Bioinformatics

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

Prediction of coronavirus 3C-like protease cleavage sites using machine-learning algorithms

1. Huiting Chen
2. Zhaozhong Zhu
3. Ye Qiu
4. Xingyi Ge
5. Heping Zheng
6. Yousong Peng

Reviewed by ScreenIT

Structural Differences In 3C-like protease (Mpro) From SARS-CoV and SARS-CoV-2: Molecular Insights For Drug Repurposing Against COVID-19 Revealed by Molecular Dynamics Simulations

1. Meet Parmar
2. Ritik Thumar
3. Bhumi Patel
4. Mohd Athar
5. Prakash C. Jha
6. Dhaval Patel

Reviewed by ScreenIT

A systematic comparison of novel and existing differential analysis methods for CyTOF data

1. Lis Arend
2. Judith Bernett
3. Quirin Manz
4. Melissa Klug
5. Olga Lazareva
6. Jan Baumbach
7. Dario Bongiovanni
8. Markus List

Reviewed by ScreenIT

Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection

1. Martina Poletti
2. Agatha Treveil
3. Luca Csabai
4. Leila Gul
5. Dezso Modos
6. Matthew Madgwick
7. Marton Olbei
8. Balazs Bohar
9. Alberto Valdeolivas
10. Denes Turei
11. Bram Verstockt
12. Sergio Triana
13. Theodore Alexandrov
14. Julio Saez-Rodriguez
15. Megan L. Stanifer
16. Steeve Boulant
17. Tamas Korcsmaros

Reviewed by ScreenIT

CytokineLink: a cytokine communication map to analyse immune responses in inflammatory and infectious diseases

1. Marton Olbei
2. John P. Thomas
3. Isabelle Hautefort
4. Agatha Treveil
5. Balazs Bohar
6. Matthew Madgwick
7. Lejla Gul
8. Luca Csabai
9. Dezso Modos
10. Tamas Korcsmaros

Reviewed by ScreenIT