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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
(Schedule and locations are subject to change. Please check back for updates.)
go directly to: [Wednesday - May 16] [Thursday - May 17]

MONDAY - May, 14 2012
4:00pm - 6:00pm Registration (Concourse Room)
4:00pm - 6:00pm Group Hike
Nichols Arboretum
www.lsa.umich.edu/mbg/see/nicholsarboretum.asp

Nichols Arboretum "the Arb" is a 123 acre living museum set in the hills adjacent to the UM main campus. Originally designed by OC Simonds in 1906. Long views are framed by the Huron River Valley and unique plants. The Total hiking trail distance is just over 2 miles, with numerous points of interest and historical areas as well as viewing points of the surrounding areas. We will follow self-guided tours in small groups depending on the number of people who join us.

We will meet at the GLBIO Registration Area in the Michigan League (2nd floor, Concourse), at 4 pm and travel as a group to the hike start.  

If you wish, you can meet us directly at the Nichols Arboretum, Washington Heights entrance (1610 Washington Heights; www.lsa.umich.edu/mbg/files/ArbGuide.pdf).  We will be arriving there around 4:15pm - 4:20pm. 

TUESDAY - May 15, 2012
  Mendelssohn Theatre  Vandenberg Room Hussey Room
8:00am - 5:00pm Registration
9:00am - 11:00am Tutorial 1
High Performance Computing in Massive Omics Data
Ma, Ping
Univ. of Illinois
Tutorial 2
RNA-Seq Approach to Study Gene Expression
Wijeratne, Asela
Ohio State Univ.
Tutorial 3
Using New Tools for Predicting 3D Structural Motifs in Non coding RNAs
Leontis, Neocles
Bowling Green
State Univ.
11:00am - 11:10am Break
11:10am  - 11:30am Industry Track 1
Bioteam

(Mendelssohn Theatre)
11:30am - 12:45pm Lunch Break (lunch on own)
12:45pm - 2:45pm Tutorial 4
An Informatics Platform for Processing Cancer Jin, Victor
Ohio State Univ.
Tutorial 5
Accessing Free, Large-scale Computation and Data Resources for Bioinformatics through the eXtreme Science and Engineering Discovery Environment (XSEDE)
Blood, Philip
Carnegie Mellon Univ.
Tutorial 6
Structural Variation Detection Using Next-generation Sequencing
Hayes, Matthew Case Western Reserve Univ.
2:45pm - 3:00pm Break
3:00pm - 5:00pm Tutorial 7
Practical Biological Network Visualization and Analysis
Jurisica, Igor
Univ. of Toronto
Tutorial 8
Knowledge-based Interpretation of High throughput Data
Farfan, Fernando
Univ. of Michigan
Tutorial 9
RNA 3D Structural Motifs: Definition, Analysis, and Prediction
Laing, Christian Wilkes Univ.
5:00pm - 5:20pm Industry Track 2
Cambridge Computer

(Mendelssohn Theatre)
5:30pm - 7:30pm Poster Session A and Reception (Ballroom)
Poster Session List by Presenter Last Name
Poster Session List By Number

WEDNESDAY - May 16, 2012
  Mendelssohn Theatre Hussey Room
8:00am - 5:00pm Registration (Concourse Room)
9:00am - 10:00am Keynote 1
Learning Population Histories from Genome
Variation Data


Russell Schwartz, Professor
Department of Biological Sciences
and Lane Center for Computational Biology
Carnegie Mellon University
Pittsburgh, PA - USA
10:00am - 10:10am Break
10:10am - 10:30am Industry Track 3
Compendia Bioscience

10:30am - 12:00pm WA1 Oral Presentations
Gene Regulations and Transcriptiomics 

OP1, OP2, OP3, OP4,
OP5, OP6
WA2 Oral Presentations
Protein Structure & Function, Databases and Ontologies
OP7, OP8, OP9, OP10, OP11, OP12

