Bioinformatics Seminars ( Past Seminars )
BMI Joint Seminar: Neurophysiology and 21st Century Technological Advances: How are we going to deal with the coming data avalanche?| Start: | Friday, April 20, 2012 12:00pm (Pacific Standard Time) | |
| End: | Friday, April 20, 2012 1:00pm (Pacific Standard Time) | |
| Where: | Garren Auditorium-Biomedical Science Building (UCSD) | |
| Who: | Jeffrey Gertsch, MD, Assistant Professor and Director, Interventional Neurophysiology Service;Department of Neurosciences, University of California San Diego School of Medicine;Senior Scientist, Warfighter Performance Department, Naval Health Research Center | |
| Description: | Understanding the human nervous system requires a unique scalar systems biological approach. For this reason, neuropathology will likely be best understood with complex rather than simple biomarkers. This concept can be applied profitably in the medical neurosciences, where the neurological examination provides sparse data in a host of patients rendered unresponsive by anesthesia, brain injury, delirium, sleep, and other conditions. The sickest subset of patients have the most to gain; the surgical and critical care neurophysiologist can employ an alternative diagnostic paradigm by gatheringcontinuous, real-time, multimodal electrophysiological data to secure a clinical correlation and reduced morbidity and mortality. Dr. Gertsch works in the emerging practice of Interventional Neurophysiology, a practice intimately tied to the technological advances necessary to observe tiny, faltering signals in this vulnerable inpatient population. This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. |
BMI Joint Seminar: Bringing the Laboratory to the People: The Role of New Wireless Technologies in Biomedical Research and Healthcare Delivery
| Start: | Friday, April 13, 2012 2:30pm (Pacific Standard Time) | |
| End: | Friday, April 13, 2012 3:30pm (Pacific Standard Time) | |
| Where: | AL 201 | |
| Who: | Dr. Bob Kaplan, the Associate Director for Behavioral and Social Sciences Research for the NIH | |
| Description: | Mobile and wireless health (mHealth), which includes a range of technologies from cellular phones to wireless sensors, has developed at an exponential pace in recent years. However, the integration and translation of these cutting-edge technologies into rigorously-evaluated health research and health care tools have lagged behind. For example, rapid advances in computer technology have yielded remarkably attractive low-cost, real-time devices to assess disease, movement, images, behavior, social interactions, environmental toxins, hormones, and other physiological variables. These new devices are miniaturized and require little energy to operate. These technologies may provide the potential to advance research, prevent disease, enhance diagnostics, improve treatment and increase access to health services and lower health care costs in ways previously unimaginable. This presentation will consider how the wireless revolution is affecting research in fields ranging from geography to pathology. It will explore NIH and NSF efforts to build programs that will systematically evaluate the benefits and the possible risks of these new technologies. |
BMI Joint Seminar: Working Record: Designing EMR System to Support Work Practices
| Start: | Friday, March 2, 2012 12:00pm (Pacific Standard Time) | |
| End: | Friday, March 2, 2012 1:00pm (Pacific Standard Time) | |
| Where: | Center for Neural Circuits and Behavior, UCSD– Large Conference Room | |
| Who: | Yunan Chen, M.D., PhD, Assistant Professor, Department of Informatics, UC Irvine | |
| Description: | Recently there has been an increasing interest in the field of Human‐Computer Interaction to study the design of Electronic Medical Record (EMR) systems. Drawn on the insights obtained from my recent ethnographic studies on the adoption, workflow, and workaround of EMR systems in various clinical settings, I will explore the concept of “working record” that emerged from my field observations. Differing from the goal of documenting precise, clear, and complete records in EMR systems, working record is the informal, transitional, and work‐in‐progress information that is essential formediating and supporting actual clinical practices. In this talk, I will conceptualize the noon of working record and exemplify the arfacts, strategies, and practices clinicians engaged in to create their own working record. This work calls for the design of EMR to not only support record keeping practices in healthcare, but also the clinical practices through which the records are written, read, and used. This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. |
BMI Joint Seminar: NLM Resources for Mining Biomedical Text
| Start: | Friday, February 3, 2012 12:00pm (Pacific Standard Time) | |
| End: | Friday, February 3, 2012 1:00pm (Pacific Standard Time) | |
| Where: | Center for Neural Circuits and Behavior, UCSD– Large Conference Room | |
| Who: | Olivier Bodenreider, PhD, Senior Scientist and Chief, Cognitive Science Branch, Lister Hill National Center for Biomedical Communications, US National Library of Medicine | |
| Description: | Over the past two decades, the National Library of Medicine (NLM) has developed resources and tools for helping researchers mine clinical text. At the core of these resources is the Unified Medical Language System (UMLS). The UMLS Metathesaurus is a large terminology integration system and a source of vocabulary for identifying biomedical entities in text. The SPECIALIST lexicon provides linguistic information about biomedical phrases including inflection and derivation. The UMLS Semantic Network provides broad categories of biomedical entities and their interrelations. Based on these resources, NLM has developed tools and services to support various aspects of text mining including spelling correction, normalization, term recognition (MetaMap), indexing (Medical Text Indexer), relation extraction (SemRep) and visualization (Semantic Medline), as well as a specialized search engine (Essie). These resources will be briefly presented and remaining challenges will be discussed. This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. |
BMI Joint Seminar: The Ethics of Medical Informatics: Is Personal Privacy the Only Worry?
