Bioinformatics, Machine Learning, Data Mining Software and Web Services Developed in the BML Lab

Protein Structure, Interaction and Function Prediction

• The open source projects on protein structure and function prediction at Github
• MULTICOM Protein Structure Prediction Toolbox (one stop for all our protein structure prediction tools and web services, funded by NIH NIGMS. [in NIH Award RePORTER].MULTICOM was ranked as one of the best methods in CASP11, 2014.)
• Deep Learning Methods for Protein Bioinformatics funded by NSF ABI program
• Deep Learning for Protein Model Quality Assessment funded by NSF III program

3D Genome Modeling

• Analysis, Construction and Visualization of 3D Genome Structure (2012 - 2017). [in NSF Award Search]
• The open source projects on 3D genome structure modeling at Github
• Genome Balance Project (funded by NSF)
• Genome Structure Database (GSDB)

Biological Network Modeling and Omics Data Analysis

• RNAMiner: an automated pipeline for mining large-scale transcriptomics (RNA-Seq) and genomics data and reconstructing biological networks
• RNAseq, Microarray, Proteomics, Genomics and Pathway Data Analysis Center (funded by NIH)
• Genomics, Transcriptomics, and Epigenomics Data Analysis of Maize Genome (funded by NSF)