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Tools

Literature Mining

  • SciMiner: Bio-NLP (Natural Language Processing) web-application for finding molecular target (gene/protein) in biomedical literatures and functional enrichment analyses (Gene, GO, MeSH, Pathway, and PPI)
  • VO-SciMiner: Brucella vaccine literature indexed with an extended version of SciMiner using Vaccine Ontology; collaboration with Dr. Yongqun Oliver He at University of Michigan
  • Ignet and Dignet: Integrated gene network and dynamic ignet, in collaboration with Dr. Yongqun Oliver He

Omics Data Analysis

  • richR: An R package for functional enrichment and network analysis
  • vennDetail: An R package for subset analysis and generating Venn diagrams up to eight sets
  • Entrez ID2Symbol Converter: A web-based conversion tool between Entrez ID and gene symbol

Cheminformatics

  • PubChemSR: An Microsoft Windows-based application for searching and downloading chemical and bioassay data from NCBI's PubChem chemical databases (v3.6.4 released on 12/18/2019)
  • Tox21 Enricher: A web-based chemical/biological functional annotation analysis tool based on Tox21 toxicity screening platform (v2.0 released on 10/01/2021)

Diabetes-Related Databases

  • Diabetic peripheral neuropathy knowledge-base (DPNKB): A web-based data repository and analysis portal of DN-related transcriptomics data. DPNKB contains 140 differentially expressed gene (DEG) sets from 18 DPN-related high-throughput gene expression profiling data. 
  • 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. 

Sequence Analysis

  • LOD Score Calculator for Sequence Modeling
  • Pairwise Protein Sequence Alignment using multiple substitution scoring matrixes
  • Simple Sequence Alignment using simple scoring scheme match/mismatch/gap
  • Sequence Fitting Alignment to fit a shorter sequence into a longer one
  • Repeat Finder to identify repeats in a string of DNA/protein sequence
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School of Medicine & Health Sciences

1301 N Columbia Rd Stop 9037
Grand Forks, ND 58202-9037

701.777.2514

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