Bioinformatics

Open Modification Searching of SARS-CoV-2–Human Protein Interaction Data Reveals Novel Viral Modification Sites

1. Charlotte Adams
2. Kurt Boonen
3. Kris Laukens
4. Wout Bittremieux

Reviewed by ScreenIT

Angiotensin-converting enzyme 2: virus accomplice or host defender?

1. Jiyan Wang
2. Hongkai Chang
3. Yaya Qiao
4. Huanran Sun
5. Xichuan Li
6. Shuofeng Yuan
7. Shuai Zhang
8. Changliang Shan

Reviewed by ScreenIT

An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant

1. Tushar Ahmed Shishir
2. Taslimun Jannat
3. Iftekhar Bin Naser

Reviewed by ScreenIT

Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins

1. Stefano Pascarelli
2. Paola Laurino

Reviewed by Review Commons

Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition

1. Jonathan Mitchel
2. M. Grace Gordon
3. Richard K. Perez
4. Evan Biederstedt
5. Raymund Bueno
6. Chun Jimmie Ye
7. Peter V. Kharchenko

Reviewed by ScreenIT

On Correlation between Structural Properties and Viral Escape Measurements from Deep Mutational Scanning

1. Leili Zhang
2. Giacomo Domeniconi
3. Chih-Chieh Yang

Reviewed by ScreenIT

Furin-cleavage site is present in an antiparallel β-strand in SARS-CoV2 Spike protein

1. Arif Bashir
2. Naveed Nazir Shah

Reviewed by ScreenIT

SARS-CoV-2 Variants Show a Gradual Declining Pathogenicity and Pro-Inflammatory Cytokine Stimulation, an Increasing Antigenic and Anti-Inflammatory Cytokine Induction, and Rising Structural Protein Instability: A Minimal Number Genome-Based Approach

1. Debmalya Barh
2. Sandeep Tiwari
3. Lucas Gabriel Rodrigues Gomes
4. Cecília Horta Ramalho Pinto
5. Bruno Silva Andrade
6. Shaban Ahmad
7. Alaa A. A. Aljabali
8. Khalid J. Alzahrani
9. Hamsa Jameel Banjer
10. Sk. Sarif Hassan
11. Elrashdy M. Redwan
12. Khalid Raza
13. Aristóteles Góes-Neto
14. Robinson Sabino-Silva
15. Kenneth Lundstrom
16. Vladimir N. Uversky
17. Vasco Azevedo
18. Murtaza M. Tambuwala

Reviewed by ScreenIT

Bioinformatic analysis of B and T cell epitopes from SARS-CoV-2 Spike, Membrane and Nucleocapsid proteins as a strategy to assess possible cross-reactivity between emerging variants, including Omicron, and other human coronaviruses

1. Diana Laura Pacheco-Olvera
2. Stephanie Saint Remy-Hernández
3. María Guadalupe García-Valeriano
4. Tania Rivera-Hernández
5. Constantino López-Macías

Reviewed by ScreenIT

Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data

1. Nighat Noureen
2. Zhenqing Ye
3. Yidong Chen
4. Xiaojing Wang
5. Siyuan Zheng

• Curated by eLife

  Evaluation Summary:

  Single-cell RNA sequencing allows us to quantify variability of gene expression patterns within a population, and thus devise patterns with prognostic, diagnostic and predictive potential, called "gene expression signatures". Here, Noureen and collaborators benchmark four methods used for identifying these gene expression signatures, and evaluate their performance at overcoming a number of analytical challenges. They conclude that caution should be exercised when using bulk sample-based methods in single-cell data analyses, and cellular contexts should be taken into consideration. With strengthening of some statistical and methodological aspects to support the validity of the conclusions, this paper will be an informative and potentially valuable addition to the literature.

  (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 #3 agreed to share their name with the authors.)

Reviewed by eLife