University Bulletin (2019-2020)

• Master of Science
• Doctor of Philosophy

The graduate program in molecular and cell biology, leading to the MS and PhD degrees is designed to provide each student with the theoretical foundations and research experience needed to become an independent and original investigator of basic biological phenomena. Preparation is achieved through the combination of (1) a flexible curriculum of required and elective courses tailored for each student's specific needs, (2) a semester of laboratory research (MS) or set of laboratory rotations (PhD) that acquaints each entering student with current research techniques and permits exploration of possible research areas, and (3) separate MS and PhD level proseminar courses specifically for first-year students and a series of journal clubs that keep students abreast of significant research findings and develop confidence with reading research literature and giving oral presentations. First-year MS and PhD students participate in all three aspects of our graduate program and are thus quickly integrated into the biological research community at Brandeis. A strength of our program is frequent interaction between students and faculty, formal and informal. Thesis research leading to the PhD degree is carried out under the personal direction of a faculty member.

A complete list of faculty research interests and recent publications can be viewed online. Potential applicants are urged to review this information. As a general orientation, the following areas of research are among those represented in the program: molecular biology of the regulation of gene expression; chromosome structure and chromosomal rearrangements; mechanisms of recombination and DNA repair; developmental genetics; behavioral genetics, neural development; biophysics of single nerve cells; learning and memory; regulation of small RNAs; immune cell differentiation and development; cytoskeletal architecture; organization of subcellular structures; structure and function of proteins; mammalian embryogenesis and the biotechnology of DNA diagnostics.

Master of Science in Molecular and Cell Biology

Graduate Outcomes

The MCB Master’s program will train students to realize their potential as independent scientists, and will foster students’ career development goals toward obtaining a position in research, teaching, or other scientific settings.

Students graduating with a Master’s degree in Molecular and Cell Biology are expected to:

1. Demonstrate a graduate-level understanding of one of the areas of research represented by the program: molecular biology of the regulation of gene expression; chromosome structure and chromosomal rearrangements; mechanisms of recombination and DNA repair; developmental genetics; behavioral genetics, neural development; biophysics of single nerve cells; learning and memory; regulation of small RNAs; immune cell differentiation and development; cytoskeletal architecture; organization of subcellular structures; structure and function of proteins; mammalian embryogenesis and the biotechnology of DNA diagnostics.
2. Explore possible research areas and techniques through a semester of independent or semi-independent research.
3. Become confident in reading primary literature, critical thinking, and presentation.
4. Learn ethical practices in the Sciences.

Doctor of Philosophy in Molecular and Cell Biology

Graduate Outcomes

Students trained in the MCB PhD program will learn the theoretical foundations and research experience needed to become an independent and original investigator of basic biological phenomena.

Students graduating with the Ph.D. in Molecular and Cell Biology are expected to:

1. Demonstrate a graduate-level understanding of one of the areas of research represented by the program: molecular biology of the regulation of gene expression; chromosome structure and chromosomal rearrangements; mechanisms of recombination and DNA repair; developmental genetics; behavioral genetics, neural development; biophysics of single nerve cells; learning and memory; regulation of small RNAs; immune cell differentiation and development; cytoskeletal architecture; organization of subcellular structures; structure and function of proteins; mammalian embryogenesis and the biotechnology of DNA diagnostics.
2. Explore possible research areas and techniques through four first-year laboratory rotations.
3. Become confident in reading primary literature, critical thinking, and presentation.
4. Become proficient in scientific writing and oral defense of original research.
5. Gain experience teaching students in a teaching assistantship role.
6. Learn ethical practices in the Sciences.
7. Complete a significant body of original work that advances the field of Biology.

The general requirements for admission to the Graduate School, given in an earlier section of this Bulletin, apply to candidates for admission to this area of study. The student's undergraduate record should ordinarily include courses equivalent to those required of undergraduates concentrating in biology at this institution. Applicants to the PhD program who have educational gaps in some of these subjects, but whose records are otherwise excellent, may make up gaps in their knowledge while they are enrolled as graduate students. In exceptional cases, students may be excused from some of these requirements. Students with serious gaps may need to add additional time to their graduate program in order to obtain a broad education in molecular and cellular biology.

The Graduate Record Examination (GRE) is not required to apply to either the MS or PhD programs, but will be considered along with other application materials if submitted.

Because the summer months provide an important opportunity for uninterrupted laboratory work, the molecular and cell biology program provides twelve-month stipend support for all full-time PhD students. Stipend support is not provided to MS students.

James Haber, Chair (Biology; Director, Rosenstiel Center) 
Genetics and molecular biology of yeast meiotic and mitotic recombination. Mating-type switching. Repair of broken chromosomes.

Susan Birren (National Center for Behavioral Genomics; Volen National Center for Complex Systems)
Developmental neurobiology.

Niels Bradshaw (Biochemistry)
Regulation of protein phosphatases and the evolution of cellular signaling.

Paul Garrity (Biology; National Center for Behavioral Genomics; Volen Center)
Neural development and behavior.

Jeff Gelles (Biochemistry)
Mechanisms of mechanoenzymes and macromolecular machines. Single-molecule light microscopy as a tool to study enzyme mechanisms.

Bruce Goode (Biology; Rosenstiel Center)
Cytoskeletal mechanisms controlling cell morphogenesis.

