IEEE Signal Processing Society, Santa Clara Valley Chapter

Workshop on Bio-informatics and Bio-signal processing

Location: Williman Room, Benson Student Center, Santa Clara University

Date: Saturday, Aug. 30, 2008

Time: 8:30am – 5:00pm

Preliminary Workshop Program

1. Molecular Biology Basics

Speaker: Dr. Craig Stephens, Santa Clara University

https://www.scu.edu/cas/biology/staffandfaculty/craig-stephens.cfm

Focus:

To introduce the background information on molecular biology for computer/electrical engineers

Outline:

1. Overview of information flow in living cells
2. Nucleic acids

• Structure of DNA and RNA molecules
• DNA replication
• Gene structure
• The genetic code

3. Proteins

• Amino acids and polypeptide chains
• Three-dimensional structures and protein function

4. Evolution at the molecular level

2. Computational Methods in Bioinformatics

Speaker: Dr. Sami Khuri, San Jose State University

https://www.cs.sjsu.edu/faculty/khuri

Focus:

This session introduces common bioinformatics tasks and investigates computational methods and algorithms for the analysis of complex biological sequence data.

Outline:

For each of the following topics, we introduce the biological motivation, algorithms to tackle the problem, and cover some examples:

1. Pairwise sequence alignment
2. Multiple sequence alignment
3. Phylogenetic tree construction
4. Gene Prediction.

3. Genomic Signal Processing: Signal Processing Models and Algorithms for RNA Sequence Analysis

Speaker: Dr. Byung-Jun Yoon, Texas A&M University, College Station

https://www.ece.tamu.edu/~bjyoon

Focus:

We will review various signal processing models and algorithms that are used in RNA sequence analysis. The main focus of the talk will be on: RNA similarity search, RNA secondary structure prediction, and the identification of novel ncRNAs.

Outline:

1. Review of noncoding RNA (ncRNA)
2. Models for RNA sequence analysis

• Stochastic context-free grammars (SCFG) and covariance models (CM)
• Profile context-sensitive HMM (profile-csHMM)

3. RNA secondary structure prediction
4. RNA similarity search
5. Identification of novel ncRNAs

4. Biostatisitcs: Statistical Analysis of Bio-data

Speaker: Dr. Ru-Fang Yeh, University of California San Francisco

https://www.biostat.ucsf.edu/rufang

Focus:

In this session we discuss the technology and analysis of high-throughput genomic data, especially from DNA microarrays and array-based ultra high-throughput sequencing in relation to their applications in clinical research.

Outline:

1. Role of bioinformatics in medical and clinical research
2. Microarray technology, applications & analysis issues
• Various array platforms
• Preprocessing: image processing, normalization
• Applications & high-level analysis: different expression, data
3. Mining, annotation
4. Ultra high-throughput sequencing, applications & analysis issues
• Technology: Solexa and 454
• Analysis issues: alignment, error assessment

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Webpage last modified: Aug 10, 2008