Systems Biology

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

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