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Course Schedule and Descriptions

Course #TitleInstructorCreditsInfo
Fall 2021 (schedule)
BMIF 6300Foundations of Biomedical InformaticsAncker3Course Plan
BMIF 6310Foundations of BioinformaticsLopez3Course Plan
BMIF 6321Scientific CommunicationRosenbloom
Davis
1Course Plan
BMIF 6331Student Journal Club and Research ColloquiumCarroll1Course Plan
BMIF 6341Research RotationStaff1Course Plan
BMIF 7340Clinical Information Systems and DatabasesWright
McCoy
3Course Plan
BMIF 7350Technology and SocietyNovak3Course Plan
BMIF 7370Evaluation Methods in Biomedical InformaticsUnertl
Peterson
3Course Plan
BMIF 7391-02Special Topics: Seminar in Biomedical Informatics: Foundations Human-Computer InteractionAnders3Course Plan
BMIF 7391-02Clinical ObservationParr
Unertl
3Course Plan
PUB 5515-01Intro to Public Health InformaticsMcPheeters2Course Plan
Spring 2022 (schedule)
BMIF 6315Methodological Foundations of Biomedical InformaticsGiuse
Davis
3Course Plan
BMIF 6322Scientific CommunicationRosenbloom
Davis
1Course Plan
BMIF 6332Student Journal Club and Research ColloquiumCarroll1Course Plan
BMIF 6342Research Rotation in Biomedical InformaticsStaff1
BMIF 7311Systems BiologyTBD3Course Plan
BMIF 7320Healthcare System and InformaticsLorenzi3Course Plan
BMIF 7380Data Privacy in BiomedicineMalin3Course Plan
BMIF 7391Special Topics: Data Management for Clinical & Translational Research3Course Plan
CS3892Special Topics: Big DataStaff3
Research Courses
BMIF 7395Directed Research Independent StudyStaff
BMIF 7999Master Thesis Research
BMIF 8999Non Candidate Research
BMIF 9999PhD Dissertation Research

Course Descriptions

BMIF 6300. Foundations of Biomedical Informatics

This introductory course examines the unique characteristics of clinical and life science data and the methods for representation and transformation of health data, information, and knowledge to improve health care. Principles of information security and confidentiality are taught, along with functional components of information systems in clinical settings and the use of databases for outcome management. Through skill modules and weekly programming exercises, the course provides an introduction to methods underlying many biomedical informatics applications, including information retrieval, medical decision making, evaluation of evidence, and knowledge representation. The historical evaluation of the field of biomedical informatics is taught concurrently, using examples of landmark systems developed by pioneers in the field. FALL. [3] Ancker

BMIF 6310. Foundations of Bioinformatics

This survey course introduces students to the experimental context and implementation of key algorithms in bioinformatics. The class begins with a review of basic biochemistry and molecular biology. The group will then focus on algorithms for matching and aligning biological sequences, given the context of molecular evolution. The emphasis will move from comparing sequences to the systems developed to enable high-throughput DNA sequencing, genome assembly, and gene annotation. Gene products will be the next focus as students consider the algorithms supporting proteomic mass spectrometry and protein structure inference and prediction. The informatics associated with transcriptional microarrays for genome-wide association studies will follow. Finally, the class will examine biological networks, including genetic regulatory networks, gene ontologies, and data integration. Formal training in software development is helpful but not required. Students will write and present individual projects. Undergraduates need the permission of the instructor to enroll. FALL. [3] Lopez

BMIF 6315. Methodological Foundations of Biomedical Informatics

In this course, students will develop foundational concepts of computation and analytical thinking that are instrumental in solving challenging problems in biomedical informatics. The course will use lectures and projects directed by co-instructors and guest lecturers. SPRING. [3] D. Giuse, Davis

BMIF 6321. Scientific Communication

The course will enhance students’ skills in written and oral scientific communication. An introductory segment covers categories of scientific writing, the peer review process, and ethical issues in research communication. Through a two-semester sequence, it provides direct, hands-on experience in writing papers, abstracts, and grant proposals; critiquing and copy editing; and preparing and giving presentations for scientific meetings. FALL, SPRING. [1-1] Rosenbloom, Davis

BMIF 6322. Scientific Communication

The course will enhance students’ skills in written and oral scientific communication. An introductory segment covers categories of scientific writing, the peer review process, and ethical issues in research communication. Through a two-semester sequence, it provides direct, hands-on experience in writing papers, abstracts, and grant proposals; critiquing and copy editing; and preparing and giving presentations for scientific meetings. FALL, SPRING. [1-1] Rosenbloom, Davis

BMIF 6331. Student Journal Club and Research Colloquium

The class meets weekly and is a seminar course that involves two revolving formats: journal club presentations and student research in progress presentations. For Biomedical Informatics graduate students only, usually taken in the second year of the program. Fall [1] Carroll

BMIF 6332. Student Journal Club and Research Colloquium

The class meets weekly and is a seminar course that involves two revolving formats: journal club presentations and student research in progress presentations. For Biomedical Informatics graduate students only, usually taken in the second year of the program. Spring [1] Carroll

BMIF 6341. Research Rotation in Biomedical Informatics

Students will perform research under the direction of a faculty adviser. FALL. [1-1] Staff.

