Advanced Educational Resources
BIOCHEM 501 Chemical Biology I Prerequisite: graduate standing. (3 credits) This course will provide a high-level overview on the structure, function and chemistry of biological macromolecules including proteins, nucleic acids and carbohydrates. Topics include protein and nucleic acid folding, energetics of macromolecular interactions (kinetics and thermodynamics), and mechanistic enzymology. Using specific examples from the current literature, each topic will stress how chemists have used molecular level tools and probes to help understand the specific systems under study. The over arching theme in this course will be that structure and function are intimately linked. Prerequisites: None.
BIOCHEM 502. Chemical Biology II Prerequisites: BIOLCHEM 501 (3 credits). This course is a continuation of Chemical Biology 501. The basic concepts obtained in Chemical Biology 501 will be applied to and demonstrated in three broad areas of interest to both chemists and biologists. The first topic will discuss combinatorial methods including SELEX and gene shuffling, combinatorial organic synthesis, high throughput screening and chemical genetics. The second topic will focus on signal transduction, emphasizing general concepts (at the molecular level) and how small molecules have been used to probe and modulate signal transduction pathways. The final topic will cover protein translation, stressing mechanistic aspects of protein synthesis and folding in vivo.
BIOCHEM 515. Introductory Biochemistry Prerequisite: graduate standing (3 credits). Biological Chemistry 515 provides a broad introduction to the fascinating field of biochemistry. Students will explore the molecular basis and chemical principles pertinent to living systems, including eukaryotes, bacteria, and viruses. The structures and functions of the four major molecules of life (proteins, lipids, carbohydrates, and nucleic acids) and their biosynthetic pathways will be examined. Students will also learn the biochemical roles of vitamins, enzyme cofactors, hormones, drugs, antibiotics, and toxins. This course is taught by medical school faculty and emphasizes the relevance of biochemistry to health, disease, physiology and medicine.
BIOCHEM 521/523. Applied Biostatistics. Prerequisite: Calculus, graduate standing. (4 credits). Fundamental statistical concepts related to the practice of public health: descriptive statistics; probability; sampling; statistical distributions; estimation; hypothesis testing; chi-square tests; simple and multiple linear regression; one-way ANOVA. Taught at a more advan.ced mathematical level than Biostat 503. Use of the computer in statistical analysis
BIOCHEM 550 Macromolecular Structure and Function Prerequisites: two terms of organic chemistry; Introductory Biochemistry or permission of instructor. Physical chemistry is recommended (3 credits). This course will relate protein structure to various aspects of protein function. The course will begin with a general introduction to three-dimensional protein structure including discussion of structure determination methods and forces in protein structure and stability. Significant sections of the course include (i) binding and allosterism, (ii) enzyme catalysis, (iii) protein-nucleic acid interaction, and (iv) signal transduction and membrane proteins. The emphasis will be to relate details of structure to the function of the proteins discussed. The course will include a molecular graphics component aimed at hands-on experience for the students.
BIOCHEM 591. Special Topics in Signal Transduction Prerequisite: graduate standing (2 credits). A literature based discussion course that will cover both seminal discoveries in signal transduction as well as recent advances in the field. The course will meet once per week for two hours, throughout the semester. Two research papers will be discussed each week. Grading is based on short weekly problem sets and a presentation by each student. Prior course work in biochemistry and cell biology is strongly encouraged.
BIOLCHEM 602. Protein Crystallography Prerequisite: graduate standing (3 credits). Protein Crystallography: Principles of Macromolecular Crystallography --- Fundamental of the methods for determining 3-dimensional structures of large molecules by x-ray crystallography. Aimed at students who expect to use crystallography as a major tool for their research, and at those who want in-depth knowledge of the methods in order to analyze structure data.
BIOCHEM 640. Regulatory RNA and Control of Gene Expression Prerequisite: graduate standing (2 credits). RNA-based mechanisms are now recognized as key regulators in biology and disease. Most mammalian genes are regulated by noncoding RNAs (e.g. microRNAs, long noncoding RNAs, piRNAs), and/or RNA-binding proteins. RNA-based mechanisms control protein translation, RNA stability, and transcription. Disruptions of these mechanisms contribute to human diseases, including cancer, neurological disorders, and cardiovascular diseases; RNA-mediated processes also are critical for stem cells and development. RNA-based techniques, such as RNA interference and CRISPR genomic modifications, are widely used as research tools to study gene function and biological processes. BiolChem 640 will cover these and related aspects of RNA-mediated control of gene expression.
BIOCHEM 650. Eukaryotic Gene Transcription Prerequisite: graduate standing (2 credits). The course will focus on recent discoveries concerning the regulation of eukaryotic gene transcription, including transcription complex architectures, chromatin organization and modifications, mechanisms of epigenetic inheritance and genome-wide functions of transcription regulatory factors. The course will be taught through a combination of lectures and discussions of current literature.
BIOCHEM 660. Molecules of Life: Protein structure, function and dynamics Prerequisite: graduate standing (2 credits). This is a literature-based course that will introduce select biological systems to illustrate how modern protein biochemistry advances our understanding of biological mechanisms. Topics include protein structure, function and dynamics; protein folding/misfolding and how this relates to disease; and the impact modification, processing, and trafficking has on protein function.
BIOINF 520. Computational Systems Biology in Physiology. Prerequisite: An introductory course in calculus is desired but not essential and one year of biology (3 credits). This course is an introduction to dynamic modeling in physiology for both experimental and theoretical inclined students. We use selected physiological systems to introduce concepts in computational systems biology. This is done through the use of increasingly more complex cellular functions modeled with scientific software.
