 |
Blog
SYNOPSIS:Cancer is a complex group of diseases with many causes. Genetic changes and epigenetic alterations in somatic tissues, as well as germ line mutations or risk alleles, all contribute to cancer development and progression. Dr. Lee will present integrated studies of breast, esophageal, and gastric cancers through collaborative research with many investigators in CCR and DCEG. He will discuss a broad range of topics: from GWAS to whole genome sequencing studies; from genomics to functional studies; from genes to signature studies; from experiments to computational analyses; and from data to knowledge discovery. Dr. Lee will talk about how interweaving high-throughput data with bioinformatics analyses enables us to gain a better understanding of cancer biology and etiology.
BIO:
Dr. Maxwell Lee is the head of the high-dimension data analysis group at NCI’s Center for Cancer Research (CCR). Dr. Lee’s group conducts collaborative research with many investigators at CCR and the Division of Cancer Epidemiology and Genetics (DCEG). The group focuses on bioinformatics analyses of high-throughput data. His research spans multiple domains, including cancer genomics and epigenomics, population genetics and epidemiology, allelic-specific gene expression and epigenetic modifications, and computational methods. Dr. Lee has published more than 60 peer-reviewed papers. He serves as an Associate Editor for BMC Cancer and is on the committees of TCGA DAC, iNCI DAC, CCRIFX RPC, and NCIP High-throughput Molecular Data Working Group.
Dr. Lee received his B.S. from the University of Science and Technology of China, Ph.D. in Biochemistry from Duke University, and completed postdoctoral training at the Johns Hopkins University School of Medicine. He joined the NCI as a tenure-track investigator in 2000.
SUMMARY:
Topic: Integrated Studies of Breast, Esophageal, and Gastric Cancers Using High-Throughput Technologies and Computational Analyses
Speaker: Maxwell Lee, Ph.D., NCI Center for Cancer Research
Date: Wednesday, March 19, 2014
Time: 11 AM – 12 PM EST
You are invited to listen to Dr. Lee's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: Download the PPT presentation. A screen cast of this presentation is not available.
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:For most people health occurs in every-day living, not in hospitals and doctor's offices. They must remember to take medications, monitor healing progress, note changes from normal, or get up and exercise — all information intensive and cognitively demanding activities. Through Project HealthDesign, an eight-year initiative funded by the Robert Wood Johnson Foundation, we learned that there is so much more to health information than what is generated in the course of care and recorded in the electronic health record. In addition to lab values and blood pressures, people attend to a wide range of data that informs them about their health status and drives them toward healthy behaviors. We call these novel data types "observations of daily living" (ODLs). ODLs represent the sensations, behaviors, attitudes, thoughts, and exposures to which people attend and draw interpretations about their health situation.
Patient-generated data includes ODLs, as well as a full range of parameters that only the individual person can provide. Programs like PCORI and the NQF Patient-reported outcomes measures project show that patient-generated data not only is useful for augmenting clinical signs and assessments in evaluating a patient's health needs, but also can be used to determine the effectiveness of care. There is growing acceptance of the importance and relevance of patient-reported data and an uptake in the sophistication of the tools used to create, store, report, and analyze it. In this presentation, Dr. Brennan will introduce the concept of patient-generated data, provide an elaboration of one novel type (ODLs), and explore the ethical and policy issues related to capture and use of patient-reported data.
Patricia Flatley Brennan, R.N., Ph.D., is the Lillian L. Moehlman Bascom Professor, School of Nursing and College of Engineering, University of Wisconsin, Madison, Wisconsin. Dr. Brennan received a Master of Science in Nursing from the University of Pennsylvania and a Ph.D. in Industrial Engineering from the University of Wisconsin, Madison. Following seven years of clinical practice in critical care nursing and psychiatric nursing, Dr. Brennan held several academic positions. Dr. Brennan is National Program Director of Project HealthDesign, a Robert Wood Johnson Foundation-funded initiative designed to stimulate the next generation of personal health records.
SUMMARY:
Topic: Patient-Generated Data: Opening a Window Into the Everyday Lives of People
Speaker: Patricia Brennan, R.N.,Ph.D.
Date: Wednesday, March 5, 2014
Time: 11 AM – 12 PM EST
You are invited to listen to Dr. Brennan's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI CBIIT Speaker Series YouTube Playlist 
.
