NCIBI Presentations

August 10 – Cytoscape Training Class
University of Michigan, Taubman Health Sciences Library

• M Brandenburg
  Cytoscape Training Class

 

July 15-19 – ISMB/ECCB 2011
Vienna, Austria
http://www.iscb.org/ismbeccb2011

• B Mirel, E Eichinger
  Gaining knowledge and coherence from complex  networks and interctive activity trails.

 

June 28-29 – NCIBI/RCMI Annual Research Meeting
University of Michigan
http://portal.ncibi.org/gateway/arm2011.html

 

May 2-4 – Great Lakes Bioinformatics Conference
Ohio University
http://www.ohiobioinformaticsconsortium.org/occbio/GL2011/

 

April 22 – Workshop on Data, Text, Web, & Social Network Mining
University of Michigan

• D Radev
  Tools for Natural Language Processing and Text Mining
• KP Unnikrishnan
  Network Discovery in Biology and Medicine through Data Mining

 

March 18 – Remote Training
University of Michigan

• M Brandenburg
  Cytoscape Remote Training

 

March 8 – Fredrick, Maryland
National Cancer Institute

• M Brandenburg
  Cytoscape and Other NCIBI Resources

 

March 7-11 - San Francisco, California
American Medical Informatics Association (AMIA) 
http://jointsummits2011.amia.org/

October 26 – Detroit, Michigan
Wayne State University

• KP Unnikrishnan
  Data Mining for Network Discovery in Biology and Medecine

 

October 21-23 – Chicago, Illinois
2010 Midwest Association of Core Directors Meeting

• J. Cavalcoli
  Panel Discussion: Bioinformatics Issues

 

September 22 – Ann Arbor, Michigan
Center for Computational Medicine and Bioinformatics (CCMB) Seminar Series

• KP Unnikrishnan
  Network Discovery in Biology and Medicine through Data Mining

 

August 23-27  – Beijing, China
23rd International Conference on Computational Linguistics

• V. Qazvinian, D. Radev, and A. Ozgur
  Citation Summarization Through Keyphrase Extraction

 

August 12-13  – New York, New York
National VIVO Conference

• B. Athey
  Collexis and VIVO: Paving the Collexis Pathway to the National Research Network

 

July  29-30  – Ann Arbor, Michigan
NCIBI/RCMI Summer Workshop on Translational Bioinformatics

• B. Athey
  Translational Infromatics 2010: Catching the Wave
• H.V. Jagadeish
  Overview of NCIBI Tools
• Charles Burant
  Metabolomics Introduction

 

July  26-28  – Toronto, Canada
CMM Brain Neuromechanics Workshop

• KP Unnikrishnan
  Graph Discovery in Neuronal Networks

 

July 18-20 – Ann Arbor, Michigan
Cytoscape Consortium Summer Retreat

• B. Athey
  CTSA Biomedical Informatics as a Means to Leverage Local and National Resources to Improve Clinical Research and Translational Effectiveness
• M. Brandenburg and Jean Song
  How to Use Cytoscape: Training the User
• B. Mirel
  Mapping complex cognitive tasks to user requirements
• G. Su
  Cytoscape plug-ins: GLay v.2 and GSearcher
• T. Weymouth
  The Cytoscape MiMI Plugin with the NCIBI/MiMI Attribute Browser

 

July  11-13  – Boston, Massachusetts
ISMB

• J. Cavalcoli
  Using the NCIBI Suite of Integrated Tools and Data

 

July  9-10  – Boston, Massachusetts
ISMB - Bio-Ontologies 2010: Semantic Applications in Life Sciences SIG

• A. Ozgur, D. Radev, and Y. He
  Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology

 

June 29 – Sacramento, California
UC Davis Annual Retreat

• B. Athey
  CTSA Biomedical Informatics as a means to leverage local and national resources and capabilities to improve clinical research and translational effectiveness

 

June 25-28 – Munich, Germany
ERA-EDTA Congress

• M. Kretzler
  Integration of Multidimensional Data Sets in Renal Disease

 

May 21-26, 2010 – Washington, DC
Medical Library Association Annual Meeting

• M. Conte, J. Song, W. Townsend
  Research by the Numbers: Assessing the Performance of Three Products for Citation Analysis.
• M. Brandenburg, J. Song
  Collaborative Teaching: Bridging Geography and Organizations.
• M. Conte, J. Song
  Assessing Institutional Compliance with the National Institutes of Health Public Access Policy.
• J. Song, M. Conte
  Developing and Promitng a University Library’s E-science Presence through an Interlibrary Collaborative Working Group.