12:00pm - 1:30pm Lunch Break (lunch on own)
1:30pm - 2:30pm Keynote 2
Pathogen Diversity from an Ecological Perspective

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
2:30pm - 4:00pm WP1 Oral Presentations
Evolution & Comp. Genomics, Population Genomics
OP13, OP14, OP15, OP16, OP17, OP18

WP2
Oral Presentations
Protein Interaction and Molecular Networks, Metagenomics
OP19, OP20, OP21, OP22, OP23, OP24

4:00pm - 4:15pm Break
4:15pm - 5:15pm S1 - Special Session
Proteins in Motion: Computational Studies in Protein Flexibility and Dynamics
S2 - Special Session
Computational Proteomics: Understanding Network Perturbations in Cancer
5:15pm - 7:15pm Poster Session B and Reception
Poster Session List by Last Name
Poster Session List By Number
7:30pm - 10:00pm 7:30pm - 8:30pm
UMICH Museum Art Viewing
...................................
8:30pm to 10:00pm
Dinner and Keynote 3 
...................................
Designing Bioinformatics for the Wetware.  Usability Challenges with Massive Amounts of Data.

Howard Cash, President
Gene Codes Corporation
Gene Codes Forensics, Inc.
Ann Arbor, MI - USA

THURSDAY - May 17, 2012
  Mendelssohn Theatre Hussey Room
8:00am - 12:00pm Registration (Concourse Room)
9:00am - 10:00am
S3 - Special Session
Creating Teams for Bioinformatics
Ohio Bioinformatics Consortium Meeting
10:00am - 10:15am Break
10:15am - 12:00pm RA1 Oral Presentations - Sequence Analysis
OP25, OP26, OP27, OP28, OP29, OP30, OP31

RA2 Oral Presentations
Algorithm & Machine Learning, Bioimaging, Disease Models & Epidemiology
OP32, OP33, OP34,
OP35, OP36, OP37, OP38
12:00pm-1:00pm Keynote 4
Mutation, Drift, and the Evolution of Subcellular Features

Michael Lynch, Professor

Department of Biology
Indiana University
Bloomington, IN - USA
1:00pm - 1:15pm Adjourn

go directly to: [TOP] [Wednesday - May 16] [Thursday - May 17]

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
(Schedule and locations are subject to change. Please check back for updates.)
go directly to: [Wednesday - May 16] [Thursday - May 17]
 

--> MONDAY - May 14, 2012

4:00pm - 6:00pm
Registration (Concourse Room)

4:00pm - 6:00pm
Group Hike
Nichols Arboretum
www.lsa.umich.edu/mbg/see/nicholsarboretum.asp

Nichols Arboretum "the Arb" is a 123 acre living museum set in the hills adjacent to the UM main campus. Originally designed by OC Simonds in 1906. Long views are framed by the Huron River Valley and unique plants. The Total hiking trail distance is just over 2 miles, with numerous points of interest and historical areas as well as viewing points of the surrounding areas. We will follow self-guided tours in small groups depending on the number of people who join us.

We will meet at the GLBIO Registration Area in the Michigan League (2nd floor, Concourse), at 4 pm and travel as a group to the hike start.  

If you wish, you can meet us directly at the Nichols Arboretum, Washington Heights entrance (1610 Washington Heights; www.lsa.umich.edu/mbg/files/ArbGuide.pdf).  We will be arriving there around 4:15pm - 4:20pm. 