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:The Computational Genomics Research group at NCI CBIIT participated in the HPN-DREAM Breast Cancer Network Inference Challenge for the first time in 2013. The challenge comprises network inference, time-course prediction, and visualization of time-course data derived from proteomic experiments in cancer cell lines and in silico simulation. The group developed a novel approach to construct consensus networks and predict phosphoprotein trajectories under the influence of each inhibitor. The time-series data were visualized with in-house R package OmicCircos which is available at bioconductor.org. This novel diagram not only maintains the network structure but also displays the time-course change, biological annotations, and topological features. The group submitted results to Synapse.org, a site that Sage Bionetworks has developed for data sharing and live scoring. Our prediction result of 20 phosphoproteins and 10 time points for the sub-challenge 2B "In silico time-course prediction" has been ranked as the best predictor.
BIO:
Chunhua Yan, Ph.D., is the bioinformatics project manager of Computational Genomics Research (CGR) at the NCI Center for Biomedical Informatics and Information Technology. The CGR group carries out the integrated analysis of cancer mutation, copy number, expression, and methylation data through collaborations with investigators both inside and outside of NCI, and participates in NCI-supported projects such as Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and The Cancer Genome Atlas (TCGA). Dr. Yan has published many articles in peer-reviewed journals covering the topics of bioinformatics software and next generation sequencing data analysis. He also has been awarded multiple U.S. patents related to the discovery of novel kinases and receptors. Dr. Yan obtained his B.S. in pharmacy from Shanghai Medical School and his Ph.D. in structural biology from University of Maryland at Baltimore.
SUMMARY:
Topic: NCI CBIIT-CGR Team Wins HPN-DREAM Breast Cancer Network Inference Challenge 2B (View presentation slides). Due to technical difficulties, a video of this presentation is not available.
Speaker: Chunhua Yan, Ph.D.
Date: Wednesday, February 19, 2014
Time: 11 AM – 12 PM
You are invited to listen to Dr. Yan's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page .
Questions? Please email us at NCICBIITcomms@mail.nih.gov .
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Of all the genomic aberrations recently observed in tumors by the TCGA program, which are expressed at the protein level? The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has begun to answer this question. With this endeavor come a number of informatics challenges, not the least of which is integrating genomic and proteomic data from a common tumor. Dr. Kinsinger will highlight findings, software tools, and data resources developed to support the next era of omics research.
BIO:
Chris Kinsinger, Ph.D., serves as a technology program manager for NCI’s Clinical Proteomic Tumor Analysis Consortium. Dr. Kinsinger focuses on the expansion and coordination of open data access and programmatic goals involving mass spectrometry, informatics, and biospecimens. In this role, he works with NCI staff and investigators to optimize proteomics technology, establish policies for sharing data and biospecimens, and generally improve the quality and reliability of proteomic measurements. Dr. Kinsinger completed postdoctoral training at National Institute of Standards and Technology (NIST), where he researched fragmentation pathways of peptide ions in mass spectrometry. He holds a Ph.D. in chemistry (2004) from the University of Minnesota.
SUMMARY:
Topic: Proteogenomic Integration of CPTAC Data
Speaker: Chris Kinsinger, Ph.D.
Date: Wednesday, February 5, 2014
Time: 11 AM – 12 PM
You are invited to listen to Dr. Kinsinger's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:The highest principle of network architecture design is interoperability. If Metcalfe's Law tells us that a network's value can scale as some exponent of the number of connections, then our job in building networks is to ensure that those connections are as numerous, as operational, and as easy to create as possible. Where we make it easy for anyone to wire in new connections, we maximize the ability of others to contribute to the value of our shared networks. Bioinformatics has, from time to time, been derided as "slidedecks full of hairballs," yet those hairballs and their ubiquity are emblematic of the fact that at its heart bioinformatics is a science of networks: networks of physical interactions, of genetic control, of degrees of similarity, or of ecological interactions among many others. Bioinformatics is also among the most networked of research communities and among the most open in the sharing of research papers, research data, tools, and even research in process in online conversations and writing.
BIO:
Cameron Neylon, Ph.D., is a practicing experimental scientist with an interest in how the Web can be effectively applied to the practice of science. Dr. Neylon is Advocacy Director at PLOS and previously was a Senior Scientist for Biomolecular Sciences, Science and Technology Facilities Council in the U.K. Dr. Neylon is in demand as a speaker and writer on the technical and social opportunities and issues that the Internet brings to scholarly communication and the ways in which the details of the scientific process can be recorded and communicated. His research has focused on the design and development of systems for capturing the research process at source and making it directly available on the web. Dr. Neylon writes regularly on these issues, as well as on the challenges the Web brings to traditional scientific practice in his blog Science in the Open.
SUMMARY:
Topic: Network Ready Research: The Role of Open Source and Open Thinking
Speaker: Cameron Neylon, Ph.D.
Date: Wednesday, January 8, 2014
Time: 11 AM – 12 PM
You are invited to listen to Dr. Neylon's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI’s CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page .
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Low-cost, high-throughput DNA sequencing has become widespread and is revolutionizing biomedical research and clinical care alike. In the era of pervasive genomics, the greatest challenge is making sense of large sequencing datasets. The Galaxy platform is a popular Web-based workbench that enables accessible, reproducible, and collaborative analysis of genomic data using high-performance computing resources. Galaxy makes it easy for anyone, regardless of programming experience, to analyze large genomic datasets. In collaboration with the Emory Winship Cancer Institute, we have extended Galaxy with tools, workflows, and visual analysis applications to better support integrative analyses of cancer genomes. Using these enhancements, we have analyzed high-throughput sequencing data from the transcriptomes of primary pancreatic adenocarcinoma tumors and a pancreatic cancer cell line. Insights derived from these analyses demonstrate how Galaxy can assist in the interpretation of cancer genomes and transcriptomes.
BIO:
Jeremy Goecks is an Assistant Professor of Computational Biology at George Washington University. The research agenda of Dr. Goecks’ laboratory centers on using high-throughput biomedical data for disease prediction and treatment, with a focus on cancer, and creating interactive computing systems for analyzing and understanding such data. He is a lead member of the Galaxy project; Galaxy is a popular Web-based platform for performing accessible, reproducible, and transparent genomics research. Dr. Goecks received his Ph.D. from the Georgia Institute of Technology and his B.S. (with Honors) from the University of Wisconsin.
SUMMARY:
Topic: Using Galaxy to Understand Cancer Genomes
Speaker: Jeremy Goecks, Ph.D., Assistant Professor of Computational Biology at George Washington University
Date: Wednesday, December 11, 2013
Time: 11 AM – 12 PM
You are invited to listen to Dr. Goecks' presentation in Room TE408/410 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI’s CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Across NIH, a number of Institutes and Centers have been active in developing or identifying common data elements (CDE) for funded investigators to use in supported research. The NIH Common Data Elements working group was established to improve the coordination and communication of these efforts across NIH and to provide a focal point for interactions with outside organizations. To date the working group has developed a Web portal to provide greater access to information about NIH CDE efforts, developed materials to promote the use of NIH CDEs, and established collaborations with outside organizations involved in data standards for clinical research. This presentation will provide an update on these activities and outline future directions.
BIO:
Jerry Sheehan is the Assistant Director for Policy Development at the National Library of Medicine, where he is responsible for issues related to scientific, technical and medical data and information. He has contributed to the formulation and implementation of policies related to clinical trials registration and results submission, genome-wide association studies, the NIH Data Sharing Policy, and the NIH Public Access Policy. In addition, Mr. Sheehan manages the trans-NIH Biomedical Informatics Coordinating Committee and serves as chair of its Common Data Elements Working Group. He is currently the Deputy Chair of CENDI (the organization of federal science, technology, and medical information managers), vice president of the International Council for Scientific and Technical Information, chair of the OECD Working Group on Innovation and Technology Policy, and served as vice chair of the Interagency Working Group on Digital Data in 2011-2012. Mr. Sheehan holds degrees in Electrical Engineering and in Technology and Policy from the Massachusetts Institute of Technology.
SUMMARY:
Topic: Making the Most of Common Data Elements: A Trans-NIH Perspective
Speaker: Jerry Sheehan, Assistant Director for Policy Development at the National Library of Medicine
Date: Wednesday, November 13, 2013
Time: 11 AM – 12 PM
You are invited to listen to Mr. Sheehan's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI’s CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov .
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Scholarly communication is going through a period of change driven by the digitization of scholarship and as a result new business models, such as open access. In many ways we are just at the beginning with the analog form of discourse now appearing as a digital PDF. We have yet to unleash the full power of the medium and go beyond the PDF, in part because of conservatism and antiquated reward systems. Biomedical informatics could drive a very positive change since the expertise exists to make change work, and the discipline comprises online data, computational methods, analysis, visualization, web based dissemination which are the raw materials for change. We will discuss what could be done and what are the implications.
BIO:
Philip E. Bourne, Ph.D., is Associate Vice Chancellor for Innovation and Industry Alliances, a Professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego, Associate Director of the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank and an Adjunct Professor at the Sanford Burnham Institute. Dr. Bourne's professional interests focus on relevant biological and educational outcomes derived from computation and scholarly communication. This implies algorithms, text mining, machine learning, metalanguages, biological databases, and visualization applied to problems in systems pharmacology, evolution, cell signaling, apoptosis, immunology and scientific dissemination. He has published over 300 papers and five books, one of which sold over 150,000 copies.
Dr. Bourne is committed to maximizing the societal benefit derived from university research. He has co-founded four companies: ViSoft Inc., Protein Vision Inc., a company distributing independent films for free and most recently SciVee. He is committed to furthering the free dissemination of science through new models of publishing and better integration and subsequent dissemination of data and results which as far as possible should be freely available to all. He is the co-founder and founding Editor-in-Chief of the open access journal PLOS Computational Biology. Dr. Bourne is a past President of the International Society for Computational Biology, and an elected fellow of the American Association for the Advancement of Science (AAAS), the International Society for Computational Biology (ISCB) and the American Medical Informatics Association (AMIA).
SUMMARY:
Topic: What Bioinformaticians Need to Know About Digital Publishing Beyond the PDF (View presentation slides). Due to technical difficulties, a video of this presentation is not available.
Speaker: Philip E. Bourne, Ph.D. Associate Vice Chancellor for Innovation and Industrial Alliances, UCSD, Professor of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD
Date: Wednesday, October 30, 2013
Time: 11 AM – 12 PM
You are invited to watch Dr. Bourne's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Cyberinfrastructure is essential in both "big" science as well as "long-tail" science. Software is a key part of cyberinfrastructure. The National Science Foundation (NSF) has a vision for its role in software as infrastructure, such as foundational research into new software, support of existing software, and community- and user-based application of software, including policy and education issues. The Division of Advanced Cyberinfrastructure (ACI) plays a role in every part of this vision, primarily through the Software Infrastructure for Sustained Innovation program. In spite of this, there are still challenges and researchers at ACI are starting to develop potential solutions.
BIO:
Daniel (Dan) S. Katz has 25 years of experience in scientific computing, engineering, geophysics, astronomy, and computer science including component models, languages, and visualization. He is a Senior Fellow in the Computation Institute at the University of Chicago and Argonne National Laboratory and is currently on assignment in the Division of Advanced Cyberinfrastructure (ACI) at the National Science Foundation (NSF). Dan is interested in the development and use of advanced cyberinfrastructure that can solve challenging problems at multiple scales. His technical research interests are in applications, algorithms, fault tolerance, and programming in parallel and distributed computing, including high-performance computing (HPC), Grid, and Cloud.
SUMMARY:
Topic: Software as Infrastructure at the National Science Foundation
Speaker: Dr. Daniel S. Katz
Date: Wednesday, September 18, 2013
Time: 11 AM – 12 PM
You are invited to watch Dr. Katz's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series videos page and on the NCI’s CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Current technology permits genome-wide generation of multidimensional molecular data assessing copy number alterations, nucleotide substitutions, insertion or deletions, rearrangements, and epigenetic changes. Furthermore, next-generation sequencing technology provides complete gene and genome sequence. The CBIIT CGR team has created approaches and tools to integrate, display, and interpret these diverse, system-wide data. The CGR team has provided tools, analytic capacity, and bioinformatics support to the specific groups in the Cancer Genomic Atlas project (TCGA) and TARGET projects as well as investigators within the NCI community. More specifically, the CBIIT-CGR team leveraged its analytic pipelines to determine the quality of data submitted to the data coordinating centers and to computationally identify features for confirmation by other groups and validation in bench-based experiments. The team performed the primary sequence analysis for the TARGET consortium.
