Course List

For a complete listing of course schedules by semester, see Banner, Brown's course registration system. (Please note that biology courses are listed under "BioMed - Biology.")

Fall Course Offerings

Quantitative Approaches in Biology (BIOL 2010) Graduate level introduction to quantitative and computational methods in modern biology. Topics include Programming, Modeling, Algorithms, Bioinformatics, Applied Statistics, Structural Biology, Molecular Dynamics, Enzyme Kinetics, and Population and Quantitative Human Genetics. Preference is given to graduate students in Molecular Biology, Cell Biology and Biochemistry and Molecular Pharmacology, Physiology, and Biotechnology. Limited to 20 students. Instructor permission required.

Foundations for Advanced Studies in Experimental Biology (BIOL 2030)
A double-credit graduate course on multidisciplinary experimental approaches to biological questions. Focusing on primary literature, the mechanism and regulation of basic cellular processes involving nucleic acids (synthesis, structure, maintenance and transmission) and proteins (synthesis, maturation, function) and their integration into more complex events (signaling, organelle biogenesis and inheritance, and cell cycle control) will be presented. Discussion sections complement lectures.

Biology of the Eukaryotic Cell (BIOL 2050)
No description available.

Topics in Biochemistry (BIOL 2210)
No description available.

Advanced Biochemistry (BIOL 2270)
No description available.

Protein Processing and Trafficking (BIOL 2280)
Explores the emerging concepts on protein trafficking, intracellular sorting and post-translational processing. Other topics are vesicular transport, exocytosis and endocytosis; sorting signals and granule membrane targeting; receptor-mediated endocytosis and lysosomal transport. Formal lectures, plus seminars presented by students on topics in the current literature. Prerequisites: Course in cell biology. and/or biochemistry. For graduate students and qualified undergraduates with permission.

Genetic Control of Cell Fate Decisions (BIOL 2320)
We will explore mechanisms underlying how neuronal cell fates are established during development and how the understanding of this process may provide insight into neurological disease and therapeutic intervention. Topics: Temporal identity in neuroblast and cerebral cortex cell fate specification, transcriptional control of lineage decisions in the spinal cord, the role of morphogen concentration and timing on cell fate decisions, micro RNA control of gene regulation, epigenetics, induced pluripotent stem cells, stem cell use in therapeutic approaches to intervene in neurological diseases. Primary literature will be discussed in lectures in the format of student-led, faculty-guided discussions. Enrollment limited to 20. Instructor permission required.

DNA Replication, Recombination & Repair (BIOL 2480)
Emphasizes critical reading and discussion of the primary literature as it relates to DNA transactions such as DNA replication and recombination in prokaryotic and eukaryotic cells. Class participation and oral presentations will be required and the basis for course grade determination. Topics of discussion will cover diverse model systems and may include: Epigenetic Regulation Via Chromatin Remodeling and Modification; Mechanisms of DNA Replication, Recombination and Repair; Transcriptional Regulation; Structural Basis of Epigenetic Regulation; RNA interference and anti-viral therapeutics; Trinucleotide Repeat Expansions and Neurological Disease; and Mechanisms of Vertebrate Development. The course is open to graduate students; advanced undergraduates with permission of the instructor. Class will meet one, three hour period per week; to be arranged.

Advanced Topics in Microbiology and Immunology (BIOL 2640)
Viral Immunology is an advanced topics course in Microbiology and Immunology which will be focused on viral immunology. Weekly meetings will cover different issues concerning defense against viral infections and pathology related to viral infection, with focus on viral-host interactions. Topics will be selected to present either important basic concepts in the context of immune responses and/or major challenges in controlling viral infections. Recent advances in understanding virus-host interactions, host responses to viruses, cytokine regulation of immune responses or cytokine-mediated pathology during viral infections will be emphasized.

Topics in Pathobiology (BIOL 2830)
Based on readings from current research literature that focus on selected topics in pathobiology. Topics for discussion rotate each semester among four general areas of pathobiological research: the molecular basis of disease, carcinogenesis, environmental pathology, and immunopathology. Includes presentations by faculty members, student presentations, and general discussions of research literature.

Molecular Mechanisms of Disease (BIOL 2860)
Examines research and modern techniques, emphasizing infectious disease and environmental exposures correlating histopathology with molecular pathogenesis: cell injury, inflammation, thrombosis and vascular disease, cancer, and toxicology. Based on BIOL 1860 lectures plus discussion section. Expected: BIOL 1290, 2050 (other 1000-level biology course with approval). Textbook plus primary lecture. Required for Pathobiology graduate students, written permission for other graduate or MPH students.

Methods of Applied Mathematics I, II (APMA 0330/0350)
Mathematical techniques involving differential equations used in the analysis of physical, biological and economic phenomena. Emphasis on the use of established methods, rather than rigorous foundations. I: First and second order differential equations. II: Applications of linear algebra to systems of equations; numerical methods; nonlinear problems and stability; introduction to partial differential equations; introduction to statistics. Prerequisite: MATH 0100, 0170, 0180, 0190, 0200, or 0350, or AP68 or AP68 for a minimum score of 5.

