Systems Biology

Dynamically linking influenza virus infection kinetics, lung injury, inflammation, and disease severity

1. Margaret A Myers
2. Amanda P Smith
3. Lindey C Lane
4. David J Moquin
5. Rosemary Aogo
6. Stacie Woolard
7. Paul Thomas
8. Peter Vogel
9. Amber M Smith

• Curated by eLife

  Evaluation Summary:

  This is an interesting synthesis of iterative model development and experimental work in an influenza model of infection in mice. The work is quite groundbreaking in the field as it is the first to use models to link dynamics of lung viral load, infected cells, inflammation, virus-specific CD8+ T cells, bystander CD8+ T cells, and disease status. The paper suggests that CD8+ T cells are vital for elimination of infected cells but can also contribute directly to lung damage and disease severity.

  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

Anti-SARS-CoV-2 potential of Cissampelos pareira L. identified by connectivity map-based analysis and in vitro studies

1. Madiha Haider
2. Vivek Anand
3. M. Ghalib Enayathullah
4. Yash Parekh
5. Sushma Ram
6. Surekha Kumari
7. Anmol
8. Gayatri Panda
9. Manjari Shukla
10. Dhwani Dholakia
11. Arjun Ray
12. Sudipta Bhattacharyya
13. Upendra Sharma
14. Kiran Kumar Bokara
15. Bhavana Prasher
16. Mitali Mukerji

Reviewed by ScreenIT

E156G and Arg158, Phe-157/del mutation in NTD of spike protein in B.1.617.2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape

1. Armi M Chaudhari
2. Dinesh Kumar
3. Madhvi Joshi
4. Amrutlal Patel
5. Chaitanya Joshi

Reviewed by ScreenIT

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

1. David E. Gordon
2. Gwendolyn M. Jang
3. Mehdi Bouhaddou
4. Jiewei Xu
5. Kirsten Obernier
6. Matthew J. O’Meara
7. Jeffrey Z. Guo
8. Danielle L. Swaney
9. Tia A. Tummino
10. Ruth Huettenhain
11. Robyn M. Kaake
12. Alicia L. Richards
13. Beril Tutuncuoglu
14. Helene Foussard
15. Jyoti Batra
16. Kelsey Haas
17. Maya Modak
18. Minkyu Kim
19. Paige Haas
20. Benjamin J. Polacco
21. Hannes Braberg
22. Jacqueline M. Fabius
23. Manon Eckhardt
24. Margaret Soucheray
25. Melanie J. Bennett
26. Merve Cakir
27. Michael J. McGregor
28. Qiongyu Li
29. Zun Zar Chi Naing
30. Yuan Zhou
31. Shiming Peng
32. Ilsa T. Kirby
33. James E. Melnyk
34. John S. Chorba
35. Kevin Lou
36. Shizhong A. Dai
37. Wenqi Shen
38. Ying Shi
39. Ziyang Zhang
40. Inigo Barrio-Hernandez
41. Danish Memon
42. Claudia Hernandez-Armenta
43. Christopher J.P. Mathy
44. Tina Perica
45. Kala B. Pilla
46. Sai J. Ganesan
47. Daniel J. Saltzberg
48. Rakesh Ramachandran
49. Xi Liu
50. Sara B. Rosenthal
51. Lorenzo Calviello
52. Srivats Venkataramanan
53. Jose Liboy-Lugo
54. Yizhu Lin
55. Stephanie A. Wankowicz
56. Markus Bohn
57. Phillip P. Sharp
58. Raphael Trenker
59. Janet M. Young
60. Devin A. Cavero
61. Joseph Hiatt
62. Theodore L. Roth
63. Ujjwal Rathore
64. Advait Subramanian
65. Julia Noack
66. Mathieu Hubert
67. Ferdinand Roesch
68. Thomas Vallet
69. Björn Meyer
70. Kris M. White
71. Lisa Miorin
72. Oren S. Rosenberg
73. Kliment A Verba
74. David Agard
75. Melanie Ott
76. Michael Emerman
77. Davide Ruggero
78. Adolfo García-Sastre
79. Natalia Jura
80. Mark von Zastrow
81. Jack Taunton
82. Alan Ashworth
83. Olivier Schwartz
84. Marco Vignuzzi
85. Christophe d’Enfert
86. Shaeri Mukherjee
87. Matt Jacobson
88. Harmit S. Malik
89. Danica G. Fujimori
90. Trey Ideker
91. Charles S. Craik
92. Stephen Floor
93. James S. Fraser
94. John Gross
95. Andrej Sali
96. Tanja Kortemme
97. Pedro Beltrao
98. Kevan Shokat
99. Brian K. Shoichet
100. Nevan J. Krogan

Reviewed by ScreenIT, preLights

Global mapping of RNA homodimers in living cells

1. Marta M. Gabryelska
2. Andrew P. Badrock
3. Jian You Lau
4. Raymond T. O'Keefe
5. Yanick J. Crow
6. Grzegorz Kudla

Reviewed by ScreenIT

A hybrid PDE–ABM model for viral dynamics with application to SARS–CoV–2 and influenza

1. Sadegh Marzban
2. Renji Han
3. Nóra Juhász
4. Gergely Röst

Reviewed by ScreenIT

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data

1. Charlie George Barker
2. Eirini Petsalaki
3. Girolamo Giudice
4. Julia Sero
5. Emmanuel Nsa Ekpenyong
6. Chris Bakal
7. Evangelia Petsalaki

Reviewed by Review Commons

The Strand-biased Transcription of SARS-CoV-2 and Unbalanced Inhibition by Remdesivir

1. Yan Zhao
2. Jing Sun
3. Yunfei Li
4. Zhengxuan Li
5. Yu Xie
6. Ruoqing Feng
7. Jincun Zhao
8. Yuhui Hu

Reviewed by ScreenIT

In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients

1. Joonho Park
2. Hyeyoon Kim
3. So Yeon Kim
4. Yeonjae Kim
5. Jee-Soo Lee
6. Moon-Woo Seong
7. Dohyun Han

Reviewed by ScreenIT

Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients

1. Michael R. Filbin
2. Arnav Mehta
3. Alexis M. Schneider
4. Kyle R. Kays
5. Jamey R. Guess
6. Matteo Gentili
7. Bánk G. Fenyves
8. Nicole C. Charland
9. Anna L.K. Gonye
10. Irena Gushterova
11. Hargun K. Khanna
12. Thomas J. LaSalle
13. Kendall M. Lavin-Parsons
14. Brendan M. Lilly
15. Carl L. Lodenstein
16. Kasidet Manakongtreecheep
17. Justin D. Margolin
18. Brenna N. McKaig
19. Maricarmen Rojas-Lopez
20. Brian C. Russo
21. Nihaarika Sharma
22. Jessica Tantivit
23. Molly F. Thomas
24. Robert E. Gerszten
25. Graham S. Heimberg
26. Paul J. Hoover
27. David J. Lieb
28. Brian Lin
29. Debby Ngo
30. Karin Pelka
31. Miguel Reyes
32. Christopher S. Smillie
33. Avinash Waghray
34. Thomas E. Wood
35. Amanda S. Zajac
36. Lori L. Jennings
37. Ida Grundberg
38. Roby P. Bhattacharyya
39. Blair Alden Parry
40. Alexandra-Chloé Villani
41. Moshe Sade-Feldman
42. Nir Hacohen
43. Marcia B. Goldberg

Reviewed by ScreenIT