BIO:
Dr. Daoud Meerzaman is the Director of R&D/Section Head of Computational Genomics Research (CGR) at the Center for Biomedical Informatics and Information Technology (CBIIT) at the National Cancer institute (NCI). Previously, Dr. Meerzaman served as the Scientific Project Manager at the Center for Cancer Research at NCI. Under his leadership, the CGR group focuses on identifying genes and their associated networks that are important in cancer. Bioinformatics analyses are used to translate genetic and genomic observations into insights concerning cancer etiology. The team has developed and continues to develop bioinformatics tools and methods to provide bioinformatics analysis support for the NCI, as well as for the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project. Dr. Meerzaman has published many articles in peer-reviewed journals and served as an invited reviewer for scientific journals. He also serves as an adjunct faculty member at the George Washington University in Washington, D.C., where he currently teaches molecular mechanisms of cancer. Dr. Meerzaman received his B.S. and doctorate degrees from the George Washington University.
SUMMARY:
Topic: Computational Tools for Cancer Genome Analysis
Speaker: Dr. Daoud Meerzaman
Date: Wednesday, July 24, 2013
Time: 11 AM – 12 PM
You are invited to watch Dr. Meerzaman's presentation at TE408-410 (East side) Training Room in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI’s CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Astronomy, like most other sciences, has become immensely data-rich. The exponential growth of data volumes, data rates, and data complexity continues. Efficient extraction of knowledge from these massive and complex data sets and data streams poses significant new challenges, many of which are common among different sciences. Their solutions are expanding on the scientific method and toolkit. In astronomy, this transformation started with the first modern digital sky surveys in the mid-1990s, which gave rise to the Virtual Observatory (VO) framework. This framework envisioned a complete and distributed environment for astronomy with massive, complex data sets. Today, VO is effectively a global data grid of astronomy, but the astroinformatics community is still struggling with the tools for an efficient knowledge discovery. This presentation will briefly review some of the lessons learned, including successes and remaining challenges. The emergence of a bridge discipline of astroinformatics — analogous to medical or bioinformatics — as a broader intellectual and technological environment for the more data-driven science and scholarship in the 21st century will be addressed.
BIO:
S. George Djorgovski is an Astronomy Professor at the California Institute of Technology (Caltech). After getting his Ph.D. from U.C. Berkeley, he was a Harvard Junior Fellow before joining the Caltech faculty in 1987. Dr. Dyorgovski has received numerous professional recognitions and awards, including the Alfred P. Sloan Fellowship and the Presidential Young Investigator Award. He is currently the author and co-author of several hundred scientific publications, covering the fields of astrophysics, cosmology, and computational science. Dr. Djorgovski was one of the co-founders of the Virtual Observatory framework, and chaired the National Virtual Observatory Science Definition Team. More recently, he fostered a development of the emerging discipline of astroinformatics. His current interests are largely in the areas of data-intensive and computationally enabled science, and the common challenges and methodological aspects that are pertinent to all scientific disciplines in the era of an exponential data growth.
SUMMARY:
Topic: Big Data Science in the 21st Century: Lessons and Experiences from Astronomy
Speaker: Dr. S. George Djorgovski
Date: Wednesday, July 10, 2013
Time: 11 AM – 12 PM
You are invited to watch Dr. Djorgovski's presentation via WebEx at 2W908 (West side) Training Room in the NCI Shady Grove Building on Medical Center Drive or from your location:
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI’s CBIIT Speaker Series YouTube Playlist. .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov .
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:Markers are becoming more important in NCI-supported clinical trials. These trials are becoming increasingly oriented toward precision medicine. Unfortunately, Program Staff do not have access to a database that tracks such markers to make sure their use can be managed. The Center for Coordinating Clinical Trials (CCCT) was mandated to create the Clinical Trials Reporting Project (CTRP) to coordinate tracking all elements of the clinical trials. CTRP now contains nearly 7,000 trials with roughly half of them including markers on all patients; 12% of said trials have integral markers that are essential for performance of the trial, e.g., mutations for eligibility for targeted therapies. The presentation will cover the CTRP Marker database and its potential as a resource for staff and potentially the public.
