Discussion SessionThursday May 15, 2008

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Find out who’s working on bioinformatics at Miami

Find out who has tools and expertise at Miami that can be applied to bioinformatics research

Get biologists and non-biologists to talk to (and maybe even understand!) each other

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Two-hour session

Brief introduction of attendees Biologists – state research problems that desire

collaboration on

Non-biologists – give tools and expertise available for collaboration on bioinformatics/biology problems

Break up into informal discussion session, with facilitation by Chun Liang and Quinn Li, botany

Valerie Cross and John Karro, computer science

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Expertise in biostatistics Analysis of dose-related tumorigenic trends in the

presence of treatment-related toxicity Analysis of pharmacokinetic data, particularly,

methods for testing the equivalence of the areas under concentration-time profile curves

Risk assessment Inverse regression/calibration problems where the

dose associated with a particular level of response is estimated and tested

Optimal design of experiments for simple compartmental models

Integration of model uncertainty in the generation of risk estimates

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Analysis and optimization of algorithms

Interested in developing efficient algorithms for finding similar sequences in genomic databases

Work with problems that have well-defined measure of similarity or difference between objects

Improve problem solutions that currently use too much memory or take too much time

Edit distance (number of operations to change one text/genomic string to another)

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Study how insect viral genes (esp. baculovirusand ascovirus) are regulated in insect cells

Baculovirus – would like bioinformatic prediction of which AATAAA used in certain processing

Ascovirus – would like bioinformatic search for particular stem loop structure, which could then be verified in lab

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Ontology - a vocabulary that represents a set of concepts of a particular domain and the relationships between those concepts

Gene Ontology (GO) guarantees the consistency of the referenced biological concepts in different databases

Use to annotate genes in various databases

Annotations used to determine similarity between genes and gene products

Group has made various ontology software tools

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Multi-view FCA

1: lagging and leading strand elongation,CDC2, DBP11, POL2

QUOTA

OntoSELF

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Primary focus on computationally-based analysis of DNA and RNA sequences

Develop tools to help with analysis

Example: Working on identification of functional genomic regions through comparison of genomes from related species

Example: Developed tools for the estimation of neutral substitution rates on a local scale

Study structure of rates

Study effect on evolution of genomic structure

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Software engineering

Software risk management and assessment

Probabilistic risk assessment

Software design methodology

Experimental verification of software design methodology effectiveness

Visual programming languages

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DNA tiling microarrays Massive data sets

Broad coverage of genome

Low signal/noise ratio

Want to extract statistically significant information to justify validation experiments in a wet lab

Seek collaboration from statisticians to develop appropriate statistics

Seek collaboration from computer scientists to effectively implement statistical and data processing algorithms

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Looking for collaboration on genomic sequence assembly and clustering

Work with expressed sequence tags (EST) from complementary DNA (cDNA) How trace a given set of ESTs back to their

original genes?

New technologies can now very quickly sequence enormous amounts of short pieces of cDNA Want computational tools to do correct

assembly and clustering

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Software development in C/C++/Fortran for numerical computation

Conversion of software for parallel computation

Application support for various physics and biophysics packages, e.g., ANSYS, Abaqus

Modeling and simulation of vascular systems

Geometric model generation

Flow solving

Data visualization

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Expertise is applied probability

Served on graduate committees in zoology

Helped graduate students with data analysis

Experience in

Analysis of variance

Markov chains

Hidden Markov Models

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Expertise in optimization and simulation of complex systems

Bioinformatics experience Sequencing by hybridization

Clustering the avian-flu viruses (with Henry Wan)

Working with Chun Liang (Botany) and CSA colleagues to cluster Expressed Sequence Tags (ESTs) to identify genes for conifers

Would like to hear from other biologists with similar research, e.g., use of ESTs for gene identification and regulation

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Has taught classes in introductory statistics, regression analysis, and time series analysis

Extensive experience applying statistics in business, social science, and natural science Time series analysis to study chemical concentrations

of stream flows into Acton Lake

Applications of regression techniques

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Scientific programming, especially C++ and MATLAB

Parallel programs on cluster

Graphical user interfaces (GUI) for programs

Mathematical modeling

Digital image processing

Basic knowledge of variety of mathematical techniques

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Works in Michael Kennedy’s lab

Seek collaboration and support for

Nuclear Magnetic Resonance (NMR) data

Use of principal component analysis (PCA)

Use of partial least squares discriminant analysis (PLS-DA)

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Installation and configuration of bioinformatics applications on the cluster

IT infrastructure planning and support -servers, network, storage, etc.

Scripting (writing programs for cluster) and help with cluster batch system

Database creation and advice on use

General support of cluster users

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Principal expertise Mathematical optimization (theory, algorithms,

software) Modeling of decision problems

Research interests Reformulating mathematical problems for efficiency Applications of optimization to data-fitting Parallel processing in optimization Optimal design of experiments

Areas of application (to date) Crystallography, statistics, hydrology, econometrics,

toxicology, engineering, ecology

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Knowledge of statistics useful in Microarray studies (separating signal from

noise, cluster analysis, missing data), image analysis

Clinical studies, forestry and wild life, public health

Specific statistical tools Bayesian hierarchical modeling and Markov

chain Monte Carlo (MCMC) algorithms

Spatial analysis (areal data and point-referenced data), including prediction and model checking

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