| Start: | Friday, December 9, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, December 9, 2011 1:00pm (Pacific Standard Time) | |
| Where: | Center for Neural Circuits and Behavior, UCSD– Large Conference Room | |
| Who: | Mary Devereaux, PhD, Director of Biomedical Ethics, UCSD | |
| Description: | The secondary use of patient health records raises a host of ethical issues. Clinicians gather personal patient information to prevent, diagnose and treat disease, advancing patient health. Some of this information may be highly confidential, including family history, genetic testing results, a diagnosis of addiction, or illegal immigration status. But all medical information, whether sensitive or not, is governed by legal and ethical requirements for privacy, confidentiality, and security, e.g., HIPAA. With the move to electronic health records (EHRs) and the growing capacity to gather andprocess terabytes of medical information, researchers understandably wish to access aggregated data to analyze patient outcomes, health demographics, and the economics of health care (Safran et al. 2007). Assuming that it's possible to de-identify information and protect patient privacy – and thatpatients give their consent – are there any other ethical issues researchers need to consider? This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. |
BMI Joint Seminar: Open-Source Software Solutions for Clinical Research: Applications for HIV
| Start: | Friday, December 2, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, December 2, 2011 1:00pm (Pacific Standard Time) | |
| Where: | Center for Neural Circuits and Behavior, UCSD– Large Conference Room | |
| Who: | Jason Young, PhD, Associated Professor, Center for AIDS Research, UCSD | |
| Description: | Modern clinical research requires flexible software tools for the management of complex data types, rapid testing of hypotheses, and secure access to and sharing of information across institutions via the web. For this purpose, we have developed an extensible, secure, and free Open source ClinicalContent Analysis and Management System (OCCAMS). At its core, OCCAMS provides methods for visit schedule and form creation, form and data versioning, integrated quality control logic and workflows, real-time web reporting of data accrual, data export, and granular permission controls. Most importantly though the modularized design and open source nature of OCCAMS encourages community development of plugins to provide new functionality addressing the specific needs of any particular area of research. As examples, OCCAMS HIV-specific plugins under development for mobile data collection, specimen storage and tracking, sequence analysis, and transmission network visualization will be discussed. This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. |
BMI Joint Seminar: Personalizing Evidence-Based Medicine with Advanced Clinical Decision Support
| Start: | Friday, November 4, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, November 4, 2011 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 107 | |
| Who: | Josh Peterson, MD, MPH, Biomedical Informatics, Vanderbilt University | |
| Description: | This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. Personalized Medicine offers the promise of improving drug efficacy and safety, enabling a tailored approach to evidence-based therapies for patients. To apply genomic data into routine practice, many HIT platforms, including electronic health records, e-prescribing systems and clinical decision support (CDS) need to be extended to integrate this new class of data with existing physiologic determinants of drug response. The presentation will review examples of successful CDS to personalize drug prescribing which has been implemented and evaluated over the last decade at Vanderbilt University Medical Center, and report on our early experience with PREDICT (Pharmacogenomics Resource for Enhanced Decisions in Care and Treatment). |
BMI Joint Seminar: Personalizing Evidence-Based Medicine with Advanced Clinical Decision Support
| Start: | Friday, September 30, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, September 30, 2011 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 107 | |
| Who: | Josh Peterson, MD, MPH, Biomedical Informatics, Vanderbilt University | |
| Description: | This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. Personalized Medicine offers the promise of improving drug efficacy and safety, enabling a tailored approach to evidence-based therapies for patients. To apply genomic data into routine practice, many HIT platforms, including electronic health records, e-prescribing systems and clinical decision support (CDS) need to be extended to integrate this new class of data with existing physiologic determinants of drug response. The presentation will review examples of successful CDS to personalize drug prescribingwhich has been implemented and evaluated over the last decade at Vanderbilt University Medical Center, and report on our early experience with PREDICT (Pharmacogenomics Resource for Enhanced Decisions in Care and Treatment). |
BMI Joint Seminar: Biomedical Technology Student Association Inaugural Talk
| Start: | Tuesday, May 3, 2011 12:00pm (Pacific Standard Time) | |
| End: | Tuesday, May 3, 2011 1:30pm (Pacific Standard Time) | |
| Where: | GMCS 405 | |
| Who: | Dr. Dean Chatham, Dean of Admissions, Applied Life Sciences, Keck Graduate Institute | |
| Description: | Dr. Dean Chatham, Dean of Admissions, Applied Life Sciences, Keck Graduate Institute |
BMI Joint Seminar: The Nationwide Health Information Network and San Diego Initiatives
| Start: | Friday, April 22, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, April 22, 2011 1:00pm (Pacific Standard Time) | |
| Where: | UCSD: CMG Large Conference Room | |
| Who: | Omar Bouhaddou, PhD., Department of Veterans Affairs& Hewlett-Packard, San Diego, CA | |
| Description: | There is currently an unprecedented opportunity for healthcare IT and informatics to help transform the healthcare system into a paperless industry. Everywhere in the world, there is an increased awareness associated with publicprivate investments and provider incentives to adopt and meaningfullyuse interoperable Electronic Health Records (EHRs). This presentation provides an overview of the United States Nationwide Health Information Network (NwHIN) initiative a secure, standardbased, Internetbased, noncentralized infrastructure for health information exchange using the Internet. Providers, consumers, hospitals, pharmacies, laboratories, and others can setup a gateway conformant to the NwHIN specifications and use a common set of protocols, messages, and a common trust agreement for data sharing including identify shared patients, represent and enforce patient preferences, and findand retrieve health information from other participants. The first bidirectional production implementation took place in San Diego. They demonstrate these standards can be implemented consistently and provide lessons learned which are informing a scalable, more plug and play scalability of the network. This event is organized by the i-DASH initiative |
BMI Joint Seminar: Genomics&"A Century of Biology"
| Start: | Wednesday, April 20, 2011 2:30pm (Pacific Standard Time) | |
| End: | Wednesday, April 20, 2011 3:30pm (Pacific Standard Time) | |
| Where: | AH 2108 | |
| Who: | Huanming Yang, PhD., Chairman and Professor, BGI (formerly Beijing Genomic Institute) | |