Quantitative Models of Biological Systems (APMA 1070)
An introduction to the use of quantitative modeling techniques in solving problems in biology. Each year one major biological area is explored in detail from a modeling perspective. The particular topic will vary from year to year. Mathematical techniques will be discussed as they arise in the context of biological problems. Prerequisites: introductory level biology, APMA 0330, 0340 or 0350, 0360, or written permission. Offered in alternate years.

Statistical Inference (APMA 1650)
APMA 1650 begins an integrated first course in mathematical statistics. The first half of APMA 1650 covers probability and the last half is statistics, integrated with its probabilistic foundation. Specific topics include probability spaces, discrete and continuous random variables, methods for parameter estimation, confidence intervals, and hypothesis testing. Prerequisite: MATH 0100, 0170, 0180, 0190, 0200, or 0350.

Virtual Reality Design for Science (CSCI 1370)
Explores the visual and human-computer interaction design process for scientific applications in Brown's immersive virtual reality Cave. Joint with RISD. Computer Science and design students learn how to work together effectively; study the process of design; learn about scientific problems; create designs applications; critique, evaluate, realize and iterate designs; and demonstrate final projects. Instructor permission required.

Computational Molecular Biology (CSCI 1810)
Processing molecular biology data (DNA, RNA, proteins) has become central to biological research and a challenge for science research. Important objectives are molecular sequence analysis, recognition of genes and regulatory elements, molecular evolution, protein structure, comparative genomics. This course models the underlying biology in the terms of computer science and presents the most significant algorithms of molecular computational biology. Prerequisites: CSCI 0160, CSCI 0180 or CSCI 0190, and CSCI 0220, or consent of instructor.

Special Topics in Computer Science (CSCI 2950)
This course will investigate active and emerging research areas in computational biology. Topics include cancer genomics; genome rearrangements and assembly; and protein and regulatory interaction networks. The course will be a mixture of lectures and student presentations of recent conference and journal papers.

Neuropharmacology and Synaptic Transmission (NEUR 1670)
Synaptic transmission will be studied from a biochemical and pharmacological point of view. We will explore the factors regulating neurotransmitter synthesis, storage, release, receptor interaction, and termination of action. Proposed mechanisms of psychoactive drugs and biochemical theories of psychiatric disorders will be examined. Prerequisites: NEUR 0010 and BIOL 0200 or the equivalent.

Advanced Molecular and Cellular Neurobiology I (NEUR 2030)
Focuses on molecular and cellular approaches used to study the CNS at the level of single molecules, individual cells and single synapses by concentrating on fundamental mechanisms of CNS information transfer, integration, and storage. Topics include biophysics of single channels, neural transmission and synaptic function. Enrollment limited to graduate students.

Introduction to Biostatistics (PHP 2500)
The first in a two-course series designed for students who seek to develop skills in biostatistical reasoning and data analysis. Offers an introduction to basic concepts and methods of statistics as applied to diverse problems in the health sciences. Methods for exploring and presenting data; direct and indirect standardization; probability; hypothesis testing; interval estimation; inference for means and proportions; simple linear regression, etc. Statistical computing is fully integrated into the course.

Spring Course Offerings

Current Topics in Biochemistry and Molecular Biology (BIOL 2200)
A critical evaluation of contemporary research in biochemistry, molecular biology, and structural biology. Intensive reading and discussion of the current literature, critical anaylsis, and student presentations in seminars.

Nuclear Hormone Receptors in Growth Differentiation & Disease (BIOL 2290B)
Key developmental and homeostatic hormones such as steroid hormones (e.g. estrogen, testosterone, glucocorticoids), and lipophilic non-steroids (e.g. retinoic acid, thyroid hormone) act through receptors that directly bind DNA and control gene expression. This course examines the activities, structures, functions, and mechanisms of action of these Nuclear Hormone Receptors and the consequences of alterations in protein or hormone function. Approaches span genetics, biochemistry, genomics, proteomics, and developmental biology.

Neuronal Signaling Meets the RNA World (BIOL 2290C)
The concept of one gene, one protein is nowhere more violated than in protein encoding genes expressed in the nervous system. We will cover a variety of post-transcriptional processing events which serve to generate protein diversity in the nervous system including alternative splicing, trans-splicing, and RNA editing. We will also address non-coding RNAs and their roles, in particular, in regulating nervous system function. Since it is clear that nervous system complexity is not a function of gene number across large phylogenetic distances, the course will be aimed at instilling a greater understanding of how the regulation of shared "toolkit" genes results in organismal complexity.

