Systems Biology

Expressive modeling and fast simulation for dynamic compartments

1. Till Köster
2. Philipp Henning
3. Tom Warnke
4. Adelinde Uhrmacher

Reviewed by preLights

Heritable epigenetic changes are constrained by the dynamics of regulatory architectures

1. Antony M Jose

• Curated by eLife

  eLife assessment

  This useful manuscript explores conditions for epigenetic inheritance by studying the stability of simple network models to permanent and transient perturbations. A novel aspect of the study is that it unifies non-genetic inheritance phenomena across cell divisions of unicellular organisms and in the germline of multicellular organisms. However, the models studied are more a collection of vignettes of numerical studies than a systematic study, therefore the evidence presented remains incomplete. As a first step towards building a more systematic theoretical framework, this work will be of interest to colleagues in the field of epigenetic inheritance.

Reviewed by eLife

The bistable mitotic switch in fission yeast

1. Béla Novák
2. John J. Tyson

Reviewed by Review Commons

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