 

--> TUESDAY - May 15, 2012

8:00am - 5:00pm  
Registration (Concourse Room)
9:00am - 11:00am
Mendelssohn Theatre
...................................
Tutorial 1
High Performance Computing in Massive Omics Data

Ping Ma, Ph.D., Department of Statistics, University of Illinois

ABSTRACT: New discoveries in genomics and proteomics are profoundly changing our view of biological sciences. Notwithstanding these exciting developments, we are at an important crossroads in this area of endeavor. While analytical technologies are evolving at unprecedented speed, the biologists engaged in this enterprise are facing major computational and analytical challenges in analyzing the massive omics data. It calls for new computing strategies for genomics and proteomics to conduct large-scale analyses of complex biological systems, and to transform the massive data into reliable information for the extraction of new knowledge. Harnessing these methods for genomics and proteomics will certainly result in new computing technologies and algorithms for data analysis.
9:00am - 11:00am
Vandenberg Room
...................................
Tutorial 2
RNA-Seq Approach to Study Gene Expression Profiles in Non-Model Organisms

Asela Wijeratne, Ph.D., Saranga Wijeratne, & Tea Meulia, Ph.D., Molecular and Cellular Imaging Center (MCIC), Ohio State University/OARDC

ABSTRACT: Transcriptome analyses provide fundamental insights into biological processes. High-throughput sequencing coupled with the development of bioinformatics tools allow transcriptome analyses in non-model organisms for which reference genome sequence and annotations are limited. We will demonstrate the use of a custom transcripome analysis pipeline, and discuss challenges for data analysis.

TUTORIAL LEVEL: Introductory to Intermediate

REQUIREMENTS: Attendees should have basic knowledge on high-throughput sequencing data technologies, familiarity with Illumina sequencing platform, knowledge of basic bioinformatics tools (Blast) and some familiarity with the GALAXY platform. As there will be hands on demonstration, participants are encouraged to bring their own laptop to the session.
9:00am - 11:00am
Hussey Room
...................................
Tutorial 3
Using New Tools for Predicting 3D Structural Motifs in Non-coding RNAs

Neocles B. Leontis, Ph.D., Department of Chemistry & Craig Zirbel, Ph.D., Department of Mathematics and Statistics, Bowling Green State University

ABSTRACT: This session covers prediction of RNA 3D structure from sequence. Participants will learn about new resources which organize RNA 3D structures and known RNA motifs. Participants will get RNA sequences, fold them using standard programs, and use a new tool called JAR3D to predict the 3D structures of the internal and hairpin loops.

TUTORIAL LEVEL: Introductory/Advanced

REQUIREMENTS: The intended audience is molecular and systems biologists interested in non-coding RNAs, RNA 3D structure, and RNA function. Participants should bring their own laptops and an interest in RNA structure and function. After an initial overview of RNA 3D structure, the workshop will provide hands-on instruction in the navigation of the author’s website and use of their software.
11:00am - 11:10am  Break
11:10am  - 11:30am
Mendelssohn Theatre
...................................
Industry Track 1
Bioteam
11:30am - 12:45pm  Lunch Break (lunch on own)
12:45pm - 2:45pm
Mendelssohn Theatre 
...................................
Tutorial 4
An Informatics Platform for Processing Cancer ‘Omics Data


Victor Jin, Ph.D. & Xun Lan, Department of Biomedical Informatics, Department of Biomedical Informatics, The Ohio State University

ABSTRACT: The tutorial will demonstrate five specific tools:
1) W-ChIPeaks: A web application for processing ChIP-chip and ChIP-seq data;
2) BALM: A bi-asymmetric-Laplace model for analyzing MBD-seq;
3) HiCPeaks: a latent Poisson model for identifying interacting loci from Hi-C data;
4) W-ChIPMotifs: a web application tool for de novo motif discovery.
5) PORT: a portable ‘omics regulatory toolkit using HRTBLDb as an example.

TUTORIAL LEVEL: Intermediate

REQUIREMENTS: The tutorial is suitable for cancer biologists who apply different high throughput technologies to study cancers, attendees with a biology background who are interested in computation,
12:45pm - 2:45pm
Vandenberg Room
...................................
Tutorial 5
Accessing Free, Large-scale Computation and Data Resources for Bioinformatics Through the eXtreme Science and Engineering Discovery Environment (XSEDE)
 
Philip Blood, Ph.D., & Alexander J. Ropelewski, Pittsburgh Supercomputing Center, Carnegie Mellon University

ABSTRACT: In certain bioinformatics applications (e.g. next generation sequencing) the cost and availability of computational and data storage resources presents a bottleneck that limits scientific progress. This tutorial will demonstrate how investigators can use NSF’s diverse, cutting-edge resources for open scientific research, integrated within XSEDE, to alleviate this bottleneck.

