Graduate Courses

As detailed in the Graduate Guide and summarized below, students enrolled in the MCDB and EE programs may fulfill degree requirements from among courses that address the following areas:

Career Development – the goal of these workshops is to assist student development of several key career skills: the ability to successfully communicate with other scientists, and the ability to successfully navigate ethical considerations unique to the research community. 

Advanced Topics – these are the core of our graduate program, and are intended to provide advanced training in a variety of current research areas.

Seminar – these courses hone the ability of our students to read and discuss the current primary scientific literature.

External courses – Can't find a course in our Department that suits your research needs?  Students have the option of taking courses from other local departments and institutions.

 

Career Development 

All graduate students in our Department are required to complete the following four workshops, with at least one completed in their first year.  These one-credit workshops are typically offered annually, and are open to all graduate students in our department.


2055 Fellowships and Grants

Nearly all academic research is supported by external grants and fellowships rather than by direct funding through the sponsoring university. However, obtaining external funding is a very competitive process and requires considerable skill. The goal of this workshop is to inform and instruct students about the grant-writing process and discuss with them necessary tools to prepare and submit a successful fellowship or grant application, and learn how to develop an application based upon current research progress. By the end of the workshop, each student will have written an NSF-style fellowship application that will be reviewed by the rest of the class as part of a mock study section. It is anticipated that many of these applications will be subsequently submitted to NSF or other appropriate agency for funding consideration.

Sample Syllabus


2056 Seminar and Poster Presentations

Successful scientists must be able to communicate their findings to members of their research fields as well as to the general public. Given the competitive nature of research and the complexity of most experimental findings, effective communication is a high-stakes game that requires effort and planning. The goals of this workshop are to teach the students effective speaking and presentation strategies, and how to apply them to a variety of different situations. The format of the workshop will include a mixture of lectures on specific topics (lecture/seminar strategies, slide layout and graphic design, how best to engage an audience, poster presentations and how they differ, written communication), and several classes devoted to giving practice presentations. The class concludes with a poster session.  Throughout the workshop, each student will give presentations that will be critiqued by the class and instructor to identify the strengths and weaknesses of their presentation. Feedback will build upon the students' strengths to assist improvement of their communication skills.

2057 Manuscript Preparation

Research findings are often complex, how can you clearly present your findings to an appropriate audience in a compelling manner given the publication constraints of a typical science journal?  In this workshop we will identify good practices for writing each section of the primary research manuscript and apply these ideas to the analysis of three Model Papers. Further, each student will develop a ~12-week schedule for the completion of a research manuscript for mock submission to a journal; weekly assignments will be devoted to the completion of this task.  In addition, we will develop criteria for writing good cover letters and manuscript reviews. For practice in peer review, students will also be assigned to write reviews of classmates’s manuscripts.

Sample Syllabus

 

2058 Ethical Practices in Scientific Research

Scientific research is not a solitary exercise, but involves constant decision-making where the outcomes affect others. This workshop will examine in turn the various common ethical issues involved in modern biological research. Ethical challenges abound, including maintaining data integrity, balancing and assessing contributions to publications, maintaining confidentiality, respecting intellectual property and avoiding plagiarism, integrating human or animal subjects into research projects, recognizing research misconduct, and bearing the responsibilities of interacting with the general public. This course combines class meeting to discuss relevant material in combination with weekly written exercises designed to stimulate participants to think deeply about each topic.

Sample Syllabus

 

Seminar Courses

All graduate students must complete 2 terms of graduate seminar courses (2450 or 2540 depending upon the program) within their first two years. These two-credit courses are offered annually both Fall and Spring terms and are open to all graduate students in the department.

 

2450 Biological Sciences Seminar

This course is taken by all MCDB graduate students.  Students read and present current research articles guided by the faculty.  The goal is to teach students to critically evaluate the research of other scientists and to communicate both the research and their evaluation in an oral presentation.  In addition, a scientific writing component is incorporated to aid students to develop skills in this area.

Sample Syllabus


2540 Ecology Seminar

This course is taken by all EE graduate students. Students will participate in the critical review of the current literature relating to a topic in ecology that is selected each term.
 

