Systems Biology

PhysiMeSS - a new physiCell addon for extracellular matrix modelling

1. Vincent Noël
2. Marco Ruscone
3. Robyn Shuttleworth
4. Cicely K. Macnamara

• Curated by GigaByte

  Editors Assessment:

  PhysiCell is an open source multicellular systems simulator for studying many interacting cells in dynamic tissue microenvironments. As part of the PhysiCell ecosystem of tools and modules this paper presents a PhysiCell addon, PhysiMeSS (MicroEnvironment Structures Simulation) which allows the user to accurately represent the extracellular matrix (ECM) as a network of fibres. This can specify rod-shaped microenvironment elements such as the matrix fibres (e.g. collagen) of the ECM, allowing the PhysiCell user the ability to investigate physical interactions with cells and other fibres. Reviewers asked for additional clarification on a number of features. And the paper now clear future releases will provide full 3D compatibility and include working on fibrogenesis, i.e. the creation of new ECM fibres by cells.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes

1. Jie Luo
2. Jeff Ranish

• Curated by eLife

  eLife Assessment

  This manuscript presents a valuable new quantitative crosslinking mass spectrometry approach using novel isobaric crosslinkers. The data are solid and the method has potential for a broad application in structural biology if more isobaric crosslinking channels are available and the quantitative information of the approach is exploited in more depth.

Reviewed by eLife

Diversity in Notch ligand-receptor signaling interactions

1. Rachael Kuintzle
2. Leah A Santat
3. Michael B Elowitz

• Curated by eLife

  eLife Assessment

  This valuable study significantly enhances our understanding of how various ligands and receptors interact within the Notch signaling pathway. By developing novel cell-based assay systems, the authors systematically analyzed the effects of different ligand-receptor combinations on pathway activation. The convincing data reveal intriguing and unexpected differences and provide a foundation for interpreting Notch signalling in both normal and disease-related contexts.

Reviewed by eLife

Proteomic and functional comparison between human induced and embryonic stem cells

1. Alejandro J Brenes
2. Eva Griesser
3. Linda V Sinclair
4. Lindsay Davidson
5. Alan R Prescott
6. Francois Singh
7. Elizabeth KJ Hogg
8. Carmen Espejo-Serrano
9. Hao Jiang
10. Harunori Yoshikawa
11. Melpomeni Platani
12. Jason R Swedlow
13. Greg M Findlay
14. Doreen A Cantrell
15. Angus I Lamond

• Curated by eLife

  eLife Assessment

  This study reports differences in proteomic profiles of embryonic versus induced pluripotent stem cells. This important finding cautions against the interchangeable use of both types of cells in biomedical research, although the mechanisms responsible for these differences remains unknown. The proteomic evidence is convincing, even though there is limited validation with other methods.

Reviewed by eLife

DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits

1. Vincent Gardeux
2. Roel PJ Bevers
3. Fabrice PA David
4. Emily Rosschaert
5. Romain Rochepeau
6. Bart Deplancke

• Curated by eLife

  eLife Assessment

  Genetic analysis of complex traits in Drosophila provides a resource for exploring the relationship between genetic and phenotypic variation. The web tool DGRPool presented in this paper makes data and results from the Drosophila Genetic Reference Panel accessible that will enable downstream analyses of genetic association. The findings of this paper are considered to be important, with practical implications beyond a single subfield, supported by convincing evidence using appropriate and validated methodology in line with current state of the art.

Reviewed by eLife

Genome-wide conditional degron libraries for functional genomics

1. Eduardo Gameiro
2. Karla A. Juárez-Núñez
3. Jia Jun Fung
4. Susmitha Shankar
5. Brian Luke
6. Anton Khmelinskii

Reviewed by Review Commons

Inference of gene regulatory networks for overcoming low performance in real-world data

1. Yusuke Hiki
2. Yuta Tokuoka
3. Takahiro G. Yamada
4. Akira Funahashi

Reviewed by Arcadia Science

Slowest possible replicative life at frigid temperatures for yeast

1. Diederik S. Laman Trip
2. Théo Maire
3. Hyun Youk

Reviewed by Arcadia Science

Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis

1. Krutik Patel
2. Matt Barter
3. Jamie Soul
4. Peter Clark
5. Carole Proctor
6. Ian Clark
7. David Young
8. Daryl P Shanley

• Curated by eLife

  eLife assessment

  This study provides valuable insight into the role of miR-199a/b-5p in cartilage formation. The evidence supporting the significance of the identified miRNA and its target mRNA transcripts is convincing. This paper will likely primarily benefit scientists focused on diseases related to this biological process, such as osteoarthritis. Furthermore, researchers with a broader interest in miRNAs may find the computational model to identify novel RNA-RNA interactions particularly helpful.

Reviewed by eLife

Delineating markers of disease-disease interaction: a systematic methodology and its application to multiple diabetes-helminth cohorts

1. Nilesh Anantha Subramanian
2. Philge Philip
3. Anuradha Rajamanickam
4. Nathella Pavan Kumar
5. Subash Babu
6. Manikandan Narayanan

Reviewed by Arcadia Science