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Bioinformatics 

Final Agenda

TUESDAY, APRIL 24

7:00 am Workshop Registration and Morning Coffee

8:00 am - 4:00 pm Pre-Conference Workshops*

  • Leveraging Saas for Next-Gen Sequencing: Case Study with the Galaxy Community
  • Data Visualization in Biology: From the Basics to Big Data

*Separate Registration Required

2:00 - 7:00 pm Main Conference Registration

4:00 Event Chairperson's Opening Remarks

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

4:05 Keynote Introduction

Sanjay Joshi, Solutions Architect, Life Sciences, EMC Isilon Storage Division

 

4:15 PLENARY KEYNOTES 

Martin LeachMartin Leach, Ph.D., CIO, Broad Institute of MIT and Harvard

Jill MesirovJill P. Mesirov, Ph.D., Associate Director and Chief Informatics Officer; Director, Computational Biology and Bioinformatics, Broad Institute of MIT and Harvard


Hitachi Data Systems5:00 - 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Drop off a business card at the CHI Sales booth for a chance to win 1 of 2 iPod touches® or 1 of 2 Xbox 360s®*!

*Apple® is not a sponsor or participant in this program


 

WEDNESDAY, APRIL 25

7:00 am Registration and Morning Coffee

7:55 Chairperson's Opening Remarks

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

8:00 Keynote Introduction

Bas Burger, President, Global Commerce, BT Global Services

 

8:15 PLENARY KEYNOTE 

Eric PerakslisEric D. Perakslis, Ph.D., CIO and Chief Scientist of Informatics, U.S. Food and Drug Administration



8:45 Benjamin Franklin Award & Laureate Presentation

9:10 Best Practices Award Program

Cycle Computing small9:45 Coffee Break in the Exhibit Hall with Poster Viewing

 


DATA MODELING AND COMPUTATIONAL INTEGRATIVE TOOLS 

10:50 Chairperson's Remarks

William O'Neill, Ph.D., Professor, Bioengineering, University of Illinois at Chicago

11:00 Translational Integrity and Continuity: Individualized Biomedical Data Integration

Xiaoming Wang, Ph.D. Fellow, Computation Institute, University of Chicago and Argonne National Laboratory

This presentation describes an established warehousing system, translational data marts (TraM), to describe the impact of conceptual modeling on the system flexibility, sustainability, and scalability; data integration workflow efficiency; application capacity and performance; and data integrity and interoperability. An oncology data mart (ONCOD) will be used as an example to illustrate a lifecycle of a data warehousing system design.

11:30 Computational Statistical Image Modeling for Lesion Diagnosis and Classification

William O'Neill, Ph.D., Professor, Bioengineering, University of Illinois at Chicago

This presentation describes a method of diagnosing and classifying lesions for cancer and cancer type using only universally available computational software. Multimodal images of brain, breast, and thyroid are modeled by partial difference equations estimated as generalized least squares realizations. Model parameters afford individual lesion statistical diagnosis while Fisher linear discriminants optimally classify models of demographic populations.

BGI12:00 pm Gene Expression Quantification and Variation Detection from RNA-Seq data

Xin Jin, Group Leader of Genetic Disorder, BGI

RNA-Seq is a promising technique for quantification analysis as well as genome-wide variation analysis. Here we introduce a project that BGI is participating in to demonstrate the utility of RNA-Seq, establish standards and develop better algorithms for the quantification analysis. Also we introduce SOAPsplice and SOAPfusion, to ab initio detect splice junctions and gene fusions at a genome-wide level by RNA-Seq.

BioFortis - small logo12:30 Luncheon Presentation
Enabling Scientific Discovery While Iteratively Cleaning and Standardizing Complex Clinical and Research Data

Matthew Clark, Ph.D., Senior Application Scientist, BioFortis, Inc.

Today's researchers have access to an ever-expanding treasure trove of electronic data. Traditionally, datasets must be cleaned and standardized before meaningful query and analysis can yield scientific insights. Large scale data cleaning efforts rarely meet desired objectives in time and on budget, delaying scientific discovery. This presentation will describe a new paradigm that allows cross-functional teams to collaboratively diagnose, repair, and circumvent data problems while delivering scientific value every step of the way.

1:40 Chairperson's Remarks

Michael Liebman, Ph.D., President & Managing Director, Strategic Medicine, Inc.

Sabrina Molinaro, Ph.D., Head, Epidemiology and Health Research Services, National Research Council of Italy

1:45 Personalized Medicine: Moving from Correlation to Causality in Breast Cancer

Michael Liebman, Ph.D., President & Managing Director, Strategic Medicine, Inc.

