacquelyn Mountcastle
3. Jennifer Balacco
4. Sylke Winkler
5. Iliana Bista
6. Anthony D Schmitt
7. Olga Vinnere Pettersson
8. Giulio Formenti
9. Karen Oliver
10. Michelle Smith
11. Wenhua Tan
12. Anne Kraus
13. Stephen Mac
14. Lisa M Komoroske
15. Tanya Lama
16. Andrew J Crawford
17. Robert W Murphy
18. Samara Brown
19. Alan F Scott
20. Phillip A Morin
21. Erich D Jarvis
22. Olivier Fedrigo
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Mar 1, 2023
Stardust: improving spatial transcriptomics data analysis through space aware modularity optimization based clustering

This article has 8 authors:
1. Simone Avesani
2. Eva Viesi
3. Luca Alessandrì
4. Giovanni Motterle
5. Vincenzo Bonnici
6. Marco Beccuti
7. Raffaele Calogero
8. Rosalba Giugno
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version May 10, 2022Latest activity Mar 1, 2023
SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data

This article has 5 authors:
1. Yunwei Zhang
2. Germaine Wong
3. Graham Mann
4. Samuel Muller
5. Jean Y H Yang
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Mar 1, 2023
Meta-Prism 2.0: Enabling algorithm for ultra-fast, accurate and memory-efficient search among millions of microbial community samples

This article has 3 authors:
1. Kai Kang
2. Hui Chong
3. Kang Ning
Reviewed by GigaScience

This article has 1 evaluationAppears in 1 listLatest version Nov 20, 2020Latest activity Mar 1, 2023
BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

This article has 6 authors:
1. Carol Moraga
2. Evelyn Sanchez
3. Mariana Galvão Ferrarini
4. Rodrigo A. Gutierrez
5. Elena A. Vidal
6. Marie-France Sagot
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Aug 7, 2020Latest activity Feb 17, 2023
Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI

This article has 6 authors:
1. Alena Kalyakulina
2. Igor Yusipov
3. Maria Giulia Bacalini
4. Claudio Franceschi
5. Maria Vedunova
6. Mikhail Ivanchenko
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version May 23, 2022Latest activity Feb 17, 2023
High-Spatiotemporal-Resolution Nanopore Sequencing of SARS-CoV-2 and Host Cell RNAs

This article has 10 authors:
1. Dóra Tombácz
2. Ákos Dörmő
3. Gábor Gulyás
4. Zsolt Csabai
5. István Prazsák
6. Balázs Kakuk
7. Ákos Harangozó
8. István Jankovics
9. Béla Dénes
10. Zsolt Boldogkői
Reviewed by GigaScience, ScreenIT

This article has 4 evaluationsAppears in 2 listsLatest version Aug 20, 2021Latest activity Feb 17, 2023
Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies

This article has 4 authors:
1. Miguel A. Naranjo-Ortiz
2. Manu Molina
3. Verónica Mixão
4. Toni Gabaldón
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version May 23, 2021Latest activity Feb 17, 2023
A curated human cellular microRNAome based on 196 primary cell types

This article has 5 authors:
1. Arun H. Patil
2. Andrea Baran
3. Zachary P. Brehm
4. Matthew N. McCall
5. Marc K. Halushka
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Aug 1, 2022Latest activity Feb 17, 2023
Association Mapping Across a Multitude of Traits Collected in Diverse Environments Identifies Pleiotropic Loci in Maize

This article has 12 authors:
1. Ravi V. Mural
2. Guangchao Sun
3. Marcin Grzybowski
4. Michael C. Tross
5. Hongyu Jin
6. Christine Smith
7. Linsey Newton
8. Carson M. Andorf
9. Margaret R. Woodhouse
10. Addie M. Thompson
11. Brandi Sigmon
12. James C. Schnable
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Feb 25, 2022Latest activity Feb 17, 2023
Spacemake: processing and analysis of large-scale spatial transcriptomics data

This article has 4 authors:
1. Tamas Ryszard Sztanka-Toth
2. Marvin Jens
3. Nikos Karaiskos
4. Nikolaus Rajewsky
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Feb 15, 2023

Evaluated articles

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

A molecular phenotypic map of malignant pleural mesothelioma

scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation

Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation

A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization

DeePVP: Identification and classification of phage virion proteins using deep learning

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Stardust: improving spatial transcriptomics data analysis through space aware modularity optimization based clustering

SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data

Meta-Prism 2.0: Enabling algorithm for ultra-fast, accurate and memory-efficient search among millions of microbial community samples

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI

High-Spatiotemporal-Resolution Nanopore Sequencing of SARS-CoV-2 and Host Cell RNAs

Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies

A curated human cellular microRNAome based on 196 primary cell types

Association Mapping Across a Multitude of Traits Collected in Diverse Environments Identifies Pleiotropic Loci in Maize

Spacemake: processing and analysis of large-scale spatial transcriptomics data