Bioinformatics

RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor

1. Siddharth Sinha
2. Benjamin Tam
3. San Ming Wang

Reviewed by ScreenIT

RNA splicing programs define tissue compartments and cell types at single-cell resolution

1. Julia Eve Olivieri
2. Roozbeh Dehghannasiri
3. Peter L Wang
4. SoRi Jang
5. Antoine de Morree
6. Serena Y Tan
7. Jingsi Ming
8. Angela Ruohao Wu
9. Tabula Sapiens Consortium
10. Stephen R Quake
11. Mark A Krasnow
12. Julia Salzman

• Curated by eLife

  Evaluation Summary:

  This manuscript describes an analysis of cell type-specific alternative splicing using 10x scRNA-seq data. This work shows that in spite of the challenges associated with the analysis of such datasets, it is possible to identify alternative exons with differential splicing between tissue compartments and to some extent reveal cell types by splicing profiles of single cells. This work is informative regarding what can be done to analyse alternative splicing using 10X data and fills in a gap in the field.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

(Machine) Learning the mutation signatures of SARS-CoV-2: a primer for predictive prognosis

1. Sunil Nagpal
2. Nishal Kumar Pinna
3. Divyanshu Srivastava
4. Rohan Singh
5. Sharmila S. Mande

Reviewed by ScreenIT

From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering

1. Andrew Melnyk
2. Fatemeh Mohebbi
3. Sergey Knyazev
4. Bikram Sahoo
5. Roya Hosseini
6. Pavel Skums
7. Alex Zelikovsky
8. Murray Patterson

Reviewed by ScreenIT

Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes

1. Christian A Balbin
2. Janelle Nunez-Castilla
3. Vitalii Stebliankin
4. Prabin Baral
5. Masrur Sobhan
6. Trevor Cickovski
7. Ananda Mohan Mondal
8. Giri Narasimhan
9. Prem Chapagain
10. Kalai Mathee
11. Jessica Siltberg-Liberles

Reviewed by ScreenIT

An open-source, high-performance tool for automated sleep staging

1. Raphael Vallat
2. Matthew P Walker

• Curated by eLife

  Evaluation Summary:

  This study describes a novel algorithm to perform fully automated sleep staging in humans. It is well validated and performs at the level of other state of the art algorithms although it does not yet include comparisons against the existing tools available in the field. Given the efforts made by the authors to ensure ease of use and accessibility it may help extend the use of automated methods in the study of sleep.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Simplifying the development of portable, scalable, and reproducible workflows

1. Stephen R Piccolo
2. Zachary E Ence
3. Elizabeth C Anderson
4. Jeffrey T Chang
5. Andrea H Bild

• Curated by eLife

  Evaluation Summary:

  This paper by Piccolo and collaborators provides a general introduction to the common workflow language (CWL) with working examples taken from bioinformatics. The authors also introduce the ToolJig web application intended as a way of interactively creating CWL documents. This work should be of interest not only to beginner bioinformaticians but also to more experienced professionals that do not routinely make use of the latest developments in reproducible research.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Modeling the SARS-CoV-2 mutation based on geographical regions and time

1. Bomin Wei
2. Yuzhe Sun
3. Xiang Gong

Reviewed by ScreenIT

Cutting epitopes to survive: the case of lambda variant

1. Stefano Pascarella
2. Massimo Ciccozzi
3. Martina Bianchi
4. Domenico Benvenuto
5. Roberto Cauda
6. Antonio Cassone

Reviewed by ScreenIT

Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins

1. Janelle Nunez-Castilla
2. Vitalii Stebliankin
3. Prabin Baral
4. Christian A. Balbin
5. Masrur Sobhan
6. Trevor Cickovski
7. Ananda Mohan Mondal
8. Giri Narasimhan
9. Prem Chapagain
10. Kalai Mathee
11. Jessica Siltberg-Liberles

Reviewed by ScreenIT