Course Descriptions

One semester survey of the molecules in a cell, their interconversions and roles in sustaining and regulating cellular function, cell replication and information transfer. The course is designed for Master's candidates in the biomedical sciences.

The Graduate Student Seminar meets weekly to provide a mechanism for graduate students to gain experience and expertise in preparing and presenting orally a research/teaching seminar.  The Journal Club is based on recent, topical paper from the primary research literature.  The paper's subject may or may not be related to the student's research.

Students in the master’s program rotate through at least one laboratory as part of the process of finding a mentor. Each rotation lasts for 4 to 5 weeks and includes approximately 15 to 20 hours per week of laboratory research under the guidance of the mentor and laboratory personnel.

The primary objective of this course is for students to become familiar with the principal, broad questions in protein structural biology and the experimental strategies used to answer them. These strategies include kinetics, specific mutagenesis, and model design and analysis. Specific topics include steady-state and transient kinetics, protein origins of enzyme catalysis, folding pathways and protein design, and protein allostery in the gating function of ion channels.

Familiarizes students with up-to-date concepts and experimental approaches used in the study of eukaryotic gene expression. Focuses on the molecular mechanisms involved in RNA polymerase II (RNAPII) transcription. Specific topics include the structure and function of RNAPII and required auxiliary factors, the molecular mechanisms of transcriptional activation and repression, the coupling of transcriptional elongation with mRNA processing, and specific examples of the role of regulated RNA polymerase II transcription in development and cellular differentiation. Each week, one to two selected papers from the scientific literature are discussed in class, with students taking turns presenting one or two figures and the instructor providing clarification and/or additional questions as appropriate.

This course focuses on how the spatial and temporal readout of the genome is achieved during development, and conversely on how forced changes in gene expression patterns can affect developmental processes. The philosophy of the course is that “development never ends” and thus examples of processes from normal or pathological embryonic, adult and aging systems may be discussed. Each session focuses on one or more fundamental principles of developmental biology/genomics using papers from the literature to illustrate the principle(s). Every effort is made to demystify developmental biology and discuss state-of-the-art experimental approaches to address questions about the genes required for normal development. While much teaching is in the form of student presentations from the primary literature, one-hour introductions are given by the course guides on each topic in the Tuesday lecture. The goal of the course is to enable students to read papers in the areas of developmental biology and genomics, to critically evaluate them, and to propose experiments that will answer questions raised in the paper.

This course introduces graduate students to the concepts and practices of bioinformatics, including computational analysis of DNA and protein sequences, analysis of large-scale DNA and protein datasets, statistical analysis of sequence alignments and gene array datasets, proteomics, and RNA and protein structure prediction. The Tuesday session is didactic lectures introducing the topic of the week and giving out assignments for completion at or prior to the Thursday lab session. The Thursday lab focuses on practical use of the concepts taught in the Tuesday lecture and is conducted by either the Tuesday lecturer, another faculty member who is expert in the particular analysis being performed or both. Assignments completed by the students for the lab sessions are graded by the appropriate instructor and used to determine the student’s grade in the course.

Guided project under the mentorship and supervision of faculty in Biochemistry. This course is designed as a capstone experience and expected to conclude in a written report, fulfilling formal requirements for an MA degree in Biochemistry. Topic and activities to be performed in this project are subject to agreement between student and faculty member, including (but not limited to) laboratory research, computational or other theoretical work, literature review, or other scientific research related to the fields of study in the department.

This elective course will cover topics in cellular signaling, including G protein-coupled receptors as well as growth factors and their receptors — including nuclear FGFR1. Other topics to be covered include mTOR signaling and neurological disease; the unfolded protein response and diabetes; and changes in signaling leading to polycystic kidney disease. The contribution of the microenvironment to cellular signaling will be studied, including the pathways that promote tissue remodeling, wound healing and cancer.

This course is cross-listed in the departments of Microbiology and Biochemistry. This course, for advanced PhD students, consists of a single, two-hour meeting per week. It utilizes a seminar/journal club format and all class readings consist of primary research articles in the general areas of DNA replication, DNA repair, and how these processes are regulated. Students taking this course should have satisfactorily completed BMS 503 or an equivalent advanced graduate-level biochemistry course covering biosynthesis of DNA in both prokaryotes and eukaryotes. In addition, students should have experience in the reading and analysis of primary research articles. Students are graded on their presentations of the primary research articles and on their participation in class discussions.

