Bioinformatics

Deep Batch Active Learning for Drug Discovery

1. Michael Bailey
2. Saeed Moayedpour
3. Ruijiang Li
4. Alejandro Corrochano-Navarro
5. Alexander Kötter
6. Lorenzo Kogler-Anele
7. Saleh Riahi
8. Christoph Grebner
9. Gerhard Hessler
10. Hans Matter
11. Marc Bianciotto
12. Pablo Mas
13. Ziv Bar-Joseph
14. Sven Jager

• Curated by eLife

  eLife assessment

  This valuable study reports novel active learning batch selection methods that have been applied to optimization tasks related to ADMET and affinity properties relevant within the drug discovery field. While the evidence is solid, the paper could have benefited from a clearer and deeper description of methods as well as interpretation of the obtained models, and a wider comparison to existing methods. The article will be of general interest to scientist working in the field of drug discovery and, in general, to researchers within the fields of machine learning and data analysis.

Reviewed by eLife

Classification of bioactive peptides: a comparative analysis of models and encodings

1. Edoardo Bizzotto
2. Guido Zampieri
3. Laura Treu
4. Pasquale Filannino
5. Raffaella Di Cagno
6. Stefano Campanaro

Reviewed by Arcadia Science

A benchmark for large language models in bioinformatics

1. Varuni Sarwal
2. Gaia Andreoletti
3. Viorel Munteanu
4. Ariel Suhodolschi
5. Dumitru Ciorba
6. Viorel Bostan
7. Mihai Dimian
8. Eleazar Eskin
9. Wei Wang
10. Serghei Mangul

Reviewed by Arcadia Science

RamanSPy: An Open-Source Python Package for Integrative Raman Spectroscopy Data Analysis

1. Dimitar Georgiev
2. Simon Vilms Pedersen
3. Ruoxiao Xie
4. Álvaro Fernández-Galiana
5. Molly M. Stevens
6. Mauricio Barahona

Reviewed by Arcadia Science

Functional annotation hypothetical proteins: a world to be explored in drug development in Trypanosomatids

1. Raissa Santos de Lima
2. Ana Carolina Silva Bulla
3. Manuela Leal da Silva

Reviewed by Arcadia Science

Variance Analysis of LC-MS Experimental Factors and Their Impact on Machine Learning

1. Tobias Greisager Rehfeldt
2. Konrad Krawczyk
3. Simon Gregersen Echers
4. Paolo Marcatili
5. Pawel Palczynski
6. Richard Röttger
7. Veit Schwämmle

Reviewed by GigaScience

When do longer reads matter? A benchmark of long read de novo assembly tools for eukaryotic genomes

1. Bianca-Maria Cosma
2. Ramin Shirali Hossein Zade
3. Erin Noel Jordan
4. Paul van Lent
5. Chengyao Peng
6. Stephanie Pillay
7. Thomas Abeel

Reviewed by GigaScience

Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities

1. Danielle C. Wrenn
2. Devin M. Drown

• Curated by GigaByte

  Editors Assessment: Antimicrobial resistance (AMR) is a global public health threat, and environmental microbial communities can act as reservoirs for resistance genes. There is a need for genomic surveillance could provide insights into how these reservoirs change and impact public health. With that goal in mind this study tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. On average adaptive sampling resulting in a target composition 4x higher than without adaptive sampling, and increased target yield in most replicates. The methods and scripts for this approach were reviewed and curated together, although the scope of this study was limited in terms of communities tested and AMR genes targeted. And the authors improved their analysis by conducting an additional analysis of a diverse microbial community. Demonstrating the method is reusable and its results are promising for developing a flexible, portable, and cost-effective AMR surveillance tool.

  *This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Learning orientation-invariant representations enables accurate and robust morphologic profiling of cells and organelles

1. James Burgess
2. Jeffrey J. Nirschl
3. Maria-Clara Zanellati
4. Sarah Cohen
5. Serena Yeung

Reviewed by Arcadia Science

A joint embedding of protein sequence and structure enables robust variant effect predictions

1. Lasse M. Blaabjerg
2. Nicolas Jonsson
3. Wouter Boomsma
4. Amelie Stein
5. Kresten Lindorff-Larsen

Reviewed by Arcadia Science