Bioinformatics

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

1. Alexander J Tarashansky
2. Jacob M Musser
3. Margarita Khariton
4. Pengyang Li
5. Detlev Arendt
6. Stephen R Quake
7. Bo Wang

• Curated by eLife

  Evaluation Summary:

  The development of single-cell genomic methods has transformed our understanding of cell types and their attributes across organisms. Here, Tarashansky et al develop SAMap (Self-Assembling Manifold mapping), a graph-based data integration method which builds upon their previously described SAM algorithm to facilitate assignment of homologous genes and cell types across diverse species. As the authors show, this empowers comparative analyses across phyla to facilitate cellular annotation and examine the evolutionary origins of cellular diversity. Overall, the manuscript is well-written and the algorithm has the potential to be foundation for comparative cellular atlasing.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome

1. Irene Unterman
2. Idit Bloch
3. Simona Cazacu
4. Gila Kazimirsky
5. Bruria Ben-Zeev
6. Benjamin P Berman
7. Chaya Brodie
8. Yuval Tabach

• Curated by eLife

  Evaluation Summary:

  The manuscript has the potential to be of broad interest to neuroscientists who are aiming to leverage concepts and tools of evolutionary biology to identify novel gene targets and much-needed therapeutic interventions. The follow up experiments are detailed, well thought out, and do a good job of proving the potential of the identified drugs in alleviating molecular signatures in in vitro disease models. However, the link between comparative genomic analysis and identification of specific drugs is not yet sufficiently established and doesn't convincingly demonstrate the usability of the evolutionary pipeline in identifying novel therapeutics.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree

1. Audrey M Hendley
2. Arjun A Rao
3. Laura Leonhardt
4. Sudipta Ashe
5. Jennifer A Smith
6. Simone Giacometti
7. Xianlu L Peng
8. Honglin Jiang
9. David I Berrios
10. Mathias Pawlak
11. Lucia Y Li
12. Jonghyun Lee
13. Eric A Collisson
14. Mark S Anderson
15. Gabriela K Fragiadakis
16. Jen Jen Yeh
17. Chun Jimmie Ye
18. Grace E Kim
19. Valerie M Weaver
20. Matthias Hebrok

• Curated by eLife

  Evaluation Summary:

  In this study, the authors present a high-resolution single-cell transcriptomic atlas of the pancreatic ductal tree. Their analysis unveiled important heterogeneity within the pancreatic ductal tree and identified unique cellular states. Overall, the results presented here suggest distinct functional roles for subpopulations of duct cells in maintenance of duct cell identity and implication in chronic pancreatic inflammation. Finally, such detailed analysis of the pancreatic duct tree is relevant also in the context of cancer biology and might help elucidating the transition from pancreatitis to pancreatic cancer and/or different predisposition to cancer.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Competitive coordination of the dual roles of the Hedgehog co-receptor in homophilic adhesion and signal reception

1. Shu Yang
2. Ya Zhang
3. Chuxuan Yang
4. Xuefeng Wu
5. Sarah Maria El Oud
6. Rongfang Chen
7. Xudong Cai
8. Xufeng S Wu
9. Ganhui Lan
10. Xiaoyan Zheng

• Curated by eLife

  Evaluation Summary:

  This is a well-conceived and well-presented study that sheds light on two critical questions related to Hedgehog signaling, namely, the dual function of the Hedgehog co-receptor Ihog in Hh signal transduction and homophilic adhesion, and the regulation of cytoneme structure.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level

1. Suraj Kannan
2. Michael Farid
3. Brian L. Lin
4. Matthew Miyamoto
5. Chulan Kwon

Reviewed by Review Commons

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses

1. Stephan Wilmes
2. Polly-Anne Jeffrey
3. Jonathan Martinez-Fabregas
4. Maximillian Hafer
5. Paul K Fyfe
6. Elizabeth Pohler
7. Silvia Gaggero
8. Martín López-García
9. Grant Lythe
10. Charles Taylor
11. Thomas Guerrier
12. David Launay
13. Suman Mitra
14. Jacob Piehler
15. Carmen Molina-París
16. Ignacio Moraga

• Curated by eLife

  Evaluation Summary:

  This study is a great example of an elaborate combination of experimental and mathematical analyses to examine an intriguing, pleiotropic immunological signaling pathway. While a good number of individual aspects of this signaling pathway have been studied and reported before, the present work pieces together many pieces and succeeds to present a conclusive and comprehensive model of this particular cytokine system. The main conclusions are well supported by the presented data and the manuscript will be of interest and relevance for the study of many other cytokine signaling pathways, being of broad relevance for immunologists and cell biologists.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser

1. Inge MN Wortel
2. Johannes Textor

Reviewed by eLife

Generating functional protein variants with variational autoencoders

1. Alex Hawkins-Hooker
2. Florence Depardieu
3. Sebastien Baur
4. Guillaume Couairon
5. Arthur Chen
6. David Bikard

Reviewed by Review Commons

Bayesian inference of kinetic schemes for ion channels by Kalman filtering

1. Jan L Münch
2. Fabian Paul
3. Ralf Schmauder
4. Klaus Benndorf

• Curated by eLife

  Summary: The manuscript is well written and overall clear, and the mathematical treatment is a rigorous tour-de-force. However, the reviewers raised a number of points that need further clarification, better discussion or amendment. These concerns are likely to be addressable largely by changes to the main text and software documentation along with some additional analyses. The study is very nice and ambitious, but clarity is a bit impaired by dealing with perhaps too many issues. The state inference and the bayesian model selection are very important but completely different issues. The authors should consider whether they may be better treated separately, or for a more specialized audience.

Reviewed by eLife

Potential role of cellular miRNAs in coronavirus-host interplay

1. Stepan Nersisyan
2. Narek Engibaryan
3. Aleksandra Gorbonos
4. Ksenia Kirdey
5. Alexey Makhonin
6. Alexander Tonevitsky

Reviewed by PeerJ, ScreenIT