Biomedical Informatics G4001 / Computer Science W4560.
Introduction to Computer Applications in Health Care and Biomedicine
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| Points: 3 |
| Instructor: M. Chiang |
| Prerequisites: Experience with computers and a passing familiarity with medicine and biology. Undergraduates in their senior or junior years may take this course only if they have adequate background in mathematics and receive permission from the instructor.
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An overview of the field of biomedical informatics, combining perspectives from medicine, computer science and social science. Use of computers and information in health care and the biomedical sciences, covering specific applications and general methods, current issues, capabilities and limitations of biomedical informatics. Biomedical Informatics studies the organization of medical information, the effective management of information using computer technology, and the impact of such technology on medical research, education, and patient care. The field explores techniques for assessing current information practices, determining the information needs of health care providers and patients, developing interventions using computer technology, and evaluating the impact of those interventions.
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Biomedical Informatics G4002/G4003.
Methods in Biomedical Informatics.
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| Points: 4 |
| Instructor: E. Mendonça |
| Prerequisites: Biomedical Informatics G4001, Computer Science W3137, and G4002 for G4003 |
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A survey of the methods underlying the field of biomedical informatics. The course explores techniques in mathematics, logic, decision science, computer science, engineering, cognitive science, management science and epidemiology, and
demonstrates the application to health care and biomedicine.
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Biomedical Informatics G4004.
Applied Clinical Information Systems.
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| Points: 3 |
| Instructor: B. Forman, S. Sengupta |
| Prerequisites: none |
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A practical overview of topics critical to the planning, implementation, and operation of clinical information systems. Subjects covered will include the governance of and strategic planning and budgeting for information technology efforts, architectural aspects of electronic medical records, health care integration middleware, systems operations, customer relationship management, the legal and regulatory aspects of clinical systems, plus risk assessment and controls.
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Biomedical Informatics G4011.
Acculturation to Medicine for Information Specialists
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| Points: 3. |
| Instructor: P. Stetson |
| Prerequisites: none |
| An introduction to the practice and culture of medicine for informaticians. Using case discussions and reviews of evidence-based literature, we will touch upon the following topics: medical language and terminology, introduction to pathology and pathophysiolgy, the process of medical decision making, and an understanding of how information flows in the practice of medicine. The seminars will be augmented with shadowing experiences in real clinical settings. |
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Biomedical Informatics G4013.
Biological Sequence Analysis
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| Points: 3. |
| Instructors: R. Friedman |
| Prerequisites: none. |
| A course in applied bioinformatics aimed primarily at experimental biologists but of interest to biomedical inforrmaticists as well. Sequential, structural, and functional genomics.
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Biomedical Informatics G4014.
Computational Biology: Functional and Integrative Genomics
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| Points: 3. |
| Instructors: Andrea Califano |
| Prerequisites: none. |
| Provides students with a broad theoretical and practical
knowledge of modern computational methods as they are applied to problems in biology. Examples will be
drawn from the primary literature, and topics in functional and integrative genomics will be emphasized.
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Biomedical Informatics G4015.
Computational Biology: Proteins, Networks, Function
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| Points: 3. |
| Instructors: D. Vitkup, B. Rost |
| Prerequisites: none. |
| Structural and functional proteomics and cellular network biology.
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Biomedical Informatics G4021.
Natural Language Processing in Biomedicine
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| Points: 3. |
| Instructor: C. Friedman |
| Prerequisites: Computer Science undergraduate degree or higher, or Methods in Biomedical Informatics and experience with one programming language.. |
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This course presents an overview of natural language processing (NLP)
methods, applications of the methods, and research issues as they pertain to
biomedical informatics. Topics include language structures and features,
biomedical resources for NLP, rule-based and corpus-based techniques, design
of an operational NLP system.
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Biomedical Informatics G4022.
