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)
Brucella vaccine literature indexed with an extended version of SciMiner using Vaccine Ontology; collaboration with Dr. Yongqun Oliver He at University of Michigan
Dignet: Integrated gene network and dynamic ignet, in collaboration with Dr. Yongqun Oliver He

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

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)

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.

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