Leslie Griffith (Biology; National Center for Behavioral Genomics; Volen Center)
Biochemistry of behavior.

Lizbeth Hedstrom (Biology)
Enzyme structure-function. Chemical biology. Protein engineering.

Tijana Ivanovic (Biochemistry; Rosenstiel Center)
Molecular mechanisms on virus translocation across biological membranes.

Sebastian Kadener (Biology; Rosenstiel Center; Volen Center)
Molecular neurobiology and RNA metabolism.

Julia Kardon (Biochemistry)
Mechanisms for control of mitochondrial protein activity, quality, and lifespan.

Isaac Krauss (Chemistry)
Organic synthesis.

Amy S.Y. Lee (Biology, Rosenstiel Center)
mRNA translation in cellular differentiation and disease.

Susan Lovett (Biology; Assistant Director, Professional Science Master’s Program in Biotechnology; Rosenstiel Center)
Genetics and molecular biology of bacteria and yeast. DNA repair. Recombination and mutogenesis.

Michael Marr (Biology; Rosenstiel Center)
Mechanisms controlling gene expression.

Maria Miara, Graduate Advising Head (Biology)
Science Education. Comparative anatomy and physiology.

Sacha Nelson (Biology; National Center for Behavioral Genomics; Volen Center)
Physiological genomics of the mammalian neocortex.

Suzanne Paradis (Biology; National Center for Behavioral Genomics; Volen Center)
Molecular mechanisms of synapse development.

Avital Rodal (Biology; Rosenstiel Center; Volen Center)
Endosomal membrane traffic in neurons.

Michael Rosbash (Biology; National Center for Behavioral Genomics; Volen Center)
Circadian rhythms, behavior, and gene expression.

W. Benjamin Rogers (Physics)
Complex fluids and biological physics, programmable self-assembly of soft materials.

Piali Sengupta (Biology; National Center for Behavioral Genomics; Volen Center)
Behavioral and neuronal development in C. elegans.

Timothy Street (Biology, Rosenstiel Center)
Mechanisms of protein folding in the cell.

Doug Theobald (Biochemistry)
Biological redox enzymes’ structure and function.

Program of Study

The program is designed to guide each student toward realizing their potential as independent scientists and foster their career development toward obtaining a position in research, teaching, or other scientific settings. Students are encouraged to become experts in the theory and practice of their chosen area of research, as well as to obtain breadth in other areas strongly represented in the program. Graduate courses are available in the areas of molecular biology, cell biology, genetics, developmental biology, biochemistry, structural biology, immunology, cancer biology, and neurobiology.

A total of six graduate-level courses, along with the attendance of appropriate Journal Clubs (at least BIOL 305a/b) for two semesters and the Graduate Student Research Seminar (BIOL 350a/b) for two semesters are required for the degree. The courses must include: BIOL 100b (or BIOL 103b, with permission of the chair), BIOL 101a (or BIOL 105b, with permission of the chair), the Masters Proseminar course (BIOL 250a) and one laboratory or research based course, with the balance of courses being graduate-level life science elective courses. However, it is the aim of the program to be flexible and allow students to fill gaps in their education. Thus, if warranted, non-graduate courses or courses outside of biology can be taken if to be agreed upon with the program advisor. The laboratory or research component can be met by a Masters Research Lab (BIOL 296a), or by a Project Laboratory (e.g. BIOL 151b, BIOL 156a, BIOL 159a, or NBIO 157a). Students who wish to fulfill the research requirement through BIOL 296a must obtain approval from the program chair and the faculty member in whose lab the research is to take place, and must submit a written laboratory report at the end of the semester. If a student takes both the Masters Research Lab course (BIOL 296a) and a Project Laboratory course, the latter will be considered an elective course. The Masters Research Lab course (BIOL 296a) cannot be considered an elective, even if taken more than once. In addition, all students are required to take CONT 300b (Responsible Conduct of Science) or attend the comparable Division of Science Responsible Conduct of Research (RCR) workshop, usually offered in the spring. In order to earn a degree from this program, the student must complete a minimum of 32 credits.

With approval of the supervising faculty member and the chair of the program, students have the option to write a Master’s Thesis (BIOL 299a) following completion of at least one full semester of Master’s Research Lab (BIOL 296a), provided that the research was performed in a single laboratory at Brandeis. Those who wish to complete a Master’s Thesis must obtain approval in the semester prior to when they will register for BIOL 299a (by November 1st if completing the thesis in the spring semester and by March 1st if completing the thesis in the fall semester). After completion and approval, the thesis must be deposited electronically in the Robert D. Farber University Archives at Brandeis.

Students must receive grades of B- or better in all courses and may be asked to leave the program at the end of a semester if their progress is found to be unsatisfactory by the graduate committee. Students wishing to be admitted to a second year of study must demonstrate adequate progress.

Residence Requirement

The minimum residence requirement is one year.

Students may take an additional one or two semesters to complete the MS degree as an Extended Master's student with approval of the chair of the program. International students may extend their time one semester if they are still completing required coursework. International students who have completed all required coursework and wish to complete the optional Master’s Thesis may stay an extra semester with advanced approval from the advising faculty, the program chair, and International Students & Scholars Office (by November 1st if completing the thesis in the spring semester and by March 1st if completing the thesis in the fall semester).