Exploration of Clinician Information Needs
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| Points: 3. |
| Instructor: J. Cimino |
| Prerequisites: Either G4002 or G4020. |
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This course will be an advanced elective, in the form of a hybrid "graduate seminar" and "project course". We will examine research on the topic of "clinician information needs", with particular relation to needs that occur while using clinical information systems. We will also examine methodologies for identifying, and resolving, information needs. Participants will prepare discussion topics related to the course themes, presented in "journal club" style. Participants will also develop projects during the semester which are relevant to the themes, including: studies of clinician needs, construction of automated methods for recognizing and/or resolving needs, and evaluation of systems (theirs or others') for resolving needs. Creating and evaluating an "infobutton" for a clinicial information system would be one example of a suiteable project, but many others are possible, based on the interests and skill sets of the participant. It is expected that project reports will be suiteable for submission to journals or conferences. Grades will be based on class submission to journals or conferences. Grades will be based on class presentations, class participation, project and project report. Potential enrollees are encouraged to contact the instructor to clarify any questions about the course, including expectations (theirs and the instructors).
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Biomedical Informatics G4024.
Biomedical Text Mining
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| Points: 3. |
| Instructors: C. Friedman / E. Mendonça |
| Prerequisites: Either i) computer science undergraduate degree or higher, or ii) Theory and Methods in Biomedical Informatics and knowledge of at least one programming language. |
This course is an advanced reading and project course concerned with text mining in the biomedical domain. Topics include text categorization, information extraction, and knowledge discovery using statistical and knowledge-based methods drawn from information retrieval, natural language processing, and machine learning. |
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Biomedical Informatics G4032.
Introduction to Biomedical Imaging Informatics
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| Points: 3. |
| Instructor: C. Imielinska |
| Prerequisites: . |
| The purpose of this course is to give students who may come from a variety of backgrounds: computer science, engineering, medicine, nursing, dentistry, and psychology, an introduction to biomedical imaging informatics. This emerging discipline defines the role of medical imaging and related technologies in medical informatics decision support and improvement of patient care and outcome. Students in the class will be expected to work together within small groups with colleagues from complementary areas. This course will teach how to design and evaluate sound and meaningful applications in biomedicine and form multidisciplinary collaborative teams.
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Biomedical Informatics G4052
Patient Preference in Health Care Decision Making.
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| Points: 3. |
| Instructor: TBA |
| Prerequisites: Biomedical Informatics G4001. |
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This course examines the theory and practice of shared decision making between patients and clinicians, methods to measure patient preferences and design, evaluation and implementation of decision support stems to incorporate patient preferences into health care decision making.
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Biomedical Informatics G4061.
Economics of Informatics: Cost and Investment Issues in Healthcare Information Technology
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| Points: 3. |
| Instructor: TBA. |
| Prerequisites: Biomedical Informatics G4001. |
The course is structured into four major sections:
- An introduction of the major economic and financial concepts associated with healthcare information technology;
- An introduction to the concepts, software applications, and tools necessary for:
- investment analysis including value chain analysis, total cost of ownership analysis and return on investment (ROI) modeling focused on healthcare information technology;
- performing healthcare IT strategic assessments and valuations;
- healthcare IT project management
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Biomedical Informatics G4062.
Public Health Informatics
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| Points: 3. |
| Instructor: R. Kukafka. |
| Prerequisites: None. |
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An overview of the field of public health informatics, combining
perspectives from public health, computer science and social and
behavioral science. This course will provide an overview of the needs and
uses of information in public health, covering specific applications,
current issues, capabilities and limitations of public health informatics.
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Biomedical Informatics G4099.
Research Seminar In Biomedical Informatics
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| Points: 0. |
| Instructor: R. Kukafka. |
| Prerequisites: Enrollment restricted to DBMI Students. Presentations are open to the public. |
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Presentations by faculty and invited international speakers in biomedical informatics, computer science, nursing informatics, library science, and related fields.
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Biomedical Informatics G5043
Cognitive Science & Biomedical Informatics: Theoretical & Methodological Issues at the
Interface
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| Points: 3. |
| Instructor: D. Kaufman |
| Prerequisites: Biomedical Informatics G4001. |
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The course presents an overview of cognitive science theories, methods and research fi
ndings as they pertain to biomedical informatics. The topics include cognitive evaluation of medical i
nformation technologies, naturalistic decision making, comprehension and medical discourse, cognitive
issues in medical artificial intelligence, and the analysis of the medical workplace.
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Biomedical Informatics G6001.
Projects In Biomedical Informatics
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| Points: 3-12. |
| Prerequisites: Advisor's permission. |
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Research in biomedical informatics under the direction of a faculty advisor.
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Biomedical Informatics G6002.
