External Presentations

August 18th, 2009 - Tallahassee, Florida
Florida A&M University

• Workshop on NCIBI Tools and Resources
  Jyoti Athanikar and Glenn Tarcea

July 29-30, 2009 - Ann Arbor, Michigan
NCIBI/RCMI: Workshop on Translational Bioinformatics

• NCIBI hosted a two-day workshop in translational bioinformatics for various Research Centers in Minority Institutions (RCMI) investigators. Participants received training in the use of NCIBI tools and resources for translational research. They also had the opportunity to learn about other programs at UM and network with UM and other RCMI researchers to build research relationships and collaborations. Click here for more information.

July 23rd, 2009 - Ann Arbor, Michigan
UM Health Sciences Library

• NCIBI Tools Workshop
  Marisa Conte and Jean Song

July 19-24, 2009 - San Diego, California
HCI International 2009

• Heuristic Evaluations of Bioinformatics Tools: A Development Case
  Barbara Mirel and Zach Wright - Download PDF

July 13th, 2009 - Las Vegas, Nevada
WORLDCOMP 2009

• HoIO & BIOCOMP'09 Keynote
  Data Explosion and Complexity in Bioinformatics (aka Cellular Systems Biology)
  Brian Athey - Download PDF
  

June 27th - July 2nd - Stockholm, Sweden
ISMB/ECCB 2009

• Technology Track: Using the NCIBI Suite of Integrated Tools and Data
  James Cavalcoli - Download PDF

March 18-19, 2009 - Las Vegas, Nevada
First Annual ORNL Biomedical Science and Engineering Conference

• Keeping up with Bioinformatics and Computational Biology as applied to Biomedicine —
  Where has it been? Where is it going?
  Keynote address by Brian Athey

March 15-17, 2009 - San Francisco, California
American Medical Informatics Association (AMIA)

Summit on Translational Bioinformatics
http://summit2009.amia.org/

• Michigan Molecular Interactions r2: From Interacting Proteins to Pathways?
  V. G. Tarcea, T. Weymouth, A. Ade, A. Bookvich, J. Gao, V. Mahavisno, Z. Wright, A. Chapman, M. Jayapandian, A. Özgür, Y. Tian, J. Cavalcoli, B. Mirel, J. Patel, D. Radev, B. Athey, D. States and H. V. Jagadish, University of Michigan
• Genomic-Scale Screening for Gene Fusions in Human Solid Tumors by Integrative Biomedical Informatics
  x. wang
• Identification of Novel Alternative Splice Isoforms using Proteomic Informatics with a Modified ECGene Database
  R. Menon; D. States; G. Omenn - Download PDF
• Integrating Tools and Data using the NCIBI Suite of Tools
  J. Cavalcoli; Y. Ikeda; B. Mirel; H. Jagadish; G. Omenn; B. Athey
• Classification and Subspace Selection of Multiple Biomedical Time-Series via Ensemble Learning
  P. Harrington; A. Rao; A. Hero
• Integrating Automated Workflows, Human Intelligence and Collaboration
  B. Mirel
• Capturing Knowledge that Spans the Translational Gap: What is Needed and Why?
  L. Hirschman; L. Hunter; Y. Lussier; D. States; C. W
• Network Analysis of Genes Regulated in Renal Diseases: Implications for a Molecular-Based Classification
  S. Bhavnani; F. Eichinger; S. Martini; P. Saxman; M. Kretzler
• Bioinformatics Framework for the Analysis and Interpretation of Metabolomic Data
  Alla Karnovsky, Jing Gao, Glenn Tarcea, Christopher Beecher, Charles Burant, Barbara Mirel, H.V. Jagadish, Gilbert S. Omenn - Download Poster
• Design of Integrated Translational Bioinformatics Systems
  Barbara Mirel, Benjamin Keller, Mor Peleg, Xiangqin Cui, Russ Altman - Download Poster

July 19-23, 2008 - Toronto, ON
ISMB 2008

SIG Presentations:

• Alternative Splicing SIG —
  "Detecting Alternative Splicing in Deep Sequencing Data"
  by Fan Meng
  