BIOINF 523. Bioinformatics Basic Biology Prerequisite: graduate standing (2 credits). Introduces basic biology to graduate students without any prior college biology. Geared towards students pursuing training in Bioinformatics or Biostatistics who have quantitative training (computer science, engineering, mathematics, statistics, physics). After a brief introduction to organic and biochemistry, bootcamp will have lectures on molecular biology, cell biology and laboratory tools used in both, as well as introductory molecular biology laboratory experiments.
BIOINF 525. Foundations in Bioinformatics and Systems Biology Prerequisite: graduate standing (1 credit for each module; students can register for any one or all 3 modules). This course is comprised of three modules. The first module is an introduction to the web resources and tools that researchers use for the retrieval of public data and the analysis of public and laboratory data. The second module is an introduction to statistics, and the third module focuses on the integration of genome-wide data sets into their functional context.
BIOINF 527. Introduction to Bioinformatics and Computational Biology Prerequisite: Upper level or graduate level Statistics or concurrent enrollment in Statistics; Calculus I & II; Biochemistry, Molecular Biology, or Cellular Biology; or permission of instructor (4 credits). This course introduces students to the fundamental theories and practices of Bioinformatics and Computational Biology via a series of integrated lectures and labs. These lectures and labs will focus on the basic knowledge required in this field, methods of high-throughput data generation, accessing public genome-related information and data, and tools for data mining and analysis. The course is divided into four areas: Basics of Bioinformatics, Computational Phylogeny (includes sequence analysis), Systems Biology and Modeling.
BIOINF 528 Advanced Application of Bioinformatics Prerequisite: BS (3 credits). This course introduces fundamental concepts and methods for bioinformatics and the advanced applications. The topics covered include bioinformatics databases, sequence and structure alignment methods, Monte Carlo simulation methods, protein folding and protein structure prediction methods, and modeling of protein-protein interactions. Emphasis is placed on the understanding of the concepts taught and on their practical utilization, with the objective of helping students use the bioinformatics tools to solve problems in their own research.
BIOINF 540 Mathematics of Biological Networks Prerequisite: None (3 credits). This course addresses methods and principles involved in constructing and studying the structure and function of biological networks using examples from real datasets. The course is structured so that any necessary background will be introduced as needed. A comprehensive website containing all reading materials and class notes will be maintained throughout the term.
BIOINF 545. High-throughput Molecular Genomic ad Epigenomic Data Analysis Prerequisite: STATS 400 (or equivalent) and graduate standing: or permission of instructor. Students should have completed at least programming class with a passing grade. Preparation in biiology or quantitative analysis also recommended (3 credits). This course will cover statistical methods used to analyze data in experimental molecular biology, with an emphasis on gene and protein expression array data. Topics: data acquisition, databases, low level processing, normalization, quality control, statistical inference (group comparisons, cyclicity, survival), multiple comparisons, statistical learning algorithms, clustering visualization, and case studies.
BIOINF 575. Programming Laboratory in Bioinformatics Prerequisite: familiarity with programming concepts is recommended (3 credits). BIOINF 575 introduces the principles and application of general computer programming, relational databases, and statistical programming as tools to solve problems in bioinformatics data analysis. General programming is taught using the object oriented language Python and statistical programming and graph generation is introduced in R. The relational database language SQL is taught in conjunction with database design, construction and querying.
BIOINF 580 Biomedical Signal and Image Analysis Prerequisite: None. The course covers some fundamental methods in biomedical data analysis. Topics include:Database management in biomedical applications, Transforms and feature extraction, Fourier transform, wavelet transform, fundamentals of information theory, and statistical methods used in signal processing, Image enhancement, image segmentation, and image feature extraction methods, Brief introduction to natural language processing, Introduction to fundamental techniques in clustering and classification, Applications in medicine and biology.
BIOINF 585. Signal Processing and Machine Learning for Systems biology and Clinical Informatics Prerequisite: See Bullitiin BIOI 586NF, CALC III or Linear Algebra. (4 credits). This course describes some fundamental methodologies to analyze biomedical data and extract characteristic features from them. Topics covered include: 1) transforms and feature extraction - Fourier transform, wavelet transform, 2) feature selection and reduction methods, 3) fundamentals of information theory and estimation theory, 4) machine learning, supervised learning, unsupervised learning, reinforcement learning, machine learning on big data, 5) introduction to text mining and natural language processing, and 6) applications in systems biology and clinical informatics.
BIOMEDE 499. Prerequisites: Graduate standing (1-4 credits). Topics of special interest selected by faculty. Lecture, seminar or laboratory.
BIOMEDE 551. Proteome Informatics Prerequisite: Bio Chem and Calculus (3 credits). Introduction to proteomics, mass spectrometry, peptide identification and protein inference, statistical methods and computational algorithms, post-translational modifications, genome annotation and alternative splicing, quantitative proteomics and differential protein expression analysis, protein-protein interaction networks and protein complexes, data mining and analysis of large-scale data sets, clinical applications, related technologies such as metabolomics and protein arrays, data integration and systems biology.
BIOMEDE 552. Biomedical Optics Prerequisites: MATH 216 (3 credits). This course provides students with an understanding of current research in biomedical optics. Topics include: fundamental theoretical principles of tissue optics; computational approaches to light transport in tissues; optical instrumentation; an overview of applications in clinical optical diagnostics and laser-based therapy; an introduction to biomedical microscopy and applications in biophotonic technology.