This advanced graduate level seminar style course is designed to teach principles and approahes used in genetic dissection of complex biological processes in model bacteria.

This is the core introductory course for students beginning a master’s degree in Biomedical Informatics or for students in other graduate degree programs seeking an introductory overview of the core theories, challenges, research methods and areas for the development of health information management systems and applications.

Building on BMI 501 as a prerequisite, this course surveys the structures and information management challenges of the U.S. health care system, public health system and biomedical research system as well as major other international health care systems. It also surveys other health care informatics application domains that build on or complement electronic health record systems.

This course provides a technical overview of the current computing and information technology systems, programming languages and software development tools available to manage, access and analyze health and biomedical research information effectively in patient care and research settings. Course work includes lectures, demonstrations and readings as well as individual and group hands-on problem exercises with test versions of representative current electronic health record and other health information databases, programming languages and internet/web health information portals.

Focusing on clinical data and research, this course surveys the essential elements of statistical data analysis methods and research strategies that are needed for health and biomedical research information systems and for health information management applications for clinicians and researchers.

This course provides an overview of the methods, systems, tools and databases available for the storage, analysis and interpretation of the increasingly voluminous molecular genome and protein data. The course focuses on the use of these biological data for research in molecular biology, systems biology, genetics and genomics as well as for translating and integrating biological data with clinical health care data to help predict and prevent disease and help clinicians, patients and consumers understand and use this information to maintain health. The course also includes a brief review of current core terminology and concepts in molecular biology, systems biology, genetics and genomics for students without previous course work or training in biomedicine.

Building on BMI 501 as a prerequisite, this course provides an in-depth survey of the data standards, data analysis tools, databases and information management systems and applications associated with clinical population research and the U.S. public health system.

Building on BMI 501 as a prerequisite, this course provides an in-depth exploration of the purpose, scope, technical structures and uses of electronic health records (EHR) and other clinical health care information systems.  Then, building on a review of current research on human cognition and decision making, the course critically reviews the purposes, scope, technical structures and ethical uses of computer-based decision support systems in clinical health care and consumer health settings.

Building on BMI 501 as a prerequisite, this course first provides a review of the theories underlying biomedical knowledge generation and the methods and tools for knowledge acquisition, modeling and representation as well as the management and maintenance of biomedical knowledge sources. The second part of the course provides an in-depth review of current theories and research underlying the development of biomedical ontologies as well as a comparative critical analysis of the major current biomedical ontologies and the methods and tools for biomedical ontology development and evaluation.

Building on BMI 501 as a prerequisite, this course reviews the interdisciplinary theoretical frameworks, design concepts and analytical foci used in human factors engineering and ergonomics for biomedical information systems. These include the physical, cognitive, organizational/social and environmental challenges of human-computer interactions and a range of human factors approaches to systems design and evaluation. The course also looks at the mediating roles of information technology on clinical and research user performance and the potential implications of a range of innovative new design concepts for biomedical information systems.

This course is required in the first two semesters of the MS degree program to give each student experience working directly with up to four members of the BMI faculty. Each semester will include work on two different faculty-mentored research or practicum projects. Each project will involve regularly scheduled weekly or bi-weekly time learning about, and helping with some aspect of a faculty member’s research or working under a faculty-member’s guidance on an informatics application development or other practicum project in a health care, public health or health-industry setting.

This course provides an overview of core business concepts for students in Biomedical Informatics. For those students who will enter management roles such as Chief Medical Informatics Officer, an understanding of business processes and methods is essential for professional success. In addition to introducing basic business topics such as accounting and finance, this course will also emphasize leadership skills, including change management and emotional intelligence.

This course, or BMI 611, is required in the final two semesters of the MS degree program. Students choosing this option will complete a biomedical informatics research project under the guidance of a member of the BMI faculty and a thesis advisory committee. The thesis research will culminate with the completion of a paper suitable for publication as well as a final oral defense, including an oral presentation of the results of the research project.

This course, or BMI 610, is required in the final two semester of the MS degree program. Students choosing this will complete a project to evaluate, test or help implement a health information system or information management process in a health care, public health, or health-related industry setting under the supervision of a member of the BMI faculty as well as a professional informatics mentor. The practicum project will culminate with the completion of a paper suitable for publication as well as a final oral presentation of the results of the practicum project.

