Skip Navigation
NIH | National Cancer Institute | NCI Wiki   New Account Help Tips
Skip to end of metadata
Go to start of metadata

Welcome to the CBIIT Speaker Series Wiki


The NCI Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring speakers on topics of interest to the biomedical informatics and research communities. General topics to be discussed include but are not limited to novel experimental approaches in basic research that require innovative informatics solutions; general informatics methodologies for specific tasks such as natural language processing and data exchange/integration; novel software applications (proprietary or open source); standards; ontologies; open-source development projects; human/computer interactions; future trends in biomedical informatics research and development; and CBIIT/NCIP partnerships inside and outside NCI/NIH.

Speaker Series Guidelines for Speakers: Download Word document

Please refer to the Speaker Calendar below for upcoming speakers.

Presentations: Please visit the NCI CBIIT Speaker Series YouTube playlist Exit Disclaimer logo to view past speakers' presentations on video.

Location: 9609 Medical Center Drive, Rockville, Maryland 20850

Questions? Please email Eve Shalley at



An invitation: If you are interested in presenting your work to our diverse audience of informaticists; basic, translational, and clinical researchers; software developers; and others interested in exploring the uses of informatics in cancer research, contact Eve Shalley at or 240-276-5194.


Upcoming Speakers:

October 14: Ramana Davuluri, Ph.D., Northwestern University Feinberg School of Medicine

October 28:  Martin Fenner, M.D., DataCite

November 4: Robert Grossman, Ph.D., University of Chicago

December 9: Ilya Shmulevich, Ph.D., Institute for Systems Biology

January 6, 2016: Deniz Kural, Seven Bridges Genomics

January 20, 2016: Gad Getz, Ph.D., Broad Institute

March 2, 2016: John Schnase, Ph.D., NASA

SYNOPSIS: With each successive discovery in genetics, the true dynamic complexity of the genome has become increasingly apparent, requiring relatively consistent updates to the technical definition of the word "gene." It is now understood that the majority of human genes produce multiple functional products, or isoforms, primarily through alternative transcription and alternative splicing. Different isoforms within the same gene have been shown to participate in different functional pathways, and the altered expression of specific isoforms have been associated with numerous diseases. While the recent advances in NGS are facilitating the goal of studying gene regulation at isoform-level, there are a number of informatics challenges and difficulties that need to be addressed to improve the current state and fulfill the promise of studying gene regulation at gene isoform-level. Dr. Davuluri will present some of the recent approaches developed by our group, with an emphasis on how those methods have led to the development of a diagnostic assay for molecular sub-typing of cancer patients. In particular, he will challenge the use of basic gene-centric approaches in cancer genomics and argue that one should go beyond simple gene-based analyses but also consider isoform-level information that include gene expression/regulation of splice-variants. Looking forward, Dr. Davuluri will discuss the integrative application of different statistical and data-mining approaches to derive platform-independent classification models for identification of isoform-level gene signatures for cancer subtyping.

Session details...


Semantic MEDLINE integrates information retrieval, advanced natural language processing, automatic summarization, and visualization into a single Web portal. The application is intended to help manage the results of PubMed searches by condensing core semantic content in the citations retrieved. Output is presented as a connected interactive graph of semantic relations, with links to the original MEDLINE citations.

The ability to manipulate salient information across documents helps users keep up with the research literature and discover connections which might otherwise go unnoticed. Such an ability can have an impact on biomedicine by supporting scientific research. Researchers can use Semantic MEDLINE to implement the literature-based discovery methodology for hypothesis generation; in addition, they can use the discovery browsing paradigm to elucidate poorly understood biomedical topics.

Session details...


In this talk, Mr. Madduri will describe Globus Genomics, a system that was developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data. This system is notable for its high degree of end-to-end automation, which encompasses every stage of the data analysis pipeline from initial data access (from remote sequencing center or database, by the Globus file transfer system) to on-demand resource acquisition by a specialized elastic provisioner (on Amazon EC2); specification, configuration, and reuse of multi-step processing pipelines (via the Galaxy workflow system); creation of custom Amazon Machine Images; and efficient scheduling of these pipelines over many processors (via the HTCondor scheduler). The system allows biomedical researchers to perform rapid analysis of large NGS datasets using just a web browser in a fully automated manner, without software installation or a need for any local computing infrastructure.

Session details...


In the era of big data, effective use of increasingly larger, complex, and diverse datasets has become a critical challenge for healthcare transformation. To meet the challenge, the scientific community must deliver innovative and scalable frameworks for interpreting the influx of information to keep pace with rapid scientific developments. The mission of a national lab is to enable scientific innovations and transformative technical breakthroughs for grand challenges by leveraging unique resources. ORNL is taking on this "Big Data to Knowledge" challenge for health innovations via its Health Data Sciences Institute (HDSI). In this presentation Dr. Tourassi will discuss informatics innovations coordinated by the institute to expand and accelerate biomedical knowledge discovery. Dr. Tourassi will illustrate the value of these innovations with two cancer-related examples from precision medicine and population health. The first example will demonstrate how linking of heterogeneous information across The Cancer Genome Atlas (TCGA) can provide novel insights into cancer-specific mutations at the individual level that can then directly inform molecular epidemiology of specific tumor states. The second example will demonstrate the use of cyber-informatics to accelerate discoveries in environmental cancer epidemiology. Underlying the two applications is a powerful semantic reasoning framework built at ORNL that enables seamless hypotheses generation for exploratory research.

Session details...

Complete List of Update Posts

Speaker Calendar


    Customise the different types of events you'd like to manage in this calendar.


    Optionally, restrict who can view or add events to the team calendar.


    Grab the calendar's URL and email it to your team, or paste it on a page to embed the calendar.


    The calendar is ready to go! Click any day on the calendar to add an event or use the Add event button.




  • No labels