BIOPHYS 440. Biophysics of Diseases Prerequisite: Graduate standing (3 credits). This course deconstructs current and emerging diseases in terms of the malfunctioning of nucleic acids, proteins, and membranes and interactions between them. The diseases covered will include Alzheimer’s, Parkinson’s, Creutzfeldt-Jakob disease (or Mad-Cow disease), HIV, a variety of bacterial infections, and other biological disorders. A variety of biophysical methods for dissecting diseases at the atomic level will be surveyed, including NMR spectroscopy, X-ray crystallography, cryo-electron microscopy, single molecule imaging, and computational methods.
BIOSTAT 501. Introduction to Biostatistics Prerequisite: elementary algebra, graduate standing (4 credits). Fundamental statistical concepts related to the practice of public health: descriptive statistics; probability; sampling; statistical distributions; estimation; hypothesis testing; chi-square tests; simple and multiple linear regression; one-way ANOVA. Use of computer in statistical analysis.
BIOSTAT 521. Applied Biostatistics Prerequisite: Calculus (4 credits). Fundamental statistical concepts related to the practice of public health: descriptive statistics; probability; sampling; statistical distributions; estimation; hypothesis testing; chi-square tests; simple and multiple linear regression; one-way ANOVA. . Taught at a more advanced mathematical level than Biostat 503. Use of the computer in statistical analysis.
BIOSTAT 522. Probability and Distribution Theory Prerequisites: BIOSTAT521; BIOSTAT501 w/ instructor permission (3 credits). A second course in applied biostatistical methods and data analysis. Concepts of data analysis and experimental design for health-related studies. Emphasis on categorical data analysis, multiple regression, analysis of variance and covariance.
BIOSTAT 553 Applied Biostatistics Prerequisite: Calculus (4 credits). Fundamental statistical concepts related to the practice of public health: descriptive statistics; probability; sampling; statistical distributions; estimation; hypothesis testing; chi-square tests; simple and multiple linear regression; one-way ANOVA. Taught at a more advanced mathematical level than Biostat 503. Use of the computer in statistical analysis.
BIOSTAT 646. High Throughput Molecular Genetic and Epigenetic Data Analysis Prerequisite: graduate standing and STAT400, BIOSTAT522, or BIOSTAT521 or permission of instructor. (3 credits) The course will cover statistical methods used to analyze data in experimental molecular biology. The course will primarily cover topics relating to gene expression data analysis, but other types of data such as genome sequence and epigenomics data that is sometimes analyzed in concert with expression data will also be covered.
CDB 530. Cell Biology Prerequisite: graduate standing (3 credits). This graduate course is designed to present basic information as well as the most recent developments in key areas of cell biology. The course consists of both lectures by faculty in their areas of expertise and small discussion groups that delve more deeply into lecture material and discuss primary literature. Both will expose students to current experimental approaches in cell biology.
CDB 550. Histology: From Stem Cells to Tissues and Organs Prerequisite: none (4 credits). The broad objective of the course is to develop a comprehensive understanding of the microscopic structure and function of tissues and organs of the body. Through lectures and laboratory work students should gain a basic understanding of: 1) How structural specializations of cells reflect their functions; 2) How cells work together to perform their specialized functions; 3) How groups of cells associate to form organs; 4) How this organization enables each organ system to carry out its function; and, 5) How stem cells contribute to tissue formation and regeneration. Students are evaluated via biweekly quizzes as well as a midterm and a final examination, all of which are online and open-book. Graduate students (CDB550) have to submit two additional question-writing assignments.
CDB 560. Quantitative Fluorescence Microscopy and Image Analysis Course resumes winter 2020 term. Prerequsitie: None (3 credits). This course trains new graduate students and upper level undergraduates in the basic theory and practice of quantitative fluorescence microscopy. Fluorescence microscopy is an indispensable technique of the Biomedical Sciences. Students have to turn to microscopy at one point or another during their graduate career, and they commonly learn it on the fly. CDB560 is designed to impart a working understanding of the key principles of fluorescence and fluorescence microscopy, as well as the quantitative analysis of fluorescence and digital image processing. Students also learn to apply this knowledge by analyzing raw microscopy data from landmark studies to replicate key results. With this training, students are expected to become proficient in rationally designing a microscopy-based assay and then devising an appropriate method to analyze the images quantitatively.
CDB 581. Developmental Genetics Prerequisite: None (3 credits). This course is an active, participation-based class covering developmental biology and genetics, with extensive connections to stem cell/regenerative biology, genomics, evolution, and human disease. Three learning styles are combined in this class: (1) short faculty lectures; (2) intensive group dissections of research papers; and (3) student presentations.
CDB 582 or 583 Organogenesis: Stem Cells to Regenerativ Biology Prerequisite: None (2 or 3 Credits). This course covers multiple aspects of organogenesis including morphological and molecular events underlying organ formation in vitro and in vivo, experimental systems, parallel pathways for organ formation in various model organisms, adult organ structure and pathology, organ regeneration and repair, stem cell systems, cell and tissue engineering, and carcinogenesis. Two modules make up the course: a) organogenesis of an organ (the organ system changes each year (2 credits)); and b) with an exercise in writing a scientific proposal (3 credits). Course objectives are: a) to provide students with a current in depth, multidisciplinary view of the processes of organogenesis; b) to highlight target areas of future research; c) to read and discuss significant papers in the field; and d) to practice the design and preparation of a research grant by writing a mini-proposal. Students who wish to take the course for a grade should enroll in CDB 583 for 3 credits. Alternatively, the course can be taken S/U without pursuit of the proposal-writing portion of the course as a 2 credit course (students interested in this option should enroll in CDB 582).