In consultation with his/her faculty advisor, each student may elect to explore a particular area of biomedical informatics in more depth with a member of the BMI faculty with expertise in this area of research or application development. The choice of topic areas will depend, in part, on the availability of the faculty with expertise during the semester the student is seeking this kind of elective. In addition, the number of credit hours and the format of the course will depend on the interests and needs of the student and whether other students are interested in taking an elective on the same topic area. Each special topic elective will include, at a minimum, a program of background, in-depth readings and “laboratory” hands-on work with resources and tools needed in this topic area of BMI research and application development.

In consultation with his/her faculty adviser, each student may also choose, as an elective, to participate in a more advanced research project with a faculty mentor. This could be to learn more about the research methods that will be needed to complete the student’s thesis or, for students planning to continue beyond the master’s degree to a PhD, to explore another possible area of research focus for a doctoral dissertation. The number of credit hours will depend on the interests and needs of each student.

Building on BMI 501, 502, 504 and 506 as prerequisites, this course provides an in-depth survey of the data standards, data analytic methods, data analysis tools, databases and information management systems and applications associated with clinical-genomic population research and the U.S. public health system. Students will learn clinical trial design and data analysis for varying populations. Students will learn genetic epidemiology. Methods will include hierarchical clustering, vector space methods, semantic clustering, machine learning, modeling and simulations (including bootstrap methods). Students will learn linear and non-linear methods of data analysis. Students will be given an introduction to complexity theory and will be shown some methods for reducing dimensionality in complex systems (including computing techniques).

Building on BMI 504 or an equivalent introductory course in biomedical statistics as a prerequisite, this course provides doctoral students with the ability to effectively understand and use a number of key advanced statistical analysis methods and tools used in biomedical informatics research. These include regression and correlation analysis, the analysis of variance and covariance, distribution-free and nonparametric analysis methods and the methods used in demography and vital statistics analysis.

Building on introductory overviews provided in BMI 503 and 504, this course provides an in-depth introduction to the needs, challenges, standards, software applications and tools for biomedical data mining and natural language processing. The most common biomedical data mining methods are reviewed with lab time for using the IBM SPSS Modeler with problem datasets. Similarly, the steps needed to automate the processing and analysis of electronic biomedical text are reviewed, with lab time for using the GATE software package with NLP problem sets. The course concludes with an in-depth review of the unique challenges of processing clinical language and a look at current NLP published research.

Building on the introduction to BMI research methods in BMI 504, this course provides an in-depth review of the methods for conducting effective and unbiased evaluations of health information systems, including economic or cost analysis studies and the challenges associated with these methods. The course includes an exploration of the place of evaluation within the field of biomedical informatics; the major objectivist (quantitative) and subjectivist (qualitative) evaluation study methods; the motivations and methods for economic (cost) analysis as a component of evaluation studies; and the strategies for proposing evaluation studies, communicating their results and dealing with ethical, legal and regulatory issues associated with information systems evaluation.

Building on BMI 505 as a prerequisite, this course provides an in-depth exploration of the purpose, scope, technical structures and uses of electronic health records (EHR) and other clinical health care information systems, in addition to a critical  review of the purposes, scope, technical structures and ethical uses of computer-based decision support systems in clinical health care and consumer health settings. Students will build an expert system and test the system against real, anonymized datasets. Students will generate order sets and computerized physician order entry (CPOE) decision rules. Then, building on BMI 507, this course engages the students to solve ethical dilemmas in the area of clinical decision-making. This course critically reviews the purposes, scope, technical structures and ethical uses of computer-based decision support systems in clinical health care and consumer health settings.

Building on BMI 506 as a prerequisite, this course provides students with hands-on experience with the methods, systems, tools and databases available for the storage, analysis and interpretation of the increasingly voluminous molecular genome and protein data.  The course focuses on exercises that make use of these biological big data for research in molecular biology, systems biology, genetics and genomics as well as for translating and integrating biological data with clinical health care data to help predict and prevent disease. Students will use BLAST (Basic Local Alignment Search Tool), Protein Structure Prediction Software and Galaxy to analyze genomic, epigenetic, gene expression and proteomic data.

Building on BMI 507 as a prerequisite, this course first provides a review of the theories underlying biomedical knowledge representation and ontology. The methods and tools for applied ontology as well as the management and maintenance of biomedical ontologies will be discussed in detail, including the principles of ontological realism and the implementation thereof in the Basic Formal Ontology (BFO). Students will gain experience with the Web Ontology Language (OWL) and the limitations thereof, and with utilities to query ontologies expressed in OWL. The students will learn how to use and evaluate classifiers and their role in subsumption. They will learn both the transitive and reflexive closure of subsumption of a KR system and its applied use in ontology development, maintenance and use. This course also provides an in-depth review of current theories and research underlying the development of biomedical ontologies, a comparative critical analysis of the major current biomedical ontologies as well as the methods and tools for biomedical ontology development, use and evaluation.

