Bioinformatics

INAEME: Integral Neoantigen Analysis with Entirety of Mutational Events

1. Vladimir Kovacevic
2. Ognjen Milicevic
3. Nevena Ilic Raicevic
4. Milica Kojicic
5. Ana Mijalkovic Lazic
6. Nikola Skundric
7. Jack DiGiovanna

Reviewed by PREreview

Context-Aware Amino Acid Embedding Advances Analysis of TCR-Epitope Interactions

1. Pengfei Zhang
2. Seojin Bang
3. Michael Cai
4. Heewook Lee

• Curated by eLife

  eLife assessment

  This study provides an important tool for predicting binding between immune cells receptors and antigens based on protein sequence data. The analysis convincingly showed the tool's effectiveness in both supervised TCR binding prediction and unsupervised clustering, surpassing existing methods in accuracy and reducing annotation costs. This study will be of interest to immunologists and computational biologists.

Reviewed by eLife

Phantasus, a web application for visual and interactive gene expression analysis

1. Maksim Kleverov
2. Daria Zenkova
3. Vladislav Kamenev
4. Margarita Sablina
5. Maxim N Artyomov
6. Alexey A Sergushichev

• Curated by eLife

  eLife assessment

  This study presents a useful tool called Phantasus, a web application to analyze gene expression data generated by microarray or RNA-seq technologies. The web application will help biologists end users, and non-bioinformatics experts to analyze new data or replicate transcriptomic studies. Local use of the Phantasus through its Bioconductor package reveals an incomplete functionality concerning the current best practices in analyzing bulk RNA-seq data.

Reviewed by eLife

Evaluating generalizability of artificial intelligence models for molecular datasets

1. Yasha Ektefaie
2. Andrew Shen
3. Daria Bykova
4. Maximillian G. Marin
5. Marinka Zitnik
6. Maha Farhat

Reviewed by Arcadia Science

Genes in Humans and Mice: Insights from Deep learning of 777K Bulk Transcriptomes

1. Zheng Su
2. Mingyan Fang
3. Andrei Smolnikov
4. Fatemeh Vafaee
5. Marcel E. Dinger
6. Emily C. Oates

Reviewed by Arcadia Science

CELEBRIMBOR: Pangenomes from metagenomes

1. Joel Hellewell
2. Samuel T. Horsfield
3. Johanna von Wachsmann
4. Tatiana Gurbich
5. Robert D. Finn
6. Zamin Iqbal
7. Leah W. Roberts
8. John A. Lees

Reviewed by Arcadia Science

Assessment of Gene Set Enrichment Analysis using curated RNA-seq-based benchmarks

1. Julián Candia
2. Luigi Ferrucci

Reviewed by Arcadia Science

Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

1. Chananchida Sang-aram
2. Robin Browaeys
3. Ruth Seurinck
4. Yvan Saeys

• Curated by eLife

  eLife assessment

  This study makes a valuable contribution to spatial transcriptomics by rigorously benchmarking cell-type deconvolution methods, assessing their performance across diverse datasets with a focus on biologically relevant, previously unconsidered aspects. The authors demonstrate the strengths of RCTD, cell2location, and SpatialDWLS for their performance, while also revealing the limitations of many methods when compared to simpler baselines. By implementing a full Nextflow pipeline, Docker containers, and a rigorous assessment of the simulator, this work offers robust insights that elevate the standards for future evaluations and provides a resource for those seeking to improve or develop new deconvolution methods. The thorough comparison and analysis of methods, coupled with a strong emphasis on reproducibility, provide solid support for the findings.

Reviewed by eLife

The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals

1. William S Henriques
2. Janet M Young
3. Artem Nemudryi
4. Anna Nemudraia
5. Blake Wiedenheft
6. Harmit S Malik

Reviewed by Arcadia Science

Pseudo-spectral angle mapping for automated pixel-level analysis of highly multiplexed tissue image data

1. Madeleine S. Durkee
2. Junting Ai
3. Gabriel Casella
4. Thao Cao
5. Anthony Chang
6. Ariel Halper-Stromberg
7. Bana Jabri
8. Marcus R. Clark
9. Maryellen L. Giger

Reviewed by Arcadia Science