Research Methodology in Biomedical Informatics
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| Points: 2. |
| Prerequisites: none |
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An introduction to conducting scientific research in informatics: observation and measurement, hypothesis formulation, design of experiments, execution of protocols, essential research skills and ethical issues in research
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Biomedical Informatics G6080.
Topics in Biomedical Informatics
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| Points: 2. |
| Instructor: TBA. |
| Prerequisites: Permission of Instructor. |
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Analysis and discussion of various topics in the Biomedical Informatics literature.
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Biomedical Informatics G6090.
Master's Essay In Biomedical Informatics I
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| Points: 1. |
| Prerequisites: Advisor's permission. |
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Development of a proposal for a research project in biomedical informatics to be carried out with the supervision of a faculty advisor.
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Biomedical Informatics G6091.
Master's Essay In Biomedical Informatics II
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| Points: 1. |
| Prerequisites: Advisor's permission. |
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Report on the results of a research project in biomedical informatics. Usually in the form of a paper for publication.
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Biomedical Informatics G8001.
Readings In Biomedical Informatics
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| Points: 3. |
| Prerequisites: Advisor's permission. |
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Readings on topics in biomedical informatics under the direction of a faculty advisor.
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Biomedical Informatics G8010.
Teaching Experience
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| Points: 2. |
| Instructor: Staff. |
| Prerequisites: permission of instructor. |
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Participation in biomedical informatics educational activities under the direction of a faculty advisor.
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Biomedical Informatics G9001.
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| Points: 0-12. |
| Doctoral Research |
| Instructor: Staff. |
| Prerequisites: completion of all M.Phil. requirements, and approval of a research proposal by the supervising faculty advisor. |
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DBMI Students should register for this course the semester following receipt of the MPhil degree after successfully completing their second qualifying examination and advancing to candidacy. This course replaces G6001 Projects in Biomedical Informatics.
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Biomedical Informatics G9999.
Doctoral Dissertation
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| Points: 0. |
| Instructor: Staff. |
| Prerequisites: complete of all M.Phil. requirements. |
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DBMI doctoral students should register for this in their final semester.
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Selected Courses Offered By Other Departments
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Introduction to Biophysical Modeling E4400
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| Points: 3 |
| Instructor: Chris Wiggins |
| Modeling of biological systems using physical and informatic methods.
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Bioinformatics of Gene Expression W4037
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| Points: 3 |
| Instructor: H. Bussemaker |
| Bioinformatics of gene expression. |
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Biochemistry and Molecular Biophysics G4250
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| Points: 3 |
| Instructor: Barry Honig - with Wayne Hendrickson, Arthur Palmer, and Arthur Karlin |
| Methods and principles involved in studying the structure and function of proteins, nucleic acids, membranes and their macromolecular assemblies.
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Computer Science W3137.
Data structures and algorithms
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| Points: 4 |
| Instructor: W. Grundy |
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Data types and Structures: arrays, stacks, singly and doubly linked lists, queues, trees, sets, and graphs. Programming techniques for processing such structures: sorting and searching, hashing, garbage collection. Storage management. Rudiments of the analysis of algorithms. This course will assume knowledge of Java as taught in W1007 or W3101.
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Computer Science W3156.
Introduction to Software engineering
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| Points: 3 |
| Instructor: C. Okasaki |
| Prerequisites: Computer Science W3137 |
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The scope of software engineering is very broad, covering economics, management, philosophy, and psychology in addition to traditional Computer Science. This course will be an intensive and hands-on introduction to a disciplined approach to producing and/or maintaining high quality, complex software that determines and fulfills its requirements on time and within budget. The course centers around Model-Based Architecting and Software Engineering (MBASE) and includes topics in software management, domain analysis, requirements analysis, human factors, cost estimation, functional specification, object oriented analysis and design with UML and the Rose CASE tool, software architecture, reliability and maintainability, team programming, testing methods, and configuration management, with special topics as time permits. Students will form small teams and be given existing MBASE projects to refine and implement. Teams will have two milestone reviews during the course and a product demonstration at the end of the course.
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Computer Science W4111.
Database systems
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| Points: 3 |
| Instructor: L. Gravano |
| Prerequisites: Computer Science W3156 |
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Introduction to database systems: data modeling; logical design of relational databases; data definition and data manipulation languages; storage and indexing techniques; concurrency control; recovery; query processing; security and integrity; system administration; essentials of distributed operation. A programming project is required.
