Systems Biology

Holimap: an accurate and efficient method for solving stochastic gene network dynamics

1. Chen Jia
2. Ramon Grima

Reviewed by preLights

A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

1. Gang Xue
2. Xiaoyi Zhang
3. Wanqi Li
4. Lu Zhang
5. Zongxu Zhang
6. Xiaolin Zhou
7. Di Zhang
8. Lei Zhang
9. Zhiyuan Li

• Curated by eLife

  eLife assessment

  The study presented in this manuscript makes important contributions to our understanding of cell fate decisions and the role of noise in gene regulatory networks. Through computational and theoretical analysis, the authors provide solid support for distinguishing distinct driving forces behind fate decisions based on noise profiles and reprogramming trajectories. While acknowledging the potential limitations of small gene regulatory networks in capturing the richness of whole-transcriptome sequencing datasets, this study offers a creative approach for formulating hypotheses about gene regulation during stem cell differentiation using single-cell sequencing data.

Reviewed by eLife

Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)

1. Atefeh Lafzi
2. Costanza Borrelli
3. Simona Baghai Sain
4. Karsten Bach
5. Jonas A Kretz
6. Kristina Handler
7. Daniel Regan-Komito
8. Xenia Ficht
9. Andreas Frei
10. Andreas Moor

Reviewed by Review Commons

Multi-omic analysis of bat versus human fibroblasts reveals altered central metabolism

1. N Suhas Jagannathan
2. Javier Yu Peng Koh
3. Younghwan Lee
4. Radoslaw Mikolaj Sobota
5. Aaron T Irving
6. Lin-fa Wang
7. Yoko Itahana
8. Koji Itahana
9. Lisa Tucker-Kellogg

Reviewed by Review Commons

Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate

1. Diana Széliová
2. Stefan Müller
3. Jürgen Zanghellini

Reviewed by Review Commons

Systematic exploration of bacterial form I rubisco maximal carboxylation rates

1. Benoit de Pins
2. Lior Greenspoon
3. Yinon M. Bar-On
4. Melina Shamshoum
5. Roee Ben-Nissan
6. Eliya Milshtein
7. Dan Davidi
8. Itai Sharon
9. Oliver Mueller-Cajar
10. Elad Noor
11. Ron Milo

Reviewed by Review Commons

Tools and methods for high-throughput single-cell imaging with the mother machine

1. Ryan Thiermann
2. Michael Sandler
3. Gursharan Ahir
4. John T Sauls
5. Jeremy Schroeder
6. Steven Brown
7. Guillaume Le Treut
8. Fangwei Si
9. Dongyang Li
10. Jue D Wang
11. Suckjoon Jun

• Curated by eLife

  eLife assessment

  This article provides a review and test of image-analysis methods for bacteria growing in the 'mother-machine' microfluidic device, introducing also a new graphical user interface for the computational analysis of mother-machine movies based on the 'Napari' environment. The tool allows users to segment cells based on two previously published methods (classical image transformation and thresholding as well as UNet-based analysis), with solid evidence for their robust performance based on comparison with other methods and use of datasets from other labs. While it was difficult to assess the user-friendliness of the new GUI, it appears to be valuable and promising for the field.

Reviewed by eLife

Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability

1. Fabien Duveau
2. Céline Cordier
3. Lionel Chiron
4. Matthias Le Bec
5. Sylvain Pouzet
6. Julie Séguin
7. Artémis Llamosi
8. Benoit Sorre
9. Jean-Marc Di Meglio
10. Pascal Hersen

• Curated by eLife

  eLife assessment

  This study presents important findings on how cells sense and respond to their surroundings, in particular when two environmental signals are presented periodically, in alternation or conjunction. The compelling analyses reveal some unexpected behaviors that could not have been drawn, from simpler experimental designs, related to the dynamic interplay between the starvation and hyper-osmotic stress responses in budding yeast, exemplifying that applying complex signals can unveil new biological insights, even for well-studied systems. The work will be of broad interest to researchers interested in fungal biology, dynamic systems, cell signaling, and cell biology.

Reviewed by eLife

Pleiotropic effects of trisomy and pharmacologic modulation on structural, functional, molecular, and genetic systems in a Down syndrome mouse model

1. Sergi Llambrich
2. Birger Tielemans
3. Ellen Saliën
4. Marta Atzori
5. Kaat Wouters
6. Vicky Van Bulck
7. Mark Platt
8. Laure Vanherp
9. Nuria Gallego Fernandez
10. Laura Grau de la Fuente
11. Harish Poptani
12. Lieve Verlinden
13. Uwe Himmelreich
14. Anca Croitor
15. Catia Attanasio
16. Zsuzsanna Callaerts-Vegh
17. Willy Gsell
18. Neus Martínez-Abadías
19. Greetje Vande Velde

• Curated by eLife

  eLife assessment

  This study presents valuable findings that examine both how Down syndrome (DS)-related physiological, behavioral, and phenotypic traits track across time, as well as how chronic treatment with green tea extracts 25 enriched in epigallocatechin-3-gallate (GTE-EGCG), administered in drinking water spanning prenatal through 5 months of age, impacts these measures in wild-type and Ts65Dn mice. The strength of the evidence is solid, due to high variability across measures, perhaps in part attributable to a failure to include sex as a factor for measures known to be sexually dimorphic. This study is of interest to scientists interested in Down Syndrome and its treatment, as well as scientists who study disorders that impact multiple organ systems.

Reviewed by eLife

A constraint-based framework to reconstruct interaction networks in microbial communities

1. Omid Oftadeh
2. Asli Sahin
3. Evangelia Vayena
4. Vassily Hatzimanikatis

Reviewed by Arcadia Science