Systems Biology

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

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

Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae

1. Maksim A. Yakovlev
2. Ke Liang
3. Carolyn R. Zaino
4. Daniel J. Vanselow
5. Andrew L. Sugarman
6. Alex Y. Lin
7. Patrick J. La Riviere
8. Yuxi Zheng
9. Justin D. Silverman
10. John C. Leichty
11. Sharon X. Huang
12. Keith C. Cheng

• Curated by eLife

  eLife assessment

  Tissue phenotyping is central to nearly all areas of biology. In this study, the authors use an advanced form of micro-CT (X-ray histotomography) in zebrafish to phenotype blood cells in the intact animal. These approaches build upon prior work from this group and others showing this is a scalable imaging method that could readily be applied to other cell types, and provide an excellent complement to histological analysis of tissues. This is important work, as it demonstrates that the method can provide an approach that is orthogonal to conventional histology. The strength of the presented data is compelling, with description of both the hardware and software needed to implement the protocol, which will make it accessible to other researchers in the field.

Reviewed by eLife

Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data

1. Idan Hekselman
2. Assaf Vital
3. Maya Ziv-Agam
4. Lior Kerber
5. Ido Yairi
6. Esti Yeger-Lotem

• Curated by eLife

  eLife assessment

  The study presents analyses linking cell-types to monogenic disorders using over-expression of known disease-associated genes in single-cell data to identify 110 disease-affected cell types for 714 Mendelian diseases. Overall this important study combines multiple data analyses to quantify the connection between cell types and human disorders. While some of the analyses are compelling, updates to the method are needed to ensure that statistical inference is appropriately stringent and rigorous.

Reviewed by eLife