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Courses of the Genetics Program

 

Required Courses

BGE 510: Graduate Genetics

This course investigates fundamental aspects of the transmission and expression of genetic information in prokaryotic and eukaryotic systems. The course is organized in a way that allows the students to appreciate the breadth of genetics research, while also gaining an in-depth understanding of selected important topics. Students explore the use of both classical and molecular genetic approaches to understand biological processes in genetics model systems including yeast, flies, worms, mouse, and man.

Spring, 3 credits, Letter graded (A, A-, B+, etc.)

MCB 503 [HBM 503]: Molecular Genetics

Introduces the classical work and current developments in lower and higher genetic systems. Covers gene structure and regulation in prokaryotic and eukaryotic organisms, mutational analysis and mapping, transposable elements, and biological DNA transfer mechanisms. Bacteriophage as well as lower and higher eukaryotic systems are used to illustrate aspects of molecular genetic structure and function. This course is offered as both MCB 503 and HBM 503. Prerequisite: matriculation in graduate program or permission of instructor

Fall, 3 credits, Letter graded (A, A-, B+, etc.)

HBH 656: Cell Biology

Introduction to the structural and functional organization of cells and tissues and to the way structure relates to function. Particular emphasis is placed on nuclear and chromosomal structure, signal transduction, protein translocation, the cytoskeleton and the extracellular matrix. The interaction of cellular structures and components and their regulation is stressed as is the organization and interaction of cells in tissues. The course is comparative and includes examples of cells and tissues from vertebrates, invertebrates, plants, and prokaryotic systems. Prerequisite: matriculation in graduate program or permission of instructor.

Spring, 4 credits, Letter graded (A, A-, B+, etc.)

​BGE 530: Laboratory Rotation

The student rotates through laboratories of four different genetics program faculty members during the first year. The selection of the laboratories is made by the student, in conjunction with individual faculty, and with the approval of the program director. By taking part in ongoing projects, the student will learn experimental procedures and techniques and become acquainted with research opportunities in the participating programs. Prerequisite: Permission of instructor

Fall and Spring, 1-8 credits, S/U grading
May be repeated 2 times for credit.
 
BGE 531: Graduate Student Seminar in Genetics

Students have the opportunity to present their research to other students and faculty on an annual basis. Students in the first or second year will present brief seminars as part of a one-day symposium with all of their classmates. Advanced students present research seminars as part of a weekly research seminar series that is attended by faculty and students. Although the first and second year students do not present in this weekly seminar series, they should attend these seminars as it provides an excellent mechanism for learning about current areas of research interest.

Fall and Spring, 0-1 credits, S/U grading
May be repeated for credit.
BGE 691: Readings in Genetics

Journal Club on thematic topics in different areas of current genetics research

Prerequisite: Permission of instructor
Fall and Spring, 1 credit, Letter graded (A, A-, B+, etc.)
May be repeated for credit.

BGE 693: Research Proposal Preparation

A course, based upon literature in the broad field of Genetics, to instruct in scientific writing and the preparation of research proposals. The course will be organized in three parts. In the first section of the course, students will become familiar with the components of the research proposal and will read and evaluate proposals written by the training faculty. Lectures given by the course co-directors will cover the basics of scientific writing, research proposal preparation, and the problems and concerns commonly voiced by reviewers of research proposals. In the second section, students will develop two short proposals for the study of genetics which are unrelated to their graduate research. One of these short proposals will be selected for development into a full proposal. In the third section, students will develop and write the full proposal. The students' skills in proposal preparation will be enhanced by critiquing the short and full proposals presented by other students in the second and third sections of the course.

Spring, 1-3 credits, Letter graded (A, A-, B+, etc.)

BGE 599: Graduate Research

Original investigation undertaken with the supervision of a member of the program.

Fall and Spring, 1-9 credits, S/U grading
May be repeated for credit.
BGE 699: Dissertation Research on Campus

Prerequisite: Advancement to candidacy (G5). Major portion of research must take place on SBU campus, at Cold Spring Harbor, or at the Brookhaven National Lab.

Fall, Spring, and Summer, 1-9 credits, S/U grading
May be repeated for credit.
BGE 800: Summer Research

May be repeated for credit.

BIO 600:  Practicum in Teaching

Fall and Spring, S/U grading
May be repeated for credit.