May 10-14, 2010 – Boston, Massachusetts
NetSci 2010 Symposium

• B. Mirel
  Building Networks to Facilitate Task-switching and Metacognition in Complex Analysis

 

April 24-28, 2010 – Anaheim, California
ASIP Annual Meeting at Experimental Biology

• A. Chinnaiyan, C. Maher
  Adventures in Translational Pathology

 

April 21, 2010 - Los Angeles, California
UCLA-Pediatric Nephrology Grand Rounds

• M. Kretzler
  Molecular Classification of Lupus Nephritis

 

April 20, 2010 - Los Angeles, California
UCLA-Cedar Sinai

• M. Kretzler
  Translational Research in Glomerular Disease

 

April 19, 2010 - Los Angeles, California
UCLA Harbor View Research Seminar

• M. Kretzler
  Systems Biology of Glomerular Disease

 

April 19, 2010 - Los Angeles, California
UCLA Harbor View Renal Grand Rounds

• M. Kretzler
  Molecular Classification of IgA Nephritis

 

April 18, 2010 - Los Angeles, California
Western Society of Pediatric Nephrology

• M. Kretzler
  The new pathology using molecular signatures

 

April 16, 2010 - Kyoto, Japan
ISN Nexus

• M. Kretzler
  Therapeutic impact on glomerular capillary failure: an interactive biology perspective.

 

April 14, 2010 - Nagoya, Japan
Special Nephrology Seminar, Nagoya School of Medicine

• M. Kretzler
  Integrative systems biology of glomerular disease.

 

April 13, 2010 - Alexandrina, Egypt
Bibliotheca

• G. Omenn, R. Menon
  Advances in Proteomic Profiling of Cancers: Alternative Splice Variants as a New Class of Cancer Biomarker Candidates
  

 

March 30, 2010 - Chicago, Illinois
University of Illinois at Chicago, Renal Grand Rounds

• M. Kretzler
  Towards molecular medicine of renal disease

 

March 25, 2010 – Victoria, British Columbia, Canada
Keystone Symposia on Molecular and Cellular Biology-New Paradigms in Cancer Therapeutics

• A.Chinnaiyan
  Targeting Gene Fusions in Prostate Cancer

 

March 23, 2010 – China
Peking Union Medical Collage

• G. Omenn - Download PDF
  Computational Medicine and Bioinformatics at the University of Michigan

 

March 12-13, 2010 - San Francisco, California
American Medical Informatics Association (AMIA)
Summit on Clinical Research Informatics
http://crisummit2010.amia.org/

• B. Mirel, Z. Wright, J. Tenenbaurm, P. Saxman, K. Smith
  User Requirements for Exploring a Resource Inventory for Clinical Research

 

March 10-12, 2010 - San Francisco, California
American Medical Informatics Association (AMIA)
Summit on Translational Bioinformatics
http://summit2010.amia.org/

Panel Discussions

• M. Musen, B. Athey
  National Centers for Biomedical Computing (NCBC) and Translational Bioinformatics: National Center for Biomedical Ontology (NCBO) and National Center for Integrative Biomedical Informatics (NCIBI)

 

Paper Presentations

• X. Wang, J. Prensner, G. Chen, Q. Cao, B. Han, S. Dhanasekaran, R. Ponnala, X. Cao, S. Varambally, D. Thomas, T. Giordano, D. Beer, N. Palanisamy, M. Sartor, G. Omenn, A. Chinnaiyan An Integrative Approach to Reveal Driver Gene Fusions from Paired-End Sequencing Data in Cancer
• J. Cavalcoli, A. Ade, B. Mirel, H.V. Jagadish, G. Omenn, B. Athey
  NCIBI NLP Tools: Foundation for Integration

