BMIR Research in Progress: Edward H. Lee “A Deep Learning Framework to Predict Survival from Medical Images of Lung Cancer Patients” @ MSOB, Conference Room X-275 | Stanford | California | United States
Edward H. Lee Graduate Student Gevaert Lab, Stanford University We present a deep learning framework to predict survival of lung cancer patients by using convolutional networks to learn high-dimensional representations of tumor phenotypes from CT[...]
BMIR Research in Progress: Marcos Martinez-Romero "CEDAR's Predictive Data Entry:  Easier and Faster Creation of High-quality Metadata" @ MSOB, Conference Room X-275 | Stanford | California | United States
  Marcos Martínez-Romero, PhD Research Software Developer BMIR, Stanford University Abstract: The ability to find and to access biomedical data that are stored in online repositories depends on the quality of the associated metadata. Despite[...]
BMIR Research Colloquium: Manuel Rivas "Finding Signals in Human Genome Sequencing Studies: Data, Models, and Inference" @ MSOB, Conference Room X-275 | Stanford | California | United States
Manuel Rivas, PhD Assistant Professor DBDS, Stanford University ABSTRACT: Genome sequencing studies applied to large case-control series, populations or biobanks with extensive phenotyping raise novel analytical challenges and present new opportunities to interrogate the human[...]
BMIR Research Colloquium: Sorin Draghici "Discovering Disease Subtypes Through the Integration of Multiple Types of Omics Data” @ MSOB, Conference Room X-275 | Stanford | California | United States
Sorin Draghici, PhD Associate Dean for Innovation and Entrepreneurship and Director of the Anderson Institute, Professor, Computer Science Wayne State University ABSTRACT: A recent paper in The New England Journal of Medicine and a follow-up in[...]
BMIR Research Colloquium: Andrew Gentles "Clinically-relevant Cell Type Cross-talk Identified from a Lung Tumor Microenvironment Interactome" @ MSOB, Conference Room X-275 | Stanford | California | United States
  Andrew Gentles Associate Professor (Research) BMIR, Stanford University ABSTRACT: Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our knowledge comes from studies isolating the interactions between malignant cells[...]
BMIR Special Research Colloquium: Ram D. Sriram “Information Technology for the Health Care Enterprise” @ MSOB, Conference Room X-275 | Stanford | California | United States
  Ram D. Sriram, PhD Chief, Software and Systems Division Information Technology Laboratory National Institute of Standards and Technology Monday, February 27th, 2017, 12:00 pm to 1:00 pm MSOB Conference Room X-275 ABSTRACT: According to[...]
BMIR Research in Progress: Katie Quinn "Mining Observational Health Data to Discover Risky Multi-drug Combinations" @ MSOB, Conference Room X-275 | Stanford | California | United States
Katie Quinn Postdoctoral Scholar Shah Lab, Stanford University Abstract: Concurrent use of multiple prescription drugs is widespread, with over 10% of Americans currently prescribed 5 or more drugs. Adverse drug reactions result in significant morbidity,[...]
BMIR Research in Progress: Yves A. Lussier, M.D. "Integrative genomics analyses unveil specific downstream biological effectors of disease polymorphisms unveiled from specific non-coding Loci" @ MSOB, Conference Room X-275 | Stanford | California | United States
Yves A. Lussier, M.D Professor, Medicine and Statistics University of Arizona, College of Medicine Tuscon Dr. Lussier has extensive experience in advising and leading computational oncology and informatics research and service groups. He established the[...]
BMIR Research in Progress: Alison Callahan "Painfully Deep Phenotyping - Extracting Patient Reported Pain from Clinical Notes" @ MSOB, Conference Room X-275 | Stanford | California | United States
Alison Callahan Research Scientist Shah Lab, Stanford University Abstract: Osteoarthritis is the most common cause of adult disability in the United States, and more than 1 million joint replacements are carried out each year to[...]
BMIR Research in Progress: Erika Bongen “Understanding Immune System Sex Differences in The Healthy Human Transcriptome” @ MSOB, Conference Room X-275 | Stanford | California | United States
Erika Bongen Graduate Student BMIR, Stanford University Thursday, April 13, 2017, 12:00pm to 1:00 pm MSOB Conference Room X-275 ABSTRACT: Sex and gender biases in the incidence of autoimmunity and infectious disease imply that women[...]
BMIR Research in Progress: Rafael Gonçalves "The OWL Reasoner Evaluation (ORE) competition" @ MSOB, Conference Room X-275 | Stanford | California | United States
Rafael Gonçalves, PhD Research Engineer “The OWL Reasoner Evaluation (ORE) competition” Co-authors: Bijan Parsia and Nicolas Matentzoglu – School of Computer Science, University of Manchester, UK Birte Glimm and Andreas Steigmiller – Institute of Artificial[...]
BMIR Research in Progress: Mu Zhou“Radiogenomics: Linking Molecular Data and Clinical Imaging Towards Non-invasive Precision Oncology” @ MSOB | Stanford | California | United States
  Mu Zhou Postdoctoral Scholar BMIR, Stanford University ABSTRACT: Growing amounts of molecular data and clinical imaging arrays offer opportunities to gain insights into translational cancer research. Exploring the interplay between these heterogeneous cancer data[...]
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[...]