TUTORIAL LEVEL: Introductory to Intermediate

REQUIREMENTS: Some familiarity with the UNIX command line will be helpful, but not necessary, for this tutorial. It will not be possible to provide attendees with access to XSEDE resources during the tutorial due to time constraints, but researchers who already have access to these resources are welcome to follow along with the demonstrations.
12:45pm - 2:45pm
Hussey Room
...................................
Tutorial 6
Structural Variation Detection using Next-Generation Sequencing

Matthew Hayes, Ph.D. student & Jing Li, Ph.D., Computational Biology Lab, Department of Electrical Engineering and Computer Science, Case Western Reserve University

ABSTRACT: The tutorial will provide a survey of structural variation (SV) detection methods. It will cover common techniques for finding variants, including depth of coverage (DOC) methods, paired-end methods, and single-read methods. We will demonstrate how sequence read alignments are visualized, and we will demonstrate the use of a few SV detection programs to find structural variants in a cancer dataset.

TUTORIAL LEVEL: Introductory

REQUIREMENTS: Basic knowledge of next-generation sequencing platforms is assumed (particularly the Illumina platform). We also assume that the participants have a basic foundation in molecular biology and nucleic acids.
2:45pm - 3:00pm   Break
3:00pm - 5:00pm
Mendelssohn Theatre 
...................................
Tutorial 7
Practical Biological Network Visualization and Analysis

Igor Jurisica, Ph.D., Ontario Cancer Institute and University of Toronto

ABSTRACT: There are many visualization software packages, such as Cytoscape, VisANT, NAViGaTOR, Pajek, Osprey, Ondex, PathwayLab, Interviewer3, Geomi, Forg3d to name a few. Individual systems differ greatly in terms of features and standards they support, and consequently diverse analyses they enable. Considering complexity and diversity of data and tasks, there is no single best layout, no single best file format or visualization tool: one size does not fit all. One way to cope with these dynamics is to support multiple scenarios and workflows. Interactive data visualization and data mining proofs a useful approach.

Exploratory data analysis through network visualization remains a challenge. Overlapping nodes and edges make the interpretation of large networks difficult, so much so that these are sometimes referred to as “hairballs”. However, integrated network analysis and visualization is emerging as a fruitful approach to revealing patterns in data. Such an approach may lead to improved understanding of complex systems. Due to many different types of users and tasks, "one size does not fit all," and a useful tool needs to be: 1) flexible in satisfying diverse user needs through various workflows, 2) intuitive to allow for different displays with a mix of automated and manual improvements, and 3) scalable in terms of memory and speed, which is especially important for large graphs.

Our goal is to emphasize importance these aspects and directly involve tool developers and biologists in a dialogue during Q&A sessions to focus future development in the most useful direction and to increase awareness of helpful features. Prior to the tutorial, we will provide example datasets online, which will enable participants to experiment with specific workflows discussed.

TUTORIAL LEVEL: Introductory/Intermediate.

REQUIREMENTS: Only rudimentary biology knowledge will be required. The tutorial will include practical examples and participants are encouraged to bring their laptops, ideally with Internet connection so that online searches and datasets can be used. Prior to the tutorial, all related datasets and workflow examples will be provided on a web server.
3:00pm - 5:00pm
Vandenberg Room
...................................
Tutorial 8
Knowledge-Based Interpretation of High Throughput Data

H.V. Jagadish, Ph.D., & Fernando Farf an, Ph.D., Department of Electrical Engineering and Computer Science, University of Michigan

ABSTRACT: In this tutorial we will showcase the use of novel approaches that exploit the rich information encapsulated in biological pathway graphs. We show how a thorough and rigorous analysis of biological pathways, using complex factors, can provide more meaningful hypotheses to describe the biological phenomena captured by high throughput experiments.

