What can I provide?

Mark

7/6/04

Who am I?

• FJU– BS: Computer Science Information Engineering

• NYU– MS: CS

• UMDNJ– PHD: Bioinformatics

Bioinformatics

• Sequences

• Protein / Molecular / Drug design

• Image Processing

• Prediction / Data mining / Machine learning

• Others

Sequences

• Fragment assembly

• Sequences alignment, compare, search.

• Trees (Phylogenetic Analysis)

• Microarray analysis

Sequences

Microarray Analysis

Protein

• Protein Structure Modeling & Prediction

• Docking

Protein Structure Modeling & Prediction

• AA sequence– TELTKCKVSHAIKDI

DGYQGISLLEWACVLFHTSGYDTQAVVNDNGSTEYGLFQISDRFW CKSSEFPESENICGISCDKLLDDELDDDIACAKKILAIKGIDYWKAYKPMCSEKLEQWRC EKP

Docking

XK-263 inhibitor binding to HIV-1 Protease

Benzamidine binding to beta-Trypsin

Molecular

• Intermolecular Interactions

• Molecular Dynamics

• Drug Discovery (QSAR)

• Conformational Search (1D, 2D, 3D search)

Intermolecular Interactions / Molecular Dynamics

Example of pulling a sodium ion (large sphere) through the gramacidin A channel

2D 3D search, alignment, QSAR

Image Processing

• Medical Image Processing and Visualization

• 3D Medical Image Processing

3D image processing for MRI

Prediction / Data mining / Machine learning

• Statistic

• Factor Analysis, Trends Analysis

• Neural Network, SVM

Others

• gene prediction, patterns recognition, Protein Classification, finding motifs.

gene prediction

ACCTGGGTCGGGTGCAGACTGCGGAGCGGGCCCTACCGTGTGCGCAGAAAGAGGAGGCGCTTGCCTTCAG CTTGTGGGAAATCCCGAAGATGGCCAAAGACAACTCAACTGTTCGTTGCTTCCAGGGCCTGCTGATTTTT

patterns recognition / finding motifs

Bioinformatics Projects

• Sequences=>Related sequences=>Papers

• Protein Modeling + Molecular Dynamics

• Automatic drug design machine

• Data cleaning

Computer Science

• Software programming

• AT&T – machine which will read emails, answer emails,

score emails, distribute emails.

Thanks

What do you want?

chiangyi at umdnj dot edu