Systems Biology

Gene networks under circadian control exhibit diurnal organization in primate organs

1. Jie Li
2. Pengxing Nie
3. Christoph W. Turck
4. Guang-Zhong Wang

Reviewed by ScreenIT

Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

1. Michael Jahn
2. Nick Crang
3. Markus Janasch
4. Andreas Hober
5. Björn Forsström
6. Kyle Kimler
7. Alexander Mattausch
8. Qi Chen
9. Johannes Asplund-Samuelsson
10. Elton Paul Hudson

• Curated by eLife

  Evaluation Summary:

  This work combines elegant experimental approaches with modelling predictions to study of metabolic adaptations in the bacterium Cupriavidus necator, a microorganism of interest given its metabolic versatility and potential industrial applications. This manuscript will be interesting for microbiologists and systems biologists who want to understand how protein production and economy and enzyme utilization differs in a versatile microorganism in different conditions.

  (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 and Reviewer #2 agreed to share their names with the authors.)

Reviewed by eLife

Synthetic lethality-based prediction of anti-SARS-CoV-2 targets

1. Lipika R. Pal
2. Kuoyuan Cheng
3. Nishanth Ulhas Nair
4. Laura Martin-Sancho
5. Sanju Sinha
6. Yuan Pu
7. Laura Riva
8. Xin Yin
9. Fiorella Schischlik
10. Joo Sang Lee
11. Sumit K. Chanda
12. Eytan Ruppin

Reviewed by ScreenIT

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

Dynamics of SARS-CoV-2 host cell interactions inferred from transcriptome analyses

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

Reviewed by ScreenIT