All 600-level courses are open to undergraduates with permission.
020.601 Current Research in Bioscience
Fall, 1 credit
020.607 Quantitative Biology Bootcamp
Quantitative and computational methods have become essential to modern biological research.
The goal of this course is to provide an introduction to basic skills that will enable students to employ these methods.
Students will learn how to work in a command line shell and use software to perform analyses of large biological datasets.
Students will learn basic programming using the Python language.
Throughout the course students will apply the skills learned to practical analysis problems emphasizing parsing and
working with biological data formats, exploratory data analysis and visualization, and numerical and statistical methods.
This course is only open to first-year students in the CMDB program.
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 reproduction.
Instructors: Van Doren, Spradling, Halpern, Bortvin, Chen, Taylor
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.
Spring, 3 hours
020.674 Graduate Biophysical Chemistry
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: Hilser, Bowman, Woodson, Roberts
Fall, 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.
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.
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.
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
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.
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 semester.
Spring - even years
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.
Fall - even years
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 attention.
Prerequisites: 020.305, 020.306, and 020.330, or the equivalent.
Spring - even years
020.640 Epigenetics & Chromosome Dynamics
It has become finally recognized that the primary structure of the DNA is not the sole and absolute determinant
of the phenotype of an organism. Much depends on the modulations of the primary information by time and tissue
specific enzymatic modifications of this information and the result is the epigenetic information potential within
the nucleus. This potential is dynamic; it can be “written and re-written” in the life-trajectory of a cell.
We will examine the various process and states of genome epigenetics, from simple genes to whole chromosomes,
chromosomal subsets and even the whole nucleus. This graduate level course will consist of few special overview
lectures given by the instructors and the rest will be student presentations. The topics will be selected by the
faculty but we will also consider the inclusion of special and timely topics suggested by the students.
The duration of each session will be 90 minutes. Upper level undergraduates may register with signature of the instructors.
The evaluation of the students for grade assignment will depend on a) the quality of the student’s oral presentation;
b) the students extent and depth of participation in the discussions of each and every seminar;
c) the completion of papers given as homework assignments. Attention is mandatory for all sessions.
No specific textbook will be assigned but the students will be sent to special Journals and books and are expected
to search relevant literature and visit references beyond those provided by the instructors and share their findings
with all in the class.
Instructors: Migeon, Moudrianakis
020.643 Graduate Virology
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.
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. Undergraduates with permission of instructor.
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
020.670 (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.
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.
Spring - even years
020.684 Fundamentals of Drug Discovery
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.
Graduate students only.
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. 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 read and thoroughly critique the assigned paper(s).
All students will submit a short, critical analysis of each paper in advance of the class session in which the paper(s)
will be covered. A student will lead each discussion (once per semester, dependent upon enrollment).
Prerequisites: 020.637, 020.668, 020.674, and 020.686
Instructors: Zappulla and Bortvin
Fall, 2 hours
020.735 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
020.739 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 discussion.
Spring, 2 hours
020.753 Logic and Methods in 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.
Graduate students only.
Instructors: Cohen-Fix, Lichten
020.801-802 Research on Biological Problems
Independent research for the Ph.D. dissertation.
020.823, .824, .825, .826 Introduction to Biological Research
Training in techniques of biological research in research laboratories.
Open to first-year biology graduate students only.
Students may also take courses on other campuses with permission of the Director of the Graduate Program.
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the Department of Biology, or the course instructor. Information on
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the CMDB Webmaster.