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Computer Science W4701.
Artificial intelligence
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| Points: 3 |
| Instructor: S. Stolfo |
| Prerequisites: Computer Science W3137 |
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Survey of the current basic techniques used for building intelligent computer systems. State-space representations, problem reduction, means-end analysis, and-or graphs. Heuristic searching, depth-first, breadth-first, best-first, hill-climbing, divide and conquer minimax, a-b . Predicate calculus, resolution theorem proving, Horn clause theorem provers. AI systems and languages: goals and contexts. Issues of knowledge representation. Learning and concept formation. Other topics as time permits.
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Computational Genomics W4761
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| Points: 3 |
| Instructor: Yechiam Yemini |
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The analysis of biological sequences and DNA microarray expression data using techniques from machine learning.
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Biochemistry and Molecular Biophysics G6300, G6301.
Biochemistry and Molecular Biology of Eukaryotes I, II
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| Points: 4.5 |
| Instructor: R. Mann, L. Greene, D. Thanos, P. Srinivasan |
| Prerequisites: |
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College Biochemistry, Biology and Chemistry
This course is for all first year Ph.D. students and provides them with a unified curriculum that covers many of the topics that students need to know to successfully carry out research in biological sciences. The topics include basic biochemical principles, processes common to all eukaryotic cells such as transcription, translation and the cell cycle, and mechanisims of cell-cell signaling.
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Nursing M8018.
Project Management
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| Points: 3 |
| Instructor: N. Curran |
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The course provides the student with tools and techniques to assess organizational readiness for innovations and process change and to manage redesign and information system technology projects. Students will learn a five-stage framework for project management: from idea generation through maintenance. Students will learn software applications needed to support various project phases.
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Nursing M8122.
Interactive Health Communication
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| Points: 3 |
| Instructor: S. Bakken, R. Kukafka |
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Introduction to use of information-based approaches to create and deliver educational and behavioral interventions. Topics include: theories related to client-health care provider communucation using electronic media; privacy, confidentiality, and security issues related to Internet communication; targeting and tailoring health messages for underserved populations; evaluating health care content on the World Wide Web.
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Nursing M8120.
Informatics for Evidence-based Practice
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| Points: 3 |
| Instructor: |
| Prerequisites: |
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Overview of informatics topics most relevant to evidence-based practice. Topics include: standardization of clinical terminology; health care standards; electronic health records; retrieval and critical analysis of digital data, information and knowledge; clinical decision making and decision support including decion analysis.
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Nursing M8123.
Introduction to Databases and Data Mining
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| Points: 3 |
| Instructor: |
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An initial database course focusing on data structures, database management, and data mining. Topics include: types of data models, data modeling techniques, normalization, data integrity, construction of databases, database management and data mining techniques such as knowledge discovery, machine learning and natural language processing.
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Public Health P6313.
Physiology
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| Points: 3 |
| Instructor: D. Brosius |
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Public Health P6103.
Introduction to Biostatistics
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| Points: 4 |
| Instructor: A. Weinberg |
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Topics covered include standard distributions, measures of central tendency and dispersion, hypothesis testing, point estimation, confidence intervals, and an introduction to correlation and regression.
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Public Health P6104.
Introduction to biostatistical methods
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| Points: 4 |
| Prerequisites: |
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An enriched core course for students majoring in biostatistics and others who expect to take additional courses in biostatistics such as Public Health P8100, P8111, P8120, or P8129. It covers in greater depth all of the topics in P6103, and is the best preparation for students anticipating a quantitative orientation in their degree programs. Topics covered include standard distributions, measures of
central tendency and dispersion, hypothesis testing, point estimation, confidence intervals, and an introduction to correlation and regression.
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Public Health P6400.
Principles Of Epidemiology I
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| Points: 3 |
| Instructor: D. Herman |
| Prerequisites: Public Health P6103 |
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The concepts, principles, and uses of epidemiology. Epidemiologic analysis of the determinants of health and disease. Study of particular diseases to illustrate the descriptions of their distributions and courses, the analysis of their causes, and approaches to prevention and control. In the main, teaching is in lecture format and autonomous small-group seminars. Research paper, exam, and student participation. Lectures, seminars, and exercises.