Building on BMI 508, this course includes an in-depth exploration of the challenges and opportunities for building effective, integrated information systems to manage and maintain clinical population data for health care outcomes management and research as well as an in-depth view of the core U.S. and international information management challenges and opportunities of public health.

Building on BMI 509 as a prerequisite, this course reviews the interdisciplinary theoretical frameworks, design concepts and analytical foci used in human factors engineering and ergonomics for biomedical information systems. It will also discuss the sociotechnical influences on health information technology (IT) and informatics. These include the physical, cognitive, organizational/social and environmental challenges of human-computer interactions and a range of human factors approaches to systems design and evaluation. The course also looks at the mediating roles of IT on clinical and research user performance and the potential implications of a range of innovative new design concepts for biomedical information systems. In addition to reviewing these concepts with more advanced examples, the students will be exposed to case studies that will allow them to gain problem-solving skills in this important informatics domain.

Repeated for the first four semesters of the PhD program, this course provides each student with experience working in the research labs of two or three members of the BMI faculty, to get a broader perspective on the research challenges of the field and to help the student choose one of the five BMI department divisions as well as the specific research questions for his or her dissertation research. The student’s faculty research mentors and research lab rotations will be chosen in consultation with each student’s initial faculty adviser, based on how the student’s interests and research goals complement those of the department’s faculty.

Building on BMI 506 as a prerequisite and BMI 706 as a highly recommended advanced selective, this course provides an in-depth exploration of the purpose, scope, technical structures and uses of referent tracking as a methodology to design information systems that are self-explanatory in terms of the data they manage and “self-aware” in terms of their interactions with users or other systems. The course includes both theoretical lectures and group discussions, the latter aimed to help integrate all aspects of referent tracking into practical applications the students will design. 

This course concerns basic concepts and contemporary issues of cell structure and function. Topics covered include cell structure and function, protein sorting and trafficking, membrane transport and excitability, signal transduction and cell cycle. A combined lecture and conference format is used with lectures emphasizing basic principles derived from original journal articles. Conferences are used to review lecture concepts, present laboratory demonstrations, analyze original literature and solve problems.

The objective of this lecture/conference course is to acquaint students with basic concepts of cell structure and function. Topics to be covered include cell organelle and membrane structure, permeation through ion channels, carriers and pumps, protein sorting and trafficking and signal transduction (receptors, G-proteins, second messengers).

The course utilizes lectures, problem solving, study of original journal articles, written examinations and research papers.

At the end of the course, students should be able to deal quantitatively with experimental data and/or the scientific literature pertaining to these aspects of cell function.

Prerequisites: Calculus, familiarity with principles of physical chemistry and consent of instructor.

Fall semester. Michael E. Duffey, PhD.

The course is designed to provide doctoral students with a comprehensive overview of biochemistry. Topics to be covered include chemical principles, protein structure and stability, enzyme kinetics, mechanism and control of enzyme, metabolic pathways, integration of metabolism, nucleic acid structure and properties, DNA replication, transcription, RNA processing and translation. The course utilizes lectures, problem solving, original journal articles and written examinations.

Prerequisites: Permission of course coordinator: Daniel J. Kosman, PhD.

Fall semester. 

The objective of this course is to acquaint students with contemporary issues of communication between cells. The course utilizes lectures, conferences, problem solving, original journal article and written examinations. Topics to be covered include properties and function of the cellular cytoskeleton, dynamics of cellular motility, structure and function of gap junctions, cell adhesion, leukocyte trafficking.

Prerequisites: Calculus, familiarity with principles of physical chemistry and consent of instructor.

First half of spring semester. Richard A. Rabin, PhD.

The objective of this course is to acquaint students with contemporary issues involved in the growth, differentiation and transformation of cells. The course utilizes lectures, conferences, problem solving, original journal article and written examinations. Topics to be covered include stem cells  apoptosis and cell death, cellular differentiation, angiogenesis, neuronal growth and differentiation.

Prerequisites: Calculus, familiarity with principles of physical chemistry and consent of instructor.

Second half of spring semester. Richard A. Rabin, PhD.