| Description: | Dr. Yang will discuss the origins and evolution of the genomic revolution and share his insights into the practical and ethical implications of its evolution for medicine, mankind and our world in “A Century of Biology.” Dr. Yang is a globally recognized leader in genetic and genomic researchand founder of BGI, one of the largest genomic organizations in the world. Dr. Yang and his collaborators at BGI have made significant contributions to the International Human Genome Project (HGP), the International Human HapMap project and the 1000 Genomes Project. In 2011, Dr. Yang was named tothe U.S. Presidential Commission for the Study of Bioethical Issues. He is a former professor and director at the Human Genome Center, Institute of Genetics, Chinese Academy of Sciences, and his research has been published in numerous peer reviewed scientific journals, including Science, Nature, Nature Genetics, and Nature Biotechnology. This event is cosponsored by the Biomedical Informatics Research Center of San Diego State University and by BGI (formerly Beijing Genomic Institute). Host: Faramarz Valafar |
BMI Joint Seminar: Bayesian Multivariate Survival Trees for Tooth Prognosis
| Start: | Wednesday, March 23, 2011 11:00am (Pacific Standard Time) | |
| End: | Wednesday, March 23, 2011 12:00pm (Pacific Standard Time) | |
| Where: | GMCS 405 | |
| Who: | Richard Levine, Professor and Co-Director, Statistics Division, SDSU | |
| Description: | Abstract: Tooth loss from periodontal disease or dental caries (decay) afflicts most adults over the course of their lives. Multivariate survival tree methods have shown potential for developing objective tooth prognosis systems, however the current technology suffers either from prohibitive computational expense or unrealistic simplifying assumptions to overcome computational demands. In this article Bayesian tree methods are developed for correlated survival data, relying on a computationally feasible, yet flexible, frailty model with piecewise constant hazard function. Bayesian stochastic search methods are detailed for tree construction and posterior ensemble averaged variable importance ranking and amalgamation procedures are developed to identify indicators of tooth prognostic groups from a forest of trees. The proposed methods are used to assign each tooth from the VA Dental Longitudinal Study to one of five prognosis categories (good, fair, poor, questionable, and hopeless) and evaluate the effects of clinical factors and genetic polymorphisms in predicting tooth loss. The prognostic rules established may be used in clinical practice to optimize tooth retention and devise periodontal treatment plans. |
BMI Joint Seminar:Mediation Technology for Neuroinformatics Data Integration: An (F)BIRN
| Start: | Friday, March 11, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, March 11, 2011 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Naveen Ashish, PhD, CalIT2, University of California Irvine | |
| Description: | This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. In this talk I will present the work done in providing integrated data access to multiple neuroscience data sources, residing at different institutions and of different kinds, using the "information mediation" technology and approach. This work is part of the "BIRN" (Biomedical Informatics Research Network) project, as a collaboration between USC/ISI and UC Irvine. We have provided integrated data access to sources such as the Human Imaging Database "HID", the eXtensible Neuroscience Archive Toolkit (XNAT)and others using mediation technology from USC/ISI. I will present the desig and implementation details in developing thsi integrated application, as well as leasons learned and directions for (ongoing) further research. |
BMI Joint Seminar: Naturalistic Human Computer Interaction: It is Not Nice to Fool Mother Nature
| Start: | Tuesday, February 1, 2011 12:00pm (Pacific Standard Time) | |
| End: | Tuesday, February 1, 2011 1:00pm (Pacific Standard Time) | |
| Where: | SDSC 145E | |
| Who: | Vilma L. Patel, PhD, DSc, School of Biomedical Informatics, University of Texas Houston | |
| Description: | This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. There is a growing recognition that many errors are neither solely attributable to lapses in human performance nor to flawed technology. Rather they develop as a product of the interaction between human beings and technology (HCI). In our view, errors are the product of cognitive activity in human adaptation to complex physical, social, and cultural environments. How well the design of health IT complements its intended setting and purpose is critically important for safe and effective performance. There are numerous obstacles to implementation and optimal performance and the ones most resilient to satisfactory resolution are related to usability and workflow. An even more disconcerting finding is that the failure to attend to human factors in the design of clinical information systems can create orfacilitate new errors and additional harm, an ironic twist in the effort to a create safer work environment. In this presentation I will discuss why is it necessary to understand the human factors and HCI concerns in naturalistic everyday work environment that make the integration of computing and clinical practice a difficult task, namely the complex and dynamic nature of health care. Examples from the investigation of Potassium chloride overdose with CPOE system and unintended consequences of EMR use in clinical environment will be used as illustrations. |
BMI Joint Seminar: What do Patients Do with All that Data? Lessons from Cancer Genetics and Genomics
| Start: | Friday, January 28, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, January 28, 2011 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Lisa Madlensky, PhD, CGC, Moores Cancer Center, UCSD | |
| Description: | This event is organized by iDASH National Biomedical Computing Center and UCSD DBMI. This seminar will include a discussion of the patient perspective of genetic information, using data from studies in the oncology and cancer risk assessment settings. Topics that will be covered include uptake ofgenetic/genomic testing; patients' understanding of genetic test results; and whether patients are likely to change their health behaviors or medical management as the result of genetic information. The discussion will also examine the current ethical and psychosocial issues that are increasingly important as large-scale genomic information becomes more accessible. |
BMI Joint Seminar: GeneWiki, Two Years After the inception-A Systems Biology Perspective for Medical Discovery
| Start: | Wednesday, January 12, 2011 1:00pm (Pacific Standard Time) | |
| End: | Wednesday, January 12, 2011 2:00pm (Pacific Standard Time) | |
| Where: | GMCS 421 | |
| Who: | Jon Huss, Novartis Institute of Genomic Research Foundation | |
| Description: | Gene Wiki is the application of Social Networking to genomic knowledge. Two years ago Gene Wiki was announced through the seminal paper published in PLoS Biology. Much potential was discussed in the paper and the follow up paper published in Nucleic Acid Research. Two years later, we present the potentials again and provide a look back at the two years to see which potentials have been materialized and which still have ways to go. |
BMI Joint Seminar: Sleep Apnea and Telemedicine-An Overview
| Start: | Friday, January 7, 2011 12:00pm (Pacific Standard Time) | |
| End: | Friday, January 7, 2011 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Dr. Carl Stepnowsky, Department of Medicine, UCSD | |
| Description: | The goal of this talk is several fold. First, some background on sleep apnea and its treatment will be provided. Then, given that background, we will discuss the role of telemedicine for both diagnostic and treatment methods related to sleep apnea. Finally, our own interventional approach will bediscussed and demonstrated. |
BMI Thesis Defense: Improving Reverse Vaccinology Selection of Bacterial Protective Antigens Using a Machine Learning Approach