GRD 500: Responsible Conduct of Research and Scholarship

This course is designed to introduce students to the major issues in the ethics of science and research. Using a combination of readings - written and web-based - videos, lectures, case discussion and other exercises, students will investigate the moral values intrinsic to science and the professional and social values with which scientists must comply. Each class will begin with an introductory lecture or video followed by discipline-based, small group discussions with the participation of faculty from the department or program from which the graduate students come.

0-1 credits, S/U grading

 

Popular Electives

AMS 534 [BGE 534]: Introduction to Systems Biology

This course is geared towards teaching essential concepts and computational skills in Systems Biology. The course is centered upon two key programming languages: Matlab for modeling applications and the R language for statistical analysis and sequence manipulation.

Spring, 3 credits, Letter graded (A, A-, B+, etc.)

AMS 572: Data Analysis I

Introduction to basic statistical procedures. Survey of elementary statistical procedures such as the t-test and chi-square test. Procedures to verify that assumptions are satisfied. Extensions of simple procedures to more complex situations and introduction to one-way analysis of variance. Basic exploratory data analysis procedures (stem and leaf plots, straightening regression lines, and techniques to establish equal variance). Offered as AMS 572 or HPH 698.

Prerequisite: AMS 312 or permission of instructor
Fall, 3 credits, Letter graded (A, A-, B+, etc.)

BEE 551: Principles of Evolution

Biological evolution, including the genetics of populations, speciation, evolution of higher taxa, and the fossil record.

Fall, 4 credits, Letter graded (A, A-, B+, etc.)

BEE 554: Population Genetics and Evolution

A general introduction to mathematical population genetics and evolutionary theory. The effects of mutation, recombination, selection, and migration are studied. Modern concepts in both theoretical and experimental population genetics are covered.

Prerequisite: BEE 552 or equivalent, and a course in evolution
Spring, odd years, 0-3 credits, Letter graded (A, A-, B+, etc.)

BEE 575: Evolutionary Ecology

The approach is to understand the theoretical basis and review empirical tests of diverse topics. The format includes both lectures and student-led discussions of primary literature.

Prerequisite: BEE 550; BEE 551, or permission of instructor
Fall, alternate years, 3 credits, Letter graded (A, A-, B+, etc.)

BME 503: Cell and Molecular Imaging

This course will cover basics of optics, microscopy, spectroscopy and fluorescence in the context of imaging at the cellular and molecular level. Recently developed advanced imaging techniques for probing protein interactions and live cell functions are also discussed. The course is organized in 3 modules.

3 credits, Letter graded (A, A-, B+, etc.)
May be repeated 2 times FOR credit.

BME 534: Functional Genomics

Course provides foundation in concepts of functional genomics and proteomics. Topics include organization and complexity of the mammalian genome and mechanisms of expression of genes, gene expression analysis technologies with a strong focus on construction and utilization of DNA microarrays, and tools for determining gene function by perturbation of gene expression.

Spring, 3 credits, Letter graded (A, A-, B+, etc.)
May be repeated 2 times FOR credit.
CHE 543: Chemical Approaches to Biology

The use of molecular concepts and methodology to solve problems in biology and medicine. The course covers methods to elucidate and control biological systems. Possible topics include chemical genomics, metabolomics, and chemotherapeutics.

Prerequisite CHE 542
Fall, 3 credits, Letter graded (A, A-, B+, etc.)

CSE 549: Computational Biology

This course focuses on current problems in computational biology and bioinformatics. Our emphasis will be algorithmic, on discovering appropriate combinatorial algorithm problems and the techniques to solve them. Primary topics will include DNA sequence assembly, DNA/protein sequence comparison, hybridization array analysis, RNA and protein folding, and phylogenic trees.

3 credits, Letter graded (A, A-, B+, etc.)

HBH 550: Statistics in Life Sciences

This course covers statistical concepts and issues in the life sciences. Basic algebra is assumed as a prerequisite. Topics covered include: descriptive statistics, foundation of statistical inference, sampling distribution, point estimate and confidence internal, comparison of independent and paired samples, analysis of categorical data, correlation, ANOVA, linear regression, and nonparametric test.

1 credit, S/U grading
May be repeated for credit.
 
HBM 522: Biology of Cancer

A short course with the emphasis on cancer as a disease of man. Lectures address human cancer as seen by the clinician and as basic research relates to human disease. This course provides students with a link between courses in cell and molecular biology and the application of this basic information to tumor management. Offered as HBM 522 and HPH 659.