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Public Health P6530.
Issues and approaches in health policy and management
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| Points: 3 |
| Instructor: TBA |
| Prerequisites: |
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Lectures, team projects, and readings on administrative problems and interventions that affect, and are affected by, all public health practitioners, as they seek to improve health care delivery, health care, and the health status of populations. Taught in both Executive and traditional formats. Individual papers required.
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Public Health P8740.
Social and economic factors in clinical decision making
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| Points: 3 |
| Instructor: TBA |
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A review of different models of clinical decision making: economic, sociological, and psychological. These models are systematically compared with each other and with the medical model in terms of the factors presumed to influence both the amount and content of diagnostic and treatment services (e.g., tests, medical vs. surgical treatment, referrals, revisits) and, more generally, clinical practice styles. Special topics: the influence of different methods of physician reimbursement, explicit standards (e.g., Diagnostic Related Groups), legal and ethical issues, organizational settings, professional norms, peer and patient pressures, and the diffusion and impact of new medical technology. Paper required.
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Public Health P8116.
Design of medical experiments
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| Points: 3 |
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Principles in the design and analysis of controlled experiments: Latin squares, incomplete block designs, crossover designs, fractional factorial designs, confounding.
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Public Health P6513.
Hospital Organization & Management
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| Points: 3 |
| Instructor: H. Karpe |
| Prerequisites: |
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Administrative elements of hospital functions, including background and theoretical concepts, and opportunities for examination and open discussion of the issues and problems of hospital management. The approach is from the general to the particular, to provide students with a workable overall knowledge of hospital organization as well as more particular insight into certain typical and key departments.
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Public Health P6503.
Introduction To Health Economics
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| Points: 3 |
| Instructor: J. Zivin |
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Economic analysis offers an analytic approach to problem solving which is particularly useful in thinking about the financing and delivery of health services. The course covers relevant aspects of microeconomic theory and their application to health care issues. Students are evaluated on the basis of homework assignments, a midterm, and a final exam.
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Public Health P8514.
Healthcare E-Commerce
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| Points: 3 |
| Instructor: S. Kachnowski |
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Public Health P6781.
The use of large scale national health care data sets
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| Points: 3 |
| Instructor: R. Arons |
| Prerequisites: |
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An overview of research methodology utilizing major publicly accessible large scale health care and social demographic data sets, including federal, state, and local level resources. Covered are (1) variable identifications and definitions; (2) record layouts; (3) data set size and analysis restrictions; (4) variable strengths and weaknesses; (5) research protocol submissions required by agencies for access to confidential data; and (6) data handling methods. These data permit a wide range of research questions to be addressed. This is demonstrated through the presentation of current and recently completed research activities and projects under development. The ability to analyze data at levels ranging from the individual patient to the national population could prove to be a valuable skill as students pursue their public health careers and advanced studies.
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Public Health P6560.
Organization theory
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| Points: 3 |
| Instructor: N. Dubbs |
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An introduction to the classical and contemporary concepts of organization and management theory. Theoretical and empirical aspects of organizational design, function, and behavior, as well as the behavior of persons who work in organizations. Develops analytical skills to enable students to apply theoretical concepts to real-life managerial problems. Take-home midterm and in-class final exam.
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Public Health P6700.
Introduction To Sociomedical Sciences
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| Points: 3 |
| Instructor: K. Hopper and A. Abraido-Lanza |
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A critical review of research illustrating the application of social science concepts and methods to health and health care. Issues include the effect of social and psychological factors (such as cultural and ethnic influences, social networks, social class, personality, and stress) on health and health behavior.
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Public health P6710.
Health communications: social marketing and the media
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| Points: 3 |
| Instructor: TBA |
| Prerequisites: |
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provide students with a broad overview of the field of health communications and social marketing. Speakers, including faculty and invited marketing/communications experts, make presentations on designing social marketing programs and understanding media relations, advertising, and marketing. Case studies of applications of social marketing principles are emphasized.
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Biomedical Engineering E3001.
Quantitative physiology I: cells and molecules
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| Points: 3 |
| Instructor: C. Hung |
| Prerequisites or corequisites: organic chemistry; BIOL C2005 |
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An introduction to the physical and chemical characteristics of biological systems, with an emphasis on subcellular biology. Thermodynamics of molecular conformational transitions, biomolecule binding and multiunit assembly, reaction kinetics, chemical pathways in cells, physical behavior of polymeric molecules, persistence length, counterion condensation, statistical mechanics of DNA, biological membranes. Topics are treated in a quantitative mathematically
intensive approach.
