Systems Biology

A kinase to cytokine explorer to identify molecular regulators and potential therapeutic opportunities

1. Marina Chan
2. Yuqi Kang
3. Shannon Osborne
4. Michael Zager
5. Taranjit S Gujral

• Curated by eLife

  eLife assessment

  This manuscript describes an important web resource for kinases connected to cytokines. The compelling information will be used by researchers across a number of fields including analysts, modelers, wet lab experimentalists and clinician-researchers, who are looking to improve our understanding of pathologies and means to correct them through modulating the immune response.

Reviewed by eLife

Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification

1. Tae-Yun Kang
2. Federico Bocci
3. Qing Nie
4. José N Onuchic
5. Andre Levchenko

• Curated by eLife

  eLife assessment

  The authors used an appropriate micro-engineered experimental model of angiogenesis coupled to mathematical model to study the early steps of the angiogenic sprouting. To this end, the authors developed a convincing model to predict how VEGF activates Delta-Notch signaling. The work affords important new insight into the complex processes involved in the onset of angiogenesis.

Reviewed by eLife

The genetic and dietary landscape of the muscle insulin signalling network

1. Julian van Gerwen
2. Stewart WC Masson
3. Harry B Cutler
4. Alexis Diaz Vegas
5. Meg Potter
6. Jacqueline Stöckli
7. Søren Madsen
8. Marin E Nelson
9. Sean J Humphrey
10. David E James

• Curated by eLife

  eLife assessment

  This fundamental study provides a unique tool for assessing the range of phosphorylation in insulin reactions due to genetic variation and dietary influence through the utilization of genetically distinct mouse strains. The discoveries of this study hold substantial importance, as they shed light on the interplay between genetic attributes and environmental conditions in shaping the insulin-signaling network within skeletal muscle, a crucial regulator of metabolism. The supporting evidence presented is compelling, and the work is anticipated to captivate a wide audience within the metabolism discipline due to its extensive appeal and by providing inspiration for further hypothesis-driven research.

Reviewed by eLife

Emergence of planar cell polarity from the interplay of local interactions and global gradients

1. Divyoj Singh
2. Sriram Ramaswamy
3. Mohit Kumar Jolly
4. Mohd Suhail Rizvi

• Curated by eLife

  eLife assessment

  This study presents a valuable model for the emergence of planar cell polarity from the interplay of local interactions and global gradient. The framework of this model is solid, although the appreciation of its result should in places be more quantitative. A quality of this model is its simplicity and its convenience for experimental testing.

Reviewed by eLife

The ability to sense the environment is heterogeneously distributed in cell populations

1. Andrew Goetz
2. Hoda Akl
3. Purushottam Dixit

• Curated by eLife

  eLife assessment

  In this valuable paper, the authors use an existing theoretical framework relying on information theory and maximum entropy inference in order to quantify how much information single cells can carry, taking into account their internal state. They reanalyze experimental data in this light. Despite some limitations of the data, the study convincingly highlights the difference between single-cell and population channel capacities. This result should be of interest to the quantitative biology community, as it contributes to explaining why channel capacities are apparently low in cells.

Reviewed by eLife

Knock-down of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection

1. Sathyabaarathi Ravichandran
2. Bharat Bhatt
3. Awantika Shah
4. Kithiganahalli Narayanaswamy Balaji
5. Nagasuma Chandra

• Curated by eLife

  eLife assessment

  The authors of this manuscript address the following question in the immunology field: what are the transcriptional regulators that allow macrophages to assume different functional phenotypes in response to immune stimuli? They generate a computational map of the gene regulatory networks involved in determining macrophage phenotypes and experimentally validate the role of putative regulatory factors in a myeloid cell line. This study represents a valuable approach to understanding how gene regulation impacts macrophage polarization but the analyses remain incomplete without further validation in primary cells or by examining the identified genes in the in vivo setting.

Reviewed by eLife

Liebig’s law of the minimum in the TGF-β/SMAD pathway

1. Yuchao Li
2. Difan Deng
3. Chris Tina Höfer
4. Jihye Kim
5. Won Do Heo
6. Quanbin Xu
7. Xuedong Liu
8. Zhike Zi

Reviewed by Review Commons

Dynamic analysis and control of a rice-pest system under transcritical bifurcations

1. Sajib Mandal
2. Sebastian Oberst
3. Md. Haider Ali Biswas
4. Md. Sirajul Islam

Reviewed by PeerJ

Inference of drug off-target effects on cellular signaling using interactome-based deep learning

1. Nikolaos Meimetis
2. Douglas A. Lauffenburger
3. Avlant Nilsson

Reviewed by preLights

Evolutionary druggability for low-dimensional fitness landscapes toward new metrics for antimicrobial applications

1. Rafael F Guerrero
2. Tandin Dorji
3. Ra'Mal M Harris
4. Matthew D Shoulders
5. C Brandon Ogbunugafor

• Curated by eLife

  eLife assessment

  This manuscript introduces two valuable new metrics - "variant vulnerability" and "drug applicability" - that would be of use to identify candidate drugs for treating infections while considering longer-term, evolution-based treatment outcomes. Despite the intuitive appeal of the metrics and their potential, the study remains incomplete, as it fails to demonstrate the generality of the approach. The work could be improved by analysing a broader range of data in a systematic way and directly tying the metrics to outcomes, which would make it possible to better assess their impact and utility.

Reviewed by eLife