 

Poster Presentations

• CTSA Inventory Resource Web Presence (CIRWP)
  T. Morris, C. Borromeo, B. Kirschner, H. Singh, J. Tenenbaum, N. Whelan, D. Gabriel, K. Anderson, T. Whetzel, C. Nyulas, B. Mirel, P. Saxman, Z. Wright, P. Boisvert, D. Rubin, B. Athey, M. Becich, K. Smith
• Developing a Disease-Centric View of Metabolic Networks
  A. Karnovsky, G. Omenn
• Exploring the Use of 3D Layouts to Analyze Disease-gene Networks
  S. Bhavnani, A. Ganesan, T. Hall, E. Maslowski, F. Eichinger, S. Martini, P. Saxman, C. Scott, M. Kretzler
• Visual Cues for Comprehending Complex Annotations of Molecular Networks
  B. Keller, N. Ramakrishnan, M. Zaki
• A Web Service to Retrieve Natural Language Processing Data Derived from Literature in PubMed and PubMed Central
  A. Ade, Z. Wright, J. Cavalcoli, H.V. Jagadish

 

March 12, 2010 – Miami Beach, Florida
Pediatric Nephrology Seminar

• M. Kretzler
  Systems Biology of Glomerular Disease

 

March 9, 2010 – Vienna, Austria
Symposium: Systems Biology of Kidney Disease

• M. Kretzler
  The Future of Applied Renal Research

 

February 25, 2010 – Sarasota, Florida
American Cancer Society Laureate Society

• A.Chinnaiyan
  Zeroing in on the Cause of Prostate Cancer

 

March 25, 2010 – Victoria, British Columbia, Canada
Keystone Symposia on Molecular and Cellular Biology-New Paradigms in Cancer Therapeutics

• A.Chinnaiyan
  Targeting Gene Fusions in Prostate Cancer

 

February 24-27, 2010 – Marco Island, Florida
Advances in Genome Biology and Technology (AGBT)

• C. Maher
  Transcriptome sequencing of ETS rearrangement negative prostate cancers reveals novel class of gene fusions.

 

February 23, 2010 - Durham, North Carolina
Duke University
NSF Workshop on HPC Center Sustainability

• B. Athey
  Integrative Biomedical Informatics at the Beginning of the 21st Century

 

February 17, 2010 – Chantilly, Virginia
Department of Defense Breast Cancer Research Program LINKS Meeting

• A.Chinnaiyan
  A Search for Gene Fusions/Translocations in Breast Cancer

 

January 25, 2010 – Miami, Florida
Internal Medicine Grand Rounds

• M. Kretzler
  Systems biology of diabetic microvascular complications

 

January 20-23, 2010 – San Juan, Puerto Rico
AACR Special Conference on Cancer Epigenetics

• Maureen A Sartor, Dana C. Dolinoy, Tamara Jones, Thomas E. Carey, Laura S. Rozek
  A Combined approach using the Illumina Infinium methylation27 beadarray and Affymetrix tiling chip set: Preliminary results illustrate methylation differences in HPV(+) and HPV(-) head and neck cancers
• A.Chinnaiyan
  Targeting Histone Modifiers in Cancers

 

January 15, 2010 – Wake Forest, North Carolina
Wake Forest University

• M. Kretzler
  Systems biology of diabetic nephropathy

 

January 12, 2010 – New Haven, Connecticut
Yale Cancer Center Grand Rounds

• A.Chinnaiyan
  The Next Generation of Gene Fusion Discovery in Cancer

December  10-12, 2009 - Aspen, Colorado
Annual Rocky Mountain Bioinformatics Conference
http://www.iscb.org/rocky09

• B. Keller, B. Mirel
  Strategies for Elaborating Cognitive Requirements of Bioinformatics Tools (Keynote address)

• A User Study of Attribute Visualization Tools and Their Role in Understanding Biological Networks
  H. Kucuk, B. Keller, T. Weymouth, B. Mirel

