Systems Biology

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity

1. Szilvia Barsi
2. Henrietta Papp
3. Alberto Valdeolivas
4. Dániel J. Tóth
5. Anett Kuczmog
6. Mónika Madai
7. László Hunyady
8. Péter Várnai
9. Julio Saez-Rodriguez
10. Ferenc Jakab
11. Bence Szalai

Reviewed by ScreenIT

Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1

1. Shida Shangguan
2. Philip K Ehrenberg
3. Aviva Geretz
4. Lauren Yum
5. Gautam Kundu
6. Kelly May
7. Slim Fourati
8. Krystelle Nganou-Makamdop
9. LaTonya D Williams
10. Sheetal Sawant
11. Eric Lewitus
12. Punnee Pitisuttithum
13. Sorachai Nitayaphan
14. Suwat Chariyalertsak
15. Supachai Rerks-Ngarm
16. Morgane Rolland
17. Daniel C Douek
18. Peter Gilbert
19. Georgia D Tomaras
20. Nelson L Michael
21. Sandhya Vasan
22. Rasmi Thomas

• Curated by eLife

  Evaluation Summary:

  Attempts to produce effective vaccines against HIV have not yet been successful, with the lack of understanding correlates of protection being a significant limitation. This paper analyses gene expression in a number of human and non-human primate vaccine trials and identifies a profile that appears to correlate with protection from infection. This profile is linked primarily to monocytes and the ability of these cells to mediate antibody dependent cellular phagocytosis. The work has implications for ongoing attempts to generate effective vaccines against HIV and perhaps other viral diseases.

  (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

Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets

1. Ahmed B. Alarabi
2. Attayeb Mohsen
3. Kenji Mizuguchi
4. Fatima Z. Alshbool
5. Fadi T. Khasawneh

Reviewed by ScreenIT

Analysis of changes occurring in Codon Positions due to mutations through the cellular automata transition rules

1. Antara Sengupta
2. Sreeya Ghosh
3. Pabitra Pal Choudhury

Reviewed by ScreenIT

Executable network of SARS-CoV-2-host interaction predicts drug combination treatments

1. Rowan Howell
2. Matthew A. Clarke
3. Ann-Kathrin Reuschl
4. Tianyi Chen
5. Sean Abbott-Imboden
6. Mervyn Singer
7. David M. Lowe
8. Clare L. Bennett
9. Benjamin Chain
10. Clare Jolly
11. Jasmin Fisher

Reviewed by ScreenIT

Tissue Specific Age Dependence of the Cell Receptors Involved in the SARS-CoV-2 Infection

1. Christian V. Forst
2. Lu Zeng
3. Qian Wang
4. Xianxiao Zhou
5. Sezen Vatansever
6. Zhidong Tu
7. Bin Zhang

Reviewed by ScreenIT

Transcriptomics-inferred dynamics of SARS-CoV-2 interactions with host epithelial cells

1. Lukas Adam
2. Megan Stanifer
3. Fabian Springer
4. Jan Mathony
5. Maik Brune
6. Chiara Di Ponzio
7. Roland Eils
8. Steeve Boulant
9. Dominik Niopek
10. Stefan M. Kallenberger

Reviewed by ScreenIT

Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast

1. Istvan T Kleijn
2. Amalia Martínez-Segura
3. François Bertaux
4. Malika Saint
5. Holger Kramer
6. Vahid Shahrezaei
7. Samuel Marguerat

Reviewed by Review Commons

Two different cell-cycle processes determine the timing of cell division in Escherichia coli

1. Alexandra Colin
2. Gabriele Micali
3. Louis Faure
4. Marco Cosentino Lagomarsino
5. Sven van Teeffelen

• Curated by eLife

  Evaluation Summary:

  How the bacterium E.coli decides when to divide is an interesting, important, unsolved and highly controversial topic of interest to readers across disciplines, including microbiology, cell biology and statistical physics. Popular "single process" models invoke regulation at the step of replication initiation or at the step of cell division per se, whereas these authors have previously proposed a "concurrent cycles" model in which both processes are relevant, with different prominences in different situations. Consistent with the authors' motivating hypothesis, in the particular perturbed condition investigated in this work, a process different from DNA replication becomes increasingly important for division control as the degree of perturbation increases, which provides a new challenge to models for cell division control.

  (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 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Systematic genome-scale identification of host factors for SARS-CoV-2 infection across models yields a core single gene dependency; ACE2

1. Katherine Chan
2. Adrian Granda Farias
3. Hunsang Lee
4. Furkan Guvenc
5. Patricia Mero
6. Kamaldeep Aulakh
7. Kevin R. Brown
8. Shahan Haider
9. Edyta Marcon
10. Ulrich Braunschweig
11. Amy Hin Yan Tong
12. Shuye Pu
13. Andrea Habsid
14. Natasha Christie-Holmes
15. Patrick Budylowski
16. Audrey Astori
17. Ayoob Ghalami
18. Samira Mubareka
19. Arinjay Banerjee
20. Karen L. Mossman
21. Jack Greenblatt
22. Scott D. Gray-Owen
23. Brian Raught
24. Benjamin J. Blencowe
25. Mikko Taipale
26. Jason Moffat

Reviewed by ScreenIT