Systems Biology

Emergence of planar cell polarity from the interplay of local interactions and global gradients

1. Divyoj Singh
2. Sriram Ramaswamy
3. Mohit Kumar Jolly
4. Mohd Suhail Rizvi

• Curated by eLife

  eLife assessment

  This study presents a valuable model for the emergence of planar cell polarity from the interplay of local interactions and global gradient. The framework of this model is solid, although the appreciation of its result should in places be more quantitative. A quality of this model is its simplicity and its convenience for experimental testing.

Reviewed by eLife

The ability to sense the environment is heterogeneously distributed in cell populations

1. Andrew Goetz
2. Hoda Akl
3. Purushottam Dixit

• Curated by eLife

  eLife assessment

  In this valuable paper, the authors use an existing theoretical framework relying on information theory and maximum entropy inference in order to quantify how much information single cells can carry, taking into account their internal state. They reanalyze experimental data in this light. Despite some limitations of the data, the study convincingly highlights the difference between single-cell and population channel capacities. This result should be of interest to the quantitative biology community, as it contributes to explaining why channel capacities are apparently low in cells.

Reviewed by eLife

Liebig’s law of the minimum in the TGF-β/SMAD pathway

1. Yuchao Li
2. Difan Deng
3. Chris Tina Höfer
4. Jihye Kim
5. Won Do Heo
6. Quanbin Xu
7. Xuedong Liu
8. Zhike Zi

Reviewed by Review Commons

Dynamic analysis and control of a rice-pest system under transcritical bifurcations

1. Sajib Mandal
2. Sebastian Oberst
3. Md. Haider Ali Biswas
4. Md. Sirajul Islam

Reviewed by PeerJ

Inference of drug off-target effects on cellular signaling using interactome-based deep learning

1. Nikolaos Meimetis
2. Douglas A. Lauffenburger
3. Avlant Nilsson

Reviewed by preLights

Evolutionary druggability for low-dimensional fitness landscapes toward new metrics for antimicrobial applications

1. Rafael F Guerrero
2. Tandin Dorji
3. Ra'Mal M Harris
4. Matthew D Shoulders
5. C Brandon Ogbunugafor

• Curated by eLife

  eLife assessment

  This manuscript introduces two valuable new metrics - "variant vulnerability" and "drug applicability" - that would be of use to identify candidate drugs for treating infections while considering longer-term, evolution-based treatment outcomes. Despite the intuitive appeal of the metrics and their potential, the study remains incomplete, as it fails to demonstrate the generality of the approach. The work could be improved by analysing a broader range of data in a systematic way and directly tying the metrics to outcomes, which would make it possible to better assess their impact and utility.

Reviewed by eLife

A unified approach to dissecting biphasic responses in cell signaling

1. Vaidhiswaran Ramesh
2. J Krishnan

• Curated by eLife

  eLife assessment

  This study presents a useful mathematical analysis of different signaling networks in an attempt to provide general rules that give rise to biphasic responses, a widely observed behavior in biology in which the outputs of the network depend non-monotonically on the inputs. Determining general conditions that underlie this behavior would be useful in engineering synthetic biological systems and for mechanistically understanding biphasic responses in biological systems. However, whereas the mathematical approach and methods are solid, as they stand, the analyses are inadequate to assess how these findings are applicable in nature and which are general.

Reviewed by eLife

Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories

1. Jeanette A.I. Johnson
2. Daniel R. Bergman
3. Heber L. Rocha
4. David L. Zhou
5. Eric Cramer
6. Ian C. Mclean
7. Yoseph W. Dance
8. Max Booth
9. Zachary Nicholas
10. Tamara Lopez-Vidal
11. Atul Deshpande
12. Randy Heiland
13. Elmar Bucher
14. Fatemeh Shojaeian
15. Matthew Dunworth
16. André Forjaz
17. Michael Getz
18. Inês Godet
19. Furkan Kurtoglu
20. Melissa Lyman
21. John Metzcar
22. Jacob T. Mitchell
23. Andrew Raddatz
24. Jacobo Solorzano
25. Aneequa Sundus
26. Yafei Wang
27. David G. DeNardo
28. Andrew J. Ewald
29. Daniele M. Gilkes
30. Luciane T. Kagohara
31. Ashley L. Kiemen
32. Elizabeth D. Thompson
33. Denis Wirtz
34. Laura D. Wood
35. Pei-Hsun Wu
36. Neeha Zaidi
37. Lei Zheng
38. Jacquelyn W. Zimmerman
39. Jude M. Phillip
40. Elizabeth M. Jaffee
41. Joe W. Gray
42. Lisa M. Coussens
43. Young Hwan Chang
44. Laura M. Heiser
45. Genevieve L. Stein-O’Brien
46. Elana J. Fertig
47. Paul Macklin

Reviewed by preLights

Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse

1. Zeyneb Kurt
2. Jenny Cheng
3. Rio Barrere-Cain
4. Caden N McQuillen
5. Zara Saleem
6. Neil Hsu
7. Nuoya Jiang
8. Calvin Pan
9. Oscar Franzén
10. Simon Koplev
11. Susanna Wang
12. Johan Björkegren
13. Aldons J Lusis
14. Montgomery Blencowe
15. Xia Yang

• Curated by eLife

  eLife assessment

  In this important study, the authors integrated genetic and genomic datasets from humans and mice to unveil shared networks and pathways associated with coronary artery disease. Their compelling analysis led to the identification of new regulatory genes and pathways in vascular tissues and in the liver, allowing for a more in-depth understanding of the pathogenesis of coronary artery disease.

Reviewed by eLife

The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion

1. Shreyas Niphadkar
2. Lavanya Karinje
3. Sunil Laxman

Reviewed by Review Commons