Advanced Topics

These two-credit courses are designed to provide in-depth coverage of contemporary research areas in biology.  Graduate students are required to take 4 of these courses (i.e., 8 credits total) within their first 2 years, with at least half of this requirement being completed in their first year.  Although these courses are open to all graduate students in our department, most of these courses are taught at an advanced level; students lacking appropriate background are encouraged to remedy major gaps in their knowledge prior to enrollment.  The following courses are typically offered every two years on a rotating basis. As a particular course is sometimes taught by a different faculty member from year to year, the specific topics covered in a given year may vary somewhat from the following descriptions.

 

2040 Protein Structure and Function

The molecular heart of biology revolves around proteins — they provide the major catalytic and structural aspects of life. Important advances in recent years have led to the development of new technologies that allow an unprecedented understanding of their function. This course will cover advanced topics in both the theoretical and practical aspects of modern protein biochemistry and biophysics: Protein structure and function, protein design, molecular graphics, molecular simulation, and homology modeling. The course will integrate lectures with student presentations on current research papers. In addition, problem sets tailored to lecture topics will be assigned to provide a hands-on understanding of the techniques discussed. This course is geared toward students who previously mastered undergraduate level courses in Biochemistry and Biophysics.

Course requirements.  This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but need to have passed the equivalence of both an undergraduate level Biochemistry (Biosc 1820 or equivalent) and Biophysics (Biosi 1470 or equivalent) course with an A- or better and obtained instructor approval.

Next/last Course offering – Fall 2013

Sample Syllabus

 

2090 Advanced Developmental Biology

Key to the creation of a higher multicellular organism is the carefully orchestrated steps that differentiate a single cell into a complex organism of billions of cells that functionally and physically interact.  This course will cover in depth five topics in modern Developmental Biology that have provided particularly novel ways of thinking about developmental problems and research: Xenopus axis formation, polarity and early cell fate decisions in the mouse, making tubular structures in development, neural crest development, and cilia function in development. Each specific topic will be introduced by a lecture, but the focus of the course is on discussion of original scientific papers (for each hour of lecture there are three hours of discussion). This course is geared toward students who have previously mastered an undergraduate course in Developmental Biology. 

Course requirements. This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but need to have received an A- or higher in Developmental Biology (Biosc 1520 or equivalent) and instructor approval.

Next/last Course Offering – Fall 2015

Sample Syllabus

  

2100 Cellular Structure & Morphology

The fundamental self-contained unit of life is the cell, and all complex organisms are composed of these building blocks. This course will focus on particularly novel ways of thinking about and investigating how cells control their characteristics and behavior to achieve complex morphogenesis.  Course format will integrate instructor lecture with student presentation and discussion of original scientific papers.  This course is geared toward students who have previously mastered an undergraduate level course in Cell Biology.

Course Requirements. This course is open to all Biological Science graduate students.  Undergraduates and students from other programs are also welcome, but need to have received an A- or higher in Cell Biology (Biosc 1500 or the equivalent) and instructor approval.

Next/last Course offering – Spring 2015

Sample Syllabus

 

2105 Cell Signaling

Cells, like individuals, do not exist in isolation; they interact in myriad ways to facilitate development and homeostasis. This course provides both an overview of  the current concepts of cell signaling and an understanding of the experimental design leading to their formulation. The format will combine  lectures on the relevant topics with discussion of the supporting primary literature.  Specific topics to be addressed include the short and long-term effects of G-protein coupled receptors, tyrosine kinase receptor activities, plus a survey of other key receptors classes that do not fall into either category. This course is geared to students who have previously mastered an undergraduate level course in Cell Biology. 

Course Requirements. This course is open to all Biological Science graduate students.  Undergraduates and students from other programs are also welcome, but need to have passed an undergraduate Cell biology course with an A- or better (Biosc 1500 or the equivalent) and additionally require instructor approval.