TUTORIAL LEVEL: Introductory
3:00pm - 5:00pm
Hussey Room
...................................
Tutorial 9
RNA 3D Structural Motifs: Definition, Analysis, and Prediction

Christian Laing, Ph.D., Department of Biology and Department of Mathematics and Computer Science, Wilkes University & Jason Wang, Ph.D., Department of Computer Science, New Jersey Institute of Technology

ABSTRACT: RNA 3D structure is highly modular, composed of several repetitive patterns called 3D motifs. Determining 3D motifs is an important step in the RNA folding problem. In this tutorial we introduce the concept of RNA 3D motifs, provide examples, and describe the recent advances on 3D motif prediction and analysis.

TUTORIAL LEVEL: Introductory

REQUIREMENTS: Suitable for an audience with interests in RNA structure prediction and analysis. An introductory knowledge of statistics and data mining is desired but not required.
5:00pm - 5:20pm
Mendelssohn Theatre
...................................
Industry Track 2
Cambridge Computer
>> Click here for abstract

5:30pm - 7:30pm
Poster Session A and Reception (Ballroom)

Poster Session list by Last Name
Poster Session list by Number

 

--> WEDNESDAY - May 16, 2012

8:00am - 5:00pm
Registration (Concourse Room)
9:00am - 10:00am
Keynote 1
...................................
Learning Population Histories from Genome Variation Data

Russell Schwartz, Professor
Department of Biological Sciences
and Lane Center for Computational Biology
Carnegie Mellon University
Pittsburgh, PA - USA
10:00am - 10:10am  Break
10:10am - 10:30am
Mendelssohn Theatre
...................................
Industry Track 3
Compendia Bioscience
10:30am - 12:00pm
Mendelssohn Theatre 
...................................
WA1 Oral Presentations
Gene Regulations and Transcriptiomics

Session Chair:  Shin-Han Shiu, Michigan State University

OP1, OP2, OP3, OP4, OP5, OP6
10:30am - 12:00pm
Hussey Room
...................................
WA2 Oral Presentations
Protein Structure & Function, Databases and Ontologies

Session Chair:  Laura Brown, Michigan Technological University

OP7, OP8, OP9, OP10, OP11, OP12
12:00pm - 1:30pm  Lunch Break (lunch on own)
1:30pm - 2:30pm
Keynote 2
...................................
Pathogen Diversity from an Ecological Perspective

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
2:30pm - 4:00pm
Mendelssohn Theatre
...................................
WP1 Oral Presentations
Evolution & Comp. Genomics, Population Genomics

Session Chair:  Helen Piontkivska, Kent State University

OP13, OP14, OP15, OP16, OP17, OP18
2:30pm - 4:00pm
Hussey Room
...................................
WP2 Oral Presentations
Protein Interaction and Molecular Networks, Metagenomics

Session Chair:  Madhavi Ganapathiraju, University of Pittsburgh

OP19, OP20, OP21, OP21, OP23, OP24
4:00pm - 4:15pm  Break
4:15pm - 5:15pm
Mendelssohn Theatre
...................................
S1 - Special Session
Proteins in Motion:
Computational Studies in Protein Flexibility and Dynamics
 
The knowledge of the dynamics and flexibility of protein structure is critical for understanding how proteins perform their functions. In recent years computational modeling of protein flexibility and dynamics has emerged and gained momentum. This modeling finds applications in various important areas, including modeling and prediction of protein disorder, protein-drug interactions, investigations of structure-function relationships, and modeling of folding and unfolding of proteins. These timely topics will be addressed in our special session.
 
