Genomics, Signal Processing, and Bioinformatics

Maurice F. Aburdene; Marie Catherine Pizzorno; Alexander P Thompson

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Conference: 2013 ASEE Annual Conference & Exposition
Location: Atlanta, Georgia
Publication Date: June 23, 2013
Start Date: June 23, 2013
End Date: June 26, 2013
ISSN: 2153-5965
Conference Session: Embedded Systems and Mobile Computing
Tagged Division: Computing & Information Technology
Page Count: 17
Page Numbers: 23.636.1 - 23.636.17
DOI: 10.18260/1-2--19650
Permanent URL: https://peer.asee.org/19650
Download Count: 597

Paper Authors

biography

Maurice F. Aburdene Bucknell University

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Maurice Felix Aburdene is a Professor of Electrical Engineering and Professor of Computer Science at Bucknell University. His teaching and research interests include control systems, parallel algorithms, simulation of dynamic systems, and signal processing.

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Marie Catherine Pizzorno Department of Biology, Bucknell University

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I received BA in Biology and Chemistry from Whittier College in 1985.
I received Ph.D. from the Biochemistry, Cellular and Molecular Biology program at Johns Hopkins School of Medicine in 1991.
I did postdoctoral work at Princeton University from 1991 to 1995. I taught in the Biology Department of Vassar College from 1995-1996. I became an Assistant Professor in the Biology Department at Bucknell University in 1996 and was promoted to Associate Professor in 2001.My primary research interests are the molecular biology of viruses that infect eukaryotes, specifically viruses that infect honeybees.

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Alexander P Thompson Bucknell University

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I am a senior Electrical Engineering student at Bucknell University. I have been studying genomic signal processing for the last two years as part of a research project through the Bucknell Presidential Fellows program. My primary role in the development of the genomic signal processing elective course is to evaluate it from the perspective of an enrolled student. In addition, I may provide assistance to Professor Aburdene in the areas of study related to my research.

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Abstract

Genomics, Signal Processing, Bioinformatics, and Imaging Maurice F. Aburdene Marie C. Pizzorno Alex ThompsonWe present our approach to teaching an elective course focusing on genomics, signal processing,bioinformatics, and medical imaging for biology, biochemistry, electrical engineering, and computerengineering students. The objective of the course is to learn about current issues in mathematicalbiology, computational biology, and bioinformatics, from an engineering perspective. The course isbeing offered for the first time in the Fall of 2012.Since today’s biologists are not only scientists, but also “engineers”, due to their ability to “buildsystems”, the course presents a multidisciplinary view of research and problem solving, which will beuseful with study of any topic, and not just genomic signal processing. The course content is broad andrequires a background in biology, mathematics, physics, chemistry, statistics, computer science andsignal processing. In addition, we draw on the resources of several academic departments and visitinglecturers to provide fundamental concepts from each field. The course outline is ambitious and willevolve, adapt, mutate, and crossover to other topics in the future.The format or course-plan and content for the course are described, along with suggestedimprovements in the future.The course contents include following topics: • Introduction to the Course and Objectives • Genetic Algorithms • Genomic Companies • DNA Sequencing Methods • Bioinformatics, Introduction to Matlab Bioinformatics Tool box, • DNA Data Bases and Sequence Search Tools • Basic Statistical Computations on DNA Sequences • Using Large Electronic Datasets for Observational Clinical Studies • DNA Indicator Sequences, Periodic Signals • Fourier Transforms, Discrete Fourier Transforms (DFT), Fast Fourier Transforms ( FFT) • Using Fourier Methods to Find Protein Coding Regions • Using correlation to compare DNA sequences • DNA Filter design (Digital Filtering)• Bioinformatics• Network Analysis of Complex Biological Systems• Applications• Peer Review of Term Papers/Projects The paper will present a critique of the course and suggestions for improvement.

Citation
Format

Aburdene, M. F., & Pizzorno, M. C., & Thompson, A. P. (2013, June), Genomics, Signal Processing, and Bioinformatics Paper presented at 2013 ASEE Annual Conference & Exposition, Atlanta, Georgia. 10.18260/1-2--19650

TY  - CPAPER
AB  -                Genomics, Signal Processing, Bioinformatics, and Imaging                                      Maurice F. Aburdene                                         Marie C. Pizzorno                                          Alex ThompsonWe present our approach to teaching an elective course focusing on genomics, signal processing,bioinformatics, and medical imaging for biology, biochemistry, electrical engineering, and computerengineering students. The objective of the course is to learn about current issues in mathematicalbiology, computational biology, and bioinformatics, from an engineering perspective. The course isbeing offered for the first time in the Fall of 2012.Since today’s biologists are not only scientists, but also “engineers”, due to their ability to “buildsystems”, the course presents a multidisciplinary view of research and problem solving, which will beuseful with study of any topic, and not just genomic signal processing. The course content is broad andrequires a background in biology, mathematics, physics, chemistry, statistics, computer science andsignal processing. In addition, we draw on the resources of several academic departments and visitinglecturers to provide fundamental concepts from each field. The course outline is ambitious and willevolve, adapt, mutate, and crossover to other topics in the future.The format or course-plan and content for the course are described, along with suggestedimprovements in the future.The course contents include following topics:    •   Introduction to the Course and Objectives    •   Genetic Algorithms    •   Genomic Companies    •   DNA Sequencing Methods    •   Bioinformatics, Introduction to Matlab Bioinformatics Tool box,    •   DNA Data Bases and Sequence Search Tools    •   Basic Statistical Computations on DNA Sequences    •   Using Large Electronic Datasets for Observational Clinical Studies    •   DNA Indicator Sequences, Periodic Signals    •   Fourier Transforms, Discrete Fourier Transforms (DFT), Fast Fourier Transforms ( FFT)    •   Using Fourier Methods to Find Protein Coding Regions    •   Using correlation to compare DNA sequences    •   DNA Filter design (Digital Filtering)•   Bioinformatics•   Network Analysis of Complex Biological Systems•   Applications•   Peer Review of Term Papers/Projects    The paper will present a critique of the course and suggestions for improvement.
AU  - Maurice F. Aburdene
AU  - Marie Catherine Pizzorno
AU  - Alexander P Thompson
CY  - Atlanta, Georgia
DA  - 2013/06/23
PB  - ASEE Conferences
TI  - Genomics, Signal Processing, and Bioinformatics
UR  - https://peer.asee.org/19650
DO  - 10.18260/1-2--19650
ER  -