Students perform research in three or four laboratories, becoming an integral part of the lab teams. During each six-to-eight-week rotation, students are introduced to the lab’s research and learn a variety of lab techniques that they can draw upon throughout their careers. Each faculty rotation adviser will describe his/her project, the experimental approach, the appropriate literature preparation, and explicit expectations for student work. Rotations also allow students to choose a specific focus and laboratory for their in-depth research as they pursue their degrees (PhD or MS). In addition, the rotations acquaint students with individual faculty-researchers, thus providing essential information for selecting a thesis mentor.

This course covers concepts, practices and an overview of principles underlying genetics and genomics as research disciplines. Specific areas of research are exemplified by extensive use of model organisms as well as large-scale genetic/genomic screens. Students learn how various models are used as research tools. Historical background information places current studies in context, offering insight into how the field should progress in the future. Lectures and paper discussions illustrate specific research areas and reinforce concepts.

This course covers the human genome, identification of disease genes, mutation types, DNA analysis/forensic medicine, chromosomes/game to genesis, typical and atypical Mendelian inheritance and animal models of disease. Other topics include population, clinical and cancer genetics; dysmorphology, congenital and developmental disorders and therapy. Students learn about fundamental approaches to research and gain an appreciation for how genetic approaches can be integrated with biochemical and molecular techniques. Each week focuses on a different concept and includes time for discussion of research papers, “make the diagnosis” exercises or dry laboratory (cytogenetics).

Moderated by senior students, this course provides experience and expertise in preparing and orally presenting research and teaching seminars. Students publically present either a Journal Club or their own degree-related research work, depending on their standing in the program.

This course covers physical mapping of chromosomes, genomics and microarrays; gene regulation and regulons; DNA damage and repair; basis of mutation, mutator genes and identification of non-mutable strains. Other topics include reversion and suppression; genetic analysis of mutants/mutations, complementation; dominance, and synthetic phenotypes; transformation; plasmids; phage; transposable elements; genetic regulation; review of paradigms; and in vitro genetics (molecular biology). Students learn about fundamental approaches to research and gain an appreciation for how genetic approaches can be integrated with biochemical and molecular techniques. Each week focuses on a different concept and includes discussion of related research papers.

Faculty mentors tutor students in research planning and laboratory techniques, and students conduct research.

The course will provide an in depth overview of microbiology, immunology, and their interface with biotechnology. The course will focus on the three major families of disease-causing microorganisms: bacteria (prokaryotes), viruses, and parasites/fungi (eukaryotes) as well as immunology and host-pathogen interactions. It will also cover key concepts in biochemistry, cell biology, and physiology. The course will consist of didactic lectures from a team of experts allowing for the presentation of cutting edge scientific research in their fields. In addition, experiment-based lectures will introduce students to cutting edge technologies used in microbiological and immunological research.

Requires successful completion of MIC 501 or BCH 503 or BMS 515 and BMS 516 with a grade of B or better.

This course covers the anatomy and function of the immune system, cell interactions, antibody formation, antigen-antibody reactions, cell-mediated immunity and biological effects of immunological reactions.

Requires successful completion of MIC 512 AND BMS 503 with a grade of B or better.

This course is for students with a strong background in biochemistry and cell biology as well as experience reading and presenting papers from the current scientific literature. It focuses on the basic biology and host interaction of select eukaryotic pathogens. The pathogens covered will vary, but will include both parasitic protozoans and fungal pathogens. Discussion encompasses aspects of molecular biology, biochemistry, cell biology and host-parasite interaction. Students will be expected to gain a working knowledge of major ideas and select primary literature in molecular parasitology, mycology and host-pathogen interactions, and be able to discuss questions, experimental approaches and evaluation of results. Several faculty members present in their areas of expertise.

Requires permission of instructor.

This course focuses on mechanisms of viral pathogenesis and the host response, as related to human disease. It covers the scientific approaches used to investigate these processes and involves studying viruses at their molecular biology and genetic levels as well as from a biophysical and evolutionary perspective. Several faculty members present in their areas of expertise. Material is based on the latest information from cutting-edge research, providing students with an awareness of the latest problems of interest in the field. Topics include, for example, virus structure, binding and entry, and alteration of host function; replication of RNA viruses; RNA virus transcription and translation; retroviruses; DNA virus life cycle and transcription; replication of DNA virus genomes; antiviral agents; emerging viruses; chronic and latent infections; and viral pathogenesis.