| Start: | Monday, December 20, 2010 2:00pm (Pacific Standard Time) | |
| End: | Monday, December 20, 2010 4:00pm (Pacific Standard Time) | |
| Where: | Stein Medical Research Building, UCSD, Room 344 a/b (3rd flr conf rm) | |
| Who: | Brett Bowman, BMI Graduate Program, SDSU | |
| Description: | ABSTRACT Since Edward Jenner's original experiments with cow-pox, researchers have sought new methods of vaccination that were safer, cheaper, and provided greater protection. The application of genomics technologies to this problem, called Reverse Vaccinology (RV), has the potential to revolutionize the identification of bacterial protective antigens (BPAs) for the development of new vaccines. In this study, we improved upon previously published RV methods by applying modern machine learning tools. We used Vaxijen, a previously published RV data set, in addition to curating our own dataset of bacterial protective antigens from the primary literature. We generated training data by applying 18 publicly available programs for protein annotation to both data sets, and classifiers were then constructed using Support Vector Machines (SVMs), Partial Least-Squares Discriminant Analysis(PLS-DA), and Linear Regression. Accuracy was assessed with stratified leave-tenth-out cross validation (LTOCV), for which we report a maximum accuracy of 92% with the BPA data set. This classifier was then assessed for its ability to recall of BPAs from the proteomes of known pathogens, for whichwe report p-values of 0.00664 (S. aureus) to<0.0001 (M. tuberculosis). To our knowledge this is the first time that machine learning has been used in Reverse Vaccinology, and our results suggest our methods would enhance current efforts to identify of protective antigens in silico.Abbreviations: RV – Reverse Vaccinology, BPA – Bacterial Protective Antigen, CSV – Comma-Separated Value, PLS-DA – Partial Least-Squares Discriminant Analysis, SVM – Support Vector Machines, LTOCV – Leave-Tenth-Out Cross-Validation Thesis Committee Chair: Dr. Faramarz Valafar, BMI Graduate Program, SDSU Second Reader: Dr. Christopher Woelk, Division of Biomedical Informatics, Department of Medicine, UCSD Third Reader: Dr. Gary Hardiman, Department of Medicine, UCSD |
BMI Thesis Defense: Isolation By Resistance Web Services
| Start: | Friday, December 10, 2010 9:00am (Pacific Standard Time) | |
| End: | Friday, December 10, 2010 11:00am (Pacific Standard Time) | |
| Where: | GMCS 329 | |
| Who: | Yoko Suzuki, BMI Graduate Program, SDSU | |
| Description: | With the emergence of landscape genetics as a new interdisciplinary field in the last decade, more sophisticated analyses have developed to examine the role of geographic features in shaping spatial patterns of genetic differentiation. An understanding of how these influence gene frequencies is important for both evolutionary biology and ecology, and can guide conservation and management efforts. In order to assess the relationship between genetic differentiation and geographic distance, the use of a “resistance distance” was proposed in 2006 by McRae. This distance is derived from an application of basic circuit theory to geography. The resistance model is predicted to correlate better with genetic divergence patterns than other more commonly used models. However, there are few ways researchers can obtain ‘resistance distance’ values. I am developing a user-friendly web interface, “Isolation By Resistance Web Service” ( view ~ibdws/googlemaps/ibrws.html), to calculate geographic distances between natural populations using resistance and other methods. This web service will help researchers better analyze spatial genetic patterns in natural populations. Andrew Bohonak, Biology and BMI Graduate Program, SDSU, Committee Chair Faramarz Valafar, Ph.D., BMI Graduate Program, SDSU, Committee Member Roger Whitney, Ph.D., Computer Science, SDSU, Committee Member |
BMI Thesis Defense: Cross-Platform Normalization of Gene Expression Data
| Start: | Thursday, December 9, 2010 1:00pm (Pacific Standard Time) | |
| End: | Thursday, December 9, 2010 3:00pm (Pacific Standard Time) | |
| Where: | LS 269 | |
| Who: | Jason Rudy, BMI Graduate Program, SDSU | |
| Description: | Abstract Simultaneous measurement of gene expression on a genomic scale can be accomplished using microarray technology or by sequencing based methods. Researchers who perform high throughput gene expression assays often deposit their data in public databases, but heterogeneity of measurement platforms leads to challenges for the integration of data sets. Researchers wishing to perform cross platform normalization face two major obstacles. First, a choice must be made about which method or methods to employ. Nine are currently available, and no rigorous comparison exists. Second, softwarefor the selected method must be obtained and incorporated into a data analysis workflow. In this work, cross-platform normalization methods are compared based on inter-platform concordance and on the consistency of gene lists obtained with transformed data using two publicly available testing data sets. Scatter and ROC-like plots are produced, and bootstrapping is employed to obtain distributions for statistics based on those plots. The consistency of platform effects across studies is explored theoretically and with respect to testing data sets. Comparisons indicate that four methods, DWD, EB, GQ, and XPN, are generally effective, while the remaining methods do not adequately correct for platform effects. Of the four successful methods, XPN generally shows the highest inter-platform concordance when treatment groups are equally sized, while DWD is most robust to differently sized treatment groups and consistently shows the smallest loss in gene detection. I provide an R package, CONOR, capable of performing the nine cross-platform normalization methods considered. Thesis Committee Faramarz Valafar, Ph.D., BMI Graduate Program, Committee Chair Barbara Bailey, Ph.D., Mathematics& Statistics, Committee MemberGary Hardiman, Ph.D., Medicine, Director of BIOGEM, UCSD, Committee Member |
BMI Joint Seminar: Human Genetic Variation
| Start: | Friday, December 3, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, December 3, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Kelly Frazer, PhD., Professor of Pediatrics, Chief, Division of Genome Information Sciences, UCSD | |
| Description: | Kelly Frazer, PhD., Professor of Pediatrics, Chief, Division of Genome Information Sciences, UCSD |
Biomedical Informatics Day: Informatics Challenges in Cutting Edge Biomedical Research
| Start: | Thursday, December 2, 2010 3:30pm (Pacific Standard Time) | |
| End: | Thursday, December 2, 2010 9:30pm (Pacific Standard Time) | |
| Where: | GMCS 333 | |
| Who: | Various from LIAI, SDSU, UCSD, and VA Hospital | |
| Description: | San Diego Researchers will present leading edge challenges in Health and Disease with a promise of informatic solution. The event is meant as a challenge for the informatic community. Talks will include: – “Future of Bioinformatics in Science and Medicine” – “Chromatin Structure andGene Regulation” – “ChIP-Sequencing in Asthma” – “DNA Methylation and Hydroxymethylation in Cancer” – “Finding Modified Bases in DNA” |
BMI Seminar: Deconstructing the super-organism
| Start: | Tuesday, November 23, 2010 2:00pm (Pacific Standard Time) | |
| End: | Tuesday, November 23, 2010 3:00pm (Pacific Standard Time) | |
| Where: | Bioscience Center Auditorium | |
| Who: | Bas E. Dutilh, PhD, Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands | |
| Description: | Only a fraction of micro-organisms can be raised in pure culture. This suggests that in the wild, microbial species form a super-organism and rely on one another for their survival. Before we can understand this dependency, we first need to know which processes take place within each of the symbionts. Metagenomic sequencing allows us to assess the composition of microbial communities at an unprecedented scale. However, many analyses to date consider the metagenome as a single entity, while most of the functional interactions between the encoded proteins will occur within the boundaries of individual cells. To solve this, it is important to assign the encountered sequences to species. However, binning is not the only challenge we need to tackle before we understand the interdependencies in microbial ecosystems. An important problem with shotgun sequencing of complex communities is that the diversity is generally sub-sampled. This leads to under-estimation but also, counter-intuitively, to over-estimation of the pathway content. I will introduce Pathway Signature Genes (PSGs), a technique designed to address these issues. PSGs predict the pathway content of the species sampled ina metagenome by correlating the encountered genes with the presence of pathways in complete genomes. This allows us to make reliable predictions about the presence or absence of known pathways. |
BMI Joint Seminar: MicroRNA Control in the Immune System
| Start: | Friday, November 19, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, November 19, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Chanchun Xiao, PhD, Scripps Research Institute | |
| Description: | MicroRNAs (miRNAs) have emerged as a major class of trans‐regulators that control gene expression at the messanger RNA level. Hundreds of miRNA have been identified and bioinformatic studies predict that more are present in the human and mouse genomes. We focus on studying the identity, function, and molecular mechanisms of miRNAs in the immune system. We use the Illumina deep sequencing technology to examine miRNA expression profile in the mouse immune system and in lymphoma specimens from a large cohort of patients with diffuse large B cell lymphoma, aiming to establish a comprehensive view of small RNAs (including miRNAs) expressed in lymphocytes under health and disease conditions, and to discover small RNAs with diagnostic and prognostic values. We employ mouse genetics and other experimental approaches to study the function of individual miRNAs in lymphocyte development, immune response, autoimmune diseases, and lymphomagenesis. Our studies have generated insights into the roles of individual of miRNA in the context of general miRNA biology. oimmune diseases, enesis. Ounergnroles of inAs ithe immune system and the ecular mechanisms underlying miRNA |
BMI Joint Seminar: A Ribosome-associated E3 Ubiquitin Ligase Implicated in Protein Quality Control
| Start: | Friday, November 12, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, November 12, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Claudio Joazeiro, PhD, Scripps Research Institute | |
| Description: | Our laboratory is interested in assigning function to, and elucidating mechanisms of, E3 ubiquitin ligases, the components of the ubiquitin-proteasome system which confer specificity to protein ubiquitylation. I will present our work leading to the annotation of over 600 putative E3s encoded inthe human genome; this has led to the realization that more than half of human E3s have not been studied at any level, so I will also describe functional genomic tools that we have developed in order to accelerate discovery in the field (1,2). In the second part of the talk, I will present our recent findings on the role of a ribosome‐associated E3 ubiquitin ligase in protein quality control (3). 1. Li et al. 2008. PLoS One 3(1):e1487 2. Deshaies and Joazeiro 1009. Annu Rev Biochem. 78:399434. 3. Bengtson and Joazeiro 2010. Nature 467:4703 . |
BMI Joint Seminar: Using Disease Models to Support Context-Sensitive Visualization and Evidence-Based Medicine
| Start: | Friday, November 5, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, November 5, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Lechtag 2A05 | |
| Who: | William Hsu, PhD, Department of Radiological Sciences, UCLA | |
| Description: | Given the large quantity of diverse, heterogeneous data in a typical patient record, clinicians spend much of their time and effort finding relevant information to help accomplish their tasks. One of the challenges in today’s healthcare environment is matching the increased capability of gathering patient data with a comparable ability to understand, analyze, and act rationally upon this information. Our group is developing informatics tools to facilitate the extraction and structuring of observational data collected during clinical practice. My research focuses on utilizing this data to build disease models and end-user applications that leverage these models to answer questions related to the diagnosis and treatment of individual patient cases. In this talk, I will describe two ongoing projects: 1) a tool for abstracting and visualizing results of clinical trials reported in literature to support disease model creation, and 2) a model-driven application that visually summarizes trends in the patient data. |
BMI Joint Seminar: Count Queries, Their Use, Challenges, and Opportunities
| Start: | Friday, October 29, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, October 29, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Staal Vinterbo, PhD, Division of Biomedical Informatics, UCSD | |
| Description: | Staal Vinterbo, PhD, Division of Biomedical Informatics, UCSD |
BMI Joint Seminar: Global microRNA Profiling Technology and Applications
| Start: | Friday, October 22, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, October 22, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 107 | |
| Who: | James Xia, Ph.D., GenoSensor Corporation, Tempe, Arizona | |
| Description: | MicroRNAs (miRNAs) are a group of small non-coding RNA molecules (~21 nt) that are widely expressed in a variety of organisms in Eukaryotes. miRNAs have impacted mRNA stability and translation, heterochromatin formation, genome rearrangement, DNA excision, and cell transformation. Thousands of miRNA sequences have been identified in many species and their expression profiling helps researchers to investigate the roles of miRNAs in many areas, including developmental biology, cancer, neuro disorders, metabolic diseases, and immune response. The seminar will discuss current miRNA detection andprofiling technologies and applications. Host: Dr. Gary Hardiman, BIOGEM |
BMI Joint Seminar: "Beta Cells and Femtocells: Surfing the Data Tsunami Toward Personal Health Knowledge"
| Start: | Tuesday, October 19, 2010 2:00pm (Pacific Standard Time) | |
| End: | Tuesday, October 19, 2010 3:00pm (Pacific Standard Time) | |
| Where: | Leichtag 205 | |
| Who: | Nathaniel Heintzman, School of Medicine, UCSD | |
| Description: | Nathaniel Heintzman, School of Medicine, UCSD |
BMI Joint Seminar: Elucidating gene function through integrative genetics and crowdsourcing
| Start: | Monday, October 18, 2010 4:00pm (Pacific Standard Time) | |
| End: | Monday, October 18, 2010 5:00pm (Pacific Standard Time) | |
| Where: | Leichtag 205 | |
| Who: | Andrew Su, Genomic Institute of Novartis Research Foundation | |
| Description: | Andrew Su, Genomic Institute of Novartis Research Foundation |
BMI Seminar: Genome-scale Metabolic Models
| Start: | Tuesday, October 12, 2010 2:00pm (Pacific Standard Time) | |
| End: | Tuesday, October 12, 2010 3:00pm (Pacific Standard Time) | |
| Where: | Bioscience Center Auditorium | |
| Who: | Chris Henry, Argonne National Laboratory | |