CDB 583. Biology of Regeneration Prerequisite: Biology 172 or 174 or genetics (BIO305) or Biochemistry (MCDB310, CHEM351 or BIOLCHEM415) or histology (CDB450). (3 credits) The objective of this course is to present basic information on the mechanisms through which mammalian tissues sense and respond to injury to regenerate. We will also discuss current approaches to study and improve regeneration. The course consists of lectures focused in the regeneration of specific organs as well as discussions of primary research literature.
CDB 595. Biology of Regeneration Prerequisites: Biology 172 or 174 or genetics (BIO305) or Biochemistry (MCDB310, CHEM351 or BIOLCHEM415) or histology (CDB450) (3 credits). The objective of this course is to present basic information on the mechanisms through which mammalian tissues sense and respond to injury to regenerate. We will also discuss current approaches to study and improve regeneration. The course consists of lectures focused in the regeneration of specific organs as well as discussions of primary research literature. The course is geared towards Juniors and Seniors.
EECS 417. Electrical Biophysics Prerequisite: EECS 492. (3 credits) Survey of recent research on learning in artificial intelligence systems. Topics include learning based on examples, instructions, analogy, discovery, experimentation, observation, problem-solving and explanation. The cognitive aspects of learning will also be studied.
EPID 515. Genetics in Public Health Prerequisite: graduate standing (3 credits). This course is designed for students with biology or genetics background, that are interested in understanding genetics in public health. This course will provide an in depth examination of genetics in public health including newborn screening diseases and practices, fundamentals of population genetics, and the genetics of common chronic diseases.
HG 541. Gene Structure and Regulation Prerequisite: undergraduate-level course in general biology required, specialized undergraduate-level course in genetics (e.g. BIOLOGY 305) is strongly recommended (3 credits). HG541, Molecular Genetics, is a course that explores how the information content of the DNA genome is (i) organized, propagated, and altered, and (ii) functionally expressed by regulated transcription into RNA - the core molecular properties and processes of genetic systems that underlie all further investigations of organismal, clinical, and population genetics. The class will focus on developing an advanced modern understanding of these molecules and reactions. We will explore what experimental research in model organisms and humans has taught us about the molecular encoding of genetic information while simultaneously exposing gaps in our understanding.
HG 542. Molecular Basis of Human Genetic Disease Prerequisite: HG 541 or an equivalent molecular genetics course with the approval of the course director (3 credits). HG542 emphasizes strategies for mapping disease-associated genetic variation, the design and interpretation of experiments to characterize the molecular pathology of implicated mutations, and how these discoveries are moved into the clinic. This is an essential course for anyone interested in molecular genetics and human variation as it relates to human disease.
HG 544. Population and Statistical Genetics. Prerequisite: A foundation in genetics and familiarity with the basic statistics and probability (3 credits). The concepts and analytic methods for studying variation in human populations are the subject matter of this course. The topics covered include the distribution of genetic variation, major forces of genetic stasis and change, quantitative traits, linkage analysis, association tests, and the role of the environment. We take a problem solving approach and present the basic models of population, quantitative, and statistical genetics at a mathematical level appropriate to students in the life sciences. Our focus is on current human genetics research. However, most of what we present is broadly useful and applies to natural populations of other species
HG 580/480. Neurobiology of Developmental Disorders Prerequisite: graduate standing (3 credits). This seminar and reading course is focused on cellular and molecular aspects of mammalian developmental neurobiology. Genetic and epigenetic principles underlying the emergence and maintenance of the mammalian nervous system will be explored in the context of human disorders that lead to structural brain abnormalities, intellectual disability and autism. The intent of this course is to present current topics in developmental neuroscience in the context of animal models and human diseases that have contributed to our understanding of the biochemical, molecular and cellular processes of brain development and function.
IMMUNO 440. Human Immunology Prerequisite: BIOLOGY 172 recommended (3 credits). This upper-level course will provide a broad overview of the rapidly advancing field of modern immunology in both the basic and clinical sciences. Topics to be covered include: Cells and Organs of the Immune System, Generation of T-Cell and B-Cell Responses, Immune Effector Mechanisms (including cellular and antibody-mediated responses), and The Immune System in Health and Disease (including AIDS and other immuno-deficiencies, immune responses to infectious diseases, vaccines, transplantation and cancer immunology and autoimmunity).
IMMUNO 850. Experimental Immuniology Prerequisite: graduate standing (3 credits). Literature based immunology techniques course aimed at providing first year students with an understanding of the theory and application of common tools used in immunology.
KINESLGY 422. Motor Learning Prerequisite: MOVESCI 320 (3 credits). An introduction to the behavioral and neurobiological basis of adaptation and motor learning. Evidence from behavioral and neuroimaging studies across beginners and expert performers will be considered with an emphasis on leveraging motor learning in rehabilitation of clinical populations. This course will be of interest to students considering careers in rehabilitation or other health-related fields.
KINESLGY 423. Sensorimotor Development Prerequisite: Graduate status; MOVESCI 320 or permission of instructor (3 credits). The purpose of this course is to study major concepts and principles fundamental to the development of sensorimotor behavior from fetal to late childhood. The overall question for this class is: How and why patterns of motor behavior change? We will study subsystems that affect behavior in real time and over developmental time. This course is intended for pediatric practitioners as well as people interested in basic science issues. We will study the origins of new motor patterns as well as the improvement of motor performance with special emphasis in the development of the nervous system from fetal to early childhood life. We will discuss observable and 'classic' changes in motor skill that occur over time, and we will examine and discuss methods to assess motor performance.