Program of Study

Students must take a total of six graduate-level courses for the degree. Two courses are taken each semester in the first year, of which three are required: BIOL 103b, BIOL 105b, and BIOL 200a (Proseminar, a workshop in primary literature reading, critical thinking, and presentation, and in grant proposal writing and defending). The remaining three courses are electives to be chosen by the student, but they must be graduate-level life science courses (BIOL, BCHM, CBIO, or NBIO; course numbers of 100 or higher). In selecting electives, students are expected to gain knowledge in at least two different disciplines represented in the program: genetics, molecular biology, cell biology, developmental biology, neuroscience, immunology, biochemistry, and structural biology. It is strongly recommended that at least one of these electives include quantitative/statistical analysis and facility in programming/coding, such as BIOL 107a or BIOL 131b. Students must complete all courses with a grade of B- or better. In addition, all students are required to take CONT 300b (Responsible Conduct of Science) or attend the comparable Division of Science Responsible Conduct of Research (RCR) workshop, typically in the spring of their first year, and again in their 5th year, but this does not count as one of the six courses toward the degree. First-year students must also complete four separate nine-week rotations (BIOL 300a/b) in four different laboratories on campus. Throughout all graduate years, students must register for and participate in Journal Clubs (at least BIOL 305a/b) and register for and (starting their third year in the program) present once per year in the Graduate Student Research Seminar (BIOL 350a/b). Presenting in the yearly Graduate Student Research Seminar is required to remain in good standing in the program. Students are also expected to continue participating in other departmental seminars and colloquia relevant to their fields of study for the entire time they are in the graduate program.

The suggested schedule of courses for the first two years is (note: students must register for all courses, even those not for credit):

First Year

Fall: BIOL 105b and BIOL 200a for credit, plus BIOL 300a, BIOL 305a, and BIOL 350a.
Spring: BIOL 103b and one elective graduate-level science course for credit, plus BIOL 305b, BIOL 350b, BIOL 300b, and CONT 300b (or comparable Division of Science Responsible Conduct of Research (RCR) workshop).

Second Year

Fall: One elective graduate-level science course for credit, plus BIOL305a and BIOL350a.
Spring: One elective graduate-level science course for credit, plus BIOL305b and BIOL350b.

At the end of the first year after completing rotations, each student must find a faculty adviser and position in that laboratory in which to perform their thesis work. Any requested extensions to this time line, e.g. for the purpose of conducting a fifth rotation over the summer, is subject to approval by the Graduate Committee. The adviser will assist the student in planning a well-balanced thesis-research program in their field of interest with the objective and expectation of publishing the work.

Qualifying Examination

Students take two qualifying exams, one at the end of the first year in May and one at the end of the second year in May. In each exam, there is a written proposal component that is submitted by the student to the members of their exam committee, followed by an oral defense of the proposal. The first exam is taken at the end of the first year and must be connected to a research area investigated during one of the student’s four laboratory rotations. The second exam is taken by the end of the second year, must be on the student’s thesis research, and outlines their planned experiments and goals for the remaining years in the PhD program. It also includes preliminary data that the student has obtained during their first two years in the program.

Teaching Requirement

As part of their PhD training, students are required to serve as teaching assistants (TAs) for two semesters, usually in their second year. With the approval of their thesis adviser, students may have the opportunity to do additional assistantships, e.g. if interested in pursuing a teaching career path, and receive additional payment for this service at a rate determined by the Department.

Residence Requirement

The minimum residence requirement is three years.

Language Requirement

There is no foreign language requirement for the PhD degree. However, students for whom English is a second language are strongly recommended and sometimes required to take English as a Second Language (ESL) courses.

Advancement in the Program

To be advanced into the second year of graduate studies, a student must earn grades of B- or better in all courses including rotations, have a satisfactory evaluation by her or his committee on the first exam/proposal, and have gained a position by mutual consent in a laboratory at Brandeis in which the thesis research is to be carried out. At the discretion of the Graduate Committee, students who do not fulfill all of these requirements after the first year may not be readmitted to the program or may be placed on probation for one year. To advance into the third year of the program and thus be “advanced to candidacy,” a student must have grades of B- or better in all six courses, have performed satisfactorily on both oral exams/proposals, and be in good standing in the thesis research laboratory. Students who had been placed on probation for the prior year must display significant improvement and perform strongly on the second exam/proposal to be advanced to candidacy. Once thesis work has begun, it is a requirement that each student must meet at least once per year with their Dissertation Committee, which includes the thesis adviser and at least two other professors, to discuss progress toward the completion of the dissertation research. These meetings must be documented with a form signed by the thesis committee members and turned into the Division of Science Graduate Affairs Office by the student. Progress will be reviewed by the Graduate Committee at the end of each year, and a student may be asked to leave the program if their progress is found to be unsatisfactory.

Dissertation and Defense

Each student will conduct an original investigation under the guidance and mentorship of their thesis adviser and write a dissertation of their results. After submission of the dissertation, the candidate will give a public seminar to the University community, and on the same day defend the work in an oral exam to the dissertation committee. The dissertation committee must include the thesis adviser, at least two additional Brandeis science faculty (at least one of whom must be listed as an MCB faculty), and one additional faculty member from outside the university - typically an expert in the area of the thesis research. The dissertation committee is selected by the student and adviser through mutual agreement. There is an expectation that students will publish a minimum of one first-author research paper from their graduate work before graduating.