| Description: | Dr. Chris Henry, Argonne National Laboratory, will talk about genome-scale metabolic modeling in Bacteria. Chris is a pioneer of the automation of metabolic modeling, and will discuss how these models can be used to refine biochemical processes including biofuel production and oil spills. He willdiscuss the efficient and accurate prediction of phenotype from genotype, an explosive area of bioinformatics research that is being revolutionized by high throughput technology. |
BMI Seminar: Lateral Gene Transfer in Prokaryotes
| Start: | Friday, October 8, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, October 8, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Bioscience Center Auditorium | |
| Who: | Gary Olsen, Professor of Microbiology, University of Illinois Urbana-Champaign | |
| Description: | Gary is one of the pioneers of bioinformatics and a leader of genomics. He has been involved in studying Archaea since their discovery, and has a long-standing research interest in identifying the origins of horizontally transferred genes. You can find out more about his research here:< view > view |
BMI Joint Seminar: Biomedical Informatics Issues in the Army Medical Department
| Start: | Wednesday, October 6, 2010 12:00pm (Pacific Standard Time) | |
| End: | Wednesday, October 6, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Rich Wilson, MS, RHIA, Major, U.S. Army | |
| Description: | The U.S. Department of Defense is the largest health care provider in the world. Both because of its size and the variety of environments that medical services are provided - ranging from battlefields in Iraq and Afghanistan to outpatient clinics - a variety of interesting informatics challenges arise. To ensure that future medical care is optimized, the Army Medical Department is collecting large masses of clinical data from which new knowledge can be derived. In this presentation I will first provide an overview of the Army Medical Department, including current operations, the state of health information technology, and the Army's biostatistical data repository. Second, I will present a project in which natural language processing of history and physical reports was used to automatically identify patients with personal and/or family history of mesothelioma. Finally, I will outline my future research directions in clinical information retrieval, as well as areas of potential areas for collaboration with the Army Medical Department. |
BMI Joint Seminar: Modeling and Visualization of Neuro-Oncology Cases
| Start: | Friday, October 1, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, October 1, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Ricky Taira, PhD, Department of Radiological Sciences, UCLA | |
| Description: | We describe the development of a prototype tool for the abstraction of patient information for the purpose of formally documenting the course of disease for a given patient. The test domain is neuro-oncology. The features of the tool include: 1)the use of natural language processing tools to assist a clinical case abstractor in structuring report information; 2) Specification of a target neuro-oncology situational ontology; 3) an interface for intra and inter-coreference tagging of findings/problems; 4) an environment for storing/retrieving and editing cases that have been previously or currently being structured. The results of this abstraction process are used in an application (to be described in a later seminar by Dr. Hsu) for visualizing both patient and population trends. Insightful anecdotal user comments and discussions of future work and scope are presented. |
BMI Thesis Proposal: Cross-Platform Normalization of Microarray Data
| Start: | Thursday, September 30, 2010 2:00pm (Pacific Standard Time) | |
| End: | Thursday, September 30, 2010 4:00pm (Pacific Standard Time) | |
| Where: | GMCS 328 | |
| Who: | Jason Rudy, BMI Graduate Program, SDSU | |
| Description: | Abstract Researchers who perform high throughput gene expression assays often deposit their data in public databases such as ArrayExpress and Gene Expression Omnibus (GEO), the latter of which currently houses 474,650 assays distributed across 7,829 platforms. A major obstacle to the full exploitation and analysis of such large scale databases is the integration of data collected using different technologies or platforms. Cross-platform microarray data normalization is the process of adjusting these data to reduce or eliminate systematic platform bias. Several methods have been proposed. For this thesis project, I provide implementation of all the most widely accepted methods in the popular R environment. This package can serve as the state of the art and most comprehensive microarray cross-platform normalization toolkit. I also propose to make use of the unique multi-platform data set provided by the Microarray Quality Control (MAQC) project to evaluate the success of each method in cross-platform normalization for Affymetrix and Illumina, the two most commonly used platforms. Using the results of this evaluation, the package will provide a “best practices” guide for platform independent microarray data analysis. The resulting toolkit can be used to significantly |
BMI Seminar: Implications of a theory of healthcare quality for computational medicine
| Start: | Friday, September 24, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, September 24, 2010 1:00pm (Pacific Standard Time) | |
| Where: | John Fontanesi, PhD, Division of Preventive Medicine, UCSD | |
| Who: | John Fontanesi, PhD, Division of Preventive Medicine, UCSD | |
| Description: | There is a rich history of Service Science that has improved the quality of IT, Call Center and Marketing Industries. What Service Science is, how it can be translated to health care quality and the implications for various aspects of computational medicine will be explored in this presentation.Light lunch will be provided |
BMI Seminar: Implementing a Health Information Exchange across San Diego County– Informatics, Clinical and Political Hurdles
| Start: | Thursday, September 16, 2010 12:00pm (Pacific Standard Time) | |
| End: | Thursday, September 16, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Anupam Goel, MD, Division of Biomedical Informatics, UCSD | |
| Description: | San Diego was selected as one of the 17 sites across the country to serve as a Beacon community to see how exchanging clinical information can improve health care quality and reduce health care costs. Over the next three years, several UCSD faculty will be partnering with clinical organizations across San Diego to share clinical information in real-time and to generate a reporting strategy to measure the program’s effectiveness. The presenter will speak about the various challenges that the project team has faced so far and their attempts to overcome those challenges. |
BMI Thesis Proposal: Improving Reverse Vaccinology Selection of Bacterial Vaccine Candidates Using a Machine Learning Approach
| Start: | Tuesday, August 31, 2010 2:00pm (Pacific Standard Time) | |
| End: | Tuesday, August 31, 2010 3:00pm (Pacific Standard Time) | |
| Where: | Stein Building, Room 344a, UCSD School of Medicine | |
| Who: | Brett N. Bowman, Bioinformatics and Medical Informatics Graduate Program, SDSU | |
