Bioinformatics

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

Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)

1. Thanh Thi Nguyen
2. Pubudu N. Pathirana
3. Thin Nguyen
4. Quoc Viet Hung Nguyen
5. Asim Bhatti
6. Dinh C. Nguyen
7. Dung Tien Nguyen
8. Ngoc Duy Nguyen
9. Douglas Creighton
10. Mohamed Abdelrazek

Reviewed by ScreenIT

On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19

1. Wenhuan Zeng
2. Anupam Gautam
3. Daniel H. Huson

Reviewed by ScreenIT

Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity

1. Debnath Pal

Reviewed by ScreenIT

Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2

1. Mercè Llabrés
2. Gabriel Valiente

Reviewed by ScreenIT

Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans

1. Rajneesh Srivastava
2. Swapna Vidhur Daulatabad
3. Mansi Srivastava
4. Sarath Chandra Janga

Reviewed by ScreenIT

Renal Carcinoma Is Associated With Increased Risk of Coronavirus Infections

1. Satyendra C. Tripathi
2. Vishwajit Deshmukh
3. Chad J. Creighton
4. Ashlesh Patil

Reviewed by ScreenIT

Snapshot of the evolution and mutation patterns of SARS-CoV-2

1. Jin Zhao
2. Jiumeng Sun
3. Wan-Ting He
4. Xiang Ji
5. Qi Gao
6. Xiaofeng Zhai
7. Marc A. Suchard
8. Samuel L. Hong
9. Guy Baele
10. Shuo Su
11. Jiyong Zhou
12. Michael Veit

Reviewed by ScreenIT

Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19

1. Philippe Youkharibache
2. Raul Cachau
3. Tom Madej
4. Jiyao Wang

Reviewed by ScreenIT

Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach

1. Rohit Pritam Das
2. Manaswini Jagadeb
3. Surya Narayan Rath

Reviewed by ScreenIT