TranslationalBioinformaticsUnit / TransformersInGenomicsPapersLinks
A curated repository designed to serve as a comprehensive guide for researchers interested in the intersection of Transformer models and genomics. This repository compiles key academic papers that demonstrate the application of transformer-based models in genomics, providing users with a valuable resource to navigate this rapidly evolving field.
☆25Updated 9 months ago
Alternatives and similar repositories for TransformersInGenomicsPapers
Users that are interested in TransformersInGenomicsPapers are comparing it to the libraries listed below
Sorting:
- Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…☆101Updated last month
- Computational Optimization of DNA Activity (CODA)☆64Updated 6 months ago
- deep learning-inspired explainable sequence model for transcription initiation☆96Updated 7 months ago
- [ISMB 2025] DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models☆115Updated 8 months ago
- ☆32Updated 8 months ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆80Updated last year
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆77Updated last month
- For fine-tuning Enformer using paired WGS & gene expression data☆22Updated last month
- NeuronMotif: deciphering cis-regulatory codes by layerwise demixing of deep neural networks☆15Updated 2 years ago
- KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph☆74Updated 7 months ago
- ☆41Updated 2 months ago
- What you need to process the Quarterly DepMap-Omics releases from Terra☆123Updated 3 weeks ago
- A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution☆37Updated 6 months ago
- code to run sei and obtain sei and sequence class predictions☆109Updated 2 years ago
- SpliceTransformer(SpTransformer) is a deep learning tool to predict tissue specific splicing site from pre-mRNA sequence☆29Updated 10 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆43Updated 2 weeks ago
- Deep Learning the T Cell Receptor Binding Specificity of Neoantigen☆86Updated 3 years ago
- NetTCR-2.0. Sequence-based prediction of peptide-TCR binding☆35Updated 3 years ago
- Comprehensive suite for evaluating perturbation prediction models☆89Updated last week
- Functional Embedding of Gene Signatures☆46Updated last year
- Knowledge-primed neural networks☆38Updated 2 years ago
- GeneCompass☆90Updated 3 months ago
- Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data☆120Updated 3 weeks ago
- Repository for the paper: "SPACE: STRING proteins as complementary embeddings"☆29Updated 2 weeks ago
- HLA-II ligand predictor.☆44Updated 2 years ago
- RNA-seq prediction with deep convolutional neural networks.☆197Updated last month
- BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity☆56Updated last year
- ☆21Updated 5 months ago
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆23Updated last year
- ☆80Updated 2 years ago