Second Annual
University of Massachusetts Bioinformatics Conference
May 2-3, University of Massachusetts, Lowell
Schedule of Events (subject to change)
Thursday, May 2
7:30-8:30AMRegistration
8:30-9:00AMOpening Remarks
Dr. Georges Grinstein, co-chair
Dr. James Lyons-Weiler, co-chair
Chancellor William T. Hogan
Plenary Session 1, Room A
9:00-9:50AMDr. James Cassatt, Ph.D.
National Institute of Health, NIGMS
Title:TBA
1 / Session 1AADVANCES IN MICROARRAY ANALYSIS 1 / Session 1B
COMPUTATIONAL STRUCTURAL BIOLOGY 1
10:00-10:30 / Bayesian Analysis of Gene Expression Levels and the Open Design of cDNA Microarray Experiments
J. Townsend, Department of Organismic & Evolutionary Biology, Harvard University / Hydrophobic Sliding Facilitates Conformational Changes And Active Site Cleft Opening In Hiv-1 ProteaseW.R.P. Scott, J. Foulkes, M.M. Prabu-Jeyabalan, J. Lavasta, C.A. Schiffer* Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School 55 Lake Ave N., Worcester, MA
10:30-11:00 / Simulation Comparisons Of Methods For The Analysis Of Global Gene Expression Patterns (J. Lyons-Weiler, Center for Bioinformatics and Computational Biology, UMass Lowell) / Substrate Conformational Transitions In The Active Site Of Chorismate Mutase: Importance Of Dynamics In Protein, Ligand Interactions And Enzymatic Catalysis H Guo, Q. Cui, W.N. Lipscomb and M. KarplusDept. of Chemistry and Chemical Biology, Harvard UniversityCambridge, MA
11:00-11:30AM Break
2 / Session 2AADVANCES IN MICROARRAY ANALYSIS 2 / Session 2B
ADVANCES IN VISUAL AND ANALYTIC DATA MINING 1
11:30-12:00 / Image Transformation Prior To Statistical Analysis Of Microarray Data R.Y., Yukhananov and A.V. Loguinov, Neurogenomic Laboratory, Pain Research Center, Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston / Using Self-Similar Geometric Structures To Represent Letter-Sequence-Indexed Statistics For Gene Regulation And Peptide Docking Studies G. Carr, George Mason University
12:00-12:30 / Sources Of Experimental Variability In Expression Data Derived From High-Density Oligonucleotide Microarrays: Practical Experience From An Academic Core Laboratory R.A. Saccone, R.K. Rauniyar, and M.-E. PattiResearch Division, Joslin Diabetes Center, Boston, MA / Visual Data Mining of High Dimensional Biological Data Research Questions G., Grinstein, Computer Science Department, UMass Lowell
12:30-1:30PMBuffet Lunch Reception
3 / Session 3AEVOLUTIONARY GENOMICS / Session 3B
STUDENT RESEARCH PRESENTATIONS
1:30-2:00 / Mitochondrial Genome Evolution In Land Plants Yin-Long Qiu, Biology Department, UMass Amherst / Using protein-protein interactions to predict protein function
Z. Gore, Center for Bioinformatics and Computational Biology, UMass Lowell
2:00-2:30 / Molecular Evolution Of The Human Growth Hormone Locus R. Adkins, Biology Department, UMass Amherst / An Empirical Comparison of Methods for the Detection of Differentially Expressed Genes: Cancer Data Sets,
S. Bhattacharya,T. Nguyen and J. Lyons-Weiler, Center for Bioinformatics and Computational Biology, UMass Lowell
2:30-3:00 / Rna Polymerases As Molecular Markers To Identify The Oldest Extant Angiosperm M. Hajibabaei, Biology Department University of Ottawa / Applying the Non-Parametric Bootstrap Technique to Measure the Significance of the Classification of Large-Scale Gene Expression Data
D. Long1,2, S. Bhattacharya1,2, J. Lyons-Weiler1,2, Center for Bioinformatics and Computational Biology2, Graduate Program in Biochemistry, UMass Lowell
3:00-3:30 / Co-Evolution And Fine-Tuning Of Rrna Subunits In Seed Plants O. Dombrovska, Y-L Qiu, Biology Department UMass Amherst / A Comparison of Methods for Detecting Differentially Expressed Genes using
Microarray Data: The Welsh et al. Epithelial Ovarian Cancer Data Set
T. Nguyen and J. Lyons-Weiler, Center for Bioinformatics and Computational Biology, UMass Lowell
3:30-4:00PM Break
4 / Session 4AFUNCTIONAL GENOMICS / Session 4B
BIOINFORMATICS IN THE CLASSROOM