Next/last Course Offering – Spring 2014

Sample Syllabus

 

2130 Genetics of Model Organisms

The basic principles of genetics have been elucidated largely by studies using a small number of species: from the peas used by Mendel to more recent examples such as the zebrafish.  In this course we will investigate many of these key species that have become model organisms, including the yeast, Saccharomyces cerevisiae, the nematode, Caenorhabditis elegans, the fruit fly, Drosophila melanogaster, the zebrafish, Danio rerio and the mouse, Mus musculus.  Why were these species chosen to study genetics?  What important findings have these studies yielded?  How do you ‘do’ genetics in these model systems?  How can experiments with these species help us to understand the basis of human genetic disease? These questions will be addressed by presentations from experts in the field and by discussions of classic and current literature. This course is geared toward students who have previously acquired a rigorous understanding of undergraduate genetics. 

Course Requirements: This course is open to all Biological Science graduate students. Undergraduates and students from other programs are also welcome, but need to have instructor approval and an A- or better in Genetics (Biosc 0350 or equivalent).

Next/last Course offering – Fall 2014

Sample Syllabus

 

2140 Genomics

Current molecular biology increasingly focuses on the collection and analysis of large sequence-based data sets with a goal to determine the organization and information structure of entire genomes. In this course, students will learn a variety of techniques in structural, functional, comparative and metagenomics directed at using genome sequence data to address questions of interest. Topics to be addressed include gene prediction, sequence alignment, homology searching, functional element identification, gene expression profiling & proteomics, and phylogenetics using whole genome/genomic data.  The course will be conducted in a lecture and discussion format with frequent reference to the current experimental literature.  This course assumes that students have previously mastered an undergraduate course in Molecular Biology.

Course Requirements. This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but need to have instructor approval and an A- or better in Molecular Biology (Biosc 1940 or the equivalent).

Next/last course offering – Fall 2015

Sample Syllabus

 

2145 Protein Life history

The goal of this course is to understand the mechanisms underlying the synthesis, folding, post-translational modification, and fates of proteins that are synthesized in various cell types.  Emphasis will be placed on the primary literature, and students will be expected to present and discuss assigned papers and background readings.  Paradigm-shifting concepts that have altered our definitions of the routes taken by proteins as they are created and mature will also be presented. The class format will alternate between lecture presentations and student presentations of relevant current literature topics. This course is geared toward students who have previously mastered undergraduate biochemistry and have a strong foundation in cell biology.

Course Requirements. This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but need to have instructor approval and/or an A- or better in biochemistry (Biosc 1000 or 1810) or an equivalent course, as well as a strong background in cell biology.

Next/last Course offering – Fall 2014

Sample Syllabus

 

2150 Nucleic Acids 

The code of life is elegantly assembled as a linear series of 4 different bases in RNA and DNA, and a large number of fascinating cellular processes are devoted to maintaining the integrity of this information. The importance of these processes cannot be underestimated, as degradation of this information is a common basis of many human maladies. Moreover, these versatile molecules have also been co-opted in numerous cases to serve catalytic functions. Course topics will stress the structure and function of nucleic acids as applied to the storage, replication, recombination, and processing of biological information. (Transcription is covered in 2155)  This course will be taught at an advanced level with an emphasis on the primary literature, and is geared toward students who have mastered undergraduate level courses in genetics, biochemistry and molecular biology.

Course Requirements. This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but need to have instructor approval and an A- or better in Genetics (Biosc 0350 or equivalent) and Molecular Biology (Biosci 1940 or equivalent).

Next/last course offering – Spring 2016

Sample Syllabus

 

2155 Gene Expression

Although all cells within an organism contain basically identical genetic material, different cells express a different array of proteins in a temporally and spatially distinct manner. In this course, we will discuss major topics in gene expression, focusing on transcription and transcription-coupled processes in eukaryotes.  We will discuss key concepts in RNA synthesis and the role of chromatin and noncoding DNA in regulating gene expression.  The format will be a mixture of lectures by the instructor and student-directed presentations of the primary literature. This course is geared toward students who have previously mastered an undergraduate course in Molecular Biology. 

Course Prerequisites. This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but need to have instructor approval and an A- or better in Molecular Biology (Biosc 1940 or the equivalent).

Next/last Course offering – Spring 2014

Sample Syllabus

 

2320 Population Biology

This course addresses population dynamics from ecological and evolutionary perspectives. It begins with the methods and models used to study demography and population growth of single species. Subsequent models build on these ideas to explore disease transmission, multi-species interactions including competition, predation, and mutualism, and how both genes and individuals move within populations (inbreeding) and between populations using a meta-population approach. Throughout the course, the application of these models to conservation and management issues is discussed, with particular emphases on extinction processes, species invasions, and human populations. Students will become familiar with a variety of mathematical models used to understand population dynamics, and will have the opportunity to discuss, in depth, some of the current topics in population biology in smaller groups.