KINESLGY 427. Mind and Brain of Expertise Prerequisite: MOVESCI 320 (3 credits). This class will examine characteristics of expertise in athletics, arts, and academics. We will focus on behavioral and brain differences between experts (athletes, musicians, chess players, etc.) and non-experts, and will engage in the nature versus nurture debate.
KINESLGY 435. Biomechanics of Human Locomotion Prerequisite: Graduate status; MOVESCI 330 or permission of instructor (3 credits). The focus of the course is on understanding how humans walk and run. Topics will include kinematics, kinetics, neuromuscular activation patterns, energetics, and musculotendon mechanics. This course is taught in a Problem-Based Learning format, requiring students to integrate knowledge of muscle physiology, neuroscience, and biomechanics to analyze normal and pathologic human locomotion. Specific projects that students may work on include clinical gait analysis, lower limb prostheses, legged robots, and human exoskeletons.
KINESLGY 443. Exercise and Succesful Aging Prerequisite: graduate standing, MOVESCI 340 or permission of instructor (3 credits). The objectives of the course are to examine three themes: (1) the role that neural and genetic programmed changes in hormone action and cumulative tissue damage and deterioration play in aging, (2) the environmental, social, and life-style determinants of aging, and (3) nutritional, exercise, and psycho-social strategies for successful aging.
KINESLGY 522. Clinical Neurophysiology Lab Prerequisite: Advisory: MOVESCI 320 (3 credits). This course is an introduction to neuroimaging techniques commonly used in neuroscience research. Techniques will be discussed in light of the study of clinical neurophysiology and neuroplasticity associated with motor control and learning deficits.
KINESLGY 533. Neuromechanics Prerequisite: Graduate standing (3 credits). This course focuses on interaction of the nervous and musculoskeletal systems during human and animal movement with a focus on basic biological and engineering principles. Topics will include neuromechanical control of movement, neurorehabilitation, biorobotics, and computer simulations of neuromechanical systems.
MATH 417. Matrix Algebra I Prerequisite: 3 mathematics courses beyond MATH 110 (3 credits). This course is an introduction to the properties of and operations on matrices with a wide variety of applications. The main emphasis is on concepts and problem-solving, but students are responsible for some of the underlying theory. Diversity rather than depth of applications is stressed. Topics include matrix operations, echelon form, general solutions of systems of linear equations, vector spaces and subspaces, linear independence and bases, linear transformations, determinants, orthogonality, characteristic polynomials, Eigenvalues and Eigenvectors, and similarity theory.
MATH 559 Computational and Mathematical Neuroscience Prerequisite: MATH 451, and 217, 419, or 420 (3 credits). Computational neuroscience investigates the brain at many different levels, from single cell activity, to small local network computation, to the dynamics of large neuronal populations. As such, this course introduces students to modeling and quantitative techniques used to investigate neural activity at these different levels.
MCDB 421. Neuropigenetics/Regeneration of Sensory Systems Prerequisite: BIOLOGY 225 and PSYCH 230 or NEUROSCI 601 (3 credits). Have you ever wondered how life experiences are translated into changes in the DNA and how these in turn affect behavior? Most of us know that a genome is the blueprint used to build and maintain an organism. While genomes are in fact hidden inside cells, they are also influenced by the “experience” of cells and organisms. These experiences, which come in the many forms, from diet to pollutants to stress, alter the chemical nature of the genome, and in turn, its function. This is particularly crucial in the brain, as its function is linked to behavior. This class will cross the lines between neuroscience, molecular biology and epigenetics to uncover the effect of the environment and life experience on brain function and behavior. We will first examine how genes determine complex behaviors, and then analyze in depth how ancestral dietary stress, maternal behavior, social stress, and more, affect gene expression to contribute to brain function and dysfunction.
MCDB 422. Brain Development, Plasticity, and Circuits Prerequisite: MCDB 310 or 311, or BIOLCHEM 415, or CHEM 351; or graduate standing ( 3 credits). The course will present studies investigating the molecular and cellular analysis of the development of the nervous system, synaptic plasticity, and circuits mediating complex behaviors.
MCDB 424. Behavioral Neurobiology Lab Prerequisite: BIOLOGY 225 or PSYCH 230 and BIOLOGY 173. The goal of the course is to provide students with fundamental concepts focused on the neurobiological basis of animal behavior. Throughout the term, students will explore a range of behaviors in Drosophila, each of which will be associated with different experimental techniques currently used in the field.
MCDB 450. Genetics and Molecular Biology of Complex Behavior Prerequisite: BIOLOGY 222 or 225; BIOLOGY 305; and, one of: MCDB 310, BIOLCHEM 415, or CHEM 351 ( 3 credits). This course explores recent advances inthe genetics and molecular biology of brain function and complex behavior. It emphasizes advances due to the application of genetic strategies that uncovered molecules important for complex behavior and brain function in organisms amenable to genetic analysis such as Drosophila, C. elegans, zebrafish and mice. The lectures introduce the basics of the field including various genetic and transgenic methods as applied to behavior and cutting edge molecular and imaging strategies for neural circuit analysis. Discussions involve the presentation of relevant research papers and research proposals based upon the knowledge gained from the course by each student.
MCDB 453. Ion Channels and their Channelpathies Prerequisite: BIOLOGY 225 (3 credits). How are brain states, such as sleep and wakefulness, attention, and motivation generated? How do these states affect sensory processing and behavior? How are memories encoded and stored, and how do brain states affect these processes? This course provides students with an overview of recent studies using electrophysiological, genetic, and behavioral techniques aimed at answering these questions.