BMIF 6342. Research Rotation in Biomedical Informatics

Research Rotation In Biomedical Informatics. Students will perform research under the direction of a faculty adviser. SPRING. [1-1] Staff.

BMIF 6390. Special Topics.

Selected topics in Biomedical Informatics. [3]

BMIF 7320. Healthcare Systems and Informatics

The purpose of this course is for students to understand the organizational world in which they will spend most of their professional lives. A better understanding will lead to strategies to build partnerships with physicians, researchers, hospitals, and academic organizations. In turn, better understanding will lead to working more closely as a team in planning future directions and implementing technological programs and changes. This course provides an overview of theoretical concepts as well as the practical tools for the student to understand and work effectively with two major topic areas: (1) understanding the health care environment; and (2) understanding organizational informatics, including the implementation of informatics systems and the concepts of behavioral change management. Prerequisite: BMIF 6300 is a required prerequisite to this course. SPRING. [3] Lorenzi.

BMIF 7340. Clinical Information Systems and Databases

This course builds on material covered in Methodological Foundations of Biomedical Informatics (BMIF 6315) by introducing and developing concepts in distributed systems and network computing: OSI stack, protocols, TCP/IP, Sockets, and DNS; clinical database concepts: synchronization, concurrency, deadlock, full-text databases; distributed database services, including high-availability techniques; and architectural considerations in the design of clinical information systems. The VUMC clinical database architecture is used as a case study. Prerequisites: for Biomedical Informatics students: BMIF 6315 or permission of instructor; for non-Biomedical Informatics students: coding ability in some standard procedural or object-oriented computer language, preferably PERL. FALL [3] D. Giuse

BMIF 7350. Technology and Society

This course engages students in discovering relationships among individuals, institutions, and technologies, and how those relationships evolved in specific cultural contexts. Students and instructors will explore this topic in four modules: 1) understanding health care actors and technologies; 2) institutions and other infrastructures, including scientific disciplines, government, and information infrastructures; 3) principles of ethics and their application in biomedical informatics research and practice; and 4) integration of the concepts. The course will be conducted as a seminar, in which students and instructors will discuss assigned readings and films. Each student will present a final case to the group. FALL [3] Novak

BMIF 7370. Evaluation Methods in Biomedical Informatics

Students are introduced to health information technology evaluation, with exposure to study design, including sampling, appropriate use of controls; data collection, including human subjects research considerations; analysis, including testing for statistical significance, definitions of sensitivity and specificity, ROC plots; and reporting of results. Quantitative and qualitative methods will be covered, as well as methods and issues specific to health care settings. FALL. [3] Peterson, Unertl

BMIF 7380. Data Privacy in Biomedicine

This course introduces students to concepts for evaluating and constructing technologies that protect personal privacy in data collected for primary care and biomedical research. Material in this course touches on topics in biomedical knowledge modeling, data mining, policy design, and law. Prerequisite: students are expected to be proficient in writing basic software programs, although no specific programming language is required. SPRING. [3] Malin.

BMIF 7391. Special Topics in Biomedical Informatics

This course is designed for faculty to offer small groups of students a study course on a topic of mutual interest and concern in the faculty member’s area of expertise

BMIF 7395. Directed Research / Independent Study

Students will work under close supervision of a specific faculty member on an ongoing research problem. Depending on the specific project, students will learn aspects of study design, research methods, data collection and analysis, research manuscript writing, and human factors engineering. Completion of Course Plan and approval of the Director of Graduate Studies is required. SPRING/FALL. [1-3] Staff.

BMIF 7999. Master’s Thesis Research

BMIF 8999. Non-Candidate Research

Research prior to entry into candidacy (completion of qualifying examination) and for special non-degree students. [Variable credit: 0-12]

BMIF 9999

Ph.D. Dissertation Research. [0-12]

PUB 5515-01 Intro to Public Health Informatics

Students will have an understanding of the role of informatics in public health practice, particularly in the context of disease surveillance.