Organized by Daisuke Kihara & Lukasz Kurgan

DESCRIPTION: The session addresses emerging developments concerning computational methods for elucidating protein flexibility and dynamics. These methods find applications in functional studies of proteins in various areas, including protein disorder, folding and unfolding of proteins, protein-drug interactions, and structure-function relationships focusing on ligand recognition.

SPEAKERS (order of the presentations):
  1. How to Mine Protein Flexibility for Inhibitor Selectivity
    Leslie Kuhn

    Department of Biochemistry & Molecular Biology
    Computer Science & Engineering
    Michigan State University

  2. Biomolecular Motors and Switches: From Machines to Drugs
    Barry Grant

    Department of Computational Medicine & Bioinformatics
    University of Michigan

  3. Disorder in Proteins: Current Characterization Efforts
    Lukasz Kurgan
    Department of Electrical and Computer Engineering
    University of Alberta, Canada

  4. Prediction of Real-Value Fluctuation of Proteins Using Static Structural Features
    Daisuke Kihara

    Department of Biological Sciences
    Computer Science
    Purdue University

4:15pm - 5:15pm
Hussey Room
...................................
S2 - Special Session
Computational Proteomics: Understanding Network Perturbations in Cancer

Organized by Rob M Ewing

>>Agenda Attached (.pdf)<<

DESCRIPTION: Interaction proteomics approaches are generating large-scale interaction maps, leading to new biological problems and computational challenges. This session will highlight analyticaland computational developments in the field of interaction proteomics and how these techniques may be applied to understanding interaction networks in cancer cells.

SPEAKERS:

  1. Rob M. Ewing, Center for Proteomics and Bioinformatics
    Case Western Reserve University
  2. Alejando Balbin, Department of Pathology
    University of Michigan Health System
  3. Mehmet Koyuturk, Electrical Engineering and Computer Science,  Case Western Reserve University

5:15pm - 7:15pm  Poster Session B and Reception

Poster Session List by Last Name
Poster Session List by Number

7:30pm - 8:30pm
UMICH Museum Art Viewing
...................................
8:30pm to 10:00pm
Dinner and Keynote 3 
...................................
Designing Bioinformatics for the Wetware.  Usability Challenges with Massive Amounts of Data.

Howard Cash, President
Gene Codes Corporation
Gene Codes Forensics, Inc.
Ann Arbor, MI - USA
 

-->  THURSDAY - May 17, 2012

8:00am - 12:00pm
Registration (Concourse Room)
9:00am - 10:00am
Mendelssohn Theatre
...................................
S3 - Special Session
Creating Teams for Bioinformatics - The educational challenge for biology and computer science at the undergraduate and graduate level: Four case studies from the Great Lakes area

Organized by Guenter Tusch

DESCRIPTION: The panel will explore the state of art of bioinformatics education in the Great Lakes Region by investigating different approaches at the undergraduate and graduate level under the aspect of future team building in research or industry.

SPEAKERS:
  1. Robert Blumenthal, Ph.D., Department of Medical Microbiology & Immunology, Director of the Program in Bioinformatics& Proteomics/Genomics, College of Medicine, University of Toledo
  2. Sorin Draghici. Ph.D., Endowed Chair in Systems Biology - Department of Obstetrics and Gynecology, Clinical and Translational Science, & Computer Science, Wayne State University
  3. Neocles Leontis, Ph.D., Department of Chemistry, Bowling Green State University
  4. Russell Schwartz, Ph.D., Department of Biological Sciences and Lane Center for Computational Biology, Carnegie Mellon University
9:00am - 10:00am
Hussey Room
Ohio Bioinformatics Consortium Meeting
10:00am - 10:15am Break
10:15am - 12:00pm
Mendelssohn Theatre
...................................
RA1 Oral Presentations - Sequence Analysis

Session Chair: 
TBA

OP25, OP26, OP27, OP28, OP29, OP30, OP31

10:15am - 12:00pm
Hussey Room
...................................
RA2 Oral Presentations
Algorithm & Machine Learning, Bioimaging, Disease Models & Epidemiology

