Evaluated articles

Showing page 8 of 21 pages of list content

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 Apr 28, 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 11, 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 May 17, 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
Loop detection using Hi-C data with HiCExplorer

This article has 3 authors:
1. Joachim Wolff
2. Rolf Backofen
3. Björn Grüning
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Mar 6, 2020Latest activity Feb 15, 2023
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks

This article has 3 authors:
1. Connah G M Johnson
2. Alexander G Fletcher
3. Orkun S Soyer
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Feb 15, 2023
Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus

This article has 14 authors:
1. R Alan Harris
2. Muthuswamy Raveendran
3. Dustin T Lyfoung
4. Fritz J Sedlazeck
5. Medhat Mahmoud
6. Trent M Prall
7. Julie A Karl
8. Harshavardhan Doddapaneni
9. Qingchang Meng
10. Yi Han
11. Donna Muzny
12. Roger W Wiseman
13. David H O'Connor
14. Jeffrey Rogers
Reviewed by GigaScience, ScreenIT

This article has 6 evaluationsAppears in 2 listsLatest version Jan 1, 2022Latest activity Feb 15, 2023
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae

This article has 11 authors:
1. Ziwei Wang
2. Mathieu Rouard
3. Manosh Kumar Biswas
4. Gaetan Droc
5. Dongli Cui
6. Nicolas Roux
7. Franc-Christophe Baurens
8. Xue-Jun Ge
9. Trude Schwarzacher
10. Pat (J S) Heslop-Harrison
11. Qing Liu
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Feb 15, 2023
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification

This article has 7 authors:
1. Chakravarthi Kanduri
2. Milena Pavlović
3. Lonneke Scheffer
4. Keshav Motwani
5. Maria Chernigovskaya
6. Victor Greiff
7. Geir K Sandve
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Feb 15, 2023
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET

This article has 8 authors:
1. Sharna D Jamadar
2. Emma X Liang
3. Shenjun Zhong
4. Phillip G D Ward
5. Alexandra Carey
6. Richard McIntyre
7. Zhaolin Chen
8. Gary F Egan
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Feb 14, 2023
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

This article has 19 authors:
1. Jean-Marc Aury
2. Stefan Engelen
3. Benjamin Istace
4. Cécile Monat
5. Pauline Lasserre-Zuber
6. Caroline Belser
7. Corinne Cruaud
8. Hélène Rimbert
9. Philippe Leroy
10. Sandrine Arribat
11. Isabelle Dufau
12. Arnaud Bellec
13. David Grimbichler
14. Nathan Papon
15. Etienne Paux
16. Marion Ranoux
17. Adriana Alberti
18. Patrick Wincker
19. Frédéric Choulet
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Nov 27, 2022
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions

This article has 12 authors:
1. D Steinke
2. S L deWaard
3. J E Sones
4. N V Ivanova
5. S W J Prosser
6. K Perez
7. T W A Braukmann
8. M Milton
9. E V Zakharov
10. J R deWaard
11. S Ratnasingham
12. P D N Hebert
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Oct 10, 2022
Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake

This article has 7 authors:
1. Luke R Thompson
2. Sean R Anderson
3. Paul A Den Uyl
4. Nastassia V Patin
5. Shen Jean Lim
6. Grant Sanderson
7. Kelly D Goodwin
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jan 1, 2022Latest activity Sep 5, 2022

Evaluated articles

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

Loop detection using Hi-C data with HiCExplorer

ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks

Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus

A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae

Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification

Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake