Bio IT World Expo 2016  
Bio IT World Expo 2016
2014 Archived Content

Cancer Informatics 

Track 12 explores the informatics trends and challenges in cancer research and care. Topics will cover data access, analysis, integration, management, and application for biological interpretation to aid in research at the benchside or care at the bedside.

Final Agenda

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7:00 am Workshop Registration and Morning Coffee

8:00 - 11:30 Morning Pre-Conference Workshops*

12:30 - 4:00 pm Afternoon Pre-Conference Workshops*

*Separate Registration Required. Click here for detailed information.

2:00 - 7:00 pm Main Conference Registration

4:00 Event Chairperson's Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute


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5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing




7:00 am Registration Open and Morning Coffee

8:00 Chairperson's Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute


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9:00 Benjamin Franklin Award & Laureate Presentation

9:30 Best Practices Awards Program

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

Collaborating in Chronic and Rare Diseases  

10:50 Chairperson's Remarks

Marcia Kean, Chairman, Strategic Initiatives, Feinstein Kean Healthcare

11:00 PANEL DISCUSSION: Patient-Powered Research Networks: Surge in the War against MS and other Diseases

Marcia Kean, Chairman, Strategic Initiatives, Feinstein Kean Healthcare

Kenneth Buetow, Ph.D., Director of Computational Sciences and Informatics, Complex Adaptive Systems Initiative (CASI), Arizona State University

Dave King, Founder and CEO, Exaptive, Inc.

Joe Laferrera, Partner, J.D., Gesmer Updegrove LLP

Sara Loud, MSEE, MBA, Repository and Operations Director, Accelerated Cure Project for Multiple Sclerosis

Driven by increasing consumer demand for knowledge, as well as the mandate of the Patient-Centered Outcomes Research Institute (PCORI), a new model for collection, integration, aggregation and analysis of data is emerging in which the patient is central. With an award from PCORI, the Accelerated Cure Project for MS, with its members and partners, are launching the iConquerMS portal for such patient empowerment, to speed and enhance research into MS and then to apply the model to other neurological diseases.  

12:00 pm Co-Presentation: Collaboration to Support Translational Research to Transform R&D

Hongyue Dai, Ph.D., Chief Bioinformatics Officer, M2Gen

Asif Dhar, Ph.D., M.D., Executive Vice President Solutions, ConvergeHEALTH by Deloitte

Join M2Gen and Deloitte as they discuss their collaboration to support personalized medicine and review case studies leveraging informatics to transform the industry.

12:15 Analysis of TCGA Data with User-Friendly Tools for Cancer Genomics
M. Michael Barmada, Ph.D., Associate Professor, Human Genetics and Biomedical Informatics, University of Pittsburgh 
Next-generation sequencing enables cancer researchers to identify biomarker, which can be used as new drug targets, prognosis, and diagnosis. However, facilitating the data analysis in a user-friendly way is still a bottleneck. Here we present the analysis of TCGA data using an intuitive and customizable software solution as an example for rapid and accurate interpretation of advanced NGS sequencing data.  

12:40 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

Modeling: Cancer 

1:50 Chairperson's Remarks

Hugo Geerts, Ph.D., MBA, BA, CSO, In Silico Biosciences; Adjunct Associate Professor, Perelman School of Medicine, University of Pennsylvania



Identifying Drug Targets from Drug-Induced Changes in Genome-Wide mRNA Expression

AviMa'ayanAvi Ma’ayan, Ph.D., Associate Professor, Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai

We collected and organized publicly available genome-wide gene expression data where hundreds of drugs were used to treat mammalian cells and changes in expression were compared to a control. We then developed computational methods that try to find the drug targets from the expression changes. We show that different steps in the analysis can contribute to approaching the right answer.

2:25 Tools for Comparison of Systematically Generated Cancer Networks vs. Literature Models

Dexter Pratt, Project Director, NDEx, Cytoscape Consortium

Cancer subtype genetic networks can be generated by systematic analysis of patient somatic mutation data. Comparison to existing models of cancer mechanisms is an important step in investigating these data-derived models. Recent work on Network Based Stratification (NBS) at the Ideker Lab will be described along with tools for network comparison under development in the NDEx project.

2:55 Integration of Text Mining and High Throughput Screening to Identify Candidate Targets for Cancer Therapy: Focus on the Autophagy Pathway

Philip L. Lorenzi, M.D., Anderson Cancer Center
Autophagy, a programmed process in which cell contents are delivered to lysosomes for degradation, appears to have both tumor-suppressive and tumor-promoting functions; both stimulation and inhibition of autophagy have been reported to induce cancer cell death, and particular genes and proteins have been associated both positively and negatively with autophagy. To provide a basis for incisive analysis of those complexities and ambiguities and to guide development of new autophagy-targeted treatments for cancer, we have compiled a comprehensive, curated inventory of autophagy modulators by integrating information from published siRNA screens, multiple pathway analysis algorithms, and extensive text-mining of the literature. The resulting inventory includes739 proteins and 385 chemicals (including drugs, small molecules, and metabolites). Because autophagy is still at an early stage of investigation, we provide extensive analysis of our sources of information and their complex relationships with each other. We conclude with a discussion of novel strategies that could potentially be used to target autophagy for cancer therapy. 

