Bioinformatics

A novel consensus‐based computational pipeline for screening of antibody therapeutics for efficacy against SARS‐CoV‐2 variants of concern including Omicron variant

1. Naveen Kumar
2. Rahul Kaushik
3. Kam Y. J. Zhang
4. Vladimir N. Uversky
5. Upasana Sahu
6. Richa Sood
7. Sandeep Bhatia

Reviewed by ScreenIT

Omicron (BA.1) and sub‐variants (BA.1.1, BA.2, and BA.3) of SARS‐CoV‐2 spike infectivity and pathogenicity: A comparative sequence and structural‐based computational assessment

1. Suresh Kumar
2. Kalimuthu Karuppanan
3. Gunasekaran Subramaniam

Reviewed by ScreenIT

Molecular Dynamics Simulations Studies On The Effects Of Mutations On The Binding Affinities Between SARS-CoV-2 Spike RBD And Human ACE2

1. Smriti Arora
2. Jeevan Patra

Reviewed by ScreenIT

Cell delivery peptides for small interfering RNAs targeting SARS-CoV-2 new variants through a bioinformatics and deep learning design

1. Ricardo D. González
2. Pedro R. Figueiredo
3. Alexandra T. P. Carvalho

Reviewed by ScreenIT

Predicting Epitope Candidates for SARS-CoV-2

1. Akshay Agarwal
2. Kristen L. Beck
3. Sara Capponi
4. Mark Kunitomi
5. Gowri Nayar
6. Edward Seabolt
7. Gandhar Mahadeshwar
8. Simone Bianco
9. Vandana Mukherjee
10. James H. Kaufman

Reviewed by ScreenIT

Genetic, metabolic, and molecular insights into the diverse outcomes of diet-induced obesity in mice

1. Alexis Maximilien Bachmann
2. Jean-David Morel
3. Gaby El Alam
4. Sandra Rodríguez-López
5. Tanes Imamura de lima
6. Ludger J.E. Goeminne
7. Giorgia Benegiamo
8. Maroun Bou Sleiman
9. Johan Auwerx

• Curated by eLife

  Evaluation Summary:

  In the present study, Bachmann and Morel et al., report a comprehensive survey of metabolic phenotypes and liver outcomes (gene expression, complex activities) in a unique subset of genetically diverse mouse strains. The authors focus on sex- and diet-dependent effects where notable differences are observed. These data will be a useful reference source for those interested in diet effects on metabolic phenotypes across various inbred mouse strains.

  (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

Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains

1. Premnath Madanagopal
2. Harshini Muthukumar
3. Kothai Thiruvengadam

Reviewed by ScreenIT

Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization

1. Gabriel Renaud
2. Maibritt Nørgaard
3. Johan Lindberg
4. Henrik Grönberg
5. Bram De Laere
6. Jørgen Bjerggaard Jensen
7. Michael Borre
8. Claus Lindbjerg Andersen
9. Karina Dalsgaard Sørensen
10. Lasse Maretty
11. Søren Besenbacher

• Curated by eLife

  Evaluation Summary:

  This work describes a shallow WGS sequencing approach (<1x) for genome‐wide cell‐free DNA fragmentation analysis using non-negative matrix factorization (NMF). The concept of utilizing 'fragmentomics' as an early cancer detection tool is a subject of intense investigation and there have been multiple recent publications in the field. This work adds an interesting unsupervised approach.

  (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

EMoMiS: A Pipeline for Epitope-based Molecular Mimicry Search in Protein Structures with Applications to SARS-CoV-2

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

Reviewed by ScreenIT

Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures

1. Dylan Lebatteux
2. Hugo Soudeyns
3. Isabelle Boucoiran
4. Soren Gantt
5. Abdoulaye Baniré Diallo

Reviewed by ScreenIT