• BOSC SIG —
  "Use the Make Utility for the Maintenance of Complex Bioinformatics Pipelines"
  by Justin Wilson
  
• Next Generation Sequencing SIG —
  "PASS: A Fast Algorithm for Illumina/SOLiD Sequence Alignment with Guaranteed Recall"
  by Manhong Dai
  
• Bio-Ontologies SIG —
  "PubOnto: Open Biomedical Ontology-Based Medline Exploration"
  by Weijain Xuan
  

Invited Plenary Presentation:

• "Identifying gene-disease associations based on centrality on a literature mined gene interaction network"
  by Arzucan Ozgur
  

Technology Track — Demonstration:

• "Working with NCBC's: Integrating Tools and Data - NCIBI Suite of Tools"
  by Jim Cavalcoli
  
  

Poster Presentations:

• "Web-based literature mining tool for target identification and functional enrichment analysis"
  by Junguk Hur
  
• "NCIBI Portal - Collaborative Biomedical Research Environment" by Yuri Ikeda
  
• "Bridging experiments using integrative tools" by Jim Cavalcoli
  
• "Automated Literature Based Metabolome Annotation Using MeSH" by Zach Wright
  
• "Bayesian Reconstruction of ROS Detoxification Pathway in E. coli" by Andrew Hodges
  
• "High throughput sequence alignment with suffix arrays and q-grams" by Justin Wilson
  
• "A Cell Line Knowledgebase" by Sira Sarntivijai
  
• "Automated Literature Based Genome Annotation Using MeSH" by Alex Ade
  
• "Exploratory Analysis of Community Structure in Biological Interactions Networks" by Gang Su

July 16-19, 2008 - Toronto, ON
Cytoscape Developer Retreat 2008

Demonstrations and Talks:

• "Normalizing Visualization with Hierarchical Community Structure"
  byGang Su
  
• "Support for Multi-Dimensional Information Through Perceptual Encoding: Next Steps"
  by Barbara Mirel and Terry Weymouth
  
• "MiMI plugin"
  by Jing Gao
  
• "Michigan and NCIBI"
  by David States
• "The Emerging Field of Translational Bioinformatics — A National Perspective"
  Keynote Address by Brian Athey
  

 

June 2-3, 2008 - Las Vegas, NV
BIOCOMP'08
The 2008 International Conference on Bioinformatics & Computational Biology

2008 Ohio Collaborative Conference on Bioinformatics (OCCBIO)
Toledo, OH

Keynote Address:

• "Indexing for Success: Scaling to Handle the Increasing Volume and Complexity of Biological Databases"
  by Jignesh Patel

Invited Plenary Presentations:

• "Analysis of cis regulation of gene expression in human brain"
  by Viktoriya Strumba
• "Bayesian analysis of gene expression microarrays"
  by Tom Blackwell
• "Detecting Modularity in Biological Interaction Networks"
  by Gang Su
• "Hunting for Biological Relationships Among Selected Genes from Type 2 Diabetes Associated Regions in Humans"
  by Yongsheng Bai

Poster Presentation:

• "Identification of gene networks of lithium treatment in bipolar disorder"
  by Haiming Chen

March 10-12, 2008 - San Francisco, CA
AMIA Summit on Translational Bioinformatics

Panel Discussions:

• "National Centers for Biomedical Computing"
  by Russ Altman, Brian Athey, Aris Floratos, Ron Kikinis, Isaac Kohane, Mark Musen, and Arthur Toga
• "High Data Dimensionality in Translational Bioinformatics"
  by David States, Aris Floratos, Isaac Kohane, Matthias Kretzler, and Gilbert Omenn
• "Towards a set of Unified NIH Computational, Data, and Community Infrastructures to Support Translational Bioinformatics"
  by Brian Athey, Michael Becich, Mark Ellisman, and Joel Saltz
  

Paper Presentations:

• A Diagram Editor for Efficient Biomedical Knowledge Capture and Integration
  Fan Meng
  
• Identifying Hypothetical Genetic Influences on Complex Disease Phenotypes
  Benjamin Keller
  