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing

4:00 Using Multiscale Systems Modeling to Design and Develop New Protein Therapeutics

Matthew Onsum, Ph.D., President, Silver Creek Pharmaceuticals

In this talk, I will present an approach to building multiscale systems models that capture drug pharmacokinetics and their effects on cell-signaling networks. I will then present two case studies that illustrate how these models can be used to design new therapies.

4:30 Biomarker Discovery to Predict Antitumor Activity through Systems Pharmacology in Drug Development and Cancer Therapy

Yasuhiro Funahashi, Ph.D., Senior Director, Biomarkers and Personalized Medicine Core Function Unit, Eisai, Inc.

NGS promotes molecular profiling of cancer and provides novel gene alterations to be targeted. But many cancer types cannot be caused by a single driver gene. A systematic approach based on pharmacology data combining PD and PG will be effective to identify biomarkers for anticancer agents targeting tumor microenvironments like angiogenesis inhibitors and chemotherapeutic agents.

5:00 A Pharmacogenomic View of the NCI-60 Cell Lines and Beyond

Ogan D. Abaan, Ph.D., Research Fellow, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH)

In this talk, we will present findings from our next-generation sequencing efforts using the NCI-60 cell lines and the pharmacogenomic data we have generated. In addition, we will discuss some new directions we have taken to mine the sequence data.

5:30 - 6:30 Best of Show Awards Reception in the Exhibit Hall


7:00 am Registration Open

7:00 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Vice President Business Development & Publisher C&EN, American Chemical Society; Founding Editor, Bio-IT World


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10:00 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

Bioinformatics across Multiple Research Initiatives 

10:30 Chairperson's Opening Remarks
Subha Madhavan, Ph.D., Director, Innovation Center for Biomedical Informatics, Oncology, Georgetown University 

10:35 Analysis of Genomics Data in an Internal Cloud Computing Environment

Philip Groth, Ph.D., IT Business Partner Genomics, R&D IT - Research, Bayer HealthCare

We have developed vCloud, an in-house cloud solution, which we have successfully deployed an analysis pipeline for Copy Number calculations and a recently published prediction algorithm for novel fusion proteins in cancer. This talk presents the technical set-up of vCloud, maintenance and running an internal cloud-computing environment, and how this set-up enables fast & secure analysis of large-scale genomics data. Results of analyzing genomic data from over 4,000 cancer patients will be presented.

11:05 Genome-Wide Multi-Omics Profiling of Colorectal Cancer Identifies Immune Determinants Strongly Associated with Relapse

Subha Madhavan, Ph.D., Director, Innovation Center for Biomedical Informatics, Oncology, Georgetown University

This presentation demonstrates the use of novel informatics methods and data integration approaches in identifying prognostic markers of cancer. The use and benefit of adjuvant chemotherapy to treat patients with state II colorectal cancer (CRC) is not well understood since the majority of these patients are cured by surgery alone. Identification of biological markers of relapse is a critical challenge to effectively target treatments to the ~20% of patients destined to relapse.

11:35 Sponsored Presentations (Opportunities Available)

12:15 pm Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

1:15 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing

Integrating Genomics into the Clinic  

1:55 Chairperson's Remarks
John Quackenbush, CEO, Genospace; Professor, Dana-Farber Cancer Institute and Harvard School of Public Health 

2:00 Enterprise-Wide Support for Individualized Treatment at a Cancer Center: Dana-Farber’s Profile Project

Barrett J. Rollins, M.D., Ph.D., CSO, Dana-Farber Cancer Institute; Linde Family Professor of Medicine, Harvard Medical School

Bringing the promise of precision medicine to cancer patients requires overcoming scientific and operational impediments. Dana-Farber Cancer Institute’s Profile project attempts to address these problems. It seeks to obtain broad genetic profiles on every patient who visits our hospital, link the data to their clinical information and make it available for research and clinical care.

2:30 PANEL DISCUSSION: From Data to Knowledge, from Research to Care – Meeting the Challenges of Genomic Medicine

Moderator: John Quackenbush, CEO, Genospace; Professor, Dana-Farber Cancer Institute and Harvard School of Public Health

Walter M. Capone, President, Multiple Myeloma Research Foundation

Andy Corts, Chief Information Officer, Sarah Cannon Research Institute

Pranil Chandra, DO, FCAP, FASCP, Director, Molecular Pathology Services, PathGroup

Joe Donahue, Senior Vice President, Thomson Reuters 

While delivering actionable personalized medicine reports to physicians seems, on the surface, like a relatively straight-forward exercise, there are many stakeholders who play a role in making the endeavor successful. Key elements in building a truly successful program include collecting and managing clinical and genomic data, integrating these in a decision support system, creating an appropriate knowledgebase to support data interpretation, and effectively delivering the data at the point of care. This panel brings together representatives from GenoSpace, Sarah Cannon Research Institute, Multiple Myeloma Research Foundation, PathGroup, and Thomson Reuters to discuss strategies to meet the challenges of genomic medicine.

4:00 Conference Adjourns

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  • Making the World's Knowledge Computable
  • Bioinformatics in the Cloud
  • The Application of Text Analytics to Drug Safety Surveillance

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