Bioinformatics

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

FAIR Header Reference genome: a TRUSTworthy standard

1. Adam Wright
2. Mark D Wilkinson
3. Christopher Mungall
4. Scott Cain
5. Stephen Richards
6. Paul Sternberg
7. Ellen Provin
8. Jonathan L Jacobs
9. Scott Geib
10. Daniela Raciti
11. Karen Yook
12. Lincoln Stein
13. David C Molik

Reviewed by Arcadia Science

A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture

1. Clare Andradi-Brown
2. Jan Stephan Wichers-Misterek
3. Heidrun von Thien
4. Yannick D Höppner
5. Judith AM Scholz
6. Helle Hansson
7. Emma Filtenborg Hocke
8. Tim Wolf Gilberger
9. Michael F Duffy
10. Thomas Lavstsen
11. Jake Baum
12. Thomas D Otto
13. Aubrey J Cunnington
14. Anna Bachmann

• Curated by eLife

  eLife assessment

  Focusing mainly on var genes, the investigators performed comprehensive computational analyses of gene expression in malaria parasites isolated from patients and assessed changes that occur as these parasites adapt to in vitro culture conditions. The study provides an improved computational pipeline for monitoring var gene expression, and importantly, the study documents changes in expression of the core genome and thus provides insights into metabolic adaptations that parasites undergo while transitioning to culture conditions. The findings are important for their technical advances that are more rigorous than the current state-of-the-art. The solid data analyses, broadly support the claims with only minor weaknesses, tell us to be cautious when interpreting results obtained only from cultured parasites.

Reviewed by eLife

Detection of new pioneer transcription factors as cell-type-specific nucleosome binders

1. Yunhui Peng
2. Wei Song
3. Vladimir B Teif
4. Ivan Ovcharenko
5. David Landsman
6. Anna R Panchenko

• Curated by eLife

  eLife assessment

  This valuable study aims to identify pioneer transcription factors, which are defined as transcription factors that compete with nucleosomes for DNA binding. The authors provide methods for identifying pioneer transcription factors on a cell type basis, using nucleosome positioning and motif information across different cell lines. The evidence to support the claims is largely solid. This work will be of interest to computational and molecular biologists working on transcription factors.

Reviewed by eLife