Analysis of Development (BIOL 2310)
No description available

Systems Biology in the Study of Development and Evolution (BIOL 2320A)
We will explore mechanisms underlying how neuronal cell fates are established during development and how the understanding of this process may provide insight into neurological disease and therapeutic intervention. Topics: Temporal identity in neuroblast and cerebral cortex cell fate specification, transcriptional control of lineage decisions in the spinal cord, the role of morphogen concentration and timing on cell fate decisions, micro RNA control of gene regulation, epigenetics, induced pluripotent stem cells, stem cell use in therapeutic approaches to intervene in neurological diseases. Primary literature will be discussed in lectures in the format of student-led, faculty-guided discussions.

The Biology of Aging (BIOL 2320D)
Studying the mechanisms underlying the process of aging promises to be one of the next great frontiers in biomedical science. Understanding the biology of aging is important not only for the long-term possibility of increasing life span, but for the more immediate benefits it will have on age-related diseases. As demographics of industrialized countries have changed, age-related diseases such as cancer, cardiovascular disease, stroke, osteoporosis, arthritis and Alzheimer's disease have assumed epidemic proportions. A thorough understanding of the aging process is an important pre-requisite for designing rational therapeutic interventions for the treatment of these age-related disorders.
We will focus on examining the biology of aging primarily through the examination of studies of a molecular, cellular, genetic and demographic nature. Lectures and presentations are based on reading of the primary and secondary literature.

Dissection of Genetic & Molecular Mechanisms (BIOL 2480B)
The transfer of traits from one individual to another is a fundamental process in biology. In this course, we will explore the diversity of molecular mechanisms underlying phenotypic inheritance through a critical evaluation of primary literature, with special emphasis on the design and implementation of novel strategies to study these processes. For graduate students and advanced undergraduates with a strong background in genetics. Expected: BIOL 0470 and BIOL 1540. Written permission required for undergraduate.

Molecular Genetics (BIOL 2540)
No description available.

Molecular Pharmacology & Physiology Seminar (BIOL 2940)
Professional development seminar required of all students in the Molecular Pharmacology and Physiology graduate program, and open to others. Instruction in effective oral presentation skills, and current topics in molecular pharmacology and physiology, including research projects directed by program faculty, statistical methods of data analysis, techniques for assessing gene function, and an overview of research at Brown and available research funding sources. Students present and participate in research seminars or planned research. Instructor permission required for undergraduates.

Introduction to Multidisciplinary Fetal Medicine (BIOL 5720)
An 8-session elective seminar for 1st and 2nd year medical school and PLME students. Emphasis is placed on the multidisciplinary approach to medical problems. The course concentrates on those conditions for which fetal and/or neonatal intervention may be indicated, from gene therapy to fetal surgical intervention.

Inference in Genomics and Molecular Biology (APMA 1080)
Sequencing of genomes (human and other) has generated a massive quantity of fundamental data that is revolutionizing the life sciences. The focus of this course is on drawing traditional and Bayesian statistical inferences from these data, including: alignment of biopolymer sequences; prediction of their structures, regulatory signals, and compositional characteristics; significances in database searches; phylogeny; and functional genomics. Emphasis is on inferences of the discrete high dimensional objects that are common in this field. Statistical topics: parameter estimation, hypothesis testing and false discovery rates, statistical decision theory, and Bayesian posterior inference. Prerequisite: APMA 1650 or MATH 1610 or equivalent; BIOL 0200 or equivalent; and experience with Matlab or another programming language.

Intro to Mathematical Models in Computational Biology (AMPA 1940N)
This course is designed to introduce students to the use of mathematical models in biology as well as some more recent topics in computational biology. Mathematical techniques will involve difference equations and dynamical systems theory, ordinary differential equations and some partial differential equations. These techinques will be applied in the study of many biological applications such as: Difference Equations: population dynamics, red blood cell production, population genetics; (ii) Ordinary Differential Equations: predator-prey models, Lotka-Volterra model, modeling the evolution of the genome, heart beat model/cycle, tranmission dynamics of HIV and gonorrhea; (iii) Partial Differential Equations: tumor growth, modeling evolution of the genome, pattern formation. Prerequisites: AM 33 and 34 (APMA 0330 and 0340).

Algorithmic Foundations of Computational Biology (CSCI 1950)
The course is devoted to computational and statistical methods as well as software tools for DNA, RNA, and protein sequence analysis. The focus is on understanding the algorithmic and mathematical foundations of the methods, the design of associated genomics software tools, as well as on their applications. Topics include: sequence alignment, genome assembly, gene prediction, regulatory genomics, and SNP's variation. The course is open to computer and mathematcial sciences students as well as biological and medical students.

Advanced Molecular and Cellular Neurobiology II (NEUR 2040) Focuses on molecular and cellular approaches used to study the CNS at the level of single molecules, individual cells and single synapses by concentrating on fundamental mechanisms of CNS information transfer, integration, and storage. Topics include biophysics of single channels, neural transmission and synaptic function. Enrollment limited to graduate students.

Advanced Topics in Neuroscience (NEUR 2940)
No description available.

Selected Topics in Biological Physics (PHYS 2620F)
No description available.