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awesome-large-biology-models's Introduction

Awesome Large Biology Models Awesome

Table of Contents

Awesome Papers and Codes

DNA Models

Title Venue Date Code Notes
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation BioArxiv 2023-09-01 - -
EpiGePT: a Pretrained Transformer model for epigenomics BioArxiv 2023-07-15 Website -
DNAGPT: A Generalized Pre-trained Tool for Versatile DNA Sequence Analysis Tasks Arxiv 2023-07-11 Github -
Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution Arxiv 2023-06-27 Github Blog
DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome Arxiv 2023-06-26 Github GUE
The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics BioRxiv 2023-01-11 Github -
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics BioRxiv 2022-10-11 - -
Effective gene expression prediction from sequence by integrating long-range interactions Nature Methods 2021-10-04 Github -
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome Bioinformatics 2021-02-04 Github -

RNA Models

Title Venue Date Code Notes
An RNA foundation model enables discovery of disease mechanisms and candidate therapeutics BioRxiv 2023-09-26 - -
CodonBERT: Large Language Models for mRNA Design and Optimization Arxiv 2023-09-09 - -
UNI-RNA: UNIVERSAL PRE-TRAINED MODELS REVOLUTIONIZE RNA RESEARCH BioArxiv 2023-07-11 - -
Self-supervised learning on millions of pre-mRNA sequences improves sequence-based RNA splicing prediction Arxiv 2023-01-31 Github -

Protein Models

Title Venue Date Code Notes
Genome-wide prediction of disease variant effects with a deep protein language model Nature Genetics 2023-08-10 Github Sequence
De novo design of protein structure and function with RFdiffusion Nature 2023-07-11 Github Structure
xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein Arxiv 2022-07-05 - Sequence
OntoProtein: Protein Pretraining With Gene Ontology Embedding ICLR22 2022-06-30 Github Sequence
Accurate proteome-wide missense variant effect prediction with AlphaMissense Science 2023-09-19 Github Sequence
Evolutionary-scale prediction of atomic-level protein structure with a language model Science 2023-03-23 Github Sequence
Protein complex prediction with AlphaFold-Multimer BioArxiv 2022-03-10 Github Sequence
ProtGPT2 is a deep unsupervised language model for protein design Nature Communications 2022-07-27 - Sequence
ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning IEEE Transactions on Pattern Analysis and Machine Intelligence 2022-10-01 Github Sequence

Single-cell Models

Title Venue Date Code Notes
GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model BioArxiv 2023-09-26 Github -
scgpt: Towards building a foundation model for single-cell multi-omics using generative ai Arxiv 2023-04-30 Github -
scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data Nature Machine Intelligence 2023-09-26 Github -

Biological Text Models

Title Venue Date Code Notes
GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information Preprint 2023-05-16 Github -
BioGPT: generative pre-trained transformer for biomedical text generation and mining Briefings in Bioinformatics 2022-12-24 Github -

Awesome Datasets

General Datasets

Name Paper Data type Link Notes
NCBI Database - DNA/RNA/Protein Link -
Ensembl Database - DNA/RNA/Protein Link -
UCSC Database - DNA/RNA Link -
RCSB PDB Database - Protein Link -
Uniprot Database - Protein Link -
STRING Database - Protein Link -

DNA Datasets

Name Paper Data type Link Notes
Genome Understanding Evaluation (GUE) DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome Sequence Classification Link -

RNA Datasets

Name Paper Data type Link Notes
Genotype-Tissue Expression (GTEx) The GTEx Consortium atlas of genetic regulatory effects across human tissues General Link -
(Master database of All possible RNA sequences (MARS) The Master Database of All Possible RNA Sequences and Its Integration with RNAcmap for RNA Homology Search General Link -

Protein Datasets

Name Paper Data type Link Notes
TBD

Single-cell Datasets

Name Paper Data type Link Notes
TBD

Biological text Datasets

Name Paper Data type Link Notes
TBD

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