BME 341/383J: Engineering Tools for Computational Biology (aka Computational Genomics Lab)

• Spring 2009
• For advanced undergraduate and beginning graduate students
• Mondays, Wednesdays and Fridays 10–11am
• Computer Studio Classroom, BME 3.312


Announcement

Jan 21:

Biomedical and Genomic Signal Processing

Jan 23:

Lab 1: Synthetic Data
Download to your desktop the executable Mathematica 6.0 code and change its suffix to .nb: Lab_1.txt
Due In-Class Feb 6
Install Mathematica on Your Computer, courtesy of the College of Engineering or the College of Natural Sciences

Jan 26:

From Darwin and Mendel to the Human Genome Project
Historical Mile Stones
• Paper 1: Artificial Transmutation of the Gene, by H. J. Muller (Science, 1927).
Muller's 1946 Nobel Lecture
Presentation 1: Lindsey M. Hieb

Jan 28:

• Paper 2: A New Five-Year Plan for the U.S. Human Genome Project, by F. S. Collins and D. Galas (Science, 1993).
Presentation 2: Vikram Agrawal
• Paper 3: A Vision for the Future of Genomics Research, by F. S. Collins et al. (Nature 2003).
Presentation 3: Nicole L. Guckert

Jan 30:

Monitoring the Flow of Biological Information with DNA Microarrays
• Paper 4: High Density Synthetic Oligonuleotide Arrays, by R. J. Lipshutz et al. (Nature Genetics, 1999).
Presentation 4: Samuel T. Poulos

Feb 2:

• Paper 5: Exploring the World of the Genome with DNA Microarrays, by P. O. Brown and D. Botstein (Nature Genetics, 1999).
Presentation 5: Lucas L. Artusi

Feb 4:

Other High-Throughput Technologies
• Paper 6: Proteomics: The First Decade and Beyond, by S. D. Patterson and R. H. Aebersold (Nature Genetics, 2003).
Presentation 6: Alina D. Daszkowski
• Paper 7: Nanoliter-Scale Synthesis of Arrayed Biomaterials and Application to Human Embryonic Stem Cells, by D. G. Anderson et al. (Nature Biotechnology, 2004).
Presentation 7: Ashley N. Foradory

Feb 6:

Lab 2: Databases
Due In-Class Feb 13

Feb 9:

Visual Correlation
Guest Presentation: Yarden Livnat, Scientific Computing and Imaging Institute, University of Utah
• A Visualization Paradigm for Network Intrusion Detection, by Y. Livnat et al. (IEEE Workshop on Information Assurance, 2002).
• Visual Correlation for Situational Awareness, by Y. Livnat et al. (IEEE Symposium on Information Visualization, 2005).
• Visual Correlation of Network Alerts, by S. Foresti et al. (IEEE Computer Graphics and Applications, 2006).

Feb 10, 3:30pm, ACES 6.304, ICES Seminar:

Yarden Livnat, Scientific Computing and Imaging Institute, University of Utah
Visual Correlation

Feb 11:

Data Sources
• Paper 8: Genome-Wide Atlas of Gene Expression in the Adult Mouse Brain, by E. S. Lein et al. (Nature, 2007).
Presentation 8: Fernando I. Cordova
• Paper 9: Comprehensive Genomic Characterization Defines Human Glioblastoma Genes and Core Pathways, by The Cancer Genome Atlas Research Network (Nature, 2008).
Presentation 9: Iris L. Kim
TCGA Online
TCGA In the News

Feb 12:

Darwin Day

Feb 13:

Lab 3: Two-Way Data Matrix Centering by Arithmetic Means
Download to your desktop the executable Mathematica 6.0 code and change its suffix to .nb: Lab_3.txt
Due In-Class Feb 20

Feb 16:

In-Class Discussion of Project 1: Large-Scale Data and Visualization
Datasets For Project 1: cell_cycle.txt, sarcoma.txt
Due In-Class Apr 13


• Paper 10: The Stanford Microarray Database, by G. Sherlock et al. (Nucleic Acids Research, 2001).
Presentation 10: Anish H. Patel
Lab 1 Solutions:
Thanks, Andrew M. Gross!: code executable by Mathematica and readable by Acrobat
Thanks, Samuel T. Poulos!: code executable by Mathematica and readable by Acrobat

Feb 18:

In-Class Work on Project 1
National Center for Biotechnology Information (NCBI) Seminar (Bethesda, Maryland, February 19, 2009)

Feb 20:

In-Class Work on Project 1
National Science Foundation (NSF) Workshop on Future Directions in Tensor-Based Computation and Modeling (Arlington, Virginia, February 20–21, 2009)

Feb 23:

In-Class Work on Project 1

Feb 25:

• Paper 11: Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization, by P. T. Spellman et al. (Molecular Biology of the Cell, 1998).
Presentation 11: Anhtuan H. Nguyen


Lab 2 Solutions: Thanks, Jeffery A. Hussmann!: problems 1–6 and problem 7 code readable by Acrobat


Lab 3 Solutions: Thanks, Ashley N. Foradory!: code executable by Mathematica and readable by Acrobat

Feb 27:

A Picture's Worth
Visualization, Part 1
Applied Mathematica: Getting Started, Getting It Done, by W. T. Shaw and J. Tiggs, Chapter 4 (Addison-Wesley, 1994).
Mathematica Package Minard.m, at M. Friendly's website
• Paper 12: Visual Correlation for Situational Awareness, by Y. Livnat et al. (IEEE Symposium on Information Visualization, 2005).
Presentation 12: Evan W. Archer

Mar 2:

• Paper 13: A Computational Analysis of Whole-Genome Expression Data Reveals Chromosomal Domains of Gene Expression, by B. A. Cohen et al. (Nature Genetics, 2000).
Presentation 13: Yann-Fuu Kou

Mar 4:

Visualization, Part 2
Clustering Algorithms, Part 1: The Traveling Salesman Problem
Clustering Algorithms, Part 2: DNA Computing
• Paper 14: Molecular Computation of Solutions to Combinatorial Problems, by L. M. Adleman (Science, 1994).
Presentation 14: Jeffery A. Hussmann

Mar 6:

Mar 9:

Mar 10, 2:00pm, Avaya Auditorium, ACES 2.302:

James Schwartz
The Long and Winding Road to the Gene: From Darwin to Hermann J. Muller

Mar 11:

In-Class Work on Project 1
2009 Algoritmy Conference on Scientific Computing (Vysoké Tatry, Slovakia, March 15–20, 2009)

Mar 13:

In-Class Work on Project 1
2009 Algoritmy Conference on Scientific Computing (Vysoké Tatry, Slovakia, March 15–20, 2009)

Mar 16–21:

Happy Spring Break!

Mar 23:

In-Class Work on Project 1
2009 Algoritmy Conference on Scientific Computing (Vysoké Tatry, Slovakia, March 15–20, 2009)

Mar 25:

Clustering Algorithms, Part 3: Pattern Recognition
• Paper 15: Cluster Analysis and Display of Genome-Wide Expression Patterns, by M. B. Eisen et al. (Proceedings of the National Academy of Sciences, 1998).
Presentation 15: Shuang Liu

Mar 27:

Extra Credit: Flowcharts for Algorithm Design
Due In-Class Apr 10

Mar 30:

• Paper 16: Interpreting Patterns of Gene Expression with Self-Organizing Maps: Methods and Application to Hematopoietic Differentiation, by P. Tamayo et al. (Proceedings of the National Academy of Sciences, 1999).
Presentation 16: Zev Gendler
• Paper 17: Algorithm for Data Clustering in Pattern Recognition Problems Based on Quantum Mechanics, by D. Horn and A. Gottlieb (Physical Review Letters, 2001).
This clustering algorithm was applied to DNA microarray data in Novel Clustering Algorithm for Microarray Expression Data in a Truncated SVD Space, by D. Horn and I. Axel (Bioinformatics, 2003).
Presentation 17: Brandon S. Nichols

Apr 1:

Clustering Algorithms, Part 4: Data Annotations and Pattern Interpretation
• Paper 18: Systematic Determination of Genetic Network Architecture, by S. Tavazoie et al. (Nature Genetics, 1998).
The Hypergeometric Distribution from Wikipedia
Presentation 18: Yi-An Chang

Apr 3:

Decompositions, Part 1: Singular Value Decomposition


In-Class Presentation of Project 1: Evan W. Archer
In-Class Presentation of Project 1: Samuel T. Poulos

Apr 6:

• Paper 19: Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling, by O. Alter et al. (Proceedings of the National Academy of Sciences, 2000).
Presentation 19: Andrew M. Gross
• Paper 20: Emergence of Single-Cell Receptive Field Properties by Learning a Sparse Code for Natural Images, by B. A. Olshausen and D. J. Field (Nature 1996).
Presentation 20: Jose A. Gutierrez

Apr 8:

In-Class Work on Project 1
National Science Foundation (NSF)

Apr 10:

In-Class Work on Project 1
National Science Foundation (NSF)

Apr 13:

In-Class Presentations of Project 1
In-Class Discussion of Project 2: Data Patterns and Interpretations

• Paper 21: Fetal Electrocardiogram Extraction by Blind Source Subspace Separation, by L. De Lathauwer et al. (IEEE Transactions on Biomedical Engineering, 2000).

Presentation 21: Matthew K. Hogan

• Paper 22: Method for Node Ranking in a Linked Database, by L. Page (United States Patent, 2001).

Presentation 22: Andrew Conrad

In-Class Work on Project 2

Decompositions, Part 2

• Paper 23: Molecular Characterisation of Soft Tissue Tumours: A Gene Expression Study, by T. O. Nielsen et al. (Lancet, 2002).

Presentation 23: Kaitlin C. Goerner

• Paper 24: A Rapid Genome-Scale Response of the Transcriptional Oscillator to Perturbation Reveals a Period-Doubling Path to Phenotypic Change, by C. M. Li and R. R. Klevecz (Proceedings of the National Academy of Sciences, 2006).

Presentation 24: Jeffrey A. Higgins

In-Class Work on Project 2

National DNA Day

• Paper 25: Regulatory Element Detection Using Correlation with Expression, by H. J. Bussemaker et al. (Nature Genetics, 2001).

Presentation 25: Joseph Jailer-Coley

In-Class Work on Project 2

In-Class Work on Project 2

In-Class Presentations of Project 2

End-of-Class Party