Systems Biology

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

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

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

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