Bioinformatics

EMImR: a Shiny application for identifying transcriptomic and epigenomic changes

1. Hiba Ben Aribi
2. Careen Naitore
3. Farah Ayadi
4. Souheila Guerbouj
5. Olaitan I. Awe

• Curated by GigaByte

  Editors Assessment:

  Coded and written up as part of the African Society for Bioinformatics and Computational Biology (ASBCB) Omicscodeathons, EMImR is a novel Shiny application for transcriptomic and epigenomic change identification and correlation wrapped up using a combination of Bioconductor and CRAN packages. Case studies are on publicly available GEO data corresponding to sequencing data of human blood cell samples of multiple sclerosis patients to demonstrate how the tool works. And a documentation and videos are provided. Peer review and the study highlighting the usefulness of the developed tool for analyzing transcriptomic and epigenomic data.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline

1. Simon Holzinger
2. Leo Schmutterer
3. Victoria Marie Rothe
4. Maria Theresia Watzlowik
5. Uwe Schwartz
6. Gernot Längst

Reviewed by Review Commons

TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing

1. Jiachen Li
2. Zhe Wang
3. Hong-Bin Shen
4. Ye Yuan

• Curated by eLife

  eLife Assessment

  This study presents a valuable tool named TSvelo, a computational framework for RNA velocity inference that models transcriptional regulation and gene-specific splicing. The evidence supporting the claims of the authors is solid, although elaboration of the computational benchmark and datasets would have strengthened the study. The work will be of interest to computational scientists working in the field of RNA biology.

Reviewed by eLife

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

1. Markus Hoffmann
2. Lina-Liv Willruth
3. Alexander Dietrich
4. Hye Kyung Lee
5. Ludwig Knabl
6. Nico Trummer
7. Jan Baumbach
8. Priscilla A. Furth
9. Lothar Hennighausen
10. Markus List

Reviewed by Rapid Reviews Infectious Diseases

MAVISp: A Modular Structure-Based Framework for Protein Variant Effects

1. Matteo Arnaudi
2. Mattia Utichi
3. Kristine Degn
4. Matteo Tiberti
5. Ludovica Beltrame
6. Karolina Krzesińska
7. Pablo Sánchez-Izquierdo Besora
8. Eleni Kiachaki
9. Simone Scrima
10. Laura Bauer
11. Katrine Meldgård
12. Anna Melidi
13. Lorenzo Favaro
14. Anu Oswal
15. Guglielmo Tedeschi
16. Terézia Dorčaková
17. Alberte Heering Estad
18. Joachim Breitenstein
19. Jordan Safer
20. Paraskevi Saridaki
21. Valentina Sora
22. Francesca Maselli
23. Philipp Becker
24. Jérémy Vinhas
25. Alberto Pettenella
26. Matteo Lambrughi
27. Claudia Cava
28. Anna Rohlin
29. Mef Nilbert
30. Sumaiya Iqbal
31. Peter Wad Sackett
32. Burcu Aykac Fas
33. Elena Papaleo

Reviewed by Review Commons

Identification and classification of ion-channels across the tree of life provide functional insights into understudied CALHM channels

1. Rahil Taujale
2. Sung Jin Park
3. Nathan Gravel
4. Saber Soleymani
5. Rayna Carter
6. Kennady Boyd
7. Sarah Keuning
8. Zheng Ruan
9. Wei Lü
10. Natarajan Kannan

• Curated by eLife

  eLife Assessment

  In this manuscript Taujale et al describe an interdisciplinary approach to mine the human channelome and further discover orthologues across diverse organisms. Further, this work provides evidence that supports a role for conserved residues in CALHM channel gating. Overall this important work presents findings that can be helpful to the ion channel community, as well as to those interested in improved methods for mining sequence space for their protein of interest. However, further validation of the improvements their approach shows over previous approaches is needed, making this a solid contribution to the literature in this field.

Reviewed by eLife

ParTIpy: A Scalable Framework for Archetypal Analysis and Pareto Task Inference

1. Philipp S. L. Schäfer
2. Leoni Zimmermann
3. Paul L. Burmedi
4. Avia Walfisch
5. Noa Goldenberg
6. Shira Yonassi
7. Einat Shaer Tamar
8. Miri Adler
9. Jovan Tanevski
10. Ricardo O. Ramirez Flores
11. Julio Saez-Rodriguez

Reviewed by Review Commons

Human single-cell atlas analysis reveals heterogeneous endothelial signaling

1. Zimo Zhu
2. Rongbin Zheng
3. Yang Yu
4. Lili Zhang
5. Kaifu Chen

Reviewed by preLights

Raw signal segmentation for estimating RNA modification from Nanopore direct RNA sequencing data

1. Guangzhao Cheng
2. Aki Vehtari
3. Lu Cheng

• Curated by eLife

  eLife Assessment

  This study presents SegPore, a valuable new method for processing direct RNA nanopore sequencing data, which improves the segmentation of raw signals into individual bases and boosts the accuracy of modified base detection. The evidence presented to benchmark SegPore is solid, and the authors provide a fully documented implementation of the method. SegPore will be of particular interest to researchers studying RNA modifications.

Reviewed by eLife

MorphoNet 2.0: An innovative approach for qualitative assessment and segmentation curation of large-scale 3D time-lapse imaging datasets

1. Benjamin Gallean
2. Tao Laurent
3. Kilian Biasuz
4. Ange Clement
5. Noura Faraj
6. Patrick Lemaire
7. Emmanuel Faure

• Curated by eLife

  eLife Assessment

  This important work presents technical and conceptual advances with the release of MorphoNet 2.0, a versatile and accessible platform for 3D+T segmentation and analysis. The authors provide compelling evidence across diverse datasets, and the clarity of the manuscript together with the software's usability broadens its impact. Although the strength of some improvements is hard to fully gauge given sample complexity, the tool is a significant step forward that will likely impact many biological imaging fields.

Reviewed by eLife