Session Chair: 
Guenther Tusch, Grand Valley State University

OP32, OP33, OP34, OP35, OP36, OP37, OP38

12:00pm -1:00pm
Keynote 4

...................................
Mutation, Drift, and the Evolution of Subcellular Features

Michael Lynch, Professor

Department of Biology
Indiana University
Bloomington, IN  USA
1:00pm - 1:15pm Adjourn
 
go directly to: [TOP] [Wednesday - May 16] [Thursday - May 17]

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

Program Committee

Updated December 14, 2011

Gerald Alter, Wright State University
Takis Benos, University of Pittsburgh
C. Titus Brown, Michigan State University
Laura Brown, Michigan Technological University
Jake Chen, Indiana University-Purdue University Indianapolis
Alan Dombkowski, Wayne State University
Zhong-Hui Duan, University of Akron
Kyle Furge, Van Andel Institute (VAI)
Madhavi Ganapathiraju, University of Pittsburgh
Elodie Ghedin, University of Pittsburgh
Xiaoxu Han, Eastern Michigan University
Paul Harrison, McGill University
Jeremy Hennig, University of Alberta
H. V. Jagadish, U of Michigan
Chandrashenkhar Joshi, Michigan Technological University
Hyun Min Kang, University of Michigan
Seyoung Kim, Carnegie Mellon University
Brian King, Bucknell University
Steve Krawetz, Wayne State University
Leslie A. Kuhn, Michigan State University
H.K. Kwan, University of Windsor
Chris Langmead, Carnegie Mellon University
Chun Liang, Miami University
David Liebovitz, Northwestern University
Nina Lin, University of Michigan
Richard Maclin, University of Minnesota,  Duluth
Chris Maher, Washington U in St Louis
Folker Meyer, Argonne National Laboratory
John Moran, University of Michigan
Helen Piontkivska, Kent State University
Timothy Pletcher, Central Michigan University
Sridhar Ramachandran, Indiana University Southeast
Gustavo Rohde, Carnegie Mellon University
Patrick Schloss, University of Michigan
David Sept, University of Michigan
Shin-Han Shiu, Michigan State University
Jinshan Tang, Michigan Technological University
Guenter Tusch, Grand Valley State University
KP Unnikrishnan, University of Michigan
Hairong Wei, Michigan Technological University
Peter White, Temple University
Elizabeth Worthey, Medical College of Wisconsin
Ji Zhu, University of Michigan

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 McKayThis email address is being protected from spambots. You need JavaScript enabled to view it.
Stephanie HagstromThis 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:

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .



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 Sciences
School 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)

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Great Lakes Bioinformatics Conference 2012

Sponsorship Opportunities

Updated February 06, 2012

This is your organization’s opportunity to become a prominent sponsor of the International Society for Computational Biology’s Great Lakes Bioinformatics Conference (GLBIO 2012)!

To participate in GLBIO 2012 please contact Stephanie Hagstrom at This email address is being protected from spambots. You need JavaScript enabled to view it..

Why you should become a sponsor
GLBIO has established a strong reputation for building relationships among a nationally prominent bioscience research community, showcasing the North American Great Lakes region as a perfect place to conduct computer-aided research in the life sciences.

Every year, the conference organizers prepare a full agenda on the latest developments in bioinformatics and biologically relevant applications. From novice to expert, attendees partake in a variety of workshops, tutorials, presentations, posters, networking, and exhibits during the conference. Your organization can play a visible role in GLBIO as attendees consider and work toward solutions to important scientific and medical problems being addressed by the bioinformatics community.

Please visit www.iscb.org/glbio2012 or contact Stephanie Hagstrom This email address is being protected from spambots. You need JavaScript enabled to view it. to become a sponsor.

Register to attend today!


