Systems Biology

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. K Patel
2. MJ Barter
3. J Soul
4. P Clark
5. CJ Proctor
6. IM Clark
7. DA Young
8. DP 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

Systems analysis of multiple diabetes-helminth cohorts reveals markers of disease-disease interaction

1. Nilesh 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

Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction

1. Saugat Poudel
2. Jason Hyun
3. Ying Hefner
4. Jon Monk
5. Victor Nizet
6. Bernhard O Palsson

• Curated by eLife

  eLife assessment

  This study presents valuable findings on core genome mutations that might have driven the emergence of the Staphylococcus aureus lineage USA300, a frequent cause of community-acquired infections. The authors present a solid novel approach that combines genome-wide association studies and RNA-expression analyses, both applied to extensive publicly available datasets. This approach generated an intriguing hypothesis that should be validated experimentally. The work will interest microbiologists working in genomic epidemiology and phenotype-genotype association studies.

Reviewed by eLife