BMIR Research Colloquium: Matthew Lange "Health, Food, and Food System Informatics--Emerging disciplines building the Internet of Food" @ MSOB, Conference Room X-275 | Stanford | California | United States
Matthew Lange, PhD Research Food and Health Informatician Principal Investigator, IC3-FOODS Associate Director, Initiative for Wireless Health & Wellness UC Davis and UC Davis Health System Abstract: The Semantic Web and Internet of Food hold[...]
BMIR Research in Progress: Juan Banda "My Odyssey with OHDSI" @ MSOB, Conference Room X-275 | Stanford | California | United States
Juan M. Banda, PhD, Research Scientist, Stanford Center for Biomedical Informatics Research , Stanford University Abstract: With over 160 collaborators in 16 countries, the Observational Health Sciences and Informatics (OHDSI) data network of over 600[...]
BMIR Research in Progress: Samson Tu & Mor Peleg "Decision Support for Multi Morbidities" @ MSOB, Conference Room X-275 | Stanford | California | United States
Samson Tu, MS, Sr. Research Engineer, Stanford Center for Biomedical Informatics Research, Stanford University, & Mor Peleg, PhD, Visiting Associate Professor, Stanford University, Dept. of Information Systems, University of Haifa ABSTRACT: Realizing the proven capabilities[...]
BMIR Research in Progress: Karishma Rohanraj Desai "Modeling Effect of Analgesic Combinations & Interactions on Post-operative Pain Outcomes" @ MSOB, Conference Room X-275 | Stanford | California | United States
Karishma Rohanraj Desai, Postdoctoral Scholar, Stanford Center for Biomedical Informatics Research, Stanford University ABSTRACT: Pain management is a major challenge for surgical patients and many are left with poorly managed pain control. In addition, concomitant[...]
BMIR Research in Progress: Ken Jung "Learning Effective Representations of EHR Data" @ MSOB, Conference Room X-275 | Stanford | California | United States
Ken Jung, Research Scientist, BMIR, Stanford University ABSTRACT: Longitudinal clinical data captured in Electronic Health Records are complex and high dimensional.  Researchers must make challenging decisions that can have a significant impact on predictive performance[...]
BMIR Research in Progress: Deendayal Dinakarpandian "Towards a Reasonable Paperless Future for Scientific Research" @ MSOB, Conference Room X-275 | Stanford | California | United States
Deendayal Dinakarpandian Visiting Associate Professor BMIR, Stanford University ABSTRACT: The nature and pace of biomedical research has changed considerably over the years. In contrast, the traditional model of publishing the results of scientific research in[...]
BMIR Research Colloquium: Matthew Lungren M.D., Darvin Yi "Optimizing Deep Learning for Medical Image Informatics" @ MSOB, Conference Room X-275 | Stanford | California | United States
Matthew Lungren M.D. Assistant Professor of Radiology (Pediatric Radiology) Darvin Yi Graduate Student Stanford University ABSTRACT: With the explosion of deep learning for computer vision, the medical imaging field is well into exploring these new[...]
BMIR Research in Progress: Madeleine Scott "Integration of Transcriptomic Data and Electronic Medical Records Enable Investigation of the Previously Overlooked Role of the Immune System in Fibrotic Disorders" @ MSOB, Conference Room X-275 | Stanford | California | United States
Title: “Integration of Transcriptomic Data and Electronic Medical Records Enable Investigation of the Previously Overlooked Role of the Immune System in Fibrotic Disorders”   Abstract: There is increasing evidence that the immune system plays a[...]
BMIR Research in Progress: Azadeh Nikfarjam "Drug Safety Information Extraction from Social Media" @ MSOB, Conference Room X-275 | Stanford | California | United States
Azadeh Nikfarjam Postdoctoral Scholar BMIR, Stanford University ABSTRACT: Adverse drug reactions (ADRs) are a major public health concern and are among the top causes of morbidity and mortality. Many ADRs, are not identified in pivotal[...]
BMIR Research in Progress: David Ouyang "Beyond Traditional Data Streams: Analysis of Organic Datasets in Healthcare" @ MSOB, Conference Room X-275 | Stanford | California | United States
David Ouyang, M.D. Stanford Health Care Stanford Medicine ABSTRACT: Many traditional data sets in healthcare, such as billing data and administrative outcome registries, are detached from direct patient care. This limitation can make analysis fraught,[...]
BMIR Research Colloquium: Teri Klein "Pharmacogenomics Knowledge for Personalized Medicine" @ MSOB, Conference Room X-275 | Stanford | California | United States
Teri Klein Member of Academic Council Professor (Research) of Biomedical Data Science and of Medicine (BMIR) Stanford University Abstract: Pharmacogenomics (PGx) focuses on the use of genomic information to guide drug therapy and is a[...]
BMIR Research in Progress: Wen-wai Yim "Classification of Hepatocellular Carcinoma Stages from Free-text Clinical and Radiology Reports" @ MSOB, Conference Room X-275 | Stanford | California | United States
Wen-Wai Yim Postdoctoral Scholar BMIR, Stanford University “Classification of Hepatocellular Carcinoma Stages from Free-text Clinical and Radiology Reports” Abstract: Cancer stage information is important for clinical research. However, they are not always explicitly noted in[...]
BMIR Research Colloquium: Anthony Juehne “Biomedical Research Transparency and Reproducibility: Causes, Impacts, and Solutions” @ MSOB, Conference Room X-275 | Stanford | California | United States
  Anthony Juehne, MPH Sr. Implementation and Evaluation Analyst The Research Data Alliance U.S Rensselaer Polytechnic Institute ABSTRACT: The scientific method depends on the verifiability and reproducibility of findings crucial to the construction of a[...]
BMIR Research In Progress: Serena Yu-Ching Yeung "Towards Ambient Intelligence in AI-Assited Hospitals" @ MSOB, Conference Room X-275 | Stanford | California | United States
  Serena Yu-Ching Yeung, Graduate Student, Stanford University ABSTRACT: Artificial intelligence has begun to impact healthcare in areas including electronic health records, medical images, and genomics. But one aspect of healthcare that has been largely[...]
BMIR Research in Progress: Hong Zheng "Benchmark of lncRNA Quantification for RNA-Seq of Cancer Samples" @ MSOB, Conference Room X-275 | Stanford | California | United States
Hong Zheng, Postdoctoral Scholar, BMIR, Stanford University ABSTRACT: Long non-coding RNAs (lncRNAs) emerge as important regulators of various biological processes. While many studies have exploited public resources such as The Cancer Genome Atlas to study[...]
BMIR Research in Progress: Aditya Rao "A Novel Multi-Cohort Analysis Framework for Analysis of Host-Response Signatures" @ MSOB, Conference Room X-275 | Stanford | California | United States
Aditya Rao, Graduate Student, ITI, Khatri Lab, Stanford University Public data repositories and other data sharing platforms have been a massive boon to researchers in the biomedical sciences. In our lab, we have developed approaches[...]
BMIR Research Colloquium: Nitesh Vijay Chawla "“Being a Dataologist: Data will see you now" @ MSOB, Conference Room X-275 | Stanford | California | United States
  Nitesh Vijay Chawla, PhD Frank M. Freimann Professor of Computer Science and Engineering Director, Interdisciplinary Center for Network Science and Applications (iCeNSA) University of Notre Dame ABSTRACT: The availability of electronic health care records[...]
BMIR Research Colloquium: Matthew Eisenberg "Health Information Exchange:  What’s taking so long, hat are the real barriers and why won’t the fax machine just die?" @ MSOB, Conference Room X-275 | Stanford | California | United States
Matthew Eisenberg, M.D., Associate Chief Medical Information Officer (ACMIO) Clinical Assistant Professor (Affiliated), Stanford Center for Biomedical Informatics Research, Stanford University Abstract: Easy access to clinical information that travels with the patient wherever she seeks[...]
BMIR Research in Progress: Hima Anbunathan “Genomic Landscape of Uveal Melanoma” @ MSOB, Conference Room X-275 | Stanford | California | United States
Postdoctoral Scholar, Gentles Lab/Mackall Lab, Stanford University     Uveal melanoma (UM) is the most common cancer of the adult eye and manifests as a highly aggressive form in approximately half of the patients. We[...]
BMIR Research in Progress: Bogdan Luca "The Derivation of a Novel Classification Framework for Prostate Cancer Using Unsupervised Bayesian Modelling of Bulk Transcriptome Data" @ MSOB, Conference Room X-275 | Stanford | California | United States
Bogdan Luca, Postdoctoral Scholar, Gentles Lab, Stanford Abstract: A critical problem in the clinical management of prostate cancer is that it is highly heterogeneous. Accurate prediction of individual cancer behaviour is therefore not achievable at[...]
Medicine Grand Rounds: Applied Biomedical Informatics: Harnessing Big Data to Optimize Patient-Valued Care @ LKSC, Berg Hall | Palo Alto | California | United States
Presenter: Tina Hernandez-Boussard                                                                 [...]
BMIR Research Colloquium: Sandy Napel  “Radiomics: Tools and Techniques” @ MSOB, Conference Room X-275 | Palo Alto | California | United States
Sandy Napel, PhD, Professor of Radiology,Co-Division-Chief, Integrative Biomedical Imaging Informatics at Stanford (IBIIS)Co-Director, Radiology 3DQ Lab Abstract: Radiomics is a process that extracts a feature vector of quantitative metrics to describe an image or a part[...]
BMIR Research Colloquium: SamsonTu "Ontologies, Information Models, and Knowledge Bases: Their Representations and Uses" @ MSOB, Conference Room X-275 | Stanford | California | United States
Samson Tu, Senior Research Scientist, Staff Emeritus Retiree, Stanford University Abstract: The boundaries between ontologies, information models, and knowledge bases are often blurred and people are often confused about the representational choices that are appropriate for each. Over[...]
BMIR Research Colloquium: Russ Greiner "An Effective Way to Estimate an Individual's Survival Distribution" @ MSOB, Conference Room X-275 | Stanford | California | United States
Russ Greiner, PhD, Professor, Department of Computing Science PI, Alberta Machine Intelligence Institute University of Alberta   Abstract: An accurate model of a patient’s survival distribution can help determine the appropriate treatment and care of[...]
Medicine Grand Rounds: Artificial Intelligence and Machine Learning in Medicine, Why, What and How? @ LKSC, Berg Hall | Palo Alto | California | United States
Presenter: Jonathan Chen, MD, PhD Assistant Professor of Biomedical Informatics Stanford University Jonathan H Chen MD, PhD is a physician-scientist with professional software development experience and graduate training in computer science. He continues to practice Internal[...]
BMIR Research In Progress: Francesco Vallania "Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations With Aging" @ MSOB, Conference Room X-275 | Rome | Georgia | United States
Francesco Vallania, Postdoctoral Scholar, ITI, Stanford University ABSTRACT: Post-translational modifications of histone proteins and exchanges of histone variants at chromatin are central to the regulation of nearly all DNA-based biological processes. However, the degree and[...]
BMIR Colloquium: Craig E. Stanley Jr., PhD Paul L. Snyder, PhD William F. Dowling, PhD Mevan S. Samarasinghe "Towards an integrated healthcare knowledge graph: Transforming and connecting dynamic healthcare data” @ MSOB, Conference Room X-275 | Stanford | California | United States
Craig E. Stanley Jr., PhD; Paul L. Snyder, PhD; William F. Dowling, PhD; Mevan S. Samarasinghe, VP Search & Discovery Elsevier ABSTRACT: As the scale and scope of healthcare information grows, practices evolve from traditional[...]
BMIR Research In Progress: Almudena Espin Perez “Genomics responses to environmental exposures in population studies: Exposome studies using systems toxicology approaches” @ MSOB, Conference Room X-275 | Stanford | California | United States
Almudena Espin-Perez Postdoctoral Scholar Gentles Lab BMIR, Stanford University Abstract: Efforts in cancer prevention have drawn increasing attention in the past few years. However, despite significant efforts the impact of biomarkers for early detection of[...]
BMIR Research In Progress: Ken Jung “Predictive models that work in the clinic” @ MSOB, Conference Room X-275 | Stanford | California | United States
Ken Jung, Research Scientist, BMIR, Shah Lab, Stanford University ABSTRACT: Most published work on predictive models intended for use in clinical applications focus narrowly on technical validation rather of the models themselves, while community wisdom[...]
BMIR Research In Progress: Hayley Warsinske "Prospective validation of a three-gene signature for tuberculosis diagnosis, predicting progression and evaluating treatment response" @ MSOB, Conference Room X275 | Stanford | California | United States
Hayley Warsinske, Postdoctoral Scholar, ITI, Stanford Abstract: The World Health Organization (WHO) has identified the need for a non-sputum based triage test for active tuberculosis disease that can be used to identify those who need[...]