MCDB 456. Genes, Circuits, and Behavior Prerequisite: BIOLOGY 222 or 225 or MCDB 422; and BIOLOGY 305 (3 credits). Newly developed methods in genetics, live-imaging, and neuroanatomy are rapidly expanding our understanding of how genetically defined neural circuits function within the nervous system to shape complex behavior. In genetically tractable model systems, both vertebrate and invertebrate, it is now possible to address the ways in which gene function, neural connectivity, and neurophysiology cooperate to determine overt animal behavior. This course is designed to provide students with an in-depth introduction to the neurobiology of model organisms that have made significant contributions toward the mechanistic understanding of brain function and behavior.
MCDB 457. Neurobiology of Sexual and Aggressive Behaviors Prerequisites: BIOLOGY 225, or PSYCH 230 (advisory) BIOLOGY 305 (3 credits). This course explores behavioral neuroscience through guided reading and discussion of recent scientific literature involving research in two “opposite” behaviors, sexual courtship and aggression. Both courtship and aggression are complex social behaviors that are highly conserved across species. Although some of their features are species-specific, there are broad similarities throughout the animal kingdom. Complex interactions between genes, environmental signals, and hormones influence the development and manifestation of these behaviors, but the core circuitries involved appear to be pre-wired in the nervous system, as animals with no previous social experience can engage in normal encounters using stereotypical behavioral patterns. The study of innate social behaviors in genetically tractable organisms offers unique opportunities to identify the underlying neuronal circuitry, understand how this circuitry is genetically specified and elucidate the contributions of neuronal sexual dimorphism to these behaviors. The class is based on students’ presentations and group discussions and it is designed to be informal and highly interactive. The main goal of the course is to help strengthen the ability to critically read works of experimental neuroscience and propose hypotheses and experiments to test them.
MCDB 459. Brain States and Behavior Prerequisites: BIOLOGY 225, (advisory) BIOLOGY 305, MCDB 351 or 352 (3 credits). How are brain states, such as sleep and wakefulness, attention, and motivation generated? How do these states affect sensory processing and behavior? How are memories encoded and stored, and how do brain states affect these processes? This course provides students with an overview of recent studies using electrophysiological, genetic, and behavioral techniques aimed at answering these questions.
MCDB 800. Biology Seminar: Neuronal Plasticity and Regeneration Prerequisite: graduate standing. (1 credit) A graduate seminar course providing opportunity to discuss current work and new developments in Molecular, Cellular, and Developmental Biology.
MCDB 801. Supervised Teaching Prerequisite: graduate standing and permission of instructor, appointment as Teaching Assistant in Biology. (1 credit) Seminars, demonstrations, and orientation for college teaching in biology. Available for all pre-candidate teaching assistants
MEDECHEM 500. Principles of Drug Action I Prerequisite: First Year PharmD Students(advisory) (3 credits). This course introduces the concepts required to understand drugs as organic chemicals whose biological activities derive from their chemical structures and physicochemical properties, including drug metabolism, signal transduction and drug-receptor interactions. The course continues with a survey of different analytical methods used to assay pharmaceuticals.
PATH 581. Tissue, Cellular and Molecular Basis of Disease Prerequisite: Biochem 580, Path 580, Anat. 530, Hum Gen. 541; or Equivalent. This course introduces to basic pathophysiologic mechanisms, the molecular basis for disease and the morphologic expression of disease. The course will begin with a review of normal histology and then focus on a rigorous presentation of cellular and molecular mechanisms which appear to be common to a number of diseases including cell response and injury, inflammation and immunity, infectious disease, disturbance of the circulation and neoplasia. Specific prototypic disease entities are then presented within the context of these mechanisms and the molecular events that govern their induction and maintenance. The course is presented in lec lab format, with the lab consisting of the examination of glass slides.
PHARMACOL 502. Intro to Scientific Communications Prerequisite: Must be in the second year or higher of a PIBS-related graduate program. Winter term (2 credits). This course introduces graduate students to essential scientific communication skills. Beginning with the relatively easy task of learning to search the literature over the internet and ending with the challenges of writing an NRSA grant application and giving a short seminar, each student will develop confidence in both written and spoken scientific communication. Class meetings alternate between presentations by local experts on various topics and student presentations of their work in progress. In-depth analysis of student writing and presentation skills will be provided in class by the instructor, by other students working in small groups, as well as by guest scientists.Through a series of assignments, each student will write a grant over the course of the semester on a topic of his or her choice. By the end of the term each student will have polished and revised the proposal to a high quality product that will be presented both orally and in written form to the rest of the class. Finally, each student will participate in a mock study section to constructively evaluate each other's grants.
PHARMACOL 601. From Molecules to Patients: Basic Quantitative Principles of Pharmacology This course examines the fundamental principles of pharmacology and their quantitative treatment as a basis for understanding the properties and mechanism of action of drugs. The course is aimed at, but not limited to students of Pharmacology, Medicinal Chemistry, Biological Chemistry, Chemical Biology, Toxicology, Bioinformatics, Bioengineering, Pharmaceutical Sciences, Pharmaceutical Engineering and Psychology.
Pre-requisites: Students enrolling in the course should have a good biochemistry and/or physiology background or permission of the instructor.
PHARMACOL 614. Seminar in Autonomic Pharmacology (3 credits)
PHARMACOL 615. Seminars in Molecular Neuropharmacology Prerequisite: Biochemistry. (2 credits) Pharmacology 615 uses a combination of textbook and literature readings and class discussions to present students with a study of central nervous system molecular neuropharmacology and neurochemistry. Topics will include neurotransmitters in the central nervous system and drugs used therapeutically in the central nervous system.
