Bioinformatics

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 in autoimmune disorders

1. Stephan Wilmes
2. Polly-Anne Jeffrey
3. Jonathan Martinez-Fabregas
4. Maximillian Hafer
5. Paul Fyfe
6. Elizabeth Pohler
7. Silvia Gaggero
8. Martín López-García
9. Grant Lythe
10. Thomas Guerrier
11. David Launay
12. Mitra Suman
13. Jacob Piehler
14. Carmen Molina-París
15. 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: build, share, and explore simulations of cells and tissues in the web browser

1. Inge M. N. 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

Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load

1. Doğa Eskier
2. Aslı Suner
3. Yavuz Oktay
4. Gökhan Karakülah

Reviewed by PeerJ, ScreenIT

Predicting cell health phenotypes using image-based morphology profiling

1. Gregory P. Way
2. Maria Kost-Alimova
3. Tsukasa Shibue
4. William F. Harrington
5. Stanley Gill
6. Federica Piccioni
7. Tim Becker
8. Hamdah Shafqat-Abbasi
9. William C. Hahn
10. Anne E. Carpenter
11. Francisca Vazquez
12. Shantanu Singh

Reviewed by Review Commons

Use of the p-value as a size-dependent function to address practical differences when analyzing large datasets

1. Estibaliz Gómez-de-Mariscal
2. Vanesa Guerrero
3. Alexandra Sneider
4. Hasini Jayatilaka
5. Jude M. Phillip
6. Denis Wirtz
7. Arrate Muñoz-Barrutia

Reviewed by eLife