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Progress and opportunities of foundation models in bioinformatics. Briefings in Bioinformatics

Last updated at Posted at 2025-08-06

Progress and opportunities of foundation models in bioinformatics. Briefings in

[22] Q. Li, Z. Hu, Y. Wang, L. Li, Y. Fan, I. King, G. Jia, S. Wang, L. Song, and Y. Li., 25:548, 9 2024. ISSN 14774054. doi: 10.1093/BIB/BBAE548. URL https://dx.doi.org/10.1093/bib/bbae548.

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A genomic mutational constraint map using variation in 76,156 human genomes
https://qiita.com/kaizen_nagoya/items/e799ad85ee98bb2a8cf6

Genomic language models: Opportunities and challenges
https://qiita.com/kaizen_nagoya/items/f797330e64e0c7d05f39

Nucleotide transformer: building and evaluating robust foundation models for human genomics
https://qiita.com/kaizen_nagoya/items/1c147c2b095364f04ef7

A genomic mutational constraint map using variation in 76,156 human genomes
https://qiita.com/kaizen_nagoya/items/e799ad85ee98bb2a8cf6

DeepSeek-AI
https://qiita.com/kaizen_nagoya/items/bb5ee9f17c03e07659d8

Codontransformer: A multispecies codon optimizer using context-aware neural networks.
https://qiita.com/kaizen_nagoya/items/d4be1d4dd9eb307f09cc

Medrax: Medical reasoning agent for chest x-ray
https://qiita.com/kaizen_nagoya/items/94c7835b2f461452b2e7

Benchmarking dna foundation models for genomic sequence classification running title: Dna foundation models benchmarking.
https://qiita.com/kaizen_nagoya/items/01e3dde0d8274fee0fd8

Lora: Low-rank adaptation of large language models,
https://qiita.com/kaizen_nagoya/items/877058f681d77808b44c

kegg pull: a software package for the restful access and pulling from the kyoto encyclopedia of gene and genomes.
https://qiita.com/kaizen_nagoya/items/05be40565793f2b4f7f3

Genegpt: augmenting large language models with domain tools for improved access to biomedical information.
https://qiita.com/kaizen_nagoya/items/8897792ff52fb5e68a46

Kegg: biological systems database as a model of the real world.
https://qiita.com/kaizen_nagoya/items/f63573043eaf8f9c6a2c

Entrez direct: E-utilities on the unix command line
https://qiita.com/kaizen_nagoya/items/cc4bbde566e67abc93d9

Clinvar: Public archive of relationships among sequence variation and human phenotype.
https://qiita.com/kaizen_nagoya/items/8149b7a5a4f930490fad

Biobert: a pre-trained biomedical language representation model for biomedical text mining.
https://qiita.com/kaizen_nagoya/items/63781eb6db1fc2ded80a

Progress and opportunities of foundation models in bioinformatics. Briefings in Bioinformatics
https://qiita.com/kaizen_nagoya/items/6ef20eaf796532fed6f8

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