Repositories list

• ML3DgenomeHeight

  Public
  Machine learning reveals 3D regulatory mechanisms for height-associated haplotypes

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Sep 10, 2025Sep 10, 2025

• spoke_genelab

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •4•4•0•0•Updated Aug 24, 2025Aug 24, 2025

• MS_note_concept_ML

  Public
  This repository contains code for predicting Multiple Sclerosis (MS) diagnosis using clinical concepts extracted from electronic health records (EHR) notes and SPOKE knowledge graph embeddings.

  Jupyter Notebook

  •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

• translator_summarization

  Public
  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Nov 16, 2024Nov 16, 2024

• versa_kg_rag_documentation

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Nov 13, 2024Nov 13, 2024

• KG_RAG

  Public
  Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

  bioinformaticsbiomedical-informaticsknowledge-graph+ 17llamagptknowledge-basecontext-awarebioinformatics-algorithmsbiomedical-applicationsrag+ 10

  Jupyter Notebook

  •

  Apache License 2.0

  •106•888•5•1•Updated Nov 9, 2024Nov 9, 2024

• Ocrelizumab_vs_rituximab

  Public
  Repo for LLM

  Python

  •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

• Biothings4SPOKE

  Public
  Batchfile

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• SpokeSigv2

  Public
  Python

  •0•1•0•0•Updated Sep 23, 2024Sep 23, 2024

• iMSMS_metabolomics

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Aug 27, 2024Aug 27, 2024

• app_patient_profile_imsms

  Public
  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 24, 2024Mar 24, 2024

• metapath_dwpc_analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• spoke_api_demo

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •1•1•0•0•Updated Mar 21, 2024Mar 21, 2024

• IMSGC_federated

  Public
  CLI python scripts for federated analysis

  Python

  •0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

• spoke_35M

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 21, 2023Sep 21, 2023

• EHR-Ranges

  Public
  ipynb for generating EHR lab ranges from patient data

  Jupyter Notebook

  •0•0•0•0•Updated Jun 28, 2023Jun 28, 2023

• VANE

  Public
  Variant Annotation with Network-enhanced Epigenetic data

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated May 5, 2023May 5, 2023

• graphRAIN

  Public
  Python

  •

  Apache License 2.0

  •0•5•0•0•Updated Feb 28, 2023Feb 28, 2023

• spoke_network_analysis

  Public
  Jupyter Notebook

  •0•0•1•0•Updated Nov 2, 2022Nov 2, 2022

• TANDEM

  Public
  This repository holds the code for TANDEM model

  Python

  •

  Apache License 2.0

  •0•1•1•0•Updated Oct 3, 2022Oct 3, 2022

• nasa_spokesig_api

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated May 5, 2022May 5, 2022

• iMSMS_study

  Public
  Gut microbiome study in multiple sclerosis

  HTML

  •4•2•0•0•Updated Apr 15, 2022Apr 15, 2022

• SPOKEsig-Workshop

  Public
  Jupyter Notebook

  •1•1•0•0•Updated Nov 18, 2021Nov 18, 2021

• SPOKEsigs

  Public
  Jupyter Notebook

  •1•2•2•0•Updated Jun 9, 2021Jun 9, 2021

• PSPG_245B

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 3, 2021Mar 3, 2021

• SPOKE_NASA_2020

  Public
  Python

  •1•1•0•0•Updated Dec 31, 2020Dec 31, 2020

• SPOKE_NASA

  Public
  Python

  •1•0•1•0•Updated Dec 31, 2020Dec 31, 2020

• RNAseq

  Public
  RNA-Seq data analysis: whole transcriptome, stranded, dUTP method

  R

  •4•0•0•0•Updated Aug 14, 2020Aug 14, 2020

• SARS-CoV-2-molecular-explorer

  Public
  This repository contains bioinformatic work from my lab in response to the COVID-19 pandemic.

  MIT License

  •0•1•0•0•Updated Apr 6, 2020Apr 6, 2020

• PSEV_guides_2

  Public
  0•0•0•0•Updated May 5, 2019May 5, 2019