Please note that the above Program of Study is typical of a student entering the PhD program directly. Students who enter the PhD program from a Brandeis Master’s program may have an altered Program of Study, to be discussed and agreed upon by the student and the Graduate Committee prior to matriculation.

Requirements for the Degree of Doctor of Philosophy in Molecular and Cell Biology with Specialization in Quantitative Biology

Program of Study

Students wishing to obtain the specialization in Quantitative Biology (QB) must first gain approval of the MCB representative for the QB program (listed online on the Brandeis QB website). This should be done as early as possible in the program, ideally during the first year. In order to receive the PhD in MCB with specialization in QB, candidates must complete (a) the requirements for the PhD described above and (b) the course requirements for the QB specialization described in the QB section of this Bulletin.

Any alteration to the QB course requirements must be approved by both the MCB Program Chair and the QB Program Chair.

BIOL 100b Advanced Cell Biology
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Prerequisites: BIOL 14a and BIOL 15b.
An advanced course on cell biology. Topics include structure and organization of the cell, principles of signal transduction, and cell division and proliferation. Usually offered every year.
Avital Rodal

BIOL 101a Molecular Biotechnology
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Prerequisite: BIOL 14a.
Develops knowledge and skills to research, choose and interpret the bext experimental approaches for answering research questions in molecular biology. Studies molecular biology techniques such as PCR, DNA sequencing, genomics, cloning, microarrays, and CRISPR, and their research applications. Usually offered every year.
Rachel Woodruff

BIOL 102b Structural Molecular Biology
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Prerequisites: BIOL 14a and BIOL 15b, or permission of the instructor.
Cells are filled with machines that carry materials about the cell, that chemically transform molecules, that transduce energy, and much more. Our understanding of how these machines work depends on understanding their structures. This introduction to the structural basis of molecular biology examines the designs of proteins, their folding and assembly, and the means whereby we visualize these structures. Usually offered every second year.
Melissa Kosinski-Collins

BIOL 103b Mechanisms of Cell Functions
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Prerequisite: BIOL 100b.
Focuses on the mechanistic basis of cell biological processes, with a heavy emphasis on how they are elucidated experimentally. Classic and modern research papers are used to illustrate a range of genetic, biochemical, and imaging-based experimental approaches. Topics include cell compartmentalization, membrane traffic, cytoskeleton, cell motility, and cell division. The primary learning goal is to understand how the scientific method is applied in cell biology research. Intended for graduate students and advanced undergraduates. Usually offered every year.
Bruce Goode

BIOL 105b Molecular Biology
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Prerequisites: BIOL 14a and BIOL 15b.
Examination of molecular processes in replication and expression of genetic information and techniques by which this understanding has been achieved. Topics include recombinant DNA and other molecular biological techniques, structure and organization of DNA in chromosomes, DNA replication, transcription and regulation of gene expression, RNA structure and processing, mRNA stability, and other mechanisms of post-translational control. Usually offered every year.
Amy Lee

BIOL 107a Data Analysis and Statistics Workshop
[ dl qr sn ]
The interpretation of data is key to making new discoveries, making optimal decisions, and designing experiments. Students will learn skills of data analysis and computer coding through hands-on, computer-based tutorials and exercises that include experimental data from the biological sciences. Knowledge of very basic statistics (mean, median) will be assumed. Usually offered every year.
Stephen Van Hooser

BIOL 111a Developmental Biology
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Prerequisites: BIOL 14a, BIOL 15b, and BIOL 18b.
How do complex organisms build themselves starting from single cells? Examines how processes such as fertilization, embryogenesis, cell differentiation, and tissue-specific gene expression occur; what is known about the key molecules and genes that orchestrate these processes; and how genetic changes affecting these processes underlie the evolution of body form. Students will learn material from class lectures and assigned readings from a textbook. To foster students’ ability to critically assess the primary scientific literature, the class will also read and discuss a number of recently published original scientific articles pertinent to class material. Usually offered every second year.
Suzanne Paradis

BIOL 112b Evolutionary Developmental Biology
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Prerequisite: BIOL 14a and BIOL 16a.
Examines both the evolution of developmental processes and the impact of development on evolution. This course will draw on the many sub-disciplines that feed into Evo-Devo including developmental biology, evolution, genetics, molecular biology, ecology and paleontology. Usually offered every second year.
Maria Miara

BIOL 122a Molecular Genetics
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Prerequisite: BIOL 14a. Recommended prerequisite: BIOL 72a or another upper-level course in genetics, genomics, or molecular biology.
A lecture- and literature-based course for students who have already taken a basic course in genetics and molecular biology. Organized somewhat historically, we will explore how genetic approaches have elucidated the nature of the gene and its regulation and the analysis of gene function. In other words, it’s a course about “genetic thinking,” with increasingly large doses of molecular biology added in as we progress. Recent advances in genomics and proteomics will be discussed. Students will be assigned one or more papers that will form the basis of part of the next lecture/discussion. To facilitate this discussion, students will be required to post questions about the reading prior to class. In addition, each student will be responsible to identify and present to the rest of the class, a topic that they found particularly creative in using genetic approaches to delve into the mysteries of cell growth and development. A written introduction to the chosen topic will also be required. Usually offered every second year.
James Haber

