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Course Listings by ajizai


									Graduate Courses
All 600-level courses are open to undergraduates with permission.
020.601 Current Research in Bioscience
Instructors: Staff
Fall, 1 credit
020.637 Genomes and Development
This course covers the genetic analysis of development, model developmental systems, cell
determination, organization of tissues and organs, cell motility and recognition, and sexual
Instructors: Van Doren, Spradling, Halpern, Bortvin
Spring, 3 hours
020.668 Advanced Molecular Biology
An advanced course in organization and function of eukaryotic and prokaryotic genes, including
discussion of techniques to analyze gene structure and transcription.
Prerequisite: 020.665.
Instructor: Schleif
Fall, 3 hours
020.674 Graduate Biophysical
Students interested in pursuing biophysical research, who have taken undergraduate physical
chemistry, may opt to take a two semester series in Molecular Biophysics (250.-689-690). This
course will provide an overview of protein and nucleic acid structure, fundamentals of
thermodynamics and kinetics, ligand binding, folding and stability of macromolecules, and the
principles of biophysical methods such as fluorescence spectroscopy, NMR, and X-ray
crystallography. Similar topics are covered in the two-semester series, but with greater emphasis
on mathematical and quantitative analysis. Students wishing to pursue this option should consult
with faculty.
Instructors: Woodson, Bowman, Brand, Hill
Spring, 3 hours
020.686 Advanced Cell Biology
All aspects of cell biology are reviewed and updated in this intensive course through critical
evaluation and discussion of the current scientific literature. Topics include protein trafficking,
membrane dynamics, cytoskeleton, signal transduction, cell cycle control, extracellular matrix,
and the integration of these processes in cells of the immune system.
Open to graduate students and advanced undergraduates by permission of the instructor.
Instructors: Staff
Fall, 3 hours
020.699 Responsible Conduct in Research (INTERSESSION)
The Johns Hopkins Departments of Biology, Biophysics, Chemistry and Carnegie Institution are
committed to promoting the highest ethical standards amoun our administration, faculty
members, and students. Therefore, all trainees and training faculty are required to attend the
discussions series, Responsible Conduct of Research. The two week series meets for 6 two hour
sessions and will be offered every January. Graduate students must attend the discussion series
during their first year of study. Science has come under increased scrutiny and scientific
misconduct has become a public issue regularly addressed in the media. Against the background
of public skepticism, each university must make a visible commitment to responsible conduct of
research. We believe that this is best accomplished by case-based discussions involving both
trainees and faculty who are active investigators. In addition to general information, such
as Honor in Science, participants will be expected to read related handouts sent to them before
each session. Copies of the material contained in the suggested reading list will also be available.
Through the use of pre/post testing and presentation evaluations, the course will respond to the
specific needs of trainees and faculty.
Instructors: Staff

Elective Courses
020.606 Molecular Evolution
A history of life on earth has been recorded in the DNA of organisms that live today. But what
language is it and how can we read that history? This course introduces basic principles of
molecular evolution plus a wide array of methodologies used to interpret molecular sequence
data. Many interesting studies of gene and genome evolution will be covered as examples of this
burgeoning area of research. This fun and popular course now includes computer labs that will
enable students to obtain first-hand experience in this exciting field of research.
Instructor: Cunningham
Spring - odd years
020.612 Introduction to the Human Brain
This course explores the outstanding problem of biology; how knowledge is represented in the
brain. Relating insights from cognitive psychology and systems neuroscience with formal theories
of learning and memory, topics include (1) anatomical and functional relations of cerebral cortex,
basal ganglia, limbic system, thalamus, cerebellum, and spinal cord; (2) cortical anatomy and
physiology including laminar/columnar organization, intrinsic cortical circuit, hierarchies of
cortical areas; (3) activity-dependent synaptic mechanism; (4) functional brain imaging; (5)
logicist and connectist theories of cognition; and (6) relation of mental representations and
natural language.
Instructor: Hedgecock
020.613 Biology Science Writing
Students will learn how to write abstracts and grant proposals, organize scientific manuscripts
and thesis dissertations by writing and rewriting about their own research and editing other
students’ work. Focus will be on structure, substance, accessibility, and clarity of writing.
Instructor: Audrey Huang
020.614 Signaling in Development and Disease
An advanced undergraduate level seminar on current topics on signal transduction mechanisms
underlying neuronal morphology, development and function. The proper functioning of the
nervous system relies on the establishment of precise neuronal circuits through a developmental
program including proliferation, neuronal migration, axonal growth and neuronal survival. This
course pertains to the extracellular cues and downstream neuronal signaling pathways that
coordinate these key events during neuronal development. The course will also cover the role of
aberrant signaling mechanisms in neuronal degeneration and disease.
Instructor: Kuruvilla
020.615 Communication Between Cells: The Synapse as Model System
All cells inform neighbors of their own activities. That act of communication frequently requires
the formation of cell junctions across which information can pass. One of the best studied of the
means of communication between cells is the synapse between neurons. This course examines
the synapse in depth. both as a means to look at the nature of neuronal comunication and as a
model for communication across cells of all types. Lectures on the physiology, structure,
biochemistry and cell biology of synapses will be used as an introduction to the function of
synapses in learning and memory and the effect on synapses of drugs and disease.
Prerequisites: Biochemistry (020.305) & Cell Biology (020.306) or Cellular Molecular
Neuroscience (080.301)
Instructor: Kirkwood
020.616 (N) Planets, Life and the Universe
This multidisciplinary course explores the origins of life, planets' formation, Earth's evolution,
extrasolar planets, habitable zones, life in extreme environments, the search for life in the
Universe, space missions and planetary protection.
Prerequisites: Three upper level (300+) courses in sciences (Biophysics, Biology, Chemistry,
Physics, Astronomy, Math, or Computer Science).
Instructors: DiRuggiero, Norman
020.620 Stem Cells
This course consists of introductory lectures given by faculty members, followed by student
presentations in the form of seminars. The introductory part will cover the basic knowledge
about stem cells, such as: What features make cells qualified as stem cells? What are the unique
cellular and molecular properties of stem cells? How do stem cells maintain their identities?
What are the mechanisms underlying stem cell differentiation and reprogramming? What are the
therapeutic applications of stem cells? The student seminar will be based on selected literatures
by the faculty. A summary mini-review paper is required for a chosen topic at the end of the
Instructor: Chen
Spring - even years
020.629 Principles of Cancer Biology
Lectures include recent findings in tumor genetics, cancer pathways, invasions and metastasis
and cancer therapies.
Instructor: Huang
020.630 Human Genetics
This course will examine the growing impact of human genetics on the biological sciences, on law
and medicine, and on our understanding of human origins. Topics include structure and evolution
of the human genome, genetic and physical mapping of human chromosomes, molecular
genetics of inherited diseases and forensic genetics.
Instructor: Hedgecock
Fall - even years
020.634 Chromatin and Gene Expression
An advanced course in molecular genetics covering various aspects of gene expression, including
the structure of the nucleosome, effects of chromatin on transcription of eukaryotic genes,
mechanisms of enhancer function, and the role of nuclear organization on gene expression. The
course will consist of lectures as well as presentations of current papers by the students.
Instructors: Moudrianakis, Beemon
Fall - even years, 2 credits
020.638 Regulation and Mechanisms of the Cell Cycle
The great progress in eukaryotic cell cycle research in the past decade was made possible by a
unique synergism between different modern biological approaches (genetic, cell biological,
biochemical, and developmental). These approaches will be highlighted in this course. We will
cover the mechanisms the cell employs to carry out its duplication cycle, such as DNA replication,
mitotic spindle function, and cytokinesis, as well as the regulatory mechanisms that govern these
processes. The relationship of cell cycle biology to the cancer problem will receive special
Prerequisites: 020.305, 020.306, and 020.330, or the equivalent.
Instructor: Hoyt
Spring - even years
020.643 643 Viruses and Anti-Virals
Viral infections are a major health problem to the entire world. The human and economic cost to
society is tremendous; however, for many of these diseases no effective cures are available. Viral
infections like HIV/AIDS, hepatitis C, herpes, HPV, SARS, avian flu, west nile virus, dengue not only
affect or threaten people in the developing world but also in the most developed regions of the
planet. Currently, fewer than 30 antivirals have been approved by the FDA, most of which
specifically target HIV/AIDS. This course will discuss current strategies and approaches for the
development of new anti-virals using a molecular and thermodynamic point of view.
Instructors: Beemon, Freire
020.644 RNA
A graduate seminar course that will explore RNA from Its beginning in the primordial RNA world
to its present-day roles in gene regulation in bacteria, mammals, and viruses. Topics will include:
The early RNA world, Riboswitches, Ribozymes, evolution of protein synthesis, splicing,
telomerase, RNA interference, microRNAs, long non-coding RNAs, Viral non-coding RNAs, and
RNA therapeutics.
Grad students only. Undergrads with permission of instructor.
Instructor: Beemon
020.646 Biological Spectroscopy
This course provides a theoretical background for fluorescence spectroscopy and demonstrates
how fluorescence can be used to advantage to address important problems in biochemistry,
biophysics, molecular biology, and cell biology.
Instructor: Brand
Fall - even years, 2 hours
020.650 Eukaryotic Molecular Biology
The field of molecular biology is fundamental for those interested in modern biological research
and medicine. In this course students examine DNA, RNA and protein synthesis (i.e., the "central
dogma" of molecular biology) in molecular detail, as well as how these processes are regulated
and interrelated. There is significant examination of molecular structure-function relationships,
with particular emphasis on RNA synthesis and processing and chromosomal organization,
nucleosome regulation and epigenetics. Modern and fundamental experimental techniques and
concepts are explored in detail. Students will learn how to use some genome databases and
bioinformatics tools available online to improve their molecular biology research skills and
knowledge. Readings are both from scientific journals as well as a textbook that includes
interactive online content. Students enrolled in 020.650 will have additional assignments
compared to those enrolled in 020.380.
Instructors: Zappulla, Moudrianakis and Beemon
Fall, one 1.5-hour and one 2.5-hour session per week
020.666 Biological Thermodynamics
An in-depth discussion of thermodynamics, statistical thermodynamics and their applications to
the conformational equilibrium and the interactions of biological macromolecules with other
macromolecules and small molecular weight ligands.
Graduate Students and Seniors with permission of Instructor.
Instructor: Freire
Fall - 2 hours
020.668 Advanced Molecular Biology
An advanced course in organization and function of eukaryotic and prokaryotic genes, including
discussion of techniques to analyze gene structure and transcription.
Prerequisite: 020.665.
Instructor: Schleif
Fall, 3 hours
020.670 (N) Emerging Strategies and Applications in Biomedical Research
Up-to-date primary literature manuscripts related to new discoveries and new strategies that are
allowing scientists to make amazing progress in biomedical research will be presented. Examples
include: labeling neurons with up to 90 different colors to trace their circuitry, evolution studies
in glowing bacteria, detecting several viruses on a single chip and using fiber optics and channel
rhodopsin to induce sleep. Students should be interested in reading primary literature research
papers and discussing them in class.
Instructor: Hattar
Spring - 3 hours
020.679 Advanced Biological Microscopy
This course is intended to build upon the basic skills students acquired in the previous course.
Students will be required to work on actual ongoing research projects. The course will emphasize
the integration and use of various light and electron microscopic techniques and their application
to various research related questions. The course will have primarily a practical “hands-on”
component; but will also include theoretical considerations as students will read, analyze, and
discuss current journal articles.
Prerequisites: Introduction to Biological Electron Microscopy and approval of the instructor.
Instructor: McCaffery
Spring - even years
020.684 Fundamentals of Drug Discovery and Development
The creation and implementation of new approaches to the drug discovery and development
process is a very active area of research. Currently, only one compound out of 5,000 that enter
preclinical studies becomes a drug. Moreover, the development process is time consuming,
lasting more than ten years on average. The rate of failure is extremely high. It has become
evident that this field is in urgent need of revolutionary changes. This course will cover drug
discovery issues ranging from the identification of hits to their optimization as drug candidates.
Current as well as novel and proposed approaches aimed at accelerating discovery, potency
optimization, selectivity, pharmacokinetics and other drug properties will be discussed.
Grad students only
Instructor: Freire
020.731 Critical Thinking in Biology (formerly Molecular Morphogenesis)
In this course, students will critically analyze modern and seminal primary research papers in
molecular, cellular and developmental biology. This analysis will emphasize the logic and
experimental design of a selected set of outstanding research publications from diverse fields.
Points of view of authors and reviewers will be actively considered. Graduate students enrolled
will develop the skills needed to efficiently understand and critique the rapidly expanding
literature and growing diversity of biological research methods. In preparation for each class, all
course participants will be expected to very thoroughly read and analyze the two assigned papers.
Instructors will facilitate highly interactive discussions in the first third of the course sessions.
Subsequently, individual students will present assigned papers to lead the discussion for the
remainder of the semester. Students presenting papers will submit a written synopsis/summary
of the paper in advance.
Biology Ph.D. students, second year and above.
Prerequisites: 020.637, 020.668, 020.674, and 020.686
Instructors: Bortvin, Ingolia and Zappulla
Fall, 2 hours
020.735 Seminar: Membrane Trafficking
The Membrane Trafficking seminar course consists of several weeks of lectures and discussions
led by the professors discussing key background concepts in the field of Membrane Trafficking.
Class meetings during the final weeks of the course are seminars on current topics in Membrane
Trafficking, led by the students. Over the course of the semester, students will learn about the
methods and logic of experiment design, model building and hypothesis testing, gain exposure to
and skills in reading and summarizing scientific literature, and get experience with preparing and
delivering an effective oral presentation.
Instructors: Wendland, McCaffery
Fall - odd years
020.738 Seminar: Biological Spectroscopy
We will discuss important recent and classical papers in biological spectroscopy with an emphasis
on steady-state and nanosecond time-resolved fluorescence. Topics will include FRET,
fluorescence anisotropy and single molecule fluorescence. We will discuss photophysics and
applications of spectroscopy to studies of proteins, membranes and nucleic acids.
Instructor: Brand
Spring - even years
020.739 Seminar: Topics in Biochemistry
Minireviews taken from the Journal of Biological Chemistry. Students select a topic of their choice
from the "Compendium of Minireviews" for the current year, and present it before the class for
Instructor: Bessman
Spring, 2 hours
020.753 Methods & Logic in Modern Biology
The purpose of this course is to gain experience in critical thinking about the logic and methods
used in modern biological research. The main approach will be the critical reading, presentation,
and discussion of primary research papers, and the preparation and presentation of a research
proposal. It is held once a week on the NIH Bethesda campus.
Grad students only.
Prerequisites: 020.637, 020.668, 020.674 and 020.686
Instructors: Lichten, Cohen-Fix
Fall - odd years
020.801-802 Research on Biological Problems
Independent research for the Ph.D. dissertation.
Instructors: Staff
020.823-826 Introduction to Biological Research
Training in techniques of biological research in research laboratories. Open to first-year biology
graduate students only.
Instructors: Staff
250.685 Proteins and Nucleic Acids
The structure of proteins, DNA, and RNA and their functions in living systems. Experimental and
theoretical approaches to macromolecules, including modeling, simulating, and visualizing
three-dimensional structures.
Instructors: Woodson, Bowman, Lecomte
250.689 Physical Chemistry of Biological Macromolecules
Introduction to the principles, methods, and approaches employed in the study of the energetics
of proteins and nucleic acids, with emphasis in understanding the relationship between structure,
energy, dynamics and biological function. Topics include classical, chemical, and statistical
thermodynamics, kinetics, theory of ligand binding, and conformational equilibria.
Instructor: Garcia-Moreno
Fall, 3 hours
250.690 Methods in Molecular Biophysics
Introduction to the methods employed in the study of energetics, structure, and function of
biological macromolecules. Topics include optical spectroscopy, transport methods, NMR, X-ray
crystallography. Course emphasizes theoretical understanding and practical knowledge through
problem solving and literature discussion.
Prerequisites, highly recommended: Proteins and Nucleic Acids (250.685) and Physical Chemistry
of Biological Macromolecules (250.689), Calculus (110.108/109), or equivalent course work.
Instructors: Bowman, Staff

Students may also take courses on other campuses with permission of the Director of the
Graduate Program.

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