Tools

UND Hur Lab GitHub

SciMiner 1.1 & 2.0: Web-based literature mining tool for gene/protein extraction and functional enrichment analysis (Gene, GO, MeSH, Pathway, and PPI)
VO-SciMiner: Vaccine literature indexed with an extended version of SciMiner using Vaccine Ontology (e.g., Brucella vaccines); collaboration with Dr. Yongqun Oliver He at University of Michigan
Ignet: Interactive gene interaction network visualization and analysis system for ontology-based literature-mined networks, in collaboration with Dr. Yongqun Oliver He
Vignet: Vaccine-focused integrative gene network; vaccine-gene interaction networks mined from PubMed literature and mapped to the Vaccine Ontology
VIOLIN: Vaccine Investigation and Online Information Network, a comprehensive vaccine knowledgebase integrating AI-driven literature analysis with ontology annotation

richR: Functional enrichment and visualization R package for comprehensive pathway analysis
VennDetail: Bioconductor R package for Venn-Pie plots and subset extraction supporting up to 8 sets
Entrez ID2Symbol Converter: A web-based conversion tool between Entrez ID and gene symbol
richCluster: C++-based hierarchical clustering algorithm wrapped in R for high-performance cluster analysis
richStudio: R Shiny application for interactive enrichment and clustering analyses (beta)
scGEN: Gene-aware embedding network for single-cell RNA-seq clustering using deep learning

PubChemSR: PubChem Search Refined, a Python cheminformatics toolkit with CLI, web dashboard, and AI-augmented ADMET prediction (v2.0 coming soon)
Tox21 Enricher: Online enrichment tool for Tox21 chemical screening data, with an R version available (v2.4.0)
ChemFuse: Multi-database cheminformatics suite integrating PubChem, ChEMBL, UniChem, BindingDB, Open Targets, and SureChEMBL (coming soon)

Diabetic peripheral neuropathy knowledgebase (DPNKB): A comprehensive knowledgebase integrating genomic, transcriptomic, and clinical data for diabetic peripheral neuropathy research; revamped successor to DNMKB2
DNMKB2: Repository and analysis portal for diabetic neuropathy transcriptomics data with 140 DEG sets (replaced by DPNKB)
ROS-Diabetes: A comprehensive list of Reactive Oxygen Species (ROS) and diabetes-related targets (genes/proteins) mined from biomedical literature
microRNA world for diabetes: A collection of web pages focusing on two miRNAs

AURORA: NIH-style asynchronous peer review of grant applications with 1-9 criterion scoring, anonymous reviewer discussion, and study-section report export (beta; account required)
IRB Assistant: AI-assisted drafting of HRP-503, HRP-503c, and HRP-398 IRB forms from uploaded study documents (beta; pilot for UND and Sanford)
NDResHub: Turns a plain-language research idea into ranked North Dakota experts, resources, and potential collaborators (beta)
Research PDF Renamer: Renames research PDFs to Author_Year_Journal_Keywords using LLM-extracted bibliographic metadata (UND network; approval needed)
SMHS Publication Atlas: Interactive dashboard of UND School of Medicine & Health Sciences publications, collaborations, and research strengths (beta)
UND Co.AI: Checks research proposals, grant applications, and project documents against UND, NDUS, state, and federal AI guidelines (beta; UND internal)