Bioinformatics

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

1. Carol Moraga
2. Evelyn Sanchez
3. Mariana Galvão Ferrarini
4. Rodrigo A. Gutierrez
5. Elena A. Vidal
6. Marie-France Sagot

Reviewed by GigaScience

Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI

1. Alena Kalyakulina
2. Igor Yusipov
3. Maria Giulia Bacalini
4. Claudio Franceschi
5. Maria Vedunova
6. Mikhail Ivanchenko

Reviewed by GigaScience

Spacemake: processing and analysis of large-scale spatial transcriptomics data

1. Tamas Ryszard Sztanka-Toth
2. Marvin Jens
3. Nikos Karaiskos
4. Nikolaus Rajewsky

Reviewed by GigaScience

Loop detection using Hi-C data with HiCExplorer

1. Joachim Wolff
2. Rolf Backofen
3. Björn Grüning

Reviewed by GigaScience

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