BIO:
Kim Jessup, M.D. is a surgical oncologist who joined the Cancer Diagnosis Program at NCI as Chief of the Diagnostics Evaluation Branch in 2006. This branch facilitates the transition of discovery-based markers into in-vitro diagnostics that are used in clinical trials. As part of this effort, Dr. Jessup helped with the creation of the Markers Database in the Clinical Trials Reporting Project as well as the creation of electronic case-report forms (eCRFs) for pharmacodynamic assays for the Experimental Therapeutics-Clinical Trials Network. He also collaborates with the FDA to standardize assays for clinical trials and assists investigators in navigating the requirements for Investigational Device Exemption. In 25 years of practice, he has focused on the multidisciplinary treatment of GI and breast cancer, melanoma, and soft tissue/skeletal sarcomas in several different academic settings. In addition, he led a research effort studying the mechanisms that underpin hepatic metastasis by human colorectal carcinoma and identified two distinct roles for the marker carcinoembryonic antigen in modulating inflammatory responses and promoting metastasis. Currently, Dr. Jessup is a Principal Investigator in the Laboratory of Experimental Carcinogenesis in the NCI Center for Cancer Research. His research targets a novel embryonic retrogene that drives cancer stem cells in metastatic human colorectal carcinoma.
SUMMARY:
Topic: The Good, The Bad and The Ugly for Clinical Markers: Possibilities For the Future
Speaker: Dr. Kim Jessup
Date: Wednesday, June 26, 2013
Time: 11 AM – 12 PM
Dr. Jessup will give his presentation in person at 2nd Floor East, Room 032-034 at the NCI Shady Grove Building on Medical Center Drive. The presentation will also be available via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page on the NCI’s CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:The standard lexicon for reporting adverse events in National Cancer Institute sponsored clinical trials is the Common Terminology Criteria for Adverse Events (CTCAE). Currently, adverse events are reported by clinicians, yet evidence suggests that compared to patient-report, clinicians may underestimate symptom severity and onset.
The NCI Patient Reported Outcomes-Common Terminology Criteria for Adverse Events (PRO-CTCAE) is a new patient-reported outcome measurement system that elicits the frequency, severity and interference of 78 treatment toxicities that can be reported from the patient perspective. This presentation offers an overview of the PRO-CTCAE measurement system and the interdisciplinary consortium in which it is being developed and tested, and suggests the trial contexts in which patient reporting of toxicity is likely to provide the greatest value and informational yield, as well as the challenges faced in developing this approach to adverse event reporting. Session details...
After outlining the factors that drive an expanding imperative to incorporate the patient perspective into the assessment of treatment tolerability and safety, the traditional approach to adverse event reporting is contrasted with a paradigm that seeks to incorporate the patient perspective. The key elements of the PRO-CTCAE measurement system are exhibited, and the research challenges, gaps in knowledge, and the issues that will need to be resolved to fully implement this new approach are examined. The presentation concludes by highlighting (i) NCI efforts to make PRO-CTCAE more widely available to investigators in the extramural community, including academic and industry investigators both in the U.S. and internationally; (ii) ongoing PRO-CTCAE consortium studies to evaluate and refine both the PRO-CTCAE items and the electronic system for patient-reported AE ascertainment and to scale up for integration into the clinical trial workflow and into existing platforms for electronic data capture and electronic health records; and (iii) envision some of the future directions for PRO-CTCAE, as both a drug development tool and as a potential platform upon which to build improvements in symptom management and care quality for patients participating in cancer clinical trials.
BIOs:
Dr. Sandra A. Mitchell is a research scientist in the Outcomes Research Branch of the Applied Research Program, Division of Cancer Control and Population Sciences, at NCI. Her work focuses on the development and testing of measures of symptom burden, physical function, and sleep and fatigue in patients with cancer, and the application of these outcomes to evaluate therapeutic response and treatment toxicity in clinical trials. Her methodologic interests include latent variable mixture modeling to characterize underlying heterogeneity, as well as analysis and interpretation issues surrounding patient-reported outcomes, including health-related quality of life.
A board certified acute-care nurse practitioner, Dr. Mitchell maintains a clinical practice as an Oncology Nurse Practitioner with the Experimental Transplantation and Immunology Branch, NCI Intramural Program, focusing on long-term survivors of allogeneic hematopoietic stem cell transplantation with chronic graft-versus-host disease. She also serves as the program director for the development and testing of PRO-CTCAE, a new measurement system to integrate patient reporting of symptomatic adverse events into cancer clinical trials.
