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, programing 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 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.

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.

Repeated for the four semesters of the third and fourth years of the PhD program, this course provides each student with more focused research experience working in the lab or labs of his or her faculty dissertation adviser or other members of his or her dissertation advisory committee. For most students, BMI 711 research work credit will be earned after completing the PhD qualifying exam, however, every student in the PhD program must pass the qualifying exam no later than the end of the first semester of BMI 711 research experience (i.e., the end of the first semester of the third year of the PhD program).

Repeated during the last two semesters (the fifth year) of the PhD program, this course provides time for the PhD candidate to complete his or her dissertation research, write the publishable dissertation thesis and prepare for the defense and formal presentation of her or his research results. During this final phase of the dissertation work, the candidate will continue to consult regularly with the members of his or her dissertation advisory committee.

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.

Laboratory rotations introduce students to disciplines, faculty, techniques and research strategies. Students participate in ongoing projects in the basic science departments. These courses are designed to assist students in identifying their research goals while enabling them to maintain a more comprehensive view of the integrative nature of life sciences.

Laboratory rotations introduce students to disciplines, faculty, techniques and research strategies. Students participate in ongoing projects in the basic science departments. These courses are designed to assist students in identifying their research goals while enabling them to maintain a more comprehensive view of the integrative nature of life sciences.

The goal of this course is to introduce students to strategies for identifying, reading, critiquing and presenting scientific literature. Students will break into small group journal clubs in which they will present a paper from the primary literature.

This course is required for all students in the PPBS program. Students will be introduced to topics relevant to their training and situations that pose potential ethical concerns. Class discussions led by faculty facilitators will explore appropriate and inappropriate ways to deal with these situations.

This lecture course is required for all students in the PPBS program. It will teach students fundamental concepts important to a broad range of biomedical research topics.

This course is a combination of lectures and research paper discussions and is required for all students in the PPBS program. This course will teach students to research methods, experimental design, data analysis and critical thinking.

Designed to expose students in the Natural Sciences Interdisciplinary masters program to current topics in the biomedical sciences. Students will be required to attend a one-hour seminar each week, chosen from the wide array of Jacobs School seminar series offered in both biomedical and clinical disciplines.

Supervised culminating project for the Natural Sciences Interdisciplinary master's program. Students will present and discuss their work in progress in individual meetings with their advisor.

This course is dual-listed with BPH 405. This course is concerned with fundamental theory and principles of various kinetic processes underlying the normal function of biological systems and membrane transport processes in biological systems. Topics include chemical kinetics, thermodynamics and statistical mechanics, osmotic forces, membrane permeation of non-electrolytes and electrolytes, membrane transport and various ionic channels in excitable cells, membrane bulk transport and intracellular vesicle trafficking processes. Theories and principles developed to the state of current research knowledge are discussed.

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).

Through this course, students prepare and defend a research proposal based on their proposed PhD work. Successful completion constitutes entrance into candidacy for the PhD degree in genetics, genomics and bioinformatics.

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.

Students prepare for and conduct an oral presentation during their annual Thesis Committee meeting. Shortly afterward, the student prepares a report detailing the committee members’ suggestions. The committee may meet more often at the discretion of the student, mentor or committee. Meetings continue until the mentor and the committee determine the student should be encouraged to prepare his/her dissertation proposal for written evaluation and oral defense.

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 BCH 503 or BMS 503 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 permission of instructor

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 permission of instructor.

This course introduces students to the process of writing a grant application. Discussion sessions follow faculty lectures on all stages of this process — from the initial steps of preparing an application to grant submission and review. In conjunction, students write short grant applications on subjects other than their thesis projects, with help from their major professors. At several stages, students submit the documents for peer evaluation and discussion, facilitated by a faculty member. Students also prepare written reviews for the final documents following the format of the National Institutes of Health, emphasizing strengths and weaknesses of their applications. In addition, students prepare and deliver short PowerPoint presentations on their proposals.

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.

Through this tutorial experience, students work one-on-one with faculty mentors to conduct research in one of the following areas:

This course provides the Graduate Students in the Graduate Neuroscience Program and other life sciences with a comprehensive overview of the principles that control the development and function of the nervous system. These principles require knowledge that cuts across all scientific disciplines. Hence, topics will be team-taught at the molecular, cellular, and systems levels. The course covers the structure and development of the nervous system, formation and function of the synapse, and the general principles of neuronal 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. Malcolm Slaughter, PhD, is the course coordinator.

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.

Course coordinators: Stanley Halvorsen, PhD, Michal Stachowiak, PhD

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.

The course is a combination of lectures, student presentations and discussions focused on the current research advances in this field. Topics include salivary gland development, formation and regulation of saliva secretion, saliva as a diagnostic fluid for oral and systemic diseases, structure/function of salivary molecules, and salivary gland diseases, dysfunction and therapy.

