Systems Biology

PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell

1. Daniel Bergman
2. Lauren Marazzi
3. Mukti Chowkwale
4. Deepa Maheshvare M
5. Supriya Bidanta
6. Tarunendu Mapder
7. Jialun Li

Reviewed by GigaByte

Transcription-replication interactions reveal principles of bacterial genome regulation

1. Andrew W. Pountain
2. Peien Jiang
3. Tianyou Yao
4. Ehsan Homaee
5. Yichao Guan
6. Magdalena Podkowik
7. Bo Shopsin
8. Victor J. Torres
9. Ido Golding
10. Itai Yanai

Reviewed by Arcadia Science

Proteome-wide systems genetics identifies UFMylation as a regulator of skeletal muscle function

1. Jeffrey Molendijk
2. Ronnie Blazev
3. Richard J Mills
4. Yaan-Kit Ng
5. Kevin I Watt
6. Daryn Chau
7. Paul Gregorevic
8. Peter J Crouch
9. James BW Hilton
10. Leszek Lisowski
11. Peixiang Zhang
12. Karen Reue
13. Aldons J Lusis
14. James E Hudson
15. David E James
16. Marcus M Seldin
17. Benjamin L Parker

• Curated by eLife

  eLife assessment

  This manuscript will be of broad interest to those working in the genetics of complex diseases, with the results strongly supporting the author's primary claims. Overall, this is an important study that demonstrates the power of proteomics-based systems genetics studies in the mouse.

Reviewed by eLife

Dynamic metabolome profiling uncovers potential TOR signaling genes

1. Stella Reichling
2. Peter F Doubleday
3. Tomas Germade
4. Ariane Bergmann
5. Robbie Loewith
6. Uwe Sauer
7. Duncan Holbrook-Smith

Reviewed by Review Commons

Patterns of interdivision time correlations reveal hidden cell cycle factors

1. Fern A Hughes
2. Alexis R Barr
3. Philipp Thomas

• Curated by eLife

  eLife assessment

  This work makes an important contribution to the study of the cell cycle and inferring mechanisms by studying correlations in division timing between single cells. By treating the problem in a general way and computing over lineage trees, the authors can infer timescales in the underlying mechanism. This approach is able to detect a general role of circadian rhythms in cell cycle control. The method is validated on data sets from bacterial and mammalian cells and can suggest when additional measurements are needed to distinguish competing models. This paper is of broad interest to scientists in the fields of cell growth, cell division, and cell-cycle control.

Reviewed by eLife

Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures

1. Felix Proulx-Giraldeau
2. Jan M Skotheim
3. Paul François

• Curated by eLife

  Evaluation Summary:

  This paper develops evolutionary simulations to identify the type of molecular networks that can give rise to size control. We now know a lot about the functional consequences and underlying molecular biology of different cell size control strategies, but comparatively less about which factors select for particular mechanisms. The authors address this point in an evolutionary framework. They show that the evolution of a specific cell size control mechanism is dependent on the cell cycle structure. The paper will interest researchers in development, evolution, and physics of biological systems.

  (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 name with the authors.)

Reviewed by eLife

Multi‐omic network analysis identified betacellulin as a novel target of omega‐3 fatty acid attenuation of western diet‐induced nonalcoholic steatohepatitis

1. Jyothi Padiadpu
2. Manuel Garcia‐Jaramillo
3. Nolan K Newman
4. Jacob W Pederson
5. Richard Rodrigues
6. Zhipeng Li
7. Sehajvir Singh
8. Philip Monnier
9. Giorgio Trinchieri
10. Kevin Brown
11. Amiran K Dzutsev
12. Natalia Shulzhenko
13. Donald B Jump
14. Andrey Morgun

Reviewed by Review Commons

A hierarchical model for external electrical control of an insect, accounting for inter-individual variation of muscle force properties

1. Dai Owaki
2. Volker Dürr
3. Josef Schmitz

• Curated by eLife

  eLife assessment

  This valuable work presents new results to characterize the relationship between electrical excitation and torque generation in stick insect joints. The evidence supporting this work is a series of torque-voltage measurements across individuals. The strength of evidence is solid in supporting the outcomes, but some details of the methodology, which could potentially shed light on the sources of this variation, are missing.

Reviewed by eLife

Deep proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice

1. Feng Xian
2. Julia Regina Sondermann
3. David Gomez Varela
4. Manuela Schmidt

• Curated by eLife

  Evaluation Summary:

  In addition to providing extensive proteomics profiling datasets. this manuscript is fundamental that sheds light on the importance of appropriate experimental design for mouse disease model which have been overlooked so far. The results look quite solid based on the proper methodology. This type of work is extremely valuable to many biomedical scientists in the field for conducting reproducible research especially in the preclinical studies and properly interpreting the results.

  (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 #3 agreed to share their name with the authors.)

Reviewed by eLife

Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains

1. Valentina Baldazzi
2. Delphine Ropers
3. Jean-Luc Gouzé
4. Tomas Gedeon
5. Hidde de Jong

• Curated by eLife

  Evaluation Summary:

  This study develops a resource allocation model for E. coli growing under steady-state conditions. The model describes both growth rate and yield and has been subjected to validation by comparison with a compiled data set. The manuscript addresses an important problem of interest to a wide range of investigators. At the same time, the authors would need to explore different assumptions for the housekeeping proteome fraction (phi_q) to ensure the model is robust.

  (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. The reviewers remained anonymous to the authors.)

Reviewed by eLife