Systems Biology

fastBMA: Scalable Network Inference and Transitive Reduction

1. Ling-Hong Hung
2. Kaiyuan Shi
3. Migao Wu
4. William Chad Young
5. Adrian E. Raftery
6. Ka Yee Yeung

Reviewed by GigaScience

Automated, high-dimensional evaluation of physiological aging and resilience in outbred mice

1. Zhenghao Chen
2. Anil Raj
3. GV Prateek
4. Andrea Di Francesco
5. Justin Liu
6. Brice E Keyes
7. Ganesh Kolumam
8. Vladimir Jojic
9. Adam Freund

• Curated by eLife

  Evaluation Summary:

  Chen et al. develop a comprehensive platform to score aging-dependent changes in mouse physiology and behavior using a multi-dimensional longitudinal phenotyping approach. Their thorough data collection and analysis reveals a diversity of trajectories in aging-related physiological and behavioral changes and helps disentangle biological aging from chronological aging, providing a reference pioneering work for future studies aimed at large-scale aging multi-dimensional phenotyping.

  (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

Evolution and regulation of microbial secondary metabolism

1. Guillem Santamaria
2. Chen Liao
3. Chloe Lindberg
4. Yanyan Chen
5. Zhe Wang
6. Kyu Rhee
7. Francisco Rodrigues Pinto
8. Jinyuan Yan
9. Joao B Xavier

• Curated by eLife

  Evaluation Summary:

  Santamaria et al. provide interesting insights into the complex regulation used by 31 Pseudomonas aeruginosa clinical strains to minimize the individual costs of cooperative phenotypes based on secondary metabolites. The data analysis is sound and of remarkable depth. Their results challenge the view that there is a tradeoff between primary and secondary metabolism in bacteria and that instead, secondary metabolites may be produced in low-stress conditions when excess carbon is available. However, the relevance of the laboratory growth conditions for these clinical strains requires additional justification.

  (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

Transiently increased intercommunity regulation characterizes concerted cell phenotypic transition

1. Weikang Wang
2. Ke Ni
3. Dante Poe
4. Jianhua Xing

Reviewed by Review Commons

Reverse engineering of metacognition

1. Matthias Guggenmos

• Curated by eLife

  Evaluation Summary:

  This paper presents a novel computational model of metacognition that parameterizes links between sensory evidence and confidence. The proposed model relies on perceptual decision-making to formalize different sources of noise and bias that impact confidence, with the aim of developing metacognitive metrics that are independent of perceptual sensitivity - a continued endeavor in the field. Despite the clear merits of this approach, more evidence is needed to validate the proposed architecture, which is particularly modular, and may therefore impair the generalizability of the proposed mechanisms.

  (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

Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock

1. Alex A Koch
2. James S Bagnall
3. Nicola J Smyllie
4. Nicola Begley
5. Antony D Adamson
6. Jennifer L Fribourgh
7. David G Spiller
8. Qing-Jun Meng
9. Carrie L Partch
10. Korbinian Strimmer
11. Thomas A House
12. Michael H Hastings
13. Andrew SI Loudon

• Curated by eLife

  Evaluation Summary:

  Koch et al. quantified the abundance of the core clock molecules and their binding affinities, thereby providing critical information for our quantitative understanding of the core transcriptional negative feedback loop of the mammalian circadian clock. Furthermore, they used mathematical modeling to incorporate the quantified information and identified the hidden role of PER:CRY complex, enhancing the mobility of BMAL1:CLOCK to new target sites. The work makes the important contribution that the displacement type repression frees CLOCK-BMAL1 to bind to other targets and activate several sets of genes. This is an important insight, but some of the data need further explanation and some statements ought to change to improve the manuscript.

  (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

Metabolic dyshomeostasis induced by SARS-CoV-2 structural proteins reveals immunological insights into viral olfactory interactions

1. Mercedes Lachén-Montes
2. Naroa Mendizuri
3. Karina Ausín
4. Miriam Echaide
5. Ester Blanco
6. Luisa Chocarro
7. María de Toro
8. David Escors
9. Joaquín Fernández-Irigoyen
10. Grazyna Kochan
11. Enrique Santamaría

Reviewed by ScreenIT

SARS-CoV-2 leverages airway epithelial protective mechanism for viral infection

1. Allison Marie Greaney
2. Micha Sam Brickman Raredon
3. Maria P. Kochugaeva
4. Laura E. Niklason
5. Andre Levchenko

Reviewed by ScreenIT

CompoundRay, an open-source tool for high-speed and high-fidelity rendering of compound eyes

1. Blayze Millward
2. Steve Maddock
3. Michael Mangan

• Curated by eLife

  Evaluation Summary:

  This work reports on a mathematical modeling system and associated software implementation for compound eye vision. A critical advance reported here is the ability to model each ommatidium with independent properties and on a software implementation that runs in real time, with tantalizing applications in both modeling biological systems such as insect compound eyes, and the exploration of the possible applications of compound eye vision in robotics.

  (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

Patient-specific Boolean models of signalling networks guide personalised treatments

1. Arnau Montagud
2. Jonas Béal
3. Luis Tobalina
4. Pauline Traynard
5. Vigneshwari Subramanian
6. Bence Szalai
7. Róbert Alföldi
8. László Puskás
9. Alfonso Valencia
10. Emmanuel Barillot
11. Julio Saez-Rodriguez
12. Laurence Calzone

• Curated by eLife

  Evaluation Summary:

  This paper presents a mathematical model for prioritizing drugs for prostate cancer patients based on signal network database. The manuscript is of broad interest to the field of oncology and precision medicine. The methodology developed is sophisticated and relevant to real patient prostate cancer data. The predictions from the model are validated in an experimental setting and provide suggestions for the personalisation of prostate cancer treatment. The study can serve as a roadmap for future development of predictive, personalized models.

  (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