Sabrina Molinaro, Ph.D., Head, Epidemiology and Health Research Services, National Research Council of Italy

Co-authored with Valentina Lorenzoni, Stefania Pieroni, and Fabio Mariani, Unit of Epidemiology and Biostatistics, Institute for Clinical Physiology, National Research Council (Italy)

We have developed a fundamental model of the disease process for breast cancer, from pre-disease through early detection, treatment and outcome, and apply a multi-scalar approach across the risk assessment-enhanced diagnosis-therapeutic decision axis and will present the modeling methodologies. We believe this approach will improve clinical decisions and also drive enhanced development of diagnostics and therapeutic interventions.

Gene Expression Data Analysis 

2:15 The Allen Mouse Brain Atlas: Towards an Infrastructure for Neuroscience Data

Chinh Dang, Senior Director, Technology, Allen Institute for Brain Science

Launched in 2003, the Allen Mouse Brain Atlas contains genome-wide cellular level gene expression data in the adult mouse brain. Since then, additional gene expression atlases of the developing mouse brain, mouse spinal cord, adult human brain, developing human brain, and non-human primate brain are freely and publicly available with associated visualization and mining tools. Learn how this data can be leveraged by the genomic, bioinformatics, and other research communities.

Teradata2:45 Teradata Drug Discovery Analytics Framework

Ed Acker, Ph.D., Vice President, Life Sciences, TeradataThe Teradata Drug Discovery Analytics Framework removes data analysis barriers to drug discovery analytics. The barriers include data volume limits, data access limits(semantic, structural,location), data analysis limits (segmentation, aggregation) and analysis performance limits (data movement, application architecture). The major components of this framework are a 3NF Logical Data Model, a Massively Parallel Processing Share Nothing Data Management Architecture, in-database analytics for structured and unstructured data, a SQL interface for unstructured data and shareable virtual data labs self-provisioned by scientists.


Elsevier small logo3:00

Speaker to be announced

 

 

 

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing

3:45 Statistical Issues in the Analysis of Genome-Wide Methylation Arrays as Compared to Gene Expression Data: A Breast Cancer Example

Sandeep Singhal, Bioinformatician, Breast Cancer Translational Research Laboratory J.C. Heuson (BCTL), Jules Bordet Institute

This presentation will highlight some statistical methods for genome wide methylation data analysis with an emphasis on what new information is gained from breast cancer studies for which both DNA methylation and gene expression data are available and what conclusions can be reached about the role of DNA methylation on gene expression.

Molecular Profiling Data 

4:15 'Omics Interpretation Solutions - A Big Pharma Practical Guide

Jack Pollard, Ph.D., Associate Director, sanofi Oncology, Translational & Experimental Medicine – Bioinformatics

Lars Greiffenberg, Ph.D, sanofi R&D-IS, Health-IT, Biology Solutions

While generating testable hypotheses from 'omics data offers one kind of challenge, implementing informatics solutions company-wide presents a different set of technology, people and process challenges. We will share our recent successful experience and practical insights at specifying and implementing an integrated solution for 'omics data management, analysis, and interpretation for sanofi R&D.

4:45 GenomeSpace: An Environment for Frictionless Bioinformatics

Michael Reich, Director, Cancer Informatics, Broad Institute of MIT and Harvard

This presentation describes GenomeSpace, a software environment that provides a connection layer between bioinformatics resources, whether they are Web-based applications, desktop packages, or simple scripts. GenomeSpace addresses the growing need for genomics researchers and bioinformaticians to have "frictionless" data transfer among the variety of analysis tools and data sources. GenomeSpace provides an open environment, which other bioinformatics resources can use to join the community of GenomeSpace-enabled tools. GenomeSpace is seeded by six prominent tools for genomics analysis: Cytoscape, Galaxy, GenePattern, Genomica, the Integrative Genomics Viewer (IGV), and the UCSC Genome Browser, and developed in collaboration with several biological research projects at the Broad Institute, Stanford University, and UCSD.

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes

 

THURSDAY, APRIL 26


8:40 Chairperson's Opening RemarksJustin H. Johnson, Director, Bioinformatics, EdgeBio; Project Lead of Validation Protocol, Archon Genomics X Prize presented by Express Scripts  


Bioinformatics & the Cloud 

8:45 An Algorithm for Identifying Multiply-Modified Endogenous Proteins Using Both Full-Scan and High Resolution Tandem Mass Spectrometric Data

Ray Fyhr, Project Lead, MRL-IT, Merck

This presentation describes a new top-down proteomics algorithm that runs on Linux clusters either in-house or clouded. This algorithm relies only on a predefined list of 'differential' modifications (i.e., phosphorylation) and a FASTA-formatted protein database, and is not constrained to full-length proteins for identification. The algorithm combines hard core computer science, protein science, and Mass Spectrometry.