The oral cavity harbors a complex and fascinating microbial ecosystem. Recent research of this micro-environment has yielded many important findings relevant to mechanisms of oral disease, with implications for infectious disease and medicine in general. This graduate course will discuss the mechanisms of oral colonization by the normal oral flora, dental and medical bacterial pathogens, review the biology of dental plaque formation and control, and the pathogenesis of oral infections including caries and periodontal disease. Emphasis will be on molecular aspects of important mechanisms. Material will be learned through group learning activities, research seminars, and student presentations. Readings will emphasize the historical background and conceptual aspects of each topic, while presentations will focus on methodology and research design.

This course is designed as a graduate level (master’s, PhD) course on concepts in immunology that are applicable to oral biology. It emphasizes oral aspects of humoral and cell-mediated immunity, covering such topics as oral vaccines, mucosal immunity and genetic basis of normal function, as well as aberrations in immunological mediators and host responses in oral diseases. Students are expected to have a basic knowledge of immunology although a review session on basic immunological concepts is provided at the beginning of the course. Emphasis is placed on the aspects of immunology that are directly pertinent to the pathogenesis, diagnosis, treatment and prophylaxis of inflammatory condition and diseases associated with the oral cavity and with oral biology. Although lecture-based, the course relies heavily on research-based current literature, and students are expected to derive information from that literature and present a review of some of those papers in the last portion of the course. Discussions of medical and research topics are part of the course and students also are evaluated on that basis.

The cell and molecular biology of bone is presented with special emphasis on the interactions involved in bone remodeling. Hormonal and growth factor effects are discussed with emphasis on signaling mechanisms and cytokine production. Pathophysiology and therapeutic intervention is studied with respect to cellular and molecular effects.

The cell membrane is the boundary between a cell and its environment, but is not simply a lipid coating: it is a vital organelle. Embedded membrane proteins facilitate the flux of ions and solutes to maintain the distinct composition of the cell interior and mediate cell excitability, while the associated cytoskeleton provides structural integrity, modulates cell movement, and the response of cells to physical stress. Having completed this course, students will have a working knowledge of the importance of membrane and structural proteins to a wide variety of physiological and pathophysiological processes. Students aiming for a career in the health sciences will benefit from this exposure to the underpinnings of medical physiology taught by instructors from the medical school faculty. In the first half of the course students will learn the fundamentals of cellular and molecular physiology. In the second half, students will apply this knowledge in faculty-led discussions of recent research developments.

Prerequisites: Calculus, cell biology (BIO201, BIO205) or consent of instructor.  

Spring semester. Cross-listed as PGY-405.

Course coordinator: Mark D. Parker, PhD

Number of students: 20-30

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course examines the understanding of the physiology of fundamental organ systems and the cellular and molecular basis of diseases of these systems. Specifically, it will examine the mechanisms by which alterations in organ system structure and function lead to disease. A combined lecture, conference and case study format are used: Lectures teach the physiological principles of the organ system being studied, conferences review original journal articles concerning the cellular and molecular basis of the disease processes being studied, and case studies show specific examples of disease processes and the cellular and molecular basis of these disease processes. At the end of the course, students should understand basic organ system physiology, and the cellular and molecular basis of disease processes affecting these organ systems. In addition, students gain valuable experience in reading scientific literature and understanding the rationale for therapeutic interventions and future scientific approaches to disease.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

This course is concerned with basic principles underlying cell and membrane physiology. Emphasis is on membrane excitability, ion channels and their modulation by cell signaling pathways.

The course offers a broad analysis of ethical issues in science including scientific misconduct, fraud and plagiarism, animal use and animal rights, clinical trials and informed consent, intellectual property rights, data handling and preservation, and issues around genetic diseases and information.

The goal of PMY 503 is to provide graduate students with an in-depth understanding of pharmacological principles as well as the ability to use and apply this information. Topics to be included: pharmacokinetic principles (e.g., absorption, distribution, metabolism, excretion, drug dosing); receptor theory and drug-receptor interactions; non-receptor targets (e.g., enzymes, biologics RNA-based therapy); pharmacogenetics; drug safety; quantifying drug effects; and target engagement and validation. Each topic will be introduced and necessary information provided through didactic lectures; subsequent sessions will focus on the use and application of this information. These sessions will involve a discussion of research papers or research problems using the Socratic Method with the faculty acting as discussion facilitators. For the more quantitative aspects of this course (e.g., pharmacokinetics and the describing of drug effects), quantitative problem-solving will also be used.

PMY 503 is dual-listed with PMY 405, intended for undergraduates, and PMY 511, for pharmacy students. These courses share a central syllabus and include a one-hour recitation tailored to the needs of each group of students.

In this course, you will learn, under supervision, how to evaluate and present original research from biomedical scientific literature.  Typically, one to two published papers are presented in a seminar (approximately 50 minutes long).  In consultation with the course director, students choose papers to be presented within the general fields of pharmacology and toxicology. A brief question and answer session follows each presentation, involving students and faculty from the Department of Pharmacology and Toxicology.

You will learn to formulate a seminar abstract, deliver work effectively in a seminar, prepare quality slides, use background information well, and evaluate papers’ methods, results and conclusions.  Your presentation will also be evaluated on your critical assessment of the presented research, ability to respond to audience questions and extent to which you place the results in a broader context of ongoing research.