Bioinformatics

GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures

1. Michael Gecht
2. Sören von Bülow
3. Camille Penet
4. Gerhard Hummer
5. Cyril Hanus
6. Mateusz Sikora

Reviewed by ScreenIT

PARROT is a flexible recurrent neural network framework for analysis of large protein datasets

1. Daniel Griffith
2. Alex S Holehouse

• Curated by eLife

  Evaluation Summary:

  The authors report a user-friendly software package (PARROT) that allows non-experts to use machine learning approaches to analyze high-throughput experiments on proteins. This package will allow more scientists to apply these powerful machine learning methods, thus increasing our ability to understand the chemistry and biological function of proteins.

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

Reviewed by eLife

Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein

1. Zhen Wah Tan
2. Wei-Ven Tee
3. Firdaus Samsudin
4. Enrico Guarnera
5. Peter J. Bond
6. Igor N. Berezovsky

Reviewed by ScreenIT

Identification and Characterization of Novel Mutants of Nsp13 Protein among Indian SARS-CoV-2 Isolates

1. Deepa Kumari
2. Namrata Kumari
3. Sudhir Kumar
4. Prabhat Kumar Sinha
5. Shivendra Kumar Shahi
6. Nihar Ranjan Biswas
7. Abhay Kumar

Reviewed by ScreenIT

Computational analysis of B cell receptor repertoires in COVID-19 patients using deep embedded representations of protein sequences

1. Inyoung Kim
2. Sang Yoon Byun
3. Sangyeup Kim
4. Sangyoon Choi
5. Jinsung Noh
6. Junho Chung
7. Byung Gee Kim

Reviewed by ScreenIT

CIGB-300 synthetic peptide, an antagonist of CK2 kinase activity, as a treatment for Covid-19. A computational biology approach

1. Jamilet Miranda
2. Ricardo Bringas
3. Jorge Fernández-de-Cossio
4. Yasser Perera

Reviewed by ScreenIT

Evolutionary dynamics of indels in SARS-CoV-2 spike glycoprotein

1. R. Shyama Prasad Rao
2. Nagib Ahsan
3. Chunhui Xu
4. Lingtao Su
5. Jacob Verburgt
6. Luca Fornelli
7. Daisuke Kihara
8. Dong Xu

Reviewed by ScreenIT

A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia

1. Xiangyi Li
2. Lin Jiang
3. Chao Xue
4. Mulin Jun Li
5. Miaoxin Li

• Curated by eLife

  Evaluation Summary:

  This manuscript describes an improved approach (MGCA) to identify risk genes for human traits and diseases using data from genome wide association studies. The authors demonstrate the utility of their approach by analyzing data from patients with schizophrenia, and narrow in meaningful biological processes and potential drug repurposing candidates. This approach will facilitate gene prioritization from large genetic datasets for downstream applications such as functional studies.

  (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

SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data

1. Christos Maniatis
2. Catalina A. Vallejos
3. Guido Sanguinetti

Reviewed by Review Commons

CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes

1. Roux-Cil Ferreira
2. Emmanuel Wong
3. Gopi Gugan
4. Kaitlyn Wade
5. Molly Liu
6. Laura Muñoz Baena
7. Connor Chato
8. Bonnie Lu
9. Abayomi S Olabode
10. Art F Y Poon

Reviewed by ScreenIT