Second Annual
University of Massachusetts Bioinformatics Conference
May 2-3, University of Massachusetts, Lowell
Schedule of Events (subject to change)
Thursday, May 2
7:30-8:30AM
Registration
8:30-9:00AM
Opening Remarks
Dr. Georges Grinstein, co-chair
Dr. James Lyons-Weiler, co-chair
Chancellor William T. Hogan
Plenary Session 1, Room A
9:00-9:50AM
1
10:0010:30
Dr. James Cassatt, Ph.D.
National Institute of Health, NIGMS
Title:TBA
Session 1A
Session 1B
ADVANCES IN MICROARRAY
ANALYSIS 1
COMPUTATIONAL
STRUCTURAL BIOLOGY 1
Bayesian Analysis of Gene Expression
Levels and the Open Design of cDNA
Microarray Experiments
Hydrophobic Sliding Facilitates
Conformational Changes And Active
Site Cleft Opening In Hiv-1 Protease
W.R.P. Scott, J. Foulkes, M.M. PrabuJeyabalan, J. Lavasta, C.A. Schiffer*
J. Townsend, Department of Organismic &
Evolutionary Biology, Harvard University
Department of Biochemistry and Molecular
Pharmacology University of Massachusetts
Medical School 55 Lake Ave N., Worcester,
MA
10:3011:00
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. Karplus Dept. of
Chemistry and Chemical Biology, Harvard
UniversityCambridge, MA
11:00-11:30AM Break
2
11:3012:00
Session 2A
Session 2B
ADVANCES IN MICROARRAY
ANALYSIS 2
ADVANCES IN VISUAL AND
ANALYTIC DATA MINING 1
Image Transformation Prior To
Statistical Analysis Of Microarray Data
R.Y., Yukhananov and A.V. Loguinov,
Using Self-Similar Geometric Structures
To Represent Letter-Sequence-Indexed
Statistics For Gene Regulation And
Peptide Docking Studies G. Carr,
Neurogenomic Laboratory, Pain Research
Center, Department of Anesthesiology,
Brigham and Women’s Hospital, Harvard
Medical School, Boston
12:00-
Sources Of Experimental Variability In
George Mason University
Visual Data Mining of High Dimensional
12:30
Expression Data Derived From HighDensity Oligonucleotide Microarrays:
Practical Experience From An
Academic Core Laboratory R.A.
Saccone, R.K. Rauniyar, and M.-E.
Patti Research Division, Joslin Diabetes
Biological Data Research Questions G.,
Grinstein, Computer Science Department,
UMass Lowell
Center, Boston, MA
12:30-1:30PM Buffet Lunch Reception
3
1:302:00
Session 3A
Session 3B
EVOLUTIONARY GENOMICS
STUDENT RESEARCH
PRESENTATIONS
Mitochondrial Genome Evolution In
Land Plants Yin-Long Qiu, Biology
Using protein-protein interactions to
predict protein function
Z. Gore, Center for Bioinformatics and
Department, UMass Amherst
Computational Biology, UMass Lowell
2:002:30
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
2:303:00
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. LyonsWeiler1,2, Center for Bioinformatics and
Computational Biology2, Graduate Program in
Biochemistry, UMass Lowell
3:003:30
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 4A
Session 4B
FUNCTIONAL GENOMICS
BIOINFORMATICS IN THE
CLASSROOM
4:004:30
Protein Classification And Prediction
From Sequence Information Alone (A.
Li, K. Marx, Chemistry Dept., Center for
Intelligent Materials, UMass Lowell)
4:305:00
TBA
Physiological Genomics
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
Bioinformatics In The Classroom M.C.
Pavao, E. Fynan, M. Shamgochian Dept
5:005:30
TBA
of Biology, Worcester State College, MA
Bioinformatics Training And Research
Opportunites At UMass Lowell A.M.
Hurley, Department of Mathematics, UMass
Lowell
5:30-7:30PM
Reception
FRIDAY, MAY 3
Plenary Session 2, Room A
9:00-9:50AM
Dr. Phil Reilly, M.D., J.D., CEO,
Interleukin Genetics Incorporated
Title:TBA
5
Session 5A
Session 5B
UNIVERSITY-INDUSTRY
RELATIONS
COMPUTATIONAL BIOLOGY
10:0010:30
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
10:3011:00
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*
1
National Center for Biotechnology
Information, National Library of Medicine,
National Institutes of Health, Bethesda MD;
2
Department of Mathematics, University of
South Carolina, Columbia, SC
11:00-11:30AM Break
6
Session 6A
Session 6B
ADVANCES IN MICROARRAY
ANALYSIS 3
ADVANCES IN VISUAL AND
ANALYTIC DATA MINING 2
11:3012:00
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
A Constrained Self-Organizing Maps To
Provide Increased Information In
Microarray Cluster Analysis (M.
Trutschl, U. Cvek, Computer Science
Department, UMass Lowell
2
UMass Lowell
12:0012:30
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 50Cancer 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
1:30-2:20PM
Plenary Session 3, Room A
Dr. Ralph Irizarry, Ph.D.
Johns Hopkins University
Exploration, Normalization, and Summaries of High Density
Oligonucleotide Array Probe Level Data
2:303:00
Session 7A
Session 7B
ADVANCES IN MICROARRAY
ANALYSIS 4
BIOINFORMATICS TOOLS: USE
AND DEVELOPMENT
Boolean Networks, Rule Association
Mining And The Peano Count Trees
(P-Trees) For Gene Expression
Profiling W.V. Granda, Plant Abiotic
Biotools II: The Next Generation
D. Lapointe, University of Massachusetts
Medical School, Worcester, MA
Stress and Bioinformatics Group, North
Dakota State University
3:003:30
Two Attempts To Beat The Curse Of
Dimensionality For The Statistical
Accuracy Of Machine Learning L.
Jones, Department of Mathematics, UMass
Free and Open Source Software in
Bioinformatics: Motivations and
Solutions
J.W. Bizzaro, Bioinformatics.Org
Lowell
3:304:00
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. LyonsWeiler, Center for Bioinformatics and
Computational Biology, UMass Lowell)
4:004:30
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