Requires success completion of MIC 501 or BCH 503 or BMS 515 AND BMS 516 with a grade of B or better

This advanced course briefly introduces general principles of bacteriology before progressing to a more comprehensive analysis of various virulence factors and specific mechanisms of bacterial pathogenesis that lead to disease. The course also covers the scientific approaches used to investigate these processes.

Students will be given the opportunity under faculty guidance to prepare and present short, introductory lectures and laboratory recitations, direct execution of experiments in the laboratory, and participate in student evaluation and improvements to course design.

Requires successful completion of BCH 503 OR BMS 503 with a grade of B or better.

This advanced seminar focuses in-depth on DNA replication, repair and damage responses. The course aims to increase knowledge in areas of DNA metabolism; improve and refine presentation skills; and hone abilities to read primary research articles and critically evaluate the work. Students also learn to organize and present a lecture independently without using a textbook as a guide.

Requires permission of instructor.

Each year, this participatory seminar focuses on different aspects of gene expression in eukaryotic pathogens. Weekly discussions are based on the most recent primary literature. Each student selects and presents a paper of high importance to the field. The presentations include relevant background information concerning the questions to be addressed.

Requires successful completion of MIC 512 with a grade of B or better.

This seminar offers a forum for discussing current scientific literature in immunology. Students present selected research papers approved by the course director. Classes are organized around groundbreaking research on topics such as vaccine development, transplantation, autoimmunity, neuroimmunology and immunopharmacology.

Requires successful completion of BMS 501 AND BMS 502 AND BMS 503 with a grade of B or better.

This course is designed to develop a working knowledge of a broad range of genetic approaches applicable to model bacteria. It covers principles and approaches used in the genetic dissection of complex biological processes in these bacteria. Participants lead in-depth discussions of the reasoning, uses and limitations of diverse methods of genetic analysis commonly used with model bacteria. These discussions are reinforced by journal club presentations that highlight the use of the technique. The course aims primarily to increase the depth of knowledge about established techniques in microbial genetics. Students also hone their abilities to read, understand and critically evaluate research articles as well as improve presentation skills.

Requires permission of instructor.

This seminar for advanced graduate students covers multiple aspects of virology at the cutting edge of current research. Students obtain a detailed understanding of various topics related to the history and process of vaccine development, including impacts on global health, economic and social issues. They critically analyze and critique the literature as well as identify novel problems in current research. Classes are organized around recent papers in the virological literature, encompassing topics such as emerging viral diseases and the hepatitis viruses. Students present, participate in discussions at a high level and demonstrate critical thinking skills.

This in-depth study of scientific literature relates to all aspects of fungal pathogenesis. Students will read, understand, interpret and critique primary scientific literature relating to the human pathogenic fungi. The course emphasizes understanding factors that contribute to host susceptibility, epidemiology and treatment, as well as fungal taxonomy and basic fungal biology. Topics range from fungal molecular biology, cell biology and biochemistry to immunology, antifungal susceptibility and clinical trials. Each course meeting will focus on a different paper chosen from the current, peer-reviewed scientific literature. Students will select papers, organize and deliver presentations, and answer questions about the paper. They are expected to attend all Journal Club meetings, participate in discussion and engage in critical questioning and scientific exchange.

Through this journal club experience, each student selects a scientific paper(s), organizes and presents relevant material, and manages a question-and-answer session. Students participate in discussion, critical questioning, scientific exchange and constructive evaluation of peer presenters.

This course is cross-listed in the departments of microbiology, biochemistry and biology. Interactions between proteins and nucleic acids facilitate all aspects of genome maintenance, including genetic recombination; DNA replication and repair; and all facets of transcription and associated mechanisms of gene regulation. Recognizing that a detailed, quantitative understanding of these interactions is key to studying and understanding all aspects of nucleic acid metabolism, this course familiarizes students with all relevant aspects of proteins and how they interact with nucleic acids, as well as with state-of-the art approaches to performing quantitative studies. It is taught by a team of faculty with expertise in these areas. 

Initial lectures cover nucleic acid structure and dynamics and protein structure as it relates to interactions with nucleic acids (that is, recognition elements). Content then progresses to cover physical biochemical aspects of protein-nucleic acid interactions, including thermodynamics, kinetics, site-size determination, binding constants, cooperativity, the kinetics of motion, the role of ATP binding and hydrolysis in regulating these interactions and comparison between bulk-phase and single-molecule studies of protein-nucleic acid interactions.