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Biomedical Engineering E3002.
Quantitative physiology to: organ systems
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| Points: 3 |
| Instructor: X. Guo |
| Prerequisites or corequisites: organic chemistry; BIOL C2005, C2006. |
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Students are introduced to a quantitative, engineering approach to cellular biology and mammalian physiology. Beginning with biological issues related to the cell, the course progresses to considerations of the major physiological systems of human body (nerves, circulatory, respiratory, renal, digestive, and skeletal).
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Biomedical Engineering E4400.
Wavelets applications in biomedical image and signal processing
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| Points: 3 |
| Instructor: A. Laine |
| Prerequisites: Instructor's permission |
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An introduction to methods of wavelet analysis and processing techniques for the quantification of biomedical images and signals. Topics include: frames and overcomplete representations, multiresolution algorithms for denoising and image restoration, multiscale texture segmentation and classification methods for computer aided diagnoses.
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Biomedical Engineering E4410.
Ultrasound in diagnostic imaging
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| Points: 3 |
| Instructor: A Laine |
| Prerequisites: Calculus, Fourier analysis |
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Physics of diagnostic ultrasound and principles of ultrasound imaging instrumentation. Propagation of plane waves and lossless medium; ultrasound propagation to biological tissues; single-element and array transducer design; pulse-echo and Doppler ultrasound instrumentation, performance evaluation of ultrasound imaging systems using tissue-mimicking phantoms, ultrasound tissue characterization; ultrasound nonlinearity and bubble activity; harmonic imaging; acoustic output of ultrasound systems; biological effects of ultrasound.
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Biomedical Engineering E4761.
Computational genomic
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| Points: 3 |
| Instructor: W. Grundy |
| Prerequisites: |
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Working knowledge of at least one programming language, and some background in probability and statistics
Computational techniques for analyzing and understanding genomic data, including DNA, RNA, protein and gene expression data. Basic concepts in molecular biology relevant to these analyses. Emphasis on techniques from artificial intelligence and machine learning. String-matching algorithms, dynamic programming, hidden Markov models, expectation-maximization, neural networks, clustering algorithms, support vector machines. Students with life science backgrounds who satisfy the prerequisites are encouraged to enroll.
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Biomedical Engineering E4894.
Biomedical imaging
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| Points: 3 |
| Instructor: TBA |
| Prerequisites: |
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This course covers image formation, methods of analysis and representation of digital images. Measures of qualitative performance in the context of clinical imaging. Algorithms fundamental to the construction of medical images via methods of computed tomography, magnetic resonance, and ultrasound. Algorithms and methods for the enhancement and quantification of specific features of clinical importance in each of these modalities.
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Biomedical Engineering E6400.
Analysis and quantification of medical images
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| Points: 3 |
| Instructor: A. Laine |
| Prerequisites: |
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Novel methods of mathematical analysis applied to problems in medical imaging. Design requirements for screening protocols, treatment therapies, and surgical planning. Sensitivity and specificity in screening mammography and chest radiographs, computer aided diagnoses systems, surgical planning in orthopedics, quantitative analysis of cardiac performance, functional magnetic resonance imaging, positron emission tomography, and echocardiography data.
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Biomedical Engineering E6480.
Computational neural modeling and neuroengineering
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| Points: 3 |
| Instructor: P. Sadja |
| Prerequisites: Signal Processing |
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Engineering perspective on the study of multiple levels of brain organization, from single neurons to cortical models and systems. Mathematical models of spiking neurons, neural dynamics, neural coding, and biologically-based computational learning. Architectures and learning principles underlying both artificial and biological neural networks. Computational models of cortical processing, with an emphasis on the visual system. Applications of principles in neuroengineering, neuroprostheses, neuromorphic systems and biomimetics. Course will include a computer simulation laboratory.
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Electrical Engineering E3060
Introduction to Genomic Information Science and Technology
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| Points: 3 |
| Instructor: Dimitris Anasstassiou |
| An introduction to thie bioinformatics for both life scientists and computer scientists/engineers.
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