BIOL 125a Immunology
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Prerequisites: BIOL14a and BIOL 15b. CHEM 25a is recommended. May not be taken for credit by students who took BIOL 70a in prior years.
Topics include properties and functions of cells involved in innate and adaptive immunity; genes, structure and function of immunoglobulins, B cell receptors and T cell receptors; lymphocyte differentiation; genetic regulation; MHC restriction; cell interactions and signaling; pathogen immunity (bacteria, viruses) and vaccines; tolerance and autoimmunity. Usually offered year.
Joan Press

BIOL 127b Introduction to Systems Biology
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Prerequisites: BIOL 14a and BIOL 15b.
Exposes students to the design principles that underlie complex biological systems. We will cover a wide range of topics, including biological networks, network motifs, dynamics in transcriptional circuits, designing and engineering synthetic circuits, prey-predator models, bacterial and animal navigation strategies. Special one-time offering, spring 2020.
Alon Zaslaver

BIOL 128a Human Genetics
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Prerequisites: BIOL 14a and BIOL 15b.
Survey of topics, including: overview of the human genome; variation; mutation and polymorphism; reproductive genetics; single-gene inheritance and complexities thereof; multifactorial conditions;risk assessment including Bayesian analysis; gene mapping including linkage analysis and genome wide association studies (GWAS); molecular methodology in genetics and genomics; cytogenetics; hemoglobinopathies; population genetics; cancer genetics; genetics of development;biochemistry of selected genetic diseases; treatment including pharmacogenetics and gene therapy; ethical considerations in genetics and genomics. Usually offered every year.
Staff

BIOL 131b Introduction to Genomics
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Prerequisites: BIOL 14a and BIOL 15b.
Focuses on the recently developing field of Genomics. During the course, the students will be introduced to general concepts and approaches for generating and analyzing large genomic datasets in the context of biological questions. Usually offered every year.
Sebastien Kadener

BIOL 132a General Microbiology
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Prerequisites: BIOL 14a, BIOL 15b, and CHEM 25a. May not be taken for credit by students who took BIOL 71a in prior years.
Topics include the physiology and properties of bacteria, viruses, and other microorganisms; microbial nutrition, metabolism, growth; bacterial genetics; horizontal gene transfer; microbial pathogenesis; immunity; antibiotics and other means of microbial control. Usually offered every year.
Susan Lovett

BIOL 134b Topics in Ecology
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Prerequisites: BIOL 23a, or permission of the instructor. Topics may vary from year to year. Please consult the Course Schedule for topic and description. Course may be repeated once for credit with permission of the instructor.
Annually, a different aspect of the global biosphere is selected for analysis. In any year the focus may be on specific ecosystems (e.g., terrestrial, aquatic, tropical, arctic), populations, system modeling, restoration ecology, or other aspects of ecology. Usually offered every year.
Dan Perlman

BIOL 151a Project Laboratory in Protein Biochemistry
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Prerequisites: BCHM 88b or BCHM 100b (recommended), BIOL 14a, BIOL 15b, BIOL 18a and 18b, and BIOL 156a.
Features experiments in protein biochemistry that are fundamental to the field of biotechnology. These include protein purification, characterization and quality assessment. Focus is placed on designing purification protocols for both tagged and untagged proteins using biochemical knowledge. The designed protocols are tested by purifying known proteins. As part of the course, students will contribute to research projects of unknown outcome by purifying and assaying novel proteins. Usually offered every year.
Kene Piasta

BIOL 152b Virus Hunter Lab
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Prerequisites: BIOL 14a, BIOL 15b, BIOL 18a, and BIOL 18b.
During this course, students will learn about a common type of virus called bacteriophage. They will isolate novel bacteriorphage from the marine environment and using modern molecular biology and bioinformatic techniques, they will sequence and annotate the viral genome. Usually offered every year.
Susan Lovett and Michael Marr

BIOL 153aj Project Lab in Biomimetics / Bioinspiration
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Prerequisites: BIOL 15b and BIOL 16a or BIOL 23a.
Explores how the natural world has been used to inspire designs solving real-world problems, identify a problem themselves, learn techniques to plan and build their own bio-inspired designs and present their products in a clear and accessible manner. Offered as part of JBS program.
Maria Miara

BIOL 156a Project Laboratory in Biotechnology
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Prerequisite: BIOL 18a and b, BIOL 14a and BIOL 15b or equivalents. Course fee: $150.
Encompasses the many facets that may present themselves to a researcher working in a laboratory setting. The primary goal of this course is to teach current methods in molecular biology in order to establish a foundational skill set that makes a student viable in today's research market. Along with this, enhancing the written format of acquired data, the art of presenting this data and scientific writing is also emphasized. Though the course meets during its scheduled time, the experimental designs contribute to real research projects from laboratories in the Biology department so that additional work will be required during off days and weekends depending on your time management. This time commitment simulates a research environment where students are responsible for their own experiments in order to prepare them for both a career in science and allow them to fully understand what attributes are necessary to be competent in the field of research. Students will be required to perform tasks when the class is not in session. Some of the techniques taught will include DNA isolation, DNA sequence analysis, generation of mutations, recombinant DNA cloning, RNA isolation, polymerase chain reaction including real-time quantitative PCR, yeast two hybrid systems, screening chemical libraries, Gateway & Gibson cloning techniques, bacterial & yeast strain constructions and DNA/RNA hybridization methods. There is a possible option of continuing the project as an independent researcher in the spring depending on the student and nature of the project. Currently we are massing useable data from past classes for publication purposes. This class has a large time commitment both during and outside of class time and should not be taken in conjunction with other research laboratories or internships. Please note that one of the goals of this course is to help place you in or on the career path you desire. Usually offered every year. Usually offered every year.
Vincent Sutera

BIOL 159a Project Laboratory in Microbiology
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Prerequisites: BIOL 18a and b. Laboratory fee: $150 per semester.
A discovery-based laboratory to study the diversity of microorganisms in particular environments. We will isolate microbes with ability to metabolize complex compounds from special environments, characterize their properties and identify them by DNA sequence analysis. This course will teach the fundamentals of microbiology through hands-on activities. Usually offered every year.
Deanni Cooper

BIOL 160b Human Reproductive and Developmental Biology
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Prerequisites: BIOL 14a and BIOL 15b.
Course deals with hormonal, cellular, and molecular aspects of gametogenesis, fertilization, pregnancy, and birth. Pathological and abnormal variations that occur and the available medical technologies for intervention, correction, and facilitation of these processes are discussed. Usually offered every year.
Judith Jackson

BIOL 162b DNA: Mechanisms and Research
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Prerequisites: BIOL 14a, BIOL 15b and CHEM 25a. May not be taken for credit by students who took BIOL 150b in prior years.
Explores DNA, and a multitude of proteins that interact with the DNA. Examines mechanisms that allow genomes to be maintained and used in cells and organisms: DNA replication, repair and multigenesis, chromatin, cohesion and segregation, DNA modifications, and more. Usually offered every second year.
Rachel Woodruff

BIOL 163b Repairing and Editing the Genome
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Prerequisites: BIOL 14a and BIOL 15b.
DNA damage must be repaired to maintain genome integrity and prevent mutations and chromosome rearrangements associated with cancer. Understanding of these repair mechanisms has opened the door to precisely modify genes, for gene therapy or even to recreate extinct mammals. Usually offered every second year.
James Haber

BIOL 172b Growth Control and Cancer
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Prerequisites: BIOL 14a and BIOL 15b, and CHEM 25a.
Examines the fundamental rules of behavior of cells in multicellular organisms. Examines the research that has revealed the molecular basis of cancer development, including the cellular and molecular mechanisms that govern cell growth, differentiation and survival in normal cells, and how this regulation is disrupted in cancer. Usually offered every second year.
Rachel Woodruff

BIOL 176b RiboNucleicAcids (RNA)
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Prerequisite: BIOL 105b.
Examines the versatility and biological functions of RiboNucleicAcides (RNA) in an upper-level seminar and primary-literature based course.Topics include splicing and the spliceosome, the ribosome, ribozymes and the RNA World Hypothesis, RNA editing, RNA interference, and long non-coding RNAs. Usually offered second every year.
Nelson Lau and Michael Rosbash

BIOL 199a Senior Research
The first of a two-semester course for students pursuing the combined BS/MS in Biology, this is an intensive research experience. The student conducts an independent research project under the supervision of a faculty member. To fulfill the BIOL 199 requirements, students must (1) submit to their research sponsor, at the conclusion of their first BIOL 199 semester, a paper that reviews the literature pertinent to their field of research, and (2) submit to their research sponsor, at the conclusion of their second BIOL 199 semester, a senior thesis that includes an abstract, an introduction, a review of materials and methods, results, discussion, and references. Students enrolled in this course must defend their thesis, receive Departmental Honors, and submit their thesis to GSAS. If a student drops out of the BS/MS program, BIOL 199 will be replaced with BIOL 99. Students must petition the department for permission to enroll in BIOL 199. Usually offered every semester.
Staff

BIOL 199b Senior Research
A continuation of BIOL 199a. See BIOL 199a for course description.
Staff

BIOL 200a Proseminar
Required seminar for first-year graduate students in MCB and Neuroscience PhD programs.
Emphasizes the reading, analysis, and presentation of scientific papers. We will examine published research on multiple topics that will cover a broad range of experimental approaches. The course will place a strong emphasis on developing writing skills and in preparing effective oral presentations. Students will be guided toward preparing a mock research proposal that will serve as a model for the first-year PhD qualifying exam. Not offered to MCB or Neuroscience MS students. Usually offered every year.
Piali Sengupta

BIOL 202d Introduction to Genetic Counseling
A two-semester sequence that provides the historical and theoretical foundations for the practice of genetic counseling and the role of genetic services within the health care delivery system. Introduces students to some of the practical aspects of genetic counseling, including case preparation, pedigree construction/interpretation, risk assessment, psychological assessment and support, patient education and medical documentation. Usually offered every year.
Gayun Chan-Smutko

BIOL 203a Proseminar: The Molecular Basis of Genetic Diseases
Covers the molecular basis of muscular dystrophy, fragile X syndrome, cystic fibrosis, Huntington's disease, and several inherited cancer syndromes. A historical perspective is used for each topic; molecular diagnostics and genetic counseling issues are addressed as well. Usually offered every year.
Judith Tsipis

BIOL 204b Clinical Genetics I
Introduces the major practice areas of clinical genetics: prenatal, pediatrics, biochemical and cancer genetics for first year students. The course is broken into fours blocks, each devoted to one of these areas. The blocks include didactic lectures from experts in the field as well as case discussions led by practicing genetic counselors meant to allow students to put what they have learned into practice. Usually offered every year.
Lauren Lichten