 

December 10, 2009 – Salt Lake City, Utah
Graduate Seminar for the Utah Department of Biomedical Informatics

• B. Athey
   Bioinformatics in the Age of Translational Medicine
  

 

October 13, 2009 – Bethesda, Maryland
The Annual P41 Directors Meeting

• B. Athey
  NCIBI – An NIH NCBC Resource to Enhance Basic and Translational Research
  

 

September 30, 2009 – Ann Arbor, Michigan
Center for Computational Medicine and Bioinformatics Seminar Series

• B. Athey
  The Relationship between Informatics and Biomedical Research & Education: Current and Future Perspectives

 

September 25-30, 2009 – Toronto, Canada
World Congress of Proteomics, Human Proteome Organization (HUPO)

• R. Menon
  Alternative Splice Variants in Cancers
• Karnovsky
  Metscape Tool for Visualizing Metabolomics

 

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

• Workshop on NCIBI Tools and Resources
  J. Athanikar J, V. G. 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. More information

 

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

• NCIBI Tools Workshop
  M. Conte, J.  Song

 

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

• B. Mirel, Z. Wright - Download PDF
  Heuristic Evaluations of Bioinformatics Tools: A Development Case
  

 

July 13, 2009 - Las Vegas, Nevada
WORLDCOMP 2009

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

 

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

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

 

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

• B. Athey
  Keeping up with Bioinformatics and Computational Biology as applied to Biomedicine —
  Where has it been? Where is it going? (Keynote address)
  

 

March 15-17, 2009 - San Francisco, California
American Medical Informatics Association (AMIA)
Summit on Translational Bioinformatics
http://summit2009.amia.org/
Panel Discussions

• L. Hirschman, L. Hunter, Y. Lussier, D. States, C. Wu
  Capturing Knowledge that Spans the Translational Gap: What is Needed and Why?
  
• I. Kohane, K. Butter, D. Osterbur, J. Song, K. Holmes
  Library-Based Bioinformatics Support and Education Initiatives at Translational Research Centers

 

Paper Presentations

• P. Harrington, A. Rao, A. Hero
  Classification and Subspace Selection of Multiple Biomedical Time-Series via Ensemble Learning
• X. Wang
  Genomic-Scale Screening for Gene Fusions in Human Solid Tumors by Integrative Biomedical Informatics

• B. Mirel, , F. Eichinger, V. Nair, and M. Kretzler
  Integrating Automated Workflows, Human Intelligence and Collaboration
• J. Cavalcoli, Y. Ikeda, B. Mirel, H. Jagadish, G. Omenn, B. Athey
  Integrating Tools and Data using the NCIBI Suite of Tools

• 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
  Michigan Molecular Interactions r2: From Interacting Proteins to Pathways?
• S. Bhavnani, F. Eichinger, S. Martini, P. Saxman, M. Kretzler
  Network Analysis of Genes Regulated in Renal Diseases: Implications for a Molecular-Based Classification

 

Poster Presentations

• Bioinformatics Framework for the Analysis and Interpretation of Metabolomic Data
  A. Karnovsky, J. Gao, G. Tarcea, C. Beecher, C. Burant, B. Mirel, H.V. Jagadish, G. Omenn - Download PDF
• Design of Integrated Translational Bioinformatics Systems
  B. Mirel, B. Keller, M. Peleg, X. Cui, R. Altman - Download PDF
• Identification of Novel Alternative Splice Isoforms using Proteomic Informatics with a Modified ECGene Database
  R. Menon, D. States, G. Omenn - Download PDF

July 19-23, 2008 - Toronto, Ontario
ISMB 2008
SIG Presentations

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

 

Invited Plenary Presentation

• A. Özgür
  Identifying gene-disease associations based on centrality on a literature mined gene interaction network

 

Technology Track — Demonstration

• Working with NCBC's: Integrating Tools and Data - NCIBI Suite of Tools
  J. Cavalcoli

 

Poster Presentations

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

 

July 16-19, 2008 - Toronto, Ontario
Cytoscape Developer Retreat 2008
Demonstrations and Talks