PHARMACOL 617. Seminars in Endocrine Pharmacology Prerequisite: Permission of Instructor (2 credits). This course is designed to provide the student with an exposure to endocrine pharmacology, with a major emphasis on the feedback mechanisms within the endocrine system that are responsible for the maintenance of normal endocrine function as well as the interventions necessary to correct disorders stemming from hormonal imbalances. Emphasis is also placed on the development of drug (hormone) therapy in treating endocrine disorders and still maintaining essential hormonal and metabolic feedback relationships.
PHARMACOL 621. Translational Pharmacology Prerequisite: Basic knowledge of pharmacologic principles and permission of instructor. (2 credits) This course will acquaint students with drug development, from the discovery process through clinical trials and FDA approval. Topics will include development and evaluation of pharmacologic targets, drug testing in animal models, clinical trial design and evaluation, statistical methods, and filing a new drug application.
PHYSIOL 502. Human Physiology Prerequisite: introduction to biology and biochemistry (4 credits). PHYSIOL 502 is an introductory graduate / advanced undergraduate course that covers the basic principles of cell physiology and the functions of the major organ systems. The course, which is 4 credit hours, is given in the winter term every year.
PHSYIOL 510. Systems & Integrative Physiology Prerequisite: Inorganic and organic chemistry; undergraduate course work in biology. (4 credits) This course addresses major principles of how the various physiological systems of the body function, both individually and as an integrated unit. The first part of the course deals with principles of physiological communication as it relates to homeostasis, biological rhythms, and both neural and endocrine communication. This is followed by consideration of various physiological regulatory systems including muscle, cardiovascular, respiratory, renal, gastrointestinal and reproductive physiology.
PHYSIOL 520/BIOINF 520. Computational Systems Biology in Physiology Prerequisite: one year of biology, an introductory course in calculus is desired but not essential. (3 credits) This course is an introduction to dynamic modeling in physiology for both experimentally and theoretically inclined students. We use selected physiological systems to introduce concepts in computational systems biology. This is done through the use of increasingly more complex cellular functions modeled with scientific software.
PHYSIOL 555. Integrative Genomics Prerequisite: none. The recent completion of the human genome opens the door to exciting new opportunities in the biomedical sciences. Integrative Genomics focuses on the study of functional biology in genetically engineered animal models. An appreciation of genetic variables, including gender and genetic background, biological variables, including organ function and issues relating to aging, and environmental variables, including, nutrition, exercise, stress, and pathogens is a central feature of the class. It is the study of the inherent complexities of genes, biology, and environment in animals that forms the unique underpinnings of the exciting new field of Integrative Genomics. The course features limited class size, and faculty from several different departments in the Medical School. Unique educational features of the class include student developed grants, oral presentations, and student-led study section evaluations of grants.
PHYSIOL 576. Signal Transduction Prerequisite: Two terms of organic chemistry; BIOLCHEM 415 or 451/452. Physical Chemistry is strongly recommended. (1 credit) A review of hormone and neurotransmitter receptors as well as the cellular effectors that are regulated by receptor activation. Oncogene products as signal transducers and the interaction of the known signaling pathways are also covered. The various techniques used to study signal transduction as well as important experimental strategies employing these techniques will also be presented.
PHYSIOL 591. Special Topics in Signal Transduction Prerequisite: NS (4 credits). An introductory course designed to acquaint students with the principles of human body function. Topics discussed include cell structure, function, and chemical composition and the functions of nerves, muscles, the lungs, heart, blood vessels, kidneys, digestive tract, endocrine glands, brain, and reproductive organs. Emphasis is placed upon the mechanisms by which cells and organs perform their functions and the interaction of the various organs in maintaining total body function. Four one-hour lectures and one hour discussion each week.
PHYSIOL 592. Integrative Neuroscience Prerequisite: Permission of instructor (2-4 credits). This is a survey course in integrative neuroscience intended for early stage graduate students or advanced undergraduates seeking broad exposure to the field of neuroscience.
PHYSIOL 600. Pathophysiology Prerequisite: Physiology 502 or equivalent ( 3 credits). This course focuses on understanding the link between altered structure and function and onset and progression of disease. Topics will include (but not be limited to) dysfunction and disorders of the skeletal muscle, cardiovascular system, respiratory system, gastrointestinal system, renal system, and hormonal systems (e.g., diabetes mellitus).
PIBS 721. Professional Research Presentation Prerequisite: None (3 credits). This course builds skills in written, visual, and oral communication, focusing mainly on professional scientific presentations. Students will create an elevator pitch, abstract, poster, 90-second "data blast," and 15-minute talk describing their own research. Students will present their work to their peers and will give and receive constructive feedback.
PSYCH 430. Advanced Topics in Biopsychology Prerequisite: PSYCH 230 or PSYCH 335 (3 credits). This course is designed to provide students, in a seminar setting, with an understanding of the process of brain development from embryogenesis through adulthood, with an emphasis on the role of the environment in directing this process. Topics to be covered include the origins of the central nervous system (including neurogenesis, cellular differentiation, synapse formation and refinement), the role of early experiences in modifying brain function (e.g., gene-environment interactions, epigenetic programming), and how changes in the developing nervous system lead to behavioral patterns in infancy and adulthood.
PSYCH 433. Advanced Topics in Neuroscience Prerequisite: BIOLOGY 225 or PSYCH 230 (3 credits). This Neuroscience course will explore recent research findings related to brain representation of behavior. The main Psychological themes to be studied will be movement and incentives for action. Relevant clinical findings will inform the discussions.