| Description: | Abstract: Since Edward Jenner's original experiments with cow-pox, researchers have sought new methods of vaccinating people that were safer, cheaper, and provided greater protection. The application of new genomics technologies to this problem, called Reverse Vaccinology (RV), has the potentialto revolutionize the identification and development of new vaccine candidates (VCs). In this study, we improve upon previously published RV methods by applying modern Machine Learning tools to the problem. We take a previously published RV datasets (Vaxijen, VIOLIN), in conjunction with a primaryliterature search to generate a list of validated VCs - to our knowledge the largest such dataset. We then applied a number of publicly available bioinformatics programs to annotate the protein data for a variety of biologically relevant features. Variables were selected and classifiers constructed on this data using Support Vector Machines (SVMs), Partial-Least Squares (PLS-DA), and Linear Regression. The most accurate SVM classifier (91.9%), as assessed by stratified leave-tenth-out cross validation, was used to assess the recall of known VCs from the whole genomes of known pathogens. This is the first time to our knowledge that Machine Learning has been applied to Reverse Vaccinology, and our results suggest that Machine Learning classifiers can be used to separate VCs from other proteins with high accuracy. |
BMI Joint Seminar:“-omics” Approaches for Studying Psychiatric Diseases
| Start: | Friday, May 28, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, May 28, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Lilia Iakoucheva Sebat, PhD. Department of Psychiatry, UCSD | |
| Description: | Genes play an important role in the etiology of psychiatric disorders. Recent genome-wide association studies and studies of copy number variants in psychiatric diseases implicated a large number of different genes including common and rare variants. Our main goal is to understand how these seemingly unrelated candidate genes contribute to psychiatric diseases, such as autism and schizophrenia. We hypothesize that defects in multiple genes that are diverse in their individual functions, but interact within the context of common cellular pathways/networks/functional modules are important for disease pathogenesis. To discover these common pathways, we are starting to build disease-focused protein-protein interaction networks using experimental and computational approaches. Our final goals are: (1) to construct comprehensive maps of protein-protein interaction networks for autism and schizophrenia candidate genes; (2) to define the splicing repertoire of the autism and schizophrenia candidate genes; (3) to integrate the splicing interactomes with the traditional interactomes; (4) to investigate the perturbations of the disease networks and functional modules by mutations identified from the patients. |
BMI Workshop on Transcriptomics, GWAS HiTS, Next Generation Sequencing and more on Illumina platforms
| Start: | Monday, May 24, 2010 8:00am (Pacific Standard Time) | |
| End: | Monday, May 24, 2010 5:00pm (Pacific Standard Time) | |
| Where: | Garren Auditorium, Biomedical Sciences Building, UCSD | |
| Who: | ||
| Description: | This workshop is jointly held with first annual San Diego Illumina users group. This all day workshop will cover topics such as Transcriptomics, GWAS HiTS, Next Generation Sequencing and more using Illumina platforms. The workshop is useful for those who simply want to learn the topics mentioned, or are familiar with the topics and are interested in finding out about what Illumina offers in each domain.Breakfast and lunch will be provided. Entrance to the workshop requires registration: view Agenda of the workshop can be found at view |
BMI Joint Seminar: Omics in Medicine
| Start: | Friday, May 21, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, May 21, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | David Perkins, MD, PhD, Department of Surgery, UCSD | |
| Description: | David Perkins, MD, PhD, Department of Surgery, UCSD |
Biomedical Informatics Open House&End of Year Celebration
| Start: | Monday, May 17, 2010 4:00pm (Pacific Standard Time) | |
| End: | Monday, May 17, 2010 6:00pm (Pacific Standard Time) | |
| Where: | GMCS 421 | |
| Who: | ||
| Description: |
BMI Joint Seminar: Algorithmic Problems in Genotype-Phenotype Correlation
| Start: | Friday, May 14, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, May 14, 2010 1:00pm (Pacific Standard Time) | |
| Where: | GMCS 421 | |
| Who: | Vineet Bafna, PhD, Department of Computer Science& Eng., UCSD | |
| Description: | The availability of inexpensive genotyping and sequencing techniques allow us the opportunity to sample the genomes of large cohorts of individuals. The associations of these genotypes with phenotypes offers novel computational challenges due to the large volumes of data, and complex inheritance patterns of the phenotypes. In this talk, I will describe recent, mostly unpublished, algorithms for correlating genotypes with phenotypes. Specifically, I will discuss the discovery of rare variants, locus locus interactions, and tests of selection. |
BMI Joint Seminar: Under-triage of Elderly Trauma Patients
| Start: | Friday, May 7, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, May 7, 2010 1:00pm (Pacific Standard Time) | |
| Where: | GMCS 421 | |
| Who: | David Chang, PhD, Department of Surgery, UCSD | |
| Description: | OBJECTIVE: To determine whether age bias is a factor in triage errors. DESIGN: Retrospective analysis of 10 years (1995-2004) of prospectively collected data in the statewide Maryland Ambulance Information System followed by surveys of emergency medical services (EMS) and trauma center personnel at regional EMS conferences and level I trauma centers, respectively. PATIENTS: Trauma patients were defined as those who met American College of Surgeons physiology, injury, and/or mechanism criteria and were subjectively declared priority I status by EMS personnel. MAIN OUTCOME MEASURE: Undertriage, defined as when trauma patients were not transported to a state-designated trauma center. RESULTS: The registry analysis identified 26 565 trauma patients. The undertriage rate was significantly higher in patients aged 65 years or older than in younger patients (49.9% vs 17.8%, P< .001). On multivariate analysis, this decrease in trauma center transports was found to start at age 50 years (odds ratio, 0.67; 95% confidence interval, 0.57-0.77), with another decrease at age 70 years (odds ratio, 0.45; 95% confidence interval, 0.39-0.53) compared with patients younger than 50 years. A total of 166 respondents participated in the follow-up surveys and ranked the top 3 causal factors for this undertriage as inadequate training, unfamiliarity with protocol, and possible age bias. CONCLUSIONS: Even when trauma is recognized and acknowledged by EMS, providers are consistently less likely to consider transporting elderly patients to a trauma center. Unconscious age bias, in both EMS in the field and receiving trauma center personnel, was identified as a possible cause. |
BMI Joint Seminar: Documenting Transitional Information in EMR
| Start: | Friday, April 30, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, April 30, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Yunan Chen, PhD, Department of Informatics, UC Irvine | |
| Description: | An observational study was conducted to examine EMR-based documentations in an Emergency Department (ED), with an emphasis on computerized documentation activities in complex flow of clinical processes. This study revealed a huge gap between formal EMR documentation and actual clinical workflow, which forces ED staff to rely on intermediate - transitional artifacts to facilitate their work. The analysis of these transitional artifacts in four different clinical workflows show that the EMR system’s inability to document procedural information, capture key information, and present information according to actual clinical workflow lead to the use of transitional artifacts. The findings of this study call for designing EMR system not only for keeping formal patients’ records, but also for documenting transitional information in the chart-writing process. |
BMI Joint Seminar: Protecting Privacy in Informatics: Are We There Yet?
