Evaluated articles

Showing page 2 of 20 pages of list content

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

This article has 11 authors:
1. Abigayle Simpson
2. Elisha M Wood-Charlson
3. Montana Smith
4. Benjamin J Koch
5. Kathleen Beilsmith
6. Jeffrey A Kimbrel
7. Matthew Kellom
8. Christopher I Hunter
9. Ramona L Walls
10. Lynn M Schriml
11. Roland C Wilhelm
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Nov 23, 2024
StereoSiTE: a framework to spatially and quantitatively profile the cellular neighborhood organized iTME

This article has 18 authors:
1. Xing Liu
2. Chi Qu
3. Chuandong Liu
4. Na Zhu
5. Huaqiang Huang
6. Fei Teng
7. Caili Huang
8. Bingying Luo
9. Xuanzhu Liu
10. Min Xie
11. Feng Xi
12. Mei Li
13. Liang Wu
14. Yuxiang Li
15. Ao Chen
16. Xun Xu
17. Sha Liao
18. Jiajun Zhang
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Nov 23, 2024
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation

This article has 19 authors:
1. Lara Fuhrmann
2. Kim Philipp Jablonski
3. Ivan Topolsky
4. Aashil A Batavia
5. Nico Borgsmüller
6. Pelin Icer Baykal
7. Matteo Carrara
8. Chaoran Chen
9. Arthur Dondi
10. Monica Dragan
11. David Dreifuss
12. Anika John
13. Benjamin Langer
14. Michal Okoniewski
15. Louis du Plessis
16. Uwe Schmitt
17. Franziska Singer
18. Tanja Stadler
19. Niko Beerenwinkel
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Nov 10, 2024
TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data

This article has 4 authors:
1. Conor Klamann
2. Christie J Lau
3. Javier Ruiz-Ramírez
4. Gregory W Schwartz
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Sep 3, 2024
MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model

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

This article has 2 evaluationsAppears in 1 listLatest version Dec 7, 2023Latest activity Aug 12, 2024
CAT: a computational anatomy toolbox for the analysis of structural MRI data

This article has 6 authors:
1. Christian Gaser
2. Robert Dahnke
3. Paul M Thompson
4. Florian Kurth
5. Eileen Luders
6. the Alzheimer's Disease Neuroimaging Initiative
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Aug 12, 2024
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit

This article has 13 authors:
1. Kari Lavikka
2. Jaana Oikkonen
3. Yilin Li
4. Taru Muranen
5. Giulia Micoli
6. Giovanni Marchi
7. Alexandra Lahtinen
8. Kaisa Huhtinen
9. Rainer Lehtonen
10. Sakari Hietanen
11. Johanna Hynninen
12. Anni Virtanen
13. Sampsa Hautaniemi
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Aug 12, 2024
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

This article has 6 authors:
1. Eva Aßmann
2. Shelesh Agrawal
3. Laura Orschler
4. Sindy Böttcher
5. Susanne Lackner
6. Martin Hölzer
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Aug 12, 2024
Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging

This article has 9 authors:
1. Laznovsky Jakub
2. Kavkova Michaela
3. Reis Alice
4. Robovska-Havelkova Pavla
5. Krivanek Jan
6. Zikmund Tomas
7. Kaiser Jozef
8. Buchtova Marcela
9. Harnos Jakub
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Jun 11, 2024Latest activity Jul 31, 2024
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes

This article has 2 authors:
1. Muzaffer Arikan
2. Thilo Muth
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Jul 31, 2024
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

This article has 6 authors:
1. Nathan J. LeRoy
2. Oleksandr Khoroshevskyi
3. Aaron O’Brien
4. Rafał Stepień
5. Alip Arslan
6. Nathan C. Sheffield
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version May 11, 2024Latest activity Jul 31, 2024
Omada: robust clustering of transcriptomes through multiple testing

This article has 7 authors:
1. Sokratis Kariotis
2. Pei Fang Tan
3. Haiping Lu
4. Christopher J Rhodes
5. Martin R Wilkins
6. Allan Lawrie
7. Dennis Wang
Reviewed by GigaScience

This article has 6 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Jul 31, 2024
Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

