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Order
Date
Presenters (alphabetically ordered)
TopicModalityTitle
year, venue
link
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010/3
Organizational meeting
3
110/10Sophia JannettyLionel Tukei Hanwen Xu
gene network analysis
single-cell transcriptomes
Transfer learning enables predictions in network biology
2023, Nature
https://www.nature.com/articles/s41586-023-06139-9
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210/17Wei QiuEthan WeinbergerAnthony WisemRNA designcodonCodonBERT: Large Language Models for mRNA design and optimization
2023, bioRxiv
https://www.biorxiv.org/content/10.1101/2023.09.09.556981
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310/24Marazzano Colon
Jasper Tran O'Leary
protein designproteinDe novo design of protein structure and function with RFdiffusion
2023, Nature
https://www.nature.com/articles/s41586-023-06415-8
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3Shengqi HangZihan Zhangprotein designproteinLarge language models generate functional protein sequences across diverse families
2023, Nature Biotech
https://www.nature.com/articles/s41587-022-01618-2
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410/31
Nuria Alina Chandra
Cassandra Maranas,
Addie Woicik
DNA --> transcriptomics
DNAGET: a foundation model of transcription across human cell types
2023, bioRxiv
https://www.biorxiv.org/content/10.1101/2023.09.24.559168v1
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511/7Saba HeraviYilun ShengXinming TuRNA activityDNA
An RNA foundation model enables discovery of disease mechanisms and candidate therapeutics
2023, bioRxiv
https://www.biorxiv.org/content/10.1101/2023.09.20.558508v11
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611/14Nuha QadirSanjay VenkataGian Marco Visaniantibody
BCR sequence
Deciphering the language of antibodies using self-supervised learning
2022, Patterns
https://www.sciencedirect.com/science/article/pii/S2666389922001052
10
711/21Jianing XuWuwei Zhang
non-coding variant effect
DNADNA language models are powerful zero-shot predictors of non-coding variant effects
2022, bioRxiv
https://www.biorxiv.org/content/10.1101/2022.08.22.504706v1
11
7Steven Golob
protein structure prediction
proteinEvolutionary-scale prediction of atomic-level protein structure with a language model
2023, Science
https://www.science.org/doi/10.1126/science.ade2574
12
811/28Ting An ChenAllison LiAnna Spiro
disease variant effect
protein sequence
Genome-wide prediction of disease variant effects with a deep protein language model
2023, Nature Genetics
https://www.nature.com/articles/s41588-023-01465-0
13
912/5Chanwoo Kim
Daphne Kontogiorgos-Heintz
Patrick Yu
single-cell cell type annotation
single-cell transcriptomes
scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data
2022, Nature Machine Intelligence
https://www.nature.com/articles/s42256-022-00534-z
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