Spring, even years, 2 credits, Letter graded (A, A-, B+, etc.)

HBM 640: Molecular Mechanisms of Microbial Pathogenesis

This course covers the principles and molecular mechanisms of pathogenesis of a selected group of the best understood viral and bacterial pathogens. A major focus of the course relates to pathogen modification of host extracellular and intracellular signalling events, as well as pathogen-host interactions pertaining to the innate, humoral and cellular responses to infection. The material is presented by invited lecturers who are leaders in their fields. This courses is directed to graduate students, post-doctorate and medical fellows, and advanced medical students, who are are contemplating careers in infectious disease research. Prerequisite: HBM, BMO 503 and BMO 520

3 credits, Letter graded (A, A-, B+, etc.)

HBM 692: Experimental Methods in Molecular Genetics and Microbiology

The goal of this course is to introduce students to the rationale underlying the wide array of new methods in biology, as well as to promote the critical analysis of scientific literature. Lectures will be given about various scientific methods and approaches, and journal articles relating to the concepts introduced will be assigned. A separate discussion section will be held to review and critique the articles, to be led by the students.

1 credit, Letter graded (A, A-, B+, etc.)

HBP 533: Immunology

Principles of immunology for graduate students in the biological sciences, including definition of antigens and antibodies, specificity of the immune response, immunoglobulin structure, the genetics of immunoglobulin synthesis, cellular cooperation in the immune response, hypersensitivity, tolerance immunogenetics. Open to advanced undergraduates.

Fall, 3 credits, Letter graded (A, A-, B+, etc.)

HBY 561: Statistical Analysis of Physiological Data

Statistical methods useful in analyzing common types of physiological data. Topics include probability, data distributions, hypothesis testing with parametric and non-parametric methods, ANOVA, regression and correlation, and power analysis. Emphasis is on experimental design and appropriate, efficient use of statistical software.

Offered Spring, 1 credit, Letter graded (A, A-, B+, etc.)

MCB 517: Biomembranes

Examines the molecular architecture of membranes; the structure, organization, functions, and assembly of lipids and proteins in biological membranes.

Prerequisite: Matriculation in Graduate Program or permission of instructor.
Fall, 1 credit, Letter graded (A, A-, B+, etc.)

MCB 520: Graduate Biochemistry I

Several topics in modern biochemistry are treated at an advanced level. Topics covered will include protein structure, enzyme kinetics and mechanisms, and enzyme regulation.

Prerequisite: undergraduate biochemistry course, matriculation in graduate program or permission of instructor
Fall, 3 credits, Letter graded (A, A-, B+, etc.)

MCB 657 [BGE 657]: Principles of Development

This course deals with developing systems at all levels from the morphological to the molecular. Illustrative material from both animal and plant kingdoms is used. Special attention is given to gametogenesis, genetic control of early development, transcriptional and translational control of protein synthesis, the role of cell division and cell movements, and cell-to-cell interactions in defining developing systems.

Prerequisite: MCB 656, matriculation in graduate program or permission of instructor.
Fall, 3 credits, Letter graded (A, A-, B+, etc.)

WRT 621: Graduate-Level Writing

This course, designed for a mixture of students from any of our graduate programs or departments, is a workshop in writing academic papers, theses, or dissertations, with attention to research methods, drafting, organizing, revising, and editing work that the students have already been assigned in their primary departments.

3 credits, S/U grading
May be repeated 1 time for credit.
 

Alan Alda Center for Communicating Science Courses (Partial Listing)

BGE 500: Introduction to News Media Concepts and Institutions

In any age when scientific, medical and environmental issues often make news, this course is designed to familiarize students with how the U.S. news media work. Students will learn how the industry is organized, and why it is undergoing fundamental change; how decisions are made about which stories to cover and how prominently to cover them; how the press weighs such values as freedom, privacy and national security; how the press attempts to deal with issues of scientific uncertainty and conflicting information. In exploring the culture and practices of American journalism, the course will focus on recent coverage of science, health and environmental developments. This course is intended for graduate students in health and science who seek a better understanding of the media context in which they will work, as well as for journalism M.S. students who do not have a background in journalism.