This article has 21 authors:
1. Riccardo Baroncelli
2. José F. Cobo-Díaz
3. Tiziano Benocci
4. Mao Peng
5. Evy Battaglia
6. Sajeet Haridas
7. William Andreopoulos
8. Kurt LaButti
9. Jasmyn Pangilinan
10. Anna Lipzen
11. Maxim Koriabine
12. Diane Bauer
13. Gaetan Le Floch
14. Miia R. Mäkelä
15. Elodie Drula
16. Bernard Henrissat
17. Igor V. Grigoriev
18. Jo Anne Crouch
19. Ronald P. de Vries
20. Serenella A. Sukno
21. Michael R. Thon
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Sep 22, 2022Latest activity Jul 1, 2024
Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

This article has 14 authors:
1. Rafael Moysés Alves
2. Vinicius A. C. de Abreu
3. Rafaely Pantoja Oliveira
4. João Victor dos Anjos Almeida
5. Mauro de Medeiros de Oliveira
6. Saura R. Silva
7. Alexandre R. Paschoal
8. Sintia S. de Almeida
9. Pedro A. F. de Souza
10. Jesus A. Ferro
11. Vitor F. O. Miranda
12. Antonio Figueira
13. Douglas S. Domingues
14. Alessandro M. Varani
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 23, 2023Latest activity Jul 1, 2024
ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection

This article has 4 authors:
1. Justin Chu
2. Jiazhen Rong
3. Xiaowen Feng
4. Heng Li
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Jul 1, 2024
Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

This article has 7 authors:
1. Scott Ferguson
2. Ashley Jones
3. Kevin Murray
4. Rose L. Andrew
5. Helen Bothwell
6. Benjamin Schwessinger
7. Justin Borevitz
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Oct 21, 2023Latest activity Jul 1, 2024
LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome

This article has 10 authors:
1. Chao Yang
2. Zhenmiao Zhang
3. Yufen Huang
4. Xuefeng Xie
5. Herui Liao
6. Jin Xiao
7. Werner Pieter Veldsman
8. Kejing Yin
9. Xiaodong Fang
10. Lu Zhang
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity Jul 1, 2024
Hecatomb: An End-to-End Research Platform for Viral Metagenomics

This article has 10 authors:
1. Michael J. Roach
2. Sarah J. Beecroft
3. Kathie A. Mihindukulasuriya
4. Leran Wang
5. Anne Paredes
6. Kara Henry-Cocks
7. Lais Farias Oliveira Lima
8. Elizabeth A. Dinsdale
9. Robert A. Edwards
10. Scott A. Handley
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Oct 5, 2022Latest activity Jul 1, 2024
IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning

This article has 9 authors:
1. Hengchuang Yin
2. Shufang Wu
3. Jie Tan
4. Qian Guo
5. Mo Li
6. Jinyuan Guo
7. Yaqi Wang
8. Xiaoqing Jiang
9. Huaiqiu Zhu
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity May 13, 2024
Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

This article has 30 authors:
1. Sungwon Jeon
2. Hansol Choi
3. Yeonsu Jeon
4. Whan-Hyuk Choi
5. Hyunjoo Choi
6. Kyungwhan An
7. Hyojung Ryu
8. Jihun Bhak
9. Hyeonjae Lee
10. Yoonsung Kwon
11. Sukyeon Ha
12. Yeo Jin Kim
13. Asta Blazyte
14. Changjae Kim
15. Yeonkyung Kim
16. Younghui Kang
17. Yeong Ju Woo
18. Chanyoung Lee
19. Jeongwoo Seo
20. Changhan Yoon
21. Dan Bolser
22. Orsolya Biro
23. Eun-Seok Shin
24. Byung Chul Kim
25. Seon-Young Kim
26. Ji-Hwan Park
27. Jongbum Jeon
28. Dooyoung Jung
29. Semin Lee
30. Jong Bhak
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2024Latest activity May 13, 2024

Evaluated articles

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

StereoSiTE: a framework to spatially and quantitatively profile the cellular neighborhood organized iTME

V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation

TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data

MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model

CAT: a computational anatomy toolbox for the analysis of structural MRI data

Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit

Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging

gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

Omada: robust clustering of transcriptomes through multiple testing

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome

Hecatomb: An End-to-End Research Platform for Viral Metagenomics

IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups