Groups and Labs
Bioinformatics Lab
Andrea Califano
Theoretical - Tuesdays, 4:00-6:00pm.
Applied - Thursday, 4:00-6:00pm.
Herbert Irving Comprehensive Cancer Center, 9th floor, Conference Room
Exploration and the application of pattern and association discovery algorithms in the context of sequence, structure, and microarray data. Reverse engineering of metabolic and gene regulatory networks using dynamical and statistical predictive models that can be validated in an experimental setting. Dissection of complex genetic traits in a whole genome context, using association discovery techniques and their related statistical models.
Biomedical Natural Language Processing
Carol Friedman, Noemie Elhadad
Mondays, 4:00-5:00pm, Conference Room A
Discussion of NLP issues, focusing on research and applications associated with the processing, normalization, and use of clinical information in the patient record, consumer and other health-related websites, and the literature. Some of the topics we explore are information granularity, summarization of information in the longitudinal record, handling of temporal information, and issues concerning the use of MedLEE.
Clinical Systems Lab
Pete Stetson, Suzanne Bakken
Thursdays, 2:00-3:00pm, VC5 Conferemce Room A
This laboratory conducts research on the complex interaction of clinicians and information systems, seeking to improve the efficiency of clinical processes, reduce errors and improve quality of care. Key questions involve how clinicians collaborate, how information is carried across transitions of care, how natural language is used to communicate information, how clinical plans are developed, and how decisions are made. The lab explores the use advanced methods for information management, including natural language processing, summarization, collaboration tools, usability evaluation, data mining, decision support, document markup standards, clinical ontologies, and web services architecture.
CognitiTION, Decision Making and Human-Computer Interation
David Kaufman
TBA
The Laboratory is a multidisciplinary research unit devoted to the study of human-computer interaction, medical decision-making, cognitive foundations of health behaviors, and the effective use of health information technologies by digital divide populations. The research is steeped in theories and methods of cognitive science, with a particular focus on the study of numeracy, eHealth literacy, analysis of medical error, information seeking behavior, naturalistic decision-making, and investigations of the productive and suboptimal use of technologies by clinicians, patients and health consumers. These studies are guided by a concern for improving performance of individuals and teams in the healthcare system.
Communication, Informatics, and Public Health Lab (CIPH)
Rita Kukafka
Every other Friday, starting September 7, 12:00-1:00pm, VC-5 Conference Room
The laboratory hosts interdisciplinary collaborations to explore ways in which communication and informatics can help meet Healthy People 2010 objectives. Research in the lab integrates methods in informatics, social and behavioral sciences, and public health.
Computational Virology LAb
Raul Rabadan
Mondays, 2:30-3:30pm, C2B2 Meeting Room
Understanding evolution through the analysis of the genome of pathogens and tumors.
Data and Text Mining Lab
George Hripcsak, Carol Friedman, Raul Rabadan
Thursdays, 9:30-10:30am, VC5 Conference Room
Machine learning and visualization are methods for discovering knowledge in large databases including text databases. This lab focuses on testing and extending existing statistical and knowledge-based discovery methods to improve their performance on clinical data and text.
Eligibility Criteria Extraction and Representation (EliXR) Lab
Chunhua Weng, Stephen Johnson
Mondays, 2:00-3:00pm, VC05 Conference Room A
Thursdays, 1:00-2:00pm, VC05-558
Eligibility criteria are specifications of "who is eligible for a research study or a treatment". They are commonly found in scientific publications, research protocols, or therapy applicability statements. Our goal is to develop a computable model of eligibility criteria that is linkable to clinical data. We design natural language processing methods to transform narrative research eligibility criteria into executable formats. We also investigate the semantic gap between eligibility criteria and clinical data and develop a semantic alignment framework that supports standards-based semantic queries over heterogeneous clinical data.
Information Seeking Lab (CIQR)
David Kaufman, Herb Chase
Thurdays, 9:30-10:30am, VC5 Conference Room A
Based on studies of clinicians' information needs (as they occur in daily workflow) and on models of expert information-retrieval strategies, the CIQR project explores 1). the degree to which spoken natural-language queries via mobile communication devices can be used to mediate information-seeking behavior and systems, 2). the use of speech-recognition, syntactic parsing, and semantic interpretation software in modeling or reproducing the methods used by professional librarians as they perform medical literature searches in response to clinicians' queries. The project seeks to improve access for physicians to the ever-enlarging body of current research data CIQR wiki.
LICOS--Laboratory for Informatics, Complexity and Organizational Study
Jacqueline Merrill
Mondays, 1:00-2:00pm, VC05-524
The mission of LICOS is to apply network, organizational and management theory and research methods to improve information management, practice, and performance in service organizations, with an emphasis on the public health system.
Pharmacovigilance Lab
Carol Friedman, George Hripcsak, Herb Chase, David Vawdrey
Mondays, 1:00-2:00pm, VC5 Conference Room
Post-marketing adverse drug events are a very serious problem world-wide. This lab focuses on development of automated methods for the discovery of novel adverse drug events. The research involves mining the electronic health record, natural language processing, statistics, information theory, knowledge representation, and mining publicly available knowledge sources and databases.
translational research informatics lab (TRI-L)
Stephen Johnson, Suzanne Bakken, Chunhua Weng, Thom Bigger
Thursdays, 10:30am-11:30pm, Irving Institute, PH10 Conference Room A
This lab conducts research on scientific collaboration across the translational spectrum, from bench to bedside to practice. We study the behavior of scientists, their research processes, workflow and social networks. Models of these phenomena are used to develop information systems that support clinical and translational research. Applications include information systems to support clinical trials management, recruiting subjects into studies, establishing a biobank that links genotype and phenotype information, using alerts to streamline the research workflow and disseminating scientific knowledge into clinical practice. Research in this lab is supported in part by the Clinical and Translation Science Award (CTSA), through the Irving Insitute.