Offered Fall, Spring, and Summer, 3 credits, Letter graded (A, A-, B+, etc.)

BGE 501: Communicating Science: Distilling Your Message

Current and future scientists and health professionals will learn to communicate clearly and engagingly with different kinds of audiences, at different levels of complexity, using different forms. We'll examine the basics of clear, two-way communication, including knowing and being responsive to your audience, overcoming "the curse of knowledge," having a point, avoiding jargon, using storytelling techniques, being personal, asking questions, and introducing complexity in stages. Students will start by crafting a short, controversial statement about their work and why it matters. We'll expand that to a longer statement, convert it into a brief piece of writing, such as a letter to the editor or a blog post, practice answering questions about it from the public and from the media, plan a public presentation, and learn to apply these skills in the classroom. Skills learned in this course can help scientists and health professionals communicate more effectively with students, potential employers or funders, public officials, family and friends, the press, and colleagues in other disciplines. JRN501, JRN502, and JRN503 are 1-credit modules, each lasting four or five weeks. Students may take all three consecutively in one semester or may take only one or two. Offered

Fall, Spring, and Summer, 1 credit, Letter graded (A, A-, B+, etc.)

BGE 502: Communicating Science: Writing for the Public

Students will practice writing about specific and health material clearly and vividly, in ways not-scientists can understand. They will learn to use analogies, examples and metaphors to illuminate unfamiliar concepts, practice using numbers clearly and translating statistics into conversational English, learn about scientific terms and concepts that are commonly misunderstood by the public. They will learn to introduce complexity gradually, to avoid overwhelming the reader while not "dumbing down" their material. Students will learn to write for different formats, including blogs, letters to the editor or to funders, and op-edits or commentary pieces.

JRN501, JRN502, and JRN503 are 1-credit modules, each lasting four or five weeks. Students may take all three consecutively in one semester or may take only one or two.
Fall, Spring, and Summer, 1 credit, Letter graded (A, A-, B+, etc.)

BGE 503: Communicating Science: Improvisation for Scientists

This innovative course uses improvisational theater techniques to help students speak more spontaneously and connect more directly and responsively with their audience and with each other. After warm-up exercises, emphasizing physical freedom and verbal spontaneity, students take part in two- and three-person exercises and situational improvisations that focus on paying attention to your listeners, and altering your approach to meet their needs. At the beginning and end of this course, students will deliver a short oral statement about their research or a scientific topic that interests them, so they can measure their progress. This course is not about acting; it's about helping current and future scientists and health professionals connect with their audiences. Science graduate students who had several sessions of improvisation training in a pilot session reported communicating better as teachers, researchers, students, and family members. A glimpse of the process can be seen in a short video on the web page of Stony Brook's Center for Communicating Science: www.stonybrook.edu/journalism/science.

JRN501, JRN502, and JRN503 are 1-credit modules, each lasting four or five weeks. Students may take all three consecutively in one semester or may take only one or two.
Fall, Spring, and Summer, 1 credit, S/U grading

BGE 504: Communicating Science: Using Digital Media

Science and health information increasingly travels by digital media, as new ways emerge for scientists to communicate directly with the public, without the intermediaries of press or public relations. Students will learn how to use blogs, podcasts, Twitter and other forms of social media for two-way communication with different segments of the public, including colleagues in other disciplines. The course will include hands-on instruction in working with digital media, tailored to students' interests and levels of experience.

Offered Fall, Spring, and Summer, 1 credit, S/U grading
May be repeated 2 times for credit.
BGE 505: Communicating Science: Connecting with the Community

Students will learn how to use communication techniques, cultural competency, and health literacy concepts to reach and mobilize the community and key stakeholders on health- and science-related issues related to their research, outreach or community education objectives. The course will incorporate role-playing and community networking skills to help students make connections with key people and groups relevant to their current interests and work. This will require contact with the instructor before the start of the course to discuss students' projects, plans or interests.

Offered Fall, Spring, and Summer, 1 credit, Letter graded (A, A-, B+, etc.)
May be repeated 2 times for credit.
BGE 506: Communicating Science: Advanced Writing for the Public

This course is for graduate students in the sciences who have taken JRN 502, Communicating Science: Writing To Be Understood, and want to continue developing and practicing their ability to write about science clearly and vividly for non-expert readers.

Offered Spring, 1 credit, S/U grading
May be repeated for credit.
 
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