Poster Presentations:

• NIH National Center for Integrative Biomedical Informatics (NCIBI)
  by James Cavalcoli

• NCIBI Portal - Collaborative Biomedical Research Environment
  by Yuri Ikeda
• An Efficient Solution for Mapping Free Text to Ontology Terms
  by Manhong Dai
• An Adaptive Tool for Biomedical Literature Retrieval
  by David States

Tuesday, March 4, 2008 — Cleveland, OH - Case Western Reserve University
Electrical Engineering and Computer Science Department Colloquium Seminar

• "Integrative Biomedical Informatics"—What Has Been Done and What is Left to Do?
  Invited Plenary Presentation by Brian Athey

Wednesday, February 20, 2008
caGrid Roadmap Workshop — Columbus, OH

• "Application and Architectural Challenges in Basic, Clinical, and Translational Research (Panel)."
  Invited Plenary Presentation by Brian Athey
  

 

Tuesday, November 27, 2007 — Rockville, MD
NIDA Genetics Consortium Meeting

• "Collaborate to Compete —An Introduction to the NIH National Center for Integrative Biomedical Informatics (NCIBI)."
  Invited Plenary Presentation by Brian Athey
  

Monday, November 5, 2007 — Washington, DC
Clinical Research Forum IT Roundtable

• "Digital Biomedical Research Driving IT Transformation at the University of Michigan Medical School and Health System — Preventative Medicine for Security Leaks."
  Invited Plenary Presentation by Brian Athey
  

Saturday, November 3, 2007 — San Francisco, CA
American Society of Nephrology (ASN) Annual Meeting

• "Introduction to a Systems View of Biology, Toolbox for Systems Biology"
  Invited Panel by Briant Athey, Peter Woolf, Michael Reich and Trey Ideker
  

Monday, October 29, 2007 — Washington, DC
Association of American Cancer Institutes (AACI) Annual Meeting

• "Interoperable Informatics Systems in Cancer Center Collaborative Networks."
  Invited Plenary Presentation by Brian Athey
  

Sunday, October 14, 2007 — Boston, MA
IEEE 7th International Symposium on Bioinformatics and Bioengineering (BIBE)

• "The NIH National Center for Biomedical Informatics (NCIBI)--Integrating Biomedical Informatics: Overview and Collaborative Opportunities."
  Keynote Address by Brian Athey
  

Monday, October 1, 2007 — Boston, MA
Harvard Biomedical HPC Leadership Summit 2007

• "Federating and Growing High Performance Computing and Data Environments to Support Research at the University of Michigan Medical School."
  Invited Plenary Presentation by Brian Athey
  

Wednesday, August 8, 2007 — Iowa City, IA
MSCCS 2007: Cyberinfrastructure-enabled Computational Science

• "The NIH National Center for Biomedical Informatics (NCIBI)--Integrating Biomedical Informatics: Overview and Collaborative Opportunities."
  Keynote Address by Brian Athey
  

Wednesday, July 25, 2007 — Vienna, Austria
ISMB/ECCB 2007

• "NCIBI Suite of Tools"
  Demo by Timothy Wiggin
  

Tuesday, July 10, 2007 — Oxford, Ohio
Ohio Collaborative Conference on Bioinformatics (OCCBIO) 2007

• "Integrating Genomics and Proteomics: Using Mass Spectrometry to Annotate the Genomes"
  Keynote Speech by David States
  

Thursday, May 31, 2007 — Indianapolis, Indiana
Indy Regional Bioinformatics Conference 2007

• "The NIH National Center for Biomedical Informatics — Overview and Collaborative Opportunities"
  Invited Talk by Brian Athey
  

Thursday, May 31, 2007 — Indianapolis, Indiana
Indy Regional Bioinformatics Conference 2007

• "Identifying Hypothetical Genetic Influences in Complex Diseases"
  Selected Abstract Presentation by Benjamin Keller
  

Wednesday, May 23, 2007 — Orlando, Florida
2007 AMIA Spring Congress

• "Collaborative Research Portal by Participatory Design"
  Presentation by Barbara Mirel