Course requirements - open to all graduate students. This course is also open to undergraduates with appropriate prerequisites as Biosc 1320.

Next/last offered - Fall 2015

Sample Syllabus

 

2350 Evolution

This course is an introduction to biological evolution. The theory, process and pattern of evolutionary change are presented. This course will encompass both microevolutionary and macroevolutionary concepts. Lecture topics will include inheritance and variation, population genetics, natural selection, speciation, adaptation, the fossil record, and phylogenetics. (Note:  3 credit course)

Prerequisites – open to all graduate students. This course is also open to undergraduates with appropriate prerequisites as Biosc 1130.

Next/last offered – this course is offered annually.

Sample Syllabus


2351 Advanced Evolution

Evolutionary Biology is a vibrant and rapidly changing research field. This course focuses on discussing recent advances and areas of major scientific growth in the study of evolution. Course time is composed of an intercalated set of topical lectures followed by literature surveys and presentations by students.

Course Requirements – This course is open to all Biological Science graduate students.  Undergraduates and students from other programs are also welcome, but they need to have instructor approval and have received an A- or better in Evolution (Biosc 1130 or the equivalent).

Next/last course offering – Fall 2014

Sample Syllabus

 

2355 Species Interactions

The goal of this course is to provide students with a highly focused look at the work of key Principle Investigators (PIs) in the field of species interactions. The specific PIs to be explored will be determined by the students, who will be responsible for summarizing the PIs research program and key contributions to the field. Basic theory and literature reviews on parasitism, mutualisms, competition, predator-prey interactions, network theory, and phylogenetics will be presented. This course is geared to students who have previously mastered an undergraduate course in Evolution. 

Course requirements. This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but they need to have instructor approval and have received an A- or better in Ecology (Biosc 0370 or the equivalent). 

Next/last Course offering – Fall 2015

Sample Syllabus

 

2361 Advanced Ecology

This course focuses on community ecology and examines how predation, competition, herbivory, and mutualisms involving bacteria to mountain lions shape how plant communities look and function.  We also cover how natural disturbances (e.g., fire and tornados) impact plant communities and ecosystems.  Topics include trophic cascades, invasive species, trait-mediated assemblages, succession, forest dynamics, super-species, coexistence theory, tropical ecology, and the maintenance of diversity.  Each class mixes a lecture with a subsequent discussion of papers from the primary literature.  Scientists from outside the University of Pittsburgh often participate and in the past have come from the University of Notre Dame, University of Wisconsin, and Ohio State University.  

Course Requirements.  This course is open to all Biological Science graduate students.  Undergraduates and students from other programs are also welcome, but they need to have instructor approval and an A- or better in Ecology (Biosc 0370 or the equivalent).

Next/last course offering – Fall 2015

Sample Syllabus


2370 Evolutionary Genetics and Development

The modern (neo-Darwinian) synthesis of evolution integrates Darwin’s ideas of natural selection with population genetics to reconcile how Mendelian traits could gradually change over time. And yet, this field necessarily had to treat the molecular mechanisms underlying phenotypic traits as a “black box”. Current advances in genetics, development, and molecular biology now render the relationship between genotype and phenotype experimentally tractable. This course will introduce evolutionary and genetic concepts that connect mechanism to phenotype. Topics will include: phylogenetic analysis, population genetics, analysis of quantitative trait loci, molecular genetics of gene variants, non-genetic (“epigenetic”) variation, and evolutionary development. Lectures will be accompanied by discussions of journal articles and written assignments. This course is geared toward students who have previously mastered undergraduate Genetics. 

Course requirements. This course is open to all Biological Sciences graduate students. Undergraduates and students from other programs are also welcome, but they need to have instructor approval and have received an A- or better in Genetics (Biosc 0350 or the equivalent).

Next/last course offering – Spring 2015

Sample Syllabus


2810 Macromolecular Structure and Function

Biochemistry is a logical way of thinking about, and experimentally probing, lifes processes at the scale of atoms and molecules.  In this course we will explore macromolecular structure, function and dynamics of protein and RNA molecules by reasoning through fundamental concepts and experimental approaches.  In addition to textbook readings, you will have exposure to the scientific literature throughout the course for real world illustrations of experimental tools and approaches. (note:  3 credit course).

Course requirements. This course is open to all Biological Sciences graduate students. This course is also open to undergraduates with appropriate prerequisites as Biosc 1810.

Next/last course offering – Fall 2015, usually taught annually

Sample Syllabus

 

2940 Molecular Biology

The goal of this course is to provide students with a current understanding of the molecules and mechanisms that define modern molecular biology. The course will emphasize experiments that have led to major developments in the field of molecular biology. Thus, students will not only learn what we know about molecular biology but how we know it. Primary literature will be emphasized. (Three credits)

Course requirements.  This course is open to all graduate students.  This course is also open to undergraduates with appropriate prerequisites as Biosc 1940.

Next/last Course offering – This course is offered annually.

Sample Syllabus

 

Relevant Courses from Outside Departments

The courses listed below are offered outside the Department and will count toward fulfilling degree requirements. Because the workload of courses offered in different departments varies, the number of credits counting toward fulfilling this requirement may differ from the number of credits listed on the graduate transcript. Relevant courses of interest not on the below list may also be taken upon prior approval of the Graduate Program Oversight Committee (GPOC, see Graduate Guide for details).

University of Pittsburgh Courses (other departments)

Course

Description  

Listed Credits

Toward degree requirements  

 BIOST_2014  

 Intro to Biostatistics for Biomedical Scientists

 3

 1

 BIOST_2041

 Intro to Statistical Methods I

 3

 2

 BIOST_2042

 Intro to Statistical Methods 2

 2

 2

 BIOINF_2051

 Intro to Bioinformatics

 3

 2

 BIOST_2055

 Statistics and Data mining in microarray analysis

 3

 2

 CLRES_2707

 Bioinformatics Resources: Data Mining

 1

 1

 CLRES_2708

 Bioinformatics Resources: Data Analysis

 1

 1

 EPIDEM_2725

 Reproductive Development

 2

 2

 IDM_2001

 Molecular Biology of Microbial Pathogens

 3

 2

 IDM_2014

 Functional Genomics of Microbial Pathogens

 3

 2

 INTBP_2040

Using PERL for Bioinformatics

 3

 2

 MOLBPH_2001

 Molecular Biophysics 1: Structure

 3

 2

 MSBMG_2510

 Biochemistry of Macromolecules

 2

 2

 MSBMG_2560

 Biology of Signal Transduction

 3

 2

 MSMGDB_3510

 Advanced Topics in Gene Expression

 3

 2 

 MSCBIO_2075

 Molecular Evolution

 3

 2

 MSMVM_3410

 Microbial Pathogenesis

 2

 2

 MSMVM_3420

 Viral Pathogenesis

 2

 2

 MSCBMP_2840

 Regulation of Membrane Traffic

 2

 2

 MSCBMP_2880

 Cell Biology of Normal and Disease States

 4

 2

 MSCBMP_2885

Imaging Cell Biology in Living Systems from Single Molecules to Animal Models

 3

 2

 MSCMP_2730

 Molecular Methods of Tissue Growth and Differentiation

 3

 2

 MSCMP_3750

 Angiogenesis

 3

 2

 MSMPHL_2310

 Principles of Pharmacology

 3

 2

 MSMPHL_3330

 DNA repair: Biochemistry to Human Disease

 2

 2

 MSMVM_3455

Antimicrobial Therapeutics

 2

 2

 MSNBIO_2112

Neurobiology of Diseases

 3

 2

 

Courses offered through Carnegie Mellon University

 Course                   

Description 

Listed Credits

Toward degree requirements

BIOSC_03-738

Physical Biochemistry 

3

2

BIOSC_04-738

Physical Biochemistry

3

2

BIOSC_03-871

Structural Biophysics 

3

2

BIOSC_03-711

Computational Molecular Biology and Genomics 

4

3

BIOSC_03-712

Computational Methods for Biological Modeling and Simulation

3

2