• The Emerging Field of Translational Bioinformatics — A National Perspective (Keynote address)
  B. Athey
• Michigan and NCIBI
  D. States
• MiMI plugin
  J. Gao
• Normalizing Visualization with Hierarchical Community Structure
  G. Su
• Support for Multi-Dimensional Information Through Perceptual Encoding: Next Steps
  B. Mirel, T. Weymouth

 

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


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

• J. Patel
  Indexing for Success: Scaling to Handle the Increasing Volume and Complexity of Biological Databases (Keynote address)
  

 

Invited Plenary Presentations

• V. Strumba
  Analysis of cis regulation of gene expression in human brain
• T. Blackwell
  Bayesian analysis of gene expression microarrays
• G. Su
  Detecting Modularity in Biological Interaction Networks
• Y. Bai
  Hunting for Biological Relationships Among Selected Genes from Type 2 Diabetes Associated Regions in Humans

 

Poster Presentation

• Identification of gene networks of lithium treatment in bipolar disorder
  H. Chen

May 16-21, 2008 - Chicago, Illinois
Medical Library Association Annual Meeting

• M. Conte, J. Song, N. Glazer, B. Mirel, D. States
  MiSearch and PubMed: Assessing an Adaptive, Profile-based PubMed Search Tool

 

March 10-12, 2008 - San Francisco, California
AMIA Summit on Translational Bioinformatics
Panel Discussions

• D.States, A.Floratos, I. Kohane, M. Kretzler, G. Omenn
  High Data Dimensionality in Translational Bioinformatics
• R. Altman, B. Athey, A. Floratos, R. Kikinis, I. Kohane, M. Musen, A. Toga
  National Centers for Biomedical Computing
• B. Athey, M. Becich, M. Ellisman, J. Saltz
  Towards a set of Unified NIH Computational, Data, and Community Infrastructures to Support Translational Bioinformatics

 

Paper Presentations

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

 

Poster Presentations

• An Adaptive Tool for Biomedical Literature Retrieval
  D. States
• An Efficient Solution for Mapping Free Text to Ontology Terms
  M. Dai
• NIH National Center for Integrative Biomedical Informatics (NCIBI)
  J. Cavalcoli
• NCIBI Portal - Collaborative Biomedical Research Environment
  Y. Ikeda

 

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

• B. Athey
  “Integrative Biomedical Informatics"—What Has Been Done and What is Left to Do?

 

February 20, 2008
caGrid Roadmap Workshop — Columbus, Ohio
Invited Plenary Presentation

• B. Athey
  Application and Architectural Challenges in Basic, Clinical, and Translational Research (Panel)

November 27, 2007 — Rockville, Maryland
NIDA Genetics Consortium Meeting

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

 

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

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

 

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

• B. Athey, P. Woolf, M. Reich, T. Ideker
  Introduction to a Systems View of Biology, Toolbox for Systems Biology (Invited panel)

 

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

• B. Athey
  Interoperable Informatics Systems in Cancer Center Collaborative Networks (Invited Plenary Presentation)

 

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

• B. Athey
  The NIH National Center for Biomedical Informatics (NCIBI)--Integrating Biomedical Informatics: Overview and Collaborative Opportunities (Keynote address) 

 

October 1, 2007 — Boston, Massachusetts
Harvard Biomedical HPC Leadership Summit 2007

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

 

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

• B. Athey
  The NIH National Center for Biomedical Informatics (NCIBI)--Integrating Biomedical Informatics: Overview and Collaborative Opportunities (Keynote address)

 

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

• NCIBI Suite of Tools (Demonstration)
  T. Wiggin

 

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

• D. States
  Integrating Genomics and Proteomics: Using Mass Spectrometry to Annotate the Genomes (Keynote address)

 

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

• B. Athey
  The NIH National Center for Biomedical Informatics — Overview and Collaborative Opportunities

• B. Keller
  Identifying Hypothetical Genetic Influences in Complex Diseases

 

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

• B. Mirel
  Collaborative Research Portal by Participatory Design