PSYCH 440. Advanced Topics in Cognitive Neuroscience Prerequisite: PSYCH 240 (3 credits). This course examines the biological underpinnings of various psychological phenomena. The first one-third of the course is devoted to lectures and readings about functional neuroimaging, concentrating especially on functional magnetic resonance imaging. Thereafter, students will make formal presentations that are based on primary empirical articles that will be assigned and that students will search out themselves.
PSYCH 447. Advanced Topics in Cognition and Cognitive Neuroscience Prerequisite: PSYCH 230, 240, 345 (3 credits). Understanding consciousness is one of the great unsolved problems in psychology. This course focuses on the scientific study of consciousness, where research has increased dramatically in recent years. We begin by considering the conceptual and philosophical underpinnings of such research, which profoundly influence their methods and interpretation.
PSYCH 531. Advanced Topics in Biopsychology Prerequisite: Psych 230 (3 credits). This course will, in a lecture setting, present topics of special interest to students and faculty. Current faculty research is addressed. Topics will vary according to the specific faculty research interest.
PSYCH 613. Advanced Statistical Methods Prerequisite: One previous course in Statistics. Graduate standing and permission of instructor. (4 credits) This is a two-term course (with PSYCH 614 in the Winter term). PSYCH 613 is a prerequisite for PSYCH 614. Students will gain experience by analyzing data and gain an appreciation for the rationale underlying the standard statistical procedures used in psychological research. Topics covered throughout the year include analysis of variance, regression, factor analysis, multidimensional scaling, and clustering.
PSYCH 614 Advanced Statistical Methods Prerequisite: PSYCH 613, graduate standing, permission of instructor (4 credits). Topics covered in this course include multidimensional scaling, cluster analysis, principal components, factor analysis, multivariate analysis of variance and canonical correlation. A brief introduction to reliability theory, structural equations modeling and hierarchical linear modeling will also be provided
PSYCH 644 Computational Modeling of Cognition Prerequisite: graduate standing (2-4 credits). This course will examine computational models of human cognitive processes.
PSYCH 731. Drugs of Abuse Prerequisite: graduate standing in Psychology or approved joint programs (3 credits). This combination lecture/seminar course provides a basic introduction to the neuropsychopharmacology of drug abuse and addiction, and has a strong natural science (neuroscience) orientation. The acute and long-term effects of selected drugs of abuse on behavior, mood, cognition, and neuronal function are discussed, and material from studies with humans is integrated with basic studies on the neurobiological basis of drug action and drug abuse — including synaptic transmission and the distribution, regulation, and integration of brain neurotransmitter systems. The focus is on addictive or illicit drugs, and all the major classes are discussed, including: opiates (heroin, morphine, opium), sedative-hypnotics (alcohol, barbituates, chloral hydrate), anxiolytics (benzodiazepines), psychomotor stimulants (amphetamine, cocaine), marijuana, hallucinogens (LSD, mescaline), hallucinogenic-stimulants (MDA, MDMA), and dissociative anaesthetics (PCP).
PSYCH 743. Human Learning and Memory Prerequisite: graduate standing in Psychology or approved joint programs and instructor permission (3 credits).
PSYCH 808. Seminar: Physiological Measurement in Behavioral Studies (3 credits) Seminar Topics
PSYCH 808. Special Seminar: Section 008, Teaching Academy Prerequisite: graduate standing. (1 credit) A seminar on special topics in psychology. Content varies by term and instructor.
PSYCH 840. Intro to Functional MRI Prerequisite: graduate standing, introductory statistics course; advanced statistics course and experience with Matlab will be an asset. (3 credits) This course will present the basic skills to design and analyze functional magnetic resonance imaging (fMRI) experiments. At the end of the course a student should be able to design, acquire and analyze a fMRI study. There are four modules of the course: Computer skills, Physics of fMRI, Experimental Design, and Statistics. We start with reviewing the basic skills necessary to manipulate image data, using Mat lab and the Unix operating system. Next we introduce the basics of MRI, principals of T1, T2 and T2*, and how images are formed. In the experimental design section we intorduce blocked and event-related designs, and how to create designs with optimal statistical power. We start the statistics section with a review of the basics of hypothesis testing and linear regression, then present the statistical tools specific to neuroimaging.
PUBPOL 650. Intro to Science and Technology Policy Analysis Prerequisite: graduate standing. (3 credits) As it exposes students to the landscape of science and technology policymaking in the US and abroad, this course introduces theories and methodologies for science and technology policy analysis, with literature drawn from a range of disciplines, including political science, economics, sociology, and history. Students will learn about the politics of science and technology policy, and how research funding decisions and regulations are made, with specific attention to the roles of government agencies, expert advisory committees, private industry, and the public. They will also gain tools for science and technology policy analysis, including research funding allocation methods, technology impact assessment, innovation theory, and deliberative democratic engagement.
STATS 531. Analysis of Time Series Prerequisite: ECON 600, 671, and 672 or STATS 610 or 611. (3 credits) Decomposition of series; trends and regression as a special case of time series; cyclic components; smoothing techniques; the variate difference method; representations including spectrogram, periodogram, etc.; stochastic difference equations, autoregressive schemes, moving averages; large sample inference and prediction; covariance structure and spectral densities; hypothesis testing and estimation and applications and other topics.
WRITING 993. Graduate Student Instructor Training: Teaching Writing in the Disciplines Prerequisite: graduate standing. (1 credit) This course is a hands-on workshop for Graduate Student Instructors (GSIs) teaching and grading Upper-Level Writing Requirement. This course is mandatory for GSIs working in these courses but may be elected with permission by other GSIs interested in the course. Topics include Upper-Level Writing Requirement course standards, writing assignment design, English as a Second Language, responding to student writing, and conferencing with students.