Dr. Mitchell received her undergraduate and master’s degrees from the University of Toronto and the University of Rochester, and received a Ph.D. from the University of Utah with a focus in quantitative methods. The author of more than 50 peer-reviewed publications in the areas of symptom management, functional status, cancer survivorship, and the application of quality-of-life outcomes in evaluating therapeutic response to treatment, Dr. Mitchell’s work has been recognized with numerous awards, including two NIH Clinical Center Director’s Awards and the Oncology Nursing Society’s Award for Excellence in Nursing-Sensitive Patient Outcomes.
SUMMARY:
Topic: Capturing Symptom Burden and Treatment Tolerability in Cancer Clinical Trials, Patient-Reported Outcomes-Common Terminology Criteria for Adverse Events (PRO-CTCAE)
Speaker: Dr. Sandra A. Mitchell
Date: Wednesday, June 12, 2013
Time: 11 AM – 12 PM
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI’s CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:
SpecL is a new declarative information modeling system developed at the Cold Spring Harbor Laboratory (CSHL) to create large complex software projects. The next generation sequencing LIMS for the CSHL Woodbury Genome Center was just completed using SpecL at its core. Traditional modeling techniques rooted in relational theory are simply not appropriate for capturing the full story of cancer research as it is emerges from laboratories across the United States and the globe. The coordination of new ideas, new processes, new workflows, new technologies, new experimental protocols, experimental designs, specific aims, intermediate results, partial results, negative results, and final published positive results require a rethink of how data and information are modeled. Data complexity, volume and size have further exacerbated the disconnect between what current methods can deliver and what is actually needed to get the job done. SpecL was designed to capture rich data models that cross cut many concerns including access, compliance, presentation, storage, and behavior. Session details...
BIOs:
Anthony Leotta earned a B.S. in Electrical Engineering from Clarkson University, Potsdam, New York, and an M.S. in Computer Science from NYU Poly, Brooklyn, New York. He joined the Wigler Lab at CSHL in 2005 as an informatics data manager specialist. He develops databases, processing pipelines, and interactive visualization software and tools. Prior to joining CSHL, Mr. Leotta was employed as a software developer for a variety of industries including financial, telecommunications, and defense.
SUMMARY:
Topic: SpecL, Information Modeling from the Top Down
Speaker: Anthony Leotta
Date: Wednesday, May 15, 2013
Time: 11 AM – 12 PM
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the CBIIT Speaker Series YouTube Playlist .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
SYNOPSIS:
Background: All U.S. transplant centers are required to report comprehensive SCT outcome data copied from SCT program databases or the EMR by manual transcription. A solution was needed to allow electronic transmission of comprehensive outcome data. The current electronic data capture method requires mandated manual data entry of 700+ unique data elements into an internet application, FormsNetR. Data is routinely transmission of comprehensive outcome data directly from departmental and institutional databases to the mandated SCT Outcomes Database (SCTOD).
Methods: MD Anderson Cancer Center designed an integration engine to extract, map, and transmit structured form data sets through a caGRID subnet (AGNIS) directly to the SCTOD from a proprietary MDACC SCT database using a secure, rules-based, and auditable method. To make this method applicable to other centers, MD Anderson collaborated with the NCI and others to expand the Biomedical Research Informatics Domain Group (BRIDG) standard data model to support a full set of granular data elements required to describe SCT outcomes. Session details ...
BIOs:
Dr. Roy Jones is a Professor of Medicine in the Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center. He chairs the American Society of Blood and Marrow Transplantation’s Informatics Committee and Quality Outcomes Committee. Dr. Jones has served as an informatics consultant to several branches of the National Cancer Institute and several other organizations. His informatics focus has been on the development of applications and databases to support clinical and translational cancer research.
Charles Martinez is the Manager of System Analysis Services in the Department of Stem Cell Transplantation Services, MD Anderson Cancer Center. Mr. Martinez is responsible for Informatics for both clinical and research for MD Anderson’s Stem Cell Transplant Department. He is also the technical chair of the American Society of Blood and Marrow Transplantation’s Informatics Committee.
SUMMARY:
Topic:
Comprehensive Stem Cell Transplant (SCT) Outcome Electronic
Data Submission
Speaker: Dr. Roy Jones and Charles Martinez
Date: Wednesday, May 1, 2013
Time: 11 AM – 12 PM
Presentation: A screen cast of the presentation will be available for viewing after the event here on our Speaker Series Videos page and on the NCI Events YouTube Channel .
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Questions? Please email us at NCICBIITcomms@mail.nih.gov.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