9:15 Large-Scale Prediction of Transcription Factor Binding Sites in Multiple Genomes Using Cloud Computing

Chuanbin Du, Ph.D., Post-Doctoral Fellow, Department of Bioinformatics and Genomics, University North Carolina at Charlotte

This presentation describes a computational method to predict transcription factor binding sites (TFBSs) accurately and efficiently using cloud computing. We designed a fast parallel algorithm based on the method GLECLUBS (GLobal Ensemble CLUsters of Binding Sites). The new algorithm is implemented on the Windows Azure platform.

9:45 The Path Toward a Medical Grade Genomce

Justin H. Johnson, Director, Bioinformatics, EdgeBio; Project Lead of Validation Protocol, Archon Genomics X Prize presented by Express Scripts  

The Archon Genomics X PRIZE presented by Express Scripts created a "Validation Protocol" that is helping to define for the first time what it means to have a complete and accurate "medical grade" whole human genome sequence. The primary role of the "Validation Protocol" is to enable the X PRIZE foundation to declare a winner of the $10 Million Competition in 2013 without controversy. This presentation will describe the Validation Protocol in detail, as well as present preliminary data on the methodologies employed to to reconstruct the fosmid data, compare sequencing technologies to minimize bias, and develop software for whole genome comparison to fosmid data for contestant grading.
 

10:15 Coffee Break in the Exhibit Hall and Poster Competition

10:45 Plenary Keynote Panel Chairperson's Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

10:50 Plenary Keynote Panel Introduction

Geoffrey Noer, Senior Director, Product Marketing, Panasas

 

11:00 Plenary Keynote Panel:
A special plenary session featuring trends and challenges in cancer research:
 

  • Julian Adams, Ph.D., President, Research and Development, Infinity Pharmaceuticals, Inc.
  • Jose Baselga, M.D., Ph.D., Chief and Bruce A. Chabner Chair, Division of Hematology/Oncology, Massachusetts General Hospital; Associate Director, Massachusetts General Hospital Cancer Center; Professor of Medicine, Harvard Medical School
  • Sir John Burn, MD, FMedSci, Professor of Clinical Genetics, Institute of Genetic Medicine, Newcastle University, UK; Genetics Lead, National Institute of Health Research, UK; Medical Director, QuantuMDx Ltd
  • John Quackenbush, Ph.D., Professor, Biostatistics and Computational Biology, Cancer Biology Center for Cancer Computational Biology, Dana-Farber Cancer Institute
 

12:15 Luncheon in the Exhibit Hall with Poster Viewing


Bioinformatics Advances and Trends 

1:55 Chairperson's Remarks

Vishal Rosha, Senior Scientist, Bioprocess Research & Development, Novartis Pharma Ag

2:00 Omics Strategies to Improve Bioprocess Development

Vishal Rosha, Senior Scientist, Bioprocess Research & Development, Novartis Pharma Ag

Mammalian and microbial cell lines are widely used in the pharmaceutical industry for the generation of peptides, recombinant proteins, etc. The product development starts with transfection of the sequence of interest into an expression system (e.g. CHO), Clone screening/selection, product quality, comparability etc. During the development process, typically several hundred clones are generated and tested for each project. The numbers of clones are stepwise reduced in order to identify the best performing clone (secretion/titer, quality, stability, etc.). Using the new custom microarray and NGS technology can reduce the development time requirement for biologics products. The aim of these studies is to systematically collect "Omics" data from cell lines under various conditions and to investigate the impact of bioprocess parameters such as time viability, stress, pH, temperature, etc. in order to optimize process conditions, cell treatment, and cell line selection towards product quality, quantity, and reproducibility. 

2:30 Persephone: Visualizing the Future of Genomics Data Integration

Timothy Swaller, Director, Information Technology and Genomics, Ceres, Inc.

Persephone is a visualization tool currently available that provides the performance and data integration capabilities needed by researchers in this age of high volume data. Persephone integrates both public and private genomic data. Learn how Persephone provides the performance and functionality required by researchers to compare, filter, query through these large, complex datasets through a visual medium.

3:00 Deconvolution of Label-Free Functional Profiles from Native Cells

Roger (Rangjiao) Liu, Ph.D., Research Manager, Bioinformatics, Life Science Development, Corning

Label-free technology is gaining momentum in drug discovery; the interpretation of label-free profiling using bioinformatics algorithms is largely unknown to the scientific world, and will be very valuable to the industry. Learn the development of label-free methods for drug discovery, the understanding and interpretation of label-free data sets, and how to generate hypotheses using pharmacology knowledgebase and bioinformatics algorithms.

3:30 Closing Featured Speaker Introduction

Jonathan Sheldon, Ph.D., Global Senior Director, Translational Medicine, Oracle Health Sciences

3:40 Closing Featured Speaker:
GeneStack — Universal Platform for Genomics Application Development

Misha Kapushesky, CEO GeneStack Ltd.

4:00 Conference Adjourns

 

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