This graduate seminar course will cover topics in infectious diseases with a focus on global health inequity in under-resourced countries. Students will draw from primary, peer-reviewed scientific literature to learn about various infectious diseases that impact under-resourced regions, and place the microbiology and immunology of these pathogens within the context of global health, health care inequity (drug access, infrastructure, malnutrition) and public health (prevention, screening, safe water and hygiene). 

Requires permission of instructor.

This seminar involves presentation, review and discussion of current scientific articles related to bacterial pathogenesis. Students will be introduced to methodologies and state-of-the-art techniques.

Requires permission of instructor.

This participatory seminar focuses on different aspects of molecular parasitology each year. Topics usually center on molecular biology or host-parasite interaction and reflect the most current primary literature. Each student selects a recent paper of high importance to the field and organizes and gives a presentation about it. Presentations include relevant background information about the questions to be addressed. Other students in the class are expected to ask and answer questions about the material presented.

Method and equipment evaluations or other short-term projects, arranged in consultation with individual faculty members.

Clinical, hospital, and research laboratories utilize a variety of analytical instruments for biomedical research and diagnosis of diseases and conditions. MT 501 lecture will cover the theoretical principles of instrumental analysis; the MT 501 laboratory will cover the operational techniques of a variety of instruments, including practical aspects of spectral, electrochemical, chromatographic, colligative and nuclear instrumentation. Students are required to take both the lecture and the laboratory.

Clinical Immunology Laboratory explores functions and mechanisms of the human immune system, including antigen-antibody reactions and their application to serological testing. Autoimmune diseases, syphilis, hepatitis, HIV-AIDS, infectious mononucleosis, cytomegalovirus infections and toxoplasmosis are among the disease states studied.

Presentation and critical evaluation of current literature; participation in group discussion. Must be taken each semester that the student is registered.

The various aspects of evaluating new procedures for the clinical laboratory will be discussed. Laboratory work involves setting up and testing a selected method, including comparison with an established procedure.

One semester rotation through various faculty laboratories to help students decide the direction of their future research.

Discusses pathological and physiological implications of electrolytes, blood gases, metabolites, enzymes, hormones, and drugs. Emphasizes developing technical competencies in analytical methods and computer-based data reduction and interpretation. Covers introductory methods of evaluation, quality control and basic statistical decision-making procedures.

Comprehensive study of the classification, etiology, pathogenicity, laboratory identification, diagnosis, and treatment of bacterial infections. Emphasizes techniques and methods used to identify and isolate bacterial pathogens. Overview of the classification and pathogenicity of viral infections. Laboratory consists of microscopic, biochemical and immunological procedures to identify pathogens from clinical specimens.

Comprehensive study of clinical hematology. The lecture focuses on the components of blood and their specific role, hematopoiesis, and the incidence, etiology, diagnosis and treatment of hematologic disorders. The laboratory complements the lecture and provides the opportunity to develop a working knowledge of the basis for hematologic laboratory testing, the development of the technical skills for the performance of a variety of laboratory procedures and the interpretation of laboratory results.

Clinical and classroom instructional design, evaluation strategies, statistical tools, and teaching skills.

Clinical Parasitology studies the relationship between human-as-host, and parasites. MT 516 will present the theory and laboratory techniques of the distribution, pathogenesis, identification and life cycles of clinically significant parasites, such as worms and protozoa, emphasizing the infective and diagnostic stages. The laboratory features identifying characteristics of parasites using prepared clinical specimens.

Managerial theory and practice, resume writing and interviewing, influence of regulatory agencies, and current issues affecting health care.

Discusses case studies using problem-solving techniques to analyze and interpret relevant clinical and laboratory data; comprehensive examination covering all program coursework.

Clinical Urinalysis and Other Body Fluids is a study of body fluids for health and disease and conditions. MT 521 will explore the theoretical and applied aspects of urinalysis and other body fluids. The laboratory will teach parameters that can be measured, such as proteins, enzymes, blood cells, and ions.

Discusses the basic biochemistry needed to understand Mendelian genetics, basic techniques used in molecular biology, practical uses of molecular biotechnology in diagnosis, research and industry, and ethical issues surrounding the use of biotechnology. Laboratory consists of hands-on and demonstration exercises illustrating techniques used in biomolecular technology and diagnosis.

