Great Lakes Bioinformatics Conference 2012

Agenda at a Glance

All meetings are being held at the Michigan League Building, University of Michigan
http://uunions.umich.edu/league/maps/floorplans/

Updated May 08, 2012

Great Lakes Bioinformatics Conference 2012

Full Agenda

All meetings are being held at the Michigan League Building, University of Michigan
http://uunions.umich.edu/league/maps/floorplans/

Updated May 10, 2012

Great Lakes Bioinformatics Conference 2012

GLBIO 2012 On-site Registration Schedule

• Monday, May 14, 2012 – 4pm – 6pm
  Michigan League Building,  2nd floor Concourse Room
  

• Tuesday, May 15, 2012 – 8am – 5pm
  Michigan League Building,  2nd floor Concourse Room
  

Great Lakes Bioinformatics Conference 2012

Keynote Speakers

Updated April 16, 2012

	Howard Cash, President Gene Codes Corporation Gene Codes Forensics, Inc. Ann Arbor, MI - USA Biosketch (.pdf) Title: Designing Bioinformatics for the Wetware.  Usability Challenges with Massive Amounts of Data. Abstract:   Gene Codes Corporation began producing DNA sequencing tools that dominated the commercial market starting in the mid-1990s.  Starting in 1997 and especially after 9/11, 2001, the company produced tools that completely changed the standard for DNA analysis software in forensic crime labs around the world.   In neither case did success depend on new discoveries or dramatically more sensitive pattern detection algorithms.  Instead, the Sequencher and M-FISys programs, respectively, raised the game on usability for the bench scientist. For people in bioinformatics, the changes in data scale have been dramatic over the last several years.  How do we make that information available to the people who will benefit from it?  If a consumer could truly get a full genome in a matter of seconds as portrayed in the dystopian movie, GATTACA, surely they would not want a listing of all of the individual data points.  So where might bioinformatics professional focus in the future?   We will briefly discuss where bioinformatics has come in the days since MolGen, UWGCG and IntelliGenetics and some of the principles that can help tool developers who focus on the data present that information so that end users can grasp its content. [TOP] [Return to Full Agenda Page]
	Michael Lynch, Professor Department of Biology Indiana University Bloomington, IN - USA CV: www.bio.indiana.edu/faculty/directory/profile.php?person=milynch Title: Mutation, Drift, and the Evolution of Subcellular Features Abstract: Understanding the mechanisms of evolution and the degree to which phylogenetic generalities exist requires information on the rate at which mutations arise and their effects at the molecular and phenotypic levels. Although procuring such data has been technically challenging, high-throughput genomic sequencing is rapidly expanding our knowledge in this area. Most notably, information on spontaneous mutations, now available in a wide variety of organisms, implies an inverse scaling of the mutation rate (per nucleotide site) with the effective population size of a lineage. The argument will be made that this pattern naturally arises as natural selection pushes the mutation rate down to a lower limit set by the power of random genetic drift rather than by intrinsic molecular limitations on repair mechanisms. Additional support for this idea derives from the relative levels of efficiency of DNA polymerases and mismatch-repair enzymes in eukaryotes relative to prokaryotes. This drift-barrier hypothesis has general implications for all aspects of evolution, including the performance of enzymes and the stability of proteins. The fundamental assumption is that as molecular adaptations become more and more refined, the room for subsequent improvement becomes diminishingly small. If this hypothesis is correct, the population-genetic environment imposes a fundamental constraint on the level of perfection that can be achieved by any molecular adaptation. It also implies that effective neutrality is the expected outcome of natural selection, an idea first suggested by Hartl et al. in 1985. Although generally viewed as an independent process, mutation also operates as a weak selective force, thereby playing a central role in “nearly neutral” hypotheses in evolution. Most notably, genes and proteins with more complex structures are subject to higher rates of mutational degeneration simply because they are larger mutational targets. However, because the mutation rate is very low at the nucleotide level, the efficiency of such mutation-associated selection becomes of diminishing significance in populations with small effective sizes. Thus, mutationally hazardous genomic and gene-structural features, which may or may not be adaptive, are expected to passively arise in lineages with small effective sizes. This general principle, the mutational-hazard theory, will be illustrated with examples including: 1) the differential expansion of intron numbers in various phylogenetic lineages; and 2) the diversification of protein-architectural features. [TOP] [Return to Full Agenda Page]
	Mercedes Pascual, Professor Department of Ecology and Evolutionary Biology Affiliate of the Center for Computational Medicine and Bioinformatics University of Michigan Ann Arbor, MI - USA CV: www.lsa.umich.edu/eeb/directory/faculty/pascual Title:  Pathogen Diversity from an Ecological Perspective Abstract: Sequence data is becoming increasingly available for many pathogens in time and space.  This presents the opportunity to describe their population structure at different scales and to address the role of this structure for epidemiology.  In particular, the genetic diversity associated with antigenic phenotypes, the variation recognized by the immune system, is of interest.  Here, conceptual models with a basis in competitive ecological interactions provide a basis to understand whether immune selection (competitive interactions between strains mediated by cross-immunity) structures pathogen populations and how this structure influences in turn the transmission dynamics of pathogens.   In this talk, I present two examples from our work on Plasmodium falciparum malaria and H3N2 influenza respectively, with individual-based models of transmission that track the history of infection of individual hosts and the genetic relatedness of the pathogen.  Empirical analyses and considerations on testing  resulting predictions on this ‘strain theory’ are discussed. [TOP] [Return to Full Agenda Page]
	Russell Schwartz, Professor Department of Biological Sciences and Lane Center for Computational Biology Carnegie Mellon University Pittsburgh, PA - USA CV: www.cmu.edu/bio/faculty/schwartz.html Title:  Learning Population Histories from Genome Variation Data Abstract: High throughput sequencing technologies have made it possible to assemble vast libraries of genetic variation data describing how genomes differ from one person to another.  Such data implicitly encode a history of our species at a population level due to the gradual accumulation of mutations in our genomes as we have developed from an initial founder population to the many diverse subpopulations that comprise our species today.  Better characterizing this history could be useful not only to basic research but also to important practical problems in improving the effectiveness of genotype/phenotype association studies and better understanding how we have adapted to historical disease threats or environmental changes.  Reconstructing this population history from the indirect evidence of random mutations is a challenging computational problem, but also an interesting problem from a computational biologist’s perspective because of a long history of different approaches reflecting different biological perspectives and drawing on different classes of computational methods.  In this talk, we will examine new strategies for characterizing population history that attempt to synthesize some of these different perspectives into a more complete model of our history as a species.  This work seeks to combine discrete algorithms and operation research methods arising from the field of phylogenetics with machine learning and statistical sampling methods arising from statistical genetic models of population substructure.  We will examine the motivation behind these approaches and explore their development from a computational perspective.  We will then see what we can learn by applying such methods to real data.  In the process, we will see some of the many ways diverse computing paradigms can contribute to current research in human genetics. [TOP] [Return to Full Agenda Page]

