Systems Biology

The metabolome of Mexican cavefish shows a convergent signature highlighting sugar, antioxidant, and Ageing-Related metabolites

1. J Kyle Medley
2. Jenna Persons
3. Tathagata Biswas
4. Luke Olsen
5. Robert Peuß
6. Jaya Krishnan
7. Shaolei Xiong
8. Nicolas Rohner

• Curated by eLife

  Evaluation Summary:

  Medley et al. study A. mexicanus, an extreme-adapted organism with important connections to human health. The authors test metabolic responses in this natural model of elevated blood glucose and extensive body fat deposits, conditions generally expected to predispose to higher risk for metabolic syndrome and higher frailty. The work is rigorous and will provide a reference for future studies aimed at dissecting the mechanistic basis underlying metabolic shifts in this uniquely attractive model. The authors also provide an open and accessible window into their data and analyses by sharing a Shiny app.

  (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

Landscape of epithelial–mesenchymal plasticity as an emergent property of coordinated teams in regulatory networks

1. Kishore Hari
2. Varun Ullanat
3. Archana Balasubramanian
4. Aditi Gopalan
5. Mohit Kumar Jolly

• Curated by eLife

  Evaluation Summary:

  In this paper, the authors identify topological metrics in gene-regulatory networks that potentially predict the kinds of phenotypic steady-states that the network allows. In particular, they apply their results to the epithelial-mesenchymal plasticity, showing that the relevant gene regulatory networks are structured as ‘teams' that may be 'strong', yielding stable phenotypes, or 'weak', yielding unstable phenotypes prone to plasticity. The work would be of interest to researchers interested in systems biology and the nonlinear dynamics of biological systems, as well as biologists interested in gene regulatory networks and their (mis)functioning in cancer cells.

  (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

Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics

1. Mayank Baranwal
2. Ryan L Clark
3. Jaron Thompson
4. Zeyu Sun
5. Alfred O Hero
6. Ophelia S Venturelli

• Curated by eLife

  Evaluation Summary:

  The ultimate goal of this work is to apply machine learning to learn from experimental data on temporal dynamics and functions of microbial communities to predict their future behavior and design new communities with desired functions. Using a significant amount of experimental data, the authors suggest that their method outperforms a commonly used approach. Overall, the work is potentially of broad interest to those working on microbiome prediction and design.

  (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

Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components

1. Jeffrey C Berry
2. Mingsheng Qi
3. Balasaheb V Sonawane
4. Amy Sheflin
5. Asaph Cousins
6. Jessica Prenni
7. Daniel P Schachtman
8. Peng Liu
9. Rebecca S Bart

• Curated by eLife

  Evaluation Summary:

  The manuscript will be of interest to researchers focusing on understanding phenotypes using data collected from field studies. It provides a rigorous strategy for how to appropriately adjust confounding effects and to perform statistical analysis of noisy data from field plots.

  (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

Zebrafish airinemes optimize their shape between ballistic and diffusive search

1. Sohyeon Park
2. Hyunjoong Kim
3. Yi Wang
4. Dae Seok Eom
5. Jun Allard

• Curated by eLife

  Evaluation Summary:

  This paper studies statistical aspects of the role of long-range cellular protrusions called airinemes as means of intracellular communication. The authors use published data showing how airinemes approach a target cell and describe these movements with a mathematical model for an unobstructed persistent random walk. The impact of this study will be on the specialised reader interested in modelling and airineme biology.

  (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

TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer

1. Amartya Singh
2. Gyan Bhanot
3. Hossein Khiabanian

Reviewed by GigaScience

Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks

1. Ermin Hodzic
2. Raunak Shrestha
3. Kaiyuan Zhu
4. Kuoyuan Cheng
5. Colin C Collins
6. S Cenk Sahinalp

Reviewed by GigaScience

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