SPONSOR AND EXHIBITOR INFORMATION

SPONSORSHIP LEVELS

$10,000 Platinum Sponsorship includes:
  • Four complimentary conference registrations
  • Company logo on conference Padfolio provided to all attendees
    (logo must be received by April 1, 2012)
  • Exclusive Named Sponsor of a Poster Session
  • Exhibit table in preferred location at Poster Sessions
  • Company logo on the conference website identified as Platinum Sponsor
  • Company name in the conference booklet identified as a Platinum Sponsor
  • Full-page black and white advertisement in program booklet
    (ad must be received by April 1, 2012)
  • Logo slide at opening session
  • Company name included on signage in registration area and poster area
  • One company brochure or marketing piece inserted in conference handouts
$7,500 Gold Sponsorship includes:
  • Three complimentary conference registrations
  • Named Sponsor of a Coffee Break
  • Exhibit table at Poster Sessions
  • Half-page black and white advertisement in program booklet
    (ad must be received by April 1, 2012)
  • Company logo on the conference website identified as a Gold Sponsor
  • Company name in the conference booklet identified as a Gold Sponsor
  • Logo slide at opening session
  • Company name included on signage in registration area
  • One company flyer inserted in the conference handouts
$5,000 Silver Sponsorship includes:
  • Two complimentary conference registrations
  • Exhibit table at Poster Sessions
  • Business card size black and white advertisement in program booklet
    (ad must be received by April 1, 2012)
  • Company logo on the conference website identified as a Silver Sponsor
  • Company name in the conference booklet identified as a Silver Sponsor
  • Logo slide at opening session
  • Company name included on signage in registration area
  • One company flyer inserted in the conference handouts
$2,000 Bronze Sponsorship includes:
  • One complimentary conference registration
  • Exhibit table at Poster Sessions
  • Company logo on the conference website identified as a Bronze Sponsor
  • Company name in the conference booklet identified as a Bronze Sponsor
  • Logo slide at opening session
  • Company name included on signage in registration area
$2,000 Industry Track Sponsorship includes:
  • One complimentary conference registration
  • 20 minute presentation (15 minutes presentation and 5 minutes Q&A) in the industry track on the Conference Agenda
  • Company logo on the conference website identified as an Industry Track Sponsor
  • Company name in the conference booklet identified as an Industry Sponsor
  • Logo slide at opening session
  • Company name included on signage in registration area
$1,000 Ruby Sponsorship includes:
  • Named Sponsor of a Keynote Speaker or Coffee Break
  • Company logo on the conference website identified as a Ruby Sponsor
  • Company name in the conference booklet identified as a Ruby Sponsor
  • Logo slide at opening session
  • Company name included on signage in registration area
$1,000 Exhibitor includes:
  • Exhibit table at Poster Sessions with two exhibit-area-only passes
  • Company logo on the conference website identified as an Exhibitor
  • Company name in the conference booklet identified as an Exhibitor
$250.00 Publisher Table includes:
  • 6’ table in registration area
  • Company name listed on the website and printed materials
OTHER SPONSORSHIP OPPORTUNITIES:
Company name will be included on signage, website and printed materials for the following:
  • $10,000 – Exclusive Banquet Sponsor (includes all Platinum level benefits except Padfolio logo placement and poster session sponsorship)
  • $1,600 – Conference Padfolios (provided to all attendees)
  • $500 and above – Sponsor a Student Travel Fellowship

Past sponsors include: Cincinnati Children’s Hospital Medical Center, Ohio University Edison Biotechnology Institute, BioOhio, Kent State University, Miami University, The Ohio State University, Ohio University, IBM, Procter & Gamble, Wittenberg University, Wright State University, Case Comprehensive Cancer Center, Diagnostic Hybrids, Mathworks, University of Akron, Agilent Technologies, International Society for Computational Biology, Ohio Supercomputer Center, University of Michigan, Genomatix Software

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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.

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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.

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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.

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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.

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