Bioinformatics

Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy

1. Tom Smith
2. Mie Monti
3. Anne E Willis
4. Lajos Kalmár

• Curated by eLife

  eLife Assessment

  This study provides an important resource by thoroughly benchmarking multiple sequencing-based tRNA quantification methods. The suggested best practice is supported by convincing evidence from in silico experiments in multiple scenarios.

Reviewed by eLife

A novel channel invariant architecture for the segmentation of cells and nuclei in multiplexed images using InstanSeg

1. Thibaut Goldsborough
2. Alan O’Callaghan
3. Fiona Inglis
4. Léo Leplat
5. Andrew Filby
6. Hakan Bilen
7. Peter Bankhead

Reviewed by Arcadia Science

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks

1. Gaetan De Waele
2. Gerben Menschaert
3. Willem Waegeman

• Curated by eLife

  eLife Assessment

  This valuable study presents a machine learning model to recommend effective antimicrobial drugs from patients' samples analysed with mass spectrometry. The evidence supporting the claims of the authors is convincing. This work will be of interest to computational biologists, microbiologists, and clinicians.

Reviewed by eLife

Modeling transcriptional profiles of gene perturbation with deep neural network

1. Wenke Liu
2. Xuya Wang
3. D R Mani
4. David Fenyö

Reviewed by preLights

TopOMetry systematically learns and evaluates the latent dimensions of single-cell atlases

1. Davi Sidarta-Oliveira
2. Ana Domingos
3. Licio A Velloso

• Curated by eLife

  eLife Assessment

  This study presents TopOMetry, an important novel dimensionality reduction method that addresses a signficant challenge in the analysis of single-cell RNA sequencing data. The authors provide convincing evidence of the method's utility across various tasks, including estimating intrinsic dimensionalities and identifying cell types. The work would benefit from more rigorous validation and a reorganization of the text.

Reviewed by eLife

Establishing comprehensive quaternary structural proteomes from genome sequence

1. Edward Alexander Catoiu
2. Nathan Mih
3. Maxwell Lu
4. Bernhard Palsson

• Curated by eLife

  eLife assessment

  This study presents an important platform for mapping mutation effects onto higher-level protein structural information, addressing a significant gap in current research. While the work is ambitious and incorporates often-overlooked aspects of higher-order structure, the strength of the evidence supporting some results seems incomplete. The quaternary structure modeling appears to underestimate oligomeric proteins compared to previous studies, and the mutation analysis lacks crucial baseline information. Despite these limitations, the method has potential for broader applications and generalization to additional organisms, warranting further development and refinement.

Reviewed by eLife

Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

1. Aurélie Anne-Gaëlle Gabriel
2. Julien Racle
3. Maryline Falquet
4. Camilla Jandus
5. David Gfeller

• Curated by eLife

  eLife assessment

  This study presents an important computational tool for the quantification of the cellular composition of human tissues profiled with ATAC-seq. The methodology and its application results on breast cancer tumor tissues are convincing. It advances existing methods by utilizing a comprehensive reference profile for major cancer-relevant cell types, compatible with a widely-used cell type deconvolution tool.

Reviewed by eLife

Assessing the ability of ChatGPT to extract natural product bioactivity and biosynthesis data from publications

1. Thomas L. Kalmer
2. Christine Mae F. Ancajas
3. Zihao Cheng
4. Abiodun S. Oyedele
5. Hunter L. Davis
6. Allison S. Walker

Reviewed by Arcadia Science

Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data

1. Michael B Hall
2. Ryan R Wick
3. Louise M Judd
4. An N Nguyen
5. Eike J Steinig
6. Ouli Xie
7. Mark Davies
8. Torsten Seemann
9. Timothy P Stinear
10. Lachlan Coin

• Curated by eLife

  eLife assessment

  This important study shows how a combination of the latest generation of Oxford Nanopore Technology long reads with state-of-the art variant callers enables bacterial variant discovery at an accuracy that matches or exceeds the current "gold standard" with short reads. The work thus heralds a new era, in which Illumina short-read sequencing no longer rules supreme. While the inclusion of a larger number of reference genomes would have enabled an even more fine-grained analysis, the evidence as it is supports the claims of the authors convincingly. The work will be of interest to anyone performing sequencing for outbreak investigations, bacterial epidemiology, or similar studies.

Reviewed by eLife

RiboSnake – a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis

1. Ann-Kathrin Dörr
2. Josefa Welling
3. Adrian Dörr
4. Jule Gosch
5. Hannah Möhlen
6. Ricarda Schmithausen
7. Jan Kehrmann
8. Folker Meyer
9. Ivana Kraiselburd

• Curated by GigaByte

  Editors Assessment:

  This new software paper presents RiboSnake, a validated, automated, reproducible analysis pipeline implemented in the popular Snakemake workflow management system for microbiome analysis. Analysing16S rRNA gene amplicon sequencing data, this uses the widely used oQIIME2 [ tool as the basis of the workflow as it offers a wide range of functionality. Users of QIIME2 can be overwhelmed by the number of options at their disposal, and this workflow provides a fully automated and fully reproducible pipeline that can be easily installed and maintained. Providing an easy-to-navigate output accessible to non bioinformatics experts, alongside sets of already validated parameters for different types of samples. Reviewers requested some clarification for testing, worked examples and documentation, and this was improved to produce a convincingly easy-to-use workflow. Hopefully opening up an already very established technique to a new group of users and assisting them with reproducible science.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte