Bioinformatics

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

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

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

AlphaFind: Discover structure similarity across the entire known proteome

1. David Prochazka
2. Terezia Slaninakova
3. Jaroslav Olha
4. Adrian Rosinec
5. Katarina Gresova
6. Miriama Janosova
7. Jakub Cillik
8. Jana Porubska
9. Radka Svobodova
10. Vlastislav Dohnal
11. Matej Antol

Reviewed by Arcadia Science