4:00-4:30 / Protein Classification And Prediction From Sequence Information Alone (A. Li, K. Marx, Chemistry Dept., Center for Intelligent Materials, UMass Lowell) / Introduction Of Computational Biochemistry Into The Chemistry Curriculum: A Modification Of Ch 415 Nucleic Acids Biochemistry To Include Bioinformatics A.D. Cooper , Professor of Chemistry, Worcester State College, MA
4:30-5:00 / TBA
Physiological Genomics / Bioinformatics In The Classroom M.C. Pavao, E. Fynan, M. ShamgochianDept of Biology, Worcester State College, MA
5:00-5:30 / TBA / Bioinformatics Training And Research Opportunites At UMass Lowell A.M. Hurley, Department of Mathematics, UMass Lowell
5:30-7:30PMReception
FRIDAY, MAY 3
Plenary Session 2, Room A
9:00-9:50AMDr. Phil Reilly, M.D., J.D., CEO,
Interleukin Genetics Incorporated
Title:TBA
5 / Session 5AUNIVERSITY-INDUSTRY RELATIONS / Session 5B
COMPUTATIONAL BIOLOGY
10:00-10:30 / Thomas Chmura
TBA / Computational Identification Of Promoters And First Exons In The Mouse Genome
I. Grosse*, R.V. Davuluri#, D. Holste*, and M.Q. Zhang*, *Cold Spring Harbor Laboratory, Cold Spring Harbor, NY #Human Cancer Genetics Program, Ohio State University, Columbus, OH
10:30-11:00 / Migrating Intellectual Property From University To Commercial Sector R.D. Gill, Ph.D., President and CEO,AnVil Inc. / Connected Gene Neighborhoods In Bacterial And Archaeal Genomes. I.B. Rogozin1, K.S. Makarova1, J. Murvai1, L. Aravind1, E. Czabarka1, Y.I. Wolf1, R.L. Tatusov1, L.A.Szekely2, and E.V. Koonin1*
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD; 2Department of Mathematics, University of South Carolina, Columbia, SC
11:00-11:30AMBreak
6 / Session 6AADVANCES IN MICROARRAY ANALYSIS 3 / Session 6B
ADVANCES IN VISUAL AND ANALYTIC DATA MINING 2
11:30-12:00 / Gene Expression Analysis Using High Dimensional Analysis And Visualization
B Jessee1, P Hoffman1, A Gee 1,2, P O'Neil1, H Li2, M McManus1 and
G Grinstein 1,2. 1AnVil, Burlington, MA 2UMass Lowell / A Constrained Self-Organizing Maps To Provide Increased Information In Microarray Cluster Analysis (M. Trutschl, U. Cvek, Computer Science Department, UMass Lowell
12:00-12:30 / A Novel Approach With Higher Sensitivity And Specificity For Affymetrix Genechip Data Analysis M. Xu,Research Computing Department, Children’s Hospital, Boston / Datamining the NCI Compound GI 50-Cancer Cell Line Dataset, K. Marx, Anvil Inc., Center For Intelligent Biomaterials Department Of Chemistry UMass Lowell
12:30-1:30PM Buffet Lunch Reception, Room A
1:30-2:20PMPlenary Session 3, Room A
Dr. Ralph Irizarry, Ph.D.
Johns Hopkins University
Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data
Session 7AADVANCES IN MICROARRAY ANALYSIS 4 / Session 7B
BIOINFORMATICS TOOLS: USE AND DEVELOPMENT
2:30-3:00 / Boolean Networks, Rule Association Mining And The Peano Count Trees (P-Trees) For Gene Expression Profiling W.V. Granda, Plant Abiotic Stress and Bioinformatics Group, North Dakota State University / Biotools II: The Next Generation
D. Lapointe, University of Massachusetts Medical School, Worcester, MA
3:00-3:30 / Two Attempts To Beat The Curse Of Dimensionality For The Statistical Accuracy Of Machine Learning L. Jones, Department of Mathematics, UMass Lowell / Free and Open Source Software in Bioinformatics: Motivations and Solutions
J.W. Bizzaro, Bioinformatics.Org
3:30-4:00 / A Multi-Level Subspace Clustering Algorithm For Mixed Data Types With Multiple Threshold Values J. D. Pawar & P. R. Rao , Department of Computer Science and Technology,
Goa University, Goa-403 206, INDIA. / The UMass Lowell Bioinformatics Web Tool Collection (S. Patel and J. Lyons-Weiler, Center for Bioinformatics and Computational Biology, UMass Lowell)
4:00-4:30 / TBA / Nomenclature In Biology: A Universal Challenge For Bioinformatics R.D. Stevenson, 1 and R.A. Morris2. 1 Dept. of Biology and, 2 Dept. of Computer Science, University of Massachusetts Boston, Boston, MA
5:00 Announcement:UMass Bioinformatics Conference Best Student Presentation
Announcement:UMass Bioinformatics Conference Best Paper
5:15 Closing Remarks