Bioinformatics

Biologically informed variational autoencoders allow predictive modeling of genetic and drug-induced perturbations

1. Daria Doncevic
2. Carl Herrmann

Reviewed by Arcadia Science

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

1. Hirotaka Suetake
2. Tsukasa Fukusato
3. Takeo Igarashi
4. Tazro Ohta

Reviewed by Arcadia Science, GigaScience

Sex-specificity of the C. elegans metabolome

1. Russell N. Burkhardt
2. Alexander B. Artyukhin
3. Erin Z. Aprison
4. Brian J. Curtis
5. Bennett W. Fox
6. Andreas H. Ludewig
7. Diana Fajardo Palomino
8. Jintao Luo
9. Amaresh Chaturbedi
10. Oishika Panda
11. Chester J. J. Wrobel
12. Victor Baumann
13. Douglas S. Portman
14. Siu Sylvia Lee
15. Ilya Ruvinsky
16. Frank C. Schroeder

Reviewed by Arcadia Science

aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow

1. Zoé Pochon
2. Nora Bergfeldt
3. Emrah Kırdök
4. Mário Vicente
5. Thijessen Naidoo
6. Tom van der Valk
7. N. Ezgi Altınışık
8. Maja Krzewińska
9. Love Dalén
10. Anders Götherström
11. Claudio Mirabello
12. Per Unneberg
13. Nikolay Oskolkov

Reviewed by Arcadia Science

GutMeta: online microbiome analysis and interactive visualization with build-in curated human gut microbiome database

1. Yiqi Jiang
2. Yanfei Wang
3. Lijia Che
4. Qian Zhou
5. Shuaicheng Li

Reviewed by Arcadia Science

The Landscape of Maize-Associated Bacteria and Fungi Across the United States

1. Corey R Schultz
2. Hanish Desai
3. Jason G Wallace

Reviewed by Arcadia Science

Robust phylogenetic tree-based microbiome association test using repeatedly measured data for composition bias

1. Kangjin Kim
2. Sungho Won

Reviewed by Arcadia Science

Training Infrastructure as a Service

1. Helena Rasche
2. Cameron Hyde
3. John Davis
4. Simon Gladman
5. Nate Coraor
6. Anthony Bretaudeau
7. Gianmauro Cuccuru
8. Wendi Bacon
9. Beatriz Serrano-Solano
10. Jennifer Hillman-Jackson
11. Saskia Hiltemann
12. Miaomiao Zhou
13. Björn Grüning
14. Andrew Stubbs

Reviewed by GigaScience

EraSOR: Erase Sample Overlap in polygenic score analyses

1. Shing Wan Choi
2. Timothy Shin Heng Mak
3. Clive J. Hoggart
4. Paul F. O’Reilly

Reviewed by GigaScience

Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

1. Sagar Patel
2. Zachary N. Harris
3. Jason P. Londo
4. Allison Miller
5. Anne Fennell

• Curated by GigaByte

  Editor’s Assessment

  Hybrid genomes are tricky to assemble, and few genomic resources are available for hybrid grapevines such as ‘Chambourcin’, a French-American interspecific hybrid grape grown in the eastern and midwestern United States. Here is an attempt to assemble Chambourcin’ using a combination of PacBio HiFi long-reads, Bionano optical maps, and Illumina short-read sequencing technologies. Producing an assembly with 26 scaffolds, an N50 length 23.3 Mb and an estimated BUSCO completeness of 97.9% that can be used for genome comparisons, functional genomic analyses, and genome-assisted breeding research. Error correction and pilon polishing was a challenge with this hybrid assembly, but after trying a few different approaches in the review process have improved it, and as they have documented what they did and are clear about the final metrics, users can assess the quality themselves.

  This assessment refers to version 2 of this preprint.

Reviewed by GigaByte