Bioinformatics

Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification

1. Chakravarthi Kanduri
2. Milena Pavlović
3. Lonneke Scheffer
4. Keshav Motwani
5. Maria Chernigovskaya
6. Victor Greiff
7. Geir K Sandve

Reviewed by GigaScience

CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing

1. Marta Sanvicente-García
2. Albert García-Valiente
3. Socayna Jouide
4. Jessica Jaraba-Wallace
5. Eric Bautista
6. Marc Escobosa
7. Avencia Sánchez-Mejías
8. Marc Güell

Reviewed by Review Commons

Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection

1. Flora Mikaeloff
2. Marco Gelpi
3. Rui Benfeitas
4. Andreas D Knudsen
5. Beate Vestad
6. Julie Høgh
7. Johannes R Hov
8. Thomas Benfield
9. Daniel Murray
10. Christian G Giske
11. Adil Mardinoglu
12. Marius Trøseid
13. Susanne D Nielsen
14. Ujjwal Neogi

• Curated by eLife

  eLife assessment

  This study systematically integrates multi-omics data to identify the metabolic at-risk profiles within people living with HIV on antiretroviral therapy and presents findings that have focused importance and scope. The methods, data, and analyses as described now only partially support the primary claims.

Reviewed by eLife

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

1. Joseph F Cardiello
2. Alberto Joven Araus
3. Sarantis Giatrellis
4. Clement Helsens
5. András Simon
6. Nicholas D Leigh

Reviewed by Review Commons

Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification

1. Cassandra Koh
2. Lionel Frangeul
3. Hervé Blanc
4. Carine Ngoagouni
5. Sébastien Boyer
6. Philippe Dussart
7. Nina Grau
8. Romain Girod
9. Jean-Bernard Duchemin
10. Maria-Carla Saleh

• Curated by eLife

  eLife assessment

  This manuscript generates a valuable new genetic resource for studying mosquitos and the pathogens that they carry. For 33 species of mosquitoes, the authors have sequenced and assembled the ribosomal RNA, which will dramatically improve the power of RNA sequencing in mosquitoes.

Reviewed by eLife

Inhibiting a promiscuous GPCR: iterative discovery of bitter taste receptor ligands

1. Fabrizio Fierro
2. Lior Peri
3. Harald Hübner
4. Alina Tabor-Schkade
5. Lukas Waterloo
6. Stefan Löber
7. Tara Pfeiffer
8. Dorothee Weikert
9. Tamir Dingjan
10. Eitan Margulis
11. Peter Gmeiner
12. Masha Y Niv

Reviewed by Arcadia Science

Longitudinal fundus imaging and its genome-wide association analysis provide evidence for a human retinal aging clock

1. Sara Ahadi
2. Kenneth A Wilson
3. Boris Babenko
4. Cory Y McLean
5. Drew Bryant
6. Orion Pritchard
7. Ajay Kumar
8. Enrique M Carrera
9. Ricardo Lamy
10. Jay M Stewart
11. Avinash Varadarajan
12. Marc Berndl
13. Pankaj Kapahi
14. Ali Bashir

• Curated by eLife

  eLife assessment

  This paper is an important contribution to the biological aging field using eye image data to create an aging clock of the retina in data from eyePACS with validation in the UK Biobank. The authors provide compelling evidence that the clock correlates with chronological and phenotypic age, predicting mortality independently of chronological age. The work identifies novel genetic loci with a top site located in the ALKAL2 region, which is functionally validated in a Drosophila model.

Reviewed by eLife

Generating colorblind-friendly scatter plots for single-cell data

1. Tejas Guha
2. Elana J Fertig
3. Atul Deshpande

• Curated by eLife

  eLife assessment

  This manuscript is extremely useful for describing an R package that provides a valuable pattern and overlay framework for producing colorblind-friendly scatter plots for the field. The utility of this tool for making plots more accessible was demonstrated compellingly. This work will be of broad interest to many biomedical scientists, especially to viewers with color-vision deficiency.

Reviewed by eLife

Applying causal discovery to single-cell analyses using CausalCell

1. Yujian Wen
2. Jielong Huang
3. Shuhui Guo
4. Yehezqel Elyahu
5. Alon Monsonego
6. Hai Zhang
7. Yanqing Ding
8. Hao Zhu

• Curated by eLife

  eLife assessment

  The paper describes an online tool, CausalCell, intended for the analysis of causal links in single-cell datasets. Regarding its significance, this work is timely and important, with potentially broad applications as a generally useful tool. However, there are major concerns about the suitability of the tool for its intended purpose, and the extent of validation in the current manuscript is incomplete.

Reviewed by eLife

Identify Non-mutational p53 Functional Deficiency in Human Cancers

1. Qianpeng Li
2. Yang Zhang
3. Sicheng Luo
4. Zhang Zhang
5. Ann L Oberg
6. David E Kozono
7. Hua Lu
8. Jann N Sarkaria
9. Lina Ma
10. Liguo Wang

• Curated by eLife

  eLife assessment:

  This study by Li et al describes an interesting attempt to predict the functional status of the p53 tumor suppressor in tumors where no DNA mutations in p53 could be identified. To this end, the authors employed SVM models to train the algorithm for the detection of 'p53 inactivation' features contrasting normal and tumor tissues. The approach could be a valuable tool for attributing tumors with unknown p53 status. The authors provide solid evidence supporting their findings and the concept of the study is solid, but in its current formulation, some of the bioinformatic analyses are incomplete, particularly related to the selection of associated genes and the potential mechanism(s).

Reviewed by eLife