BIOL 205a Masters Proseminar
Enrollment limited to Life Science Masters students.
In the life sciences, theories, methods and discoveries must be communicated effectively. Equally important is the ability to interpret and evaluate the work done by others. Students will have opportunities to learn, practice and evaluate oral and written methods of scientific communication. Usually offered every year.
Maria Miara and Neil Simister

BIOL 205b Counseling Theory and Technique
A comprehensive overview of counseling theory and practice. Topics include listening, observation, and interview skills and strategies; family dynamics and development; coping and adaptation processes; referral and consultation procedures; and ethical principles. Students are provided an opportunity to integrate clinical experiences with the coverage of topics. Usually offered every year.
Terri Queler

BIOL 206d Genetic Counseling Journal Club
Noncredit.
Informal biweekly meeting of students and faculty at which recent papers are discussed. Usually offered every year.
Gretchen Schneider

BIOL 207a Genetic Counseling: Case Conferences and Family Counseling
Examines case studies providing the basis for discussion of a variety of genetic disorders and the application of counseling modalities. Students have an opportunity to share experiences gained during clinical internships. Discussions emphasize the interplay of medical, psychological, ethical, legal, social, and cultural factors in genetic counseling. Co-taught by a clinical psychologist and a certified genetic counselor. Usually offered every year.
Terri Queler

BIOL 211a Genetic Counseling Fieldwork Placement: Part I
Students work one day per week in a community-based health service organization, school, clinic, or public health agency to develop awareness of disability-related issues and the variety of community-based services for individuals with special needs. Students also observe in a genetics clinic twenty to thirty hours over the course of the semester to gain exposure to concepts learned in BIOL 202d (Introduction to Genetic Counseling). Periodic course discussions supplement the fieldwork experience. Usually offered every year.
Gayun Chan-Smutko

BIOL 211b Genetic Counseling Fieldwork Placement: Part II
To begin preparing for clinical genetics internships, students participate in a variety of experiences that serve to foster and integrate the concepts introduced in courses and presentations. Students are exposed to procedures in clinical labs through lectures, site visits, and/or lab work. In addition, students continue observations in a genetics clinic and meet several times with a family with a child with a disability. Periodic course discussions supplement the fieldwork experience.
Gayun Chan-Smutko

BIOL 212a Genetic Counseling Internship I
Students complete a 30 contact day clinical genetic internship under the supervision of a genetic counselor or other qualified clinician. Students increase their knowledge of clinical genetics and master genetic counseling skills by offering genetic counseling services in a prenatal, pediatric, cancer, general, adult ,or specialty clinic setting. Usually offered every summer.
Lauren Lichten

BIOL 212b Genetic Counseling Internship II
Students complete a 25-30 contact day clinical genetic internship under the supervision of a genetic counselor or other qualified clinician. Students increase their knowledge of clinical genetics and master genetic counseling skills by offering genetic counseling services in a prenatal, pediatric, cancer, general, adult, or specialty clinic setting. Usually offered every year.
Lauren Lichten

BIOL 213a Genetic Counseling Research I
In the summer semester students chose a research project, do a review of the literature and summarize key findings, and write a research proposal for a thesis project (to be done in the following fall/spring semesters). Usually offered in the summer.
Cassandra Buck

BIOL 213b Genetic Counseling Research II
Prerequisite: BIOL 213a.
Students are introduced to the principles and basic techniques of social science research in a series of seminars while they implement their thesis research projects. Usually offered fall and spring.
Cassandra Buck

BIOL 214c Genetic Counseling Process Group
Students share and learn from their collective experiences in their internships, courses, and individual lives and have the opportunity to process and integrate the experience of becoming a genetic counselor. Usually offered every semester.
Joseph Cunningham

BIOL 216b Professional Development Seminar Series
This is a noncredit seminar required for all genetic counseling students.
Students meet once a week for a series of lectures, presentations and mock sessions that explore issues related to advanced practice in genetic counseling. Topics include advanced genetic counseling case management, Baysian analysis, and the use of the NSGC code of ethics. Usually offered every year.
Gretchen Schneider

BIOL 220a Clinical Genetics II
Prerequisite: BIOL 204b or permission of the instructor.
Continuation of BIOL 204b with emphasis on the genetic and developmental disorders of most major organ systems. The course includes discussion of neurogenetics, neuromuscular, hematological, cardiovascular, connective tissue, skeletal dysplasias and craniosynostoses, vision and hearing disorders as well as coverage of renal, immunological and GI and pulmonary disorders. Each week covers a different system in both a didactic lecture and a case discussion. Usually offered every year.
Lauren Lichten

BIOL 235b American Health Policy & Practice and the Delivery of Genomic Health Care
Enrollment limited to Genetic Counseling or Health Policy graduate students or with permission of the instructor.
The continuous discovery of genetic markers for common diseases is leading to an increasing demand for genetic services, and for the integration of traditional medical genetics with mainstream medicine and public health care. In addition, the American healthcare system is evolving and huge changes in how is accessed, financed and delivered can be expected in the coming years. Those providing genetic services will therefore need a strong background in the structure of the American health care system and how public policy is influencing the field of medical genetics. This course is specifically designed to meet this objective using a mixture of readings from the literature, writing assignments, lecture, class discussion, guest speakers and student presentations. Usually offered every second year.
Staff

BIOL 236b Genetics, Law, and Social Policy
Explores legal doctrines, developing skills in analyzing legal and policy issues arising in professional practice and preparing students to actively participate in the development of institutional and public policies. Topics covered include confidentiality, patient autonomy, regulation of genetic, reproductive rights, and genetic discrimination. Usually offered every second year.
Alice Noble

BIOL 296a Master's Research Lab
Prerequisite: Permission of the Program Director.
Students engage in biological research by working in the laboratory of a faculty member for a minimum of 10 hours per week for one semester. Intended for students in the MS Program in Molecular and Cell Biology. Usually offered every semester.
Staff

BIOL 297a Readings in Molecular and Cell Biology
Usually offered every year.
Staff

BIOL 298a Independent Study in Molecular and Cell Biology
Usually offered every year.
Staff

BIOL 299a Master's Research Project
Usually offered every year.
Staff

BIOL 300a Biological Research
Primarily for the first-year student, with the purpose of introducing him or her to biological research and to the work in progress in the laboratories of a number of faculty members. In consultation with the graduate adviser, the student plans a sequence of such tenures, each comprising nine weeks, and then carries out experimental investigations under the guidance of the faculty members involved. Usually offered every year.
Staff

BIOL 300b Biological Research
Primarily for the first-year student, with the purpose of introducing him or her to biological research and to the work in progress in the laboratories of a number of faculty members. In consultation with the graduate adviser, the student plans a sequence of such tenures, each comprising nine weeks, and then carries out experimental investigations under the guidance of the faculty members involved. Usually offered every year.
Staff

BIOL 301b Biological Research
Yields half-course credit.
See BIOL 300a for course description.
Staff

BIOL 305a Topics in Molecular Genetics and Development
Usually offered every year.
Staff

BIOL 305b Topics in Molecular Genetics and Development
Usually offered every year.
Staff

BIOL 316a Mechanisms of Recombination
Usually offered every year.
James Haber and Susan Lovett

BIOL 316b Mechanisms of Recombination
Usually offered every year.
James Haber and Susan Lovett

BIOL 350a Graduate Student Research Seminar
Usually offered every year.
Staff

BIOL 350b Graduate Student Research Seminar
Usually offered every year.
Staff

BIOL 401d Dissertation Research
Independent research for PhD candidates. Specific sections for individual faculty members as requested.
Staff

BCHM 102a Quantitative Approaches to Biochemical Systems
[ dl sn ]
Prerequisite: BCHM 100a or equivalent and Math 10a and b or equivalent.
Introduces quantitative approaches to analyzing macromolecular structure and function. Emphasizes the use of basic thermodynamics and single-molecule and ensemble kinetics to elucidate biochemical reaction mechanisms. Also discusses the physical bases of spectroscopic and diffraction methods commonly used in the study of proteins and nucleic acids. Usually offered every year.
Maria-Eirini Pandelia

BIOL 107a Data Analysis and Statistics Workshop
[ dl qr sn ]
The interpretation of data is key to making new discoveries, making optimal decisions, and designing experiments. Students will learn skills of data analysis and computer coding through hands-on, computer-based tutorials and exercises that include experimental data from the biological sciences. Knowledge of very basic statistics (mean, median) will be assumed. Usually offered every year.
Stephen Van Hooser

COSI 178a Computational Molecular Biology
[ dl sn ]
Open to advanced undergraduate students and graduate students.
Information and computing technologies are becoming indispensable to modern biological research due to significant advances of high-throughput experimental technologies in recent years. This course presents an overview of the systemic development and application of computing systems and computational algorithms/techniques to the analysis of biological data, such as sequences, gene expression, protein expression, and biological networks. Hands-on training will be provided. Usually offered every other year.
Pengyu Hong

NBIO 136b Computational Neuroscience
[ dl sn ]
Prerequisite: MATH 10a and either NBIO 140b or PHYS 10a or approved equivalents.
An introduction to concepts and methods in computer modeling and analysis of neural systems. Topics include single and multicompartmental models of neurons, information representation and processing by populations of neurons, synaptic plasticity and models of learning, working memory, decision making and neural oscillations. The course will be based on in-class computer tutorials, assuming no prior coding experience, with reading assignments and preparation as homework. Usually offered every second year.
Paul Miller

PHYS 105a Biological Physics
[ sn ]
Physical forces in living matter are studied from the perspective offered by statistical mechanics, elasticity theory, and fluid dynamics. Quantitative models for biological structure and function are developed and used to discuss recent experiments in single-molecule biology. Usually offered every second year.
Michael Hagan

QBIO 110a Numerical Modeling of Biological Systems
[ sn ]
Prerequisite: MATH 10a and b or equivalent.
Modern scientific computation applied to problems in molecular and cell biology. Covers techniques such as numerical integration of differential equations, molecular dynamics and Monte Carlo simulations. Applications range from enzymes and molecular motors to cells. Usually offered every second year.
Michael Hagen

QBIO 120b Quantitative Biology Instrumentation Laboratory
[ sn ]
Focuses on optical and other instruments commonly used in biomedical laboratories to make quantitative measurements in vivo and in vitro. Students disassemble and reconfigure modular instruments in laboratory exercises that critically evaluate instrument reliability and usability and investigate the origins of noise and systematic error in measurements. Usually offered every year.
Tijana Ivanovic