| Start: | Friday, April 23, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, April 23, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Anand Sarwate, PhD, Information Theory And Applications Center, UCSD | |
| Description: | Privacy is a loaded term in the English language; if you ask 5 different people what they think it means, they will give you 5 different answers. In information processing systems, guaranteeing privacy most often means "protecting against re-identification." In medical informatics this is spelledout in the HIPAA Privacy Rule. In this talk I will give a survey of different ways in which sensitive information may be handled and describe approaches towards developing a quantitative definition of privacy. I will describe "state of the art" methods that guarantee statistical privacy and will show their limitations for clinical and research applications. Privacy in these settings must be addressed by systems incorporating statistical methods, access control, regulation, and repercussions for misuse. |
BMI Joint Seminar: Effects of EMR on Medication Safety in Primary Care Practices
| Start: | Friday, April 16, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, April 16, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Grace Kuo, PharmD, MPH | |
| Description: | Context: Evidence for effective strategies of medication reconciliation in the ambulatory care setting is lacking. Study Objectives: To compare medication reconciliation practices between primary care clinics using electronic medical record (EMR) and clinics using paper medical record (PMR). Study Design: Cross-sectional observational and time motion workflow study. Setting: Five primary care clinics in San Diego. Participants: 150 adult patients taking at least two medications completed the study (with a total of 1,238 medications). Essential feature of study: Outpatient medication reconciliation accuracy. Outcome measures: Frequency and type of medication reconciliation. Results: Of the 1,238 medications, the frequency of medication reconciliation by names only was similar between EMR and PMR clinics (96% vs. 97%, p=0.209) but the frequency of medication reconciliation by names plus directions was more in PMR clinics (42% vs. 65%, p<0.001). However, the accuracy of medication review was better in the EMR group. In the study, 57% of medications were reviewed and names reconciled (64%EMR vs. 47%PMR, p<0.001), 25% were medications reportedly used by patients but not recorded in the chart (19%EMR vs. 35%PMR, p<0.001), 18% were medications recorded in the chart but not used by patients (17%EMR vs. 18%PMR, p=0.580). Medication names were reviewed by 90% of nurses and 85% of providers (or 96% by any). Conclusions: Medication reconciliation occurred almost always by names in both EMR and PMR clinics but only half of the time by names plus directions– more frequently in PMR clinics. Medication reconciliation accuracy occurred in half of medications; the use of EMR appears to be significantly better compared with the use of PMR. Times spent by nurses and providers in reviewing medication names only and medication names plus directions were significantly different between groups but not significantly different within groups. |
BMI Joint Seminar: Clinical Informatics and Telemedicine in Urban Safety Net Clinics
| Start: | Friday, April 9, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, April 9, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Leichtag 2A05 | |
| Who: | Lola Ogunyemi, PhD | |
| Description: | Urban, safety net clinics work primarily with uninsured and underinsured patients who often have chronic conditions that need to be addressed. In this talk, I will discuss the role that informatics can play in enhancing the quality of care at such clinics; focusing on two projects that the Centerfor Biomedical Informatics at Charles Drew University has with seven urban, safety net clinics in South Los Angeles. One involves computerized decision support for diabetes care in a Los Angeles County health center and the other involves teleretinal screening for diabetic retinopathy at six federally qualified health centers. |
BMI Joint Seminar: "Contemporary Clinical Research: An Informatics Approach"
| Start: | Tuesday, March 23, 2010 12:00pm (Pacific Standard Time) | |
| End: | Tuesday, March 23, 2010 1:00pm (Pacific Standard Time) | |
| Where: | Stein Room 344A | |
| Who: | ||
| Description: | Peter Szolovits, PhD,Massachusetts Institute of Technology, Clinical trials are very expensive, slow, and tend to be limited to a modest number of patients. Inspired by our field’s growing ability to perform high-throughput measurements of genes and their expression, we explore the possibility of using ordinaryclinical data sets to stand as a proxy for high-throughput determination of phenotype and environment. If successful, this promises to speed up translational research, make better use of existing data, and reduce the costs of studies. I describe our experience in applying this model to an exploratory study of rheumatoid arthritis. In addition to describing our process, I will also introduce the machinery developed by the Partners Healthcare i2b2 project to support such efforts, describe a clever and privacy-protecting mechanism developed at the Brigham and Women’s Hospital for using discarded blood samples to speed study accrual, and then elaborate on the medical natural language approaches we have taken to extracting meaningful data from the narrative text that forms much of clinical records. |
Seminar: The Electronic Medical Record in the Post-genomic Era
| Start: | Friday, March 12, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, March 12, 2010 1:00pm (Pacific Standard Time) | |
| Where: | UCSD - Leichtag 2A05 | |
| Who: | ||
| Description: | Speaker: Vibha Bhatnagar, MD, MPHThe electronic medical record (EMR) can be used to create very large scale databases for genetic studies and “virtual cohorts” for the study of complex chronic diseases in a setting representative of clinical practice. Increasingly, genetic studies are expected to leverage the EMR for accuratepatient phenotyping Hypertension and renal failure are examples of a complex traits, determined by the interplay of multiple genes, lifestyle and medical comorbid factors, that may be best studied in the primary care (or clinical cohort) arena rather than smaller experimental (clinical trial) settings. One of the key features of our work was to take advantage of the large-scale, comprehensive and integrated EMR in the Veteran’s Administration Healthcare System known as VistA (Veterans Health Information Systems and Technology Architecture< view > ) and explore the predictive value of genetic markers for antihypertensive drug response and hypertension related comorbid disease. The VA EMR can be accessed via a graphical user interface known as the Computerized Patient Record System (CPRS< view > ), an intuitive single interface for health care providers to review and update a patient’s EMR. VASDHS is a part of the Veterans Integrated Service Network 22 (VISN-22), spanning Southern California and Southern Nevada. VISN-22 provides research support by abstracting electronic medical data from individual VA healthcare facilities and makes the data accessible to investigators for research purposes in a “data warehouse”. |
Seminar: Next-generation Proteomics: The Computational Engine of Mass Spectrometry Discoveries
| Start: | Friday, February 12, 2010 12:00pm (Pacific Standard Time) | |
| End: | Friday, February 12, 2010 1:00pm (Pacific Standard Time) | |
| Where: | UCSD - Leichtag Building | |
| Who: | ||
| Description: | Speaker: Nuno Bandeira, PhDThe ongoing quest for understanding the cellular role of proteins is riddled with Bioinformatics computational puzzles whose solutions could dramatically affect health care, bioenergy and biotechnology in general. The main generator of these protein puzzles is mass spectrometry – a technology whose development merited a Nobel Prize in Chemistry (2002) and continues to expand and improve at an impressive rate. In mass spectrometry, proteins are represented by ‘spectrum fingerprints’ whose identification is key to understanding cellular proteomics states – a task typically addressed bydatabase search techniques. This talk will focus on a novel computational framework for the analysis of mass spectrometry data (Spectral Networks) and discuss the underlying algorithmic and machine learning problems. Consequent applications of these algorithms include protein identification in cataractous lens, characterization of monoclonal antibody drugs, sequencing snake venoms and high-throughput elucidation of bioactive cyclic peptides. |