Systems Biology

CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data

1. Franck Simon
2. Maria Colomba Comes
3. Tiziana Tocci
4. Louise Dupuis
5. Vincent Cabeli
6. Nikita Lagrange
7. Arianna Mencattini
8. Maria Carla Parrini
9. Eugenio Martinelli
10. Hervé Isambert

• Curated by eLife

  eLife assessment

  In this fundamental study, the authors describe a new data processing pipeline that can be used to discover causal interactions from time-lapse imaging data. The utility of this pipeline was convincingly illustrated using tumor-on-chip ecosystem data. The newly developed pipeline could be used to better understand cell-cell interactions and could also be applied to perform temporal causal discovery in other areas of science, meaning this work could potentially have a wide range of applications.

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

Transplantation of exogenous mitochondria mitigates myocardial dysfunction after cardiac arrest

1. Zhen Wang
2. Jie Zhu
3. Mengda Xu
4. Xuyuan Ma
5. Maozheng Shen
6. Jingyu Yan
7. Guosheng Gan
8. Xiang Zhou

• Curated by eLife

  eLife assessment

  This study presents valuable findings on how mitochondrial transplantation affects post-cardiac arrest myocardial dysfunction (PAMD). The authors demonstrate that mitochondrial transplantation enhances cardiac function, increases survival rates after the return of spontaneous circulation (ROSC). While the findings are promising, the organization of the paper, along with the analysis and interpretation of the results, are inadequate and need revision.

Reviewed by eLife

Unveiling Gene Perturbation Effects through Gene Regulatory Networks Inference from single-cell transcriptomic data

1. Clelia Corridori
2. Merrit Romeike
3. Giorgio Nicoletti
4. Christa Buecker
5. Samir Suweis
6. Sandro Azaele
7. Graziano Martello

Reviewed by Review Commons

Systems genomics of salinity stress response in rice

1. Sonal Gupta
2. Simon C Groen
3. Maricris L Zaidem
4. Andres Godwin C Sajise
5. Irina Calic
6. Mignon A Natividad
7. Kenneth L McNally
8. Georgina V Vergara
9. Rahul Satija
10. Steven J Franks
11. Rakesh K Singh
12. Zoé Joly-Lopez
13. Michael D Purugganan

• Curated by eLife

  eLife assessment

  Working with a diverse panel of field-grown rice accessions, this valuable study measures changes in transcript abundance, tests for patterns of selection on gene expression, and maps the genetic basis of variation in gene expression in normal and high salinity conditions. The authors provide solid evidence that salinity treatment increases the number of genes with mean expression levels away from the optimum, and that a relatively small number of genes are hotspots for genetic variants that affect genome-wide patterns of variation in gene expression under high salinity. The design, clarity, and interpretation of several statistical analyses can be improved, additional opportunities for integration among datasets and analyses could be realized, and genetic manipulation would be required to confirm the functional involvement of any specific genes in regulatory networks or organismal traits that confer adaptation to higher salinity conditions. The manuscript will not only be of interest to evolutionary biologists studying the genetics of complex traits, but it will also be a resource for plant biologists studying mechanisms of abiotic stress tolerance.

Reviewed by eLife

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

Sfp1 integrates TORC1 and PKA activity towards yeast ribosome biogenesis

1. Luc-Alban Vuillemenot
2. Franz Y. Ho
3. Andreas Milias-Argeitis

Reviewed by Review Commons