This course covers the multiple styles of presentation that are required for effective technical communication, emphasizing the ability to accurately analyze and present data and technical information in both written and oral formats. Written formats to be covered include preparation of a poster, writing SOPS/materials and methods, figures, tables and legends, and best practices for lab notebooks. Oral formats to be covered will include journal club discussion, PowerPoint and a poster presentation. Additional lectures will cover avoiding common errors in grammar and usage, accessing peer-reviewed library resources, and constructing a formatted bibliography. The course will also cover scientific vocabulary and best practices in software commonly used in technical communications, including EndNote, Track Changes in Word, and PowerPoint.

Clinical Biochemistry is the study of basic human biochemistry, with an emphasis on biomolecular structure, metabolic pathways and their relationship to human health and disease. MT 401/527 will cover the fundamental structures, function and interactions of biological macromolecules, including nucleic acids (RNA and DNA), proteins, carbohydrates and lipids. Accepted Biotechnology Students will use MT 401/527 as a foundation for MT 430/530 Bioseparation Techniques, taught each Spring; Accepted Medical Technology Students will use MT 401/527 as a foundation for MT 407/507 Clinical Chemistry.

Introduces the field of forensic science, including the general areas of forensic serology, DNA analysis, chemistry/drug analysis, firearms/tool marks, arson, and trace evidence.

Mycology is the study of fungi and human fungal infections. MT 529/429 is a comprehensive study of the classification, etiology, pathogenicity, diagnosis and treatment of fungal infections. Emphasizes techniques and methods used to isolate and identify fungal pathogens. The laboratory consists of microscopic and biochemical procedures to identify molds and yeasts from clinical specimens.

Lectures are presented to introduce the biochemistry of selected laboratory experiments designed to provide the student experience with common analytical techniques associated with the isolation, quantification and characterization of biomolecules with an emphasis on instrumentation.  Multiple bioseparation techniques including thin layer, classical column, high performance liquid and gas chromatography as well as electrophoretic separations are practiced.  Automated and semi-automated chemistry systems are also employed.

Hemostasis is the study of the components of the coagulation and fibrinolytic systems and related disorders. In lecture students will comprehensively study these systems and develop an understanding of mechanisms involved in their normal function as well as the clinical and diagnostic features of the disorders of each system. In the laboratory component students will learn the basis of the laboratory tests performed to assess the coagulation and fibrinolytic systems and become technically proficient in performing these tests. Case studies will also be used for the clinical application of the material.

Medical Genetics is the study of the basic principles of hereditary medical, including basic Mendelian genetics, molecular and biochemical basis of genetics, developmental genetics, genetics of complex diseases, the genetics of cancer, genetic counseling, and prenatal diagnosis.

Lectures are presented to introduce the concepts of cell and tissue culture, with specific laboratory exercises designed to expose the student, through the use of primary and established cell lines, to sterile technique, media preparation, quality control and cell line validation, passaging of nonadherent and adherent cells, cryopreservation, and microscopy and digital photography.   Cellular assays for viability, proliferation, invasion, and apoptosis will be performed.

Human blood group antigens and antibodies; compatibility testing for blood transfusions and problem solving involving case studies.

In depth study of current clinically used tumor markers, current research on tumor markers and student presentation of a research project concerning the past, present and future of particular tumor antigens.

Attend lectures pertaining to education, Fall semester cr; participate in teaching of an undergraduate course at least one semester. May elect to present lectures, develop teaching materials.

Minimum 6 credits required. Guided research.

This course provides graduate students in the neuroscience program and other life sciences with a comprehensive overview of the principles that control the properties of neurons and their function in the nervous system. It covers the structure, development and migration of neurons; formation and function of the synapse; and the general principles of neuronal excitability and synaptic function. The student is expected to gain (1) the necessary background to pursue in greater depth any selected facet of neuroscience and (2) an appreciation of the beauty and excitement offered by the intellectual challenge posed by analyzing how the nervous system functions.

This course focuses on current research in the development of the nervous system and on diseases and dysfunctions of the brain. The format includes short lectures but is primarily based on student-led discussions of original journal articles.

Topics covered include: retinal tectal topography - both gradient and activity based; N-methylation during development; calcium waves; stem cells; delta/notch; trophic factors; synapse development in the CNS; neurotoxicology; Parkinson's disease; viral neurotoxicity; HIV/AIDS; encephalopathy.

This is an advanced course for students who have already taken NRS 520 or the equivalent.

Only required for the MS program, as PhD students take research rotations during their PPBS year.

This one-credit course is designed to introduce students to the wide spectrum of subject areas in neuroscience by attending seminars hosted by the Neuroscience Program and associated departments.