Great Lakes Bioinformatics Conference 2012

Poster Presentation List

Great Lakes Bioinformatics Conference 2012

Steering Committee

Honorary Conference Chairs:
• Brian Athey, University of Michigan - This email address is being protected from spambots. You need JavaScript enabled to view it.
• Robert Murphy, Carnegie Mellon University - This email address is being protected from spambots. You need JavaScript enabled to view it.

Conference Chairs:

• Lonnie Welch, Ohio University - This email address is being protected from spambots. You need JavaScript enabled to view it.

Program Chairs:
• Laura Brown, Michigan Technological University - This email address is being protected from spambots. You need JavaScript enabled to view it.
• Margit Burmeister, University of Michigan - This email address is being protected from spambots. You need JavaScript enabled to view it.
• Elodie Ghedin, University of Pittsburgh - This email address is being protected from spambots. You need JavaScript enabled to view it.

ISCB:
• B.J. Morrison McKay – This email address is being protected from spambots. You need JavaScript enabled to view it.
• Stephanie Hagstrom – This email address is being protected from spambots. You need JavaScript enabled to view it.

Great Lakes Bioinformatics Conference 2012

Conference Sponsors

Updated May 04, 2012

SILVER:

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BRONZE:


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INDUSTRY TRACK:


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RUBY:


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Case Western Reserve University
Case Center for Proteomics & Bioinformatics
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The Ohio State University – Center for Applied Plant Science

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Department of Computer Science
Department of Biological SciencesSchool of Forest Resources and Environmental Science (SFRES)
School of Technology (SOT)
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University of Pittsburgh

EXHIBITOR:


Research and Economic Development
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Michigan Metabolomics and Obesity Center

PUBLISHER TABLE:

GENERAL:

Great Lakes Bioinformatics Consortium
(a regional Affiliate of the International Society of Computational Biology)

[TOP]

Great Lakes Bioinformatics Conference 2012

Industry Tracks

Updated May 07, 2012

Industry Track 2
5:00 pm - 5:20 pm
Mendelssohn Theatre
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Presenter:  Chris Robertson, Solution Architect, Cambridge Computer

Topic:  Reigning in Research Data: Adding Intelligence to Conventional File Systems

Description: There is a growing need to put structure on unstructured research data, being driven by a number of different factors:

• Granting agencies are requiring investigators to specify and conform to data management plans that preserve and make data available to other researchers

• Research institutions are seeking to charge storage consumption back to individual grants and projects

• Data storage administrators need better content classification in order to manage data protection and life cycle management
  

• As capacity grows and time progresses, it becomes futile to rely on any given individual's memory as the only means for content classification

Unfortunately, research scientists are fundamentally resistant to traditional efforts to put structure on their unstructured data. Commercial content management systems are seen as cumbersome to operate, not to mention that they might add latency to high-performance processing jobs. As such, many scientists have no tools other than directory names to identify their data. Others rely on spreadsheets and home-grown software applications to track their files, but often these links break as files are moved and renamed. Cambridge Computer has embarked on a project to define the best practices for content classification of research data. We are collaborating with a number of leading institutions and have completed development of a working prototype. The purpose of this talk is to share the highlights of our work, stimulate discussion, and make contact with potential collaborators.

[Return to Full Agenda]