GRAD > BIOL
Biology Courses
BIOL 506 Marine and Coastal Ecological Research +
Description:
This course emphasized supervised independent research into the adaptations and interactions of organisms of Nantucket's beaches, salt marshes, sand dunes, watershed, and embayments. Students will be exposed to tools, techniques and statistical analyses used in community ecology, oceanography and related fields. Individualized research projects have included in the past a wide variety of topics such as plant/animal interactions in the marsh, impact of nitrogen on marsh plants, and the impact of tidal cycles on plankton community dynamics. More Info
Offered in:- TBA
BIOL 514 Developmental Biology +
Description:
This course studies plant function with emphasis on nutrition, translocation, metabolism, signal transduction and gene expression, photosynthesis and respiration, hormonal controls during vegetative and reproductive growth, and responses to environmental signals and stresses. More Info
Offered in:BIOL 518 Neurobiology Lecture +
Description:
This course examines the nervous system, beginning at the membrane and cellular level and then moving on to the organization of sensory and motor systems. Special topics include the biological basis of various neurological and psychiatric diseases. More Info
Offered in:BIOL 523 Plant Physiology (Lecture only) +
Description:
A study of plant function with emphasis on nutrition, translocation, metabolism, signal transduction and gene expression, photosynthesis and respiration, hormonal controls during vegetative and reproductive growth, and responses to environmental signals and stresses. More Info
Offered in:- TBA
BIOL 529 Plant Life Lecture +
BIOL 533 Marine Invertebrates Lecture +
Description:
This course provides and essential background for those planning to concentrate in organismic biology, evolution, ecology, or applied environmental science. The course covers life histories, ecological roles, adaptations, morphologies, evolution, and classification of marine invertebrate animals. More Info
Offered in:- TBA
BIOL 534 Microbiology +
Description:
This course focuses on the study of viruses, bacteria, algae, fungi, and protozoa, to include their characterization, classification, and relationship to humans and the environment. Lecture topics include microbial biochemistry, cell biology, genetics, taxonomy, pathogenic bacteriology, food and industrial microbiology, and ecology. The laboratory emphasizes aseptic techniques to isolate, culture, observe, and identify bacteria. More Info
Offered in:BIOL 539 Comparative Animal Physiology +
Description:
This course considers physiological principles and problems in a phylogenetic perspective. An integrated view of physiological solutions from the cellular to organismal level is used to discuss adaptations to environments and constraints on life history. Major topics to be considered include temperature responses, biological clocks, allometry, respiration, circulation, energetics, locomotion, and salt and water balance. More Info
Offered in:- TBA
BIOL 540 Marine Mammal Biology +
Description:
This upper-level course covers the biologic ecology of marine mammals (Pinnipeds, Cetaceans, Sirenians) with emphasis on applied populations population ecology and conservation issues. Topics include adaptations to marine environments, effects of human exploitation, case studies of population recovery, and multispecies interactions. Many topics make use of mathematical equations. More Info
Offered in:- TBA
BIOL 542 Ecology Lecture +
Description:
This course studies population and community ecology. Topics include theory and case studies of population dynamics, competition, predation, niche concepts, life history strategies, behavioral interactions, energetics and productivity, community structure and organization, and biogeography. More Info
Offered in:BIOL 545L Biology in Society: Critical Thinking +
Description:
Current and historical cases are used to examine the political, ethical, and other social dimensions of the life sciences. Close examination of developments in the life sciences can lead to questions about the social influences shaping scientists' work or its application. This, in turn, can lead to new questions and alternative approaches for educators, biologists, health professionals, and concerned citizens. The specific thematic emphasis each semester is publicized by the Program. More Info
Offered in:- TBA
BIOL 552 Evolution (Lecture only) +
Description:
This course focuses on evolution as the unifying concept of biology. Topics include population genetics, adaptive strategies, sex and breeding systems, speciation and population differentiation, fossil histories, and the evolution of man. More Info
Offered in:BIOL 572 Molecular Biology (Lecture only) +
Description:
This course studies the molecular biology and biochemistry of gene expression in prokaryotes and eukaryotes. Topics include DNA structure/physical biochemistry, recombinant DNA technology, techniques in research, DNA synthesis, RNA synthesis, protein synthesis, operons, chromatin structure and gene regulation, oncogenes, hormones and growth factors and signal transductions, transposons, mutagenesis and repair, flowering, photosynthesis, development, circadian rhythms. More Info
Offered in:BIOL 580 Intro to Immunology Lecture +
Description:
This course is an introduction to the principles of immunology, including definition of antigens and antibodies, specificity of the immune response, immunoglobulin synthesis, cellular cooperation in the immune response, mechanism of inflammation, transplantation, and diseases associated with responsiveness of the immune system. More Info
Offered in:BIOL 607 Biostatistics and Experimental Design +
Description:
This course will cover the basic statistical knowledge necessary for students in biology to design, execute, and analyze a basic research project. The course aims to have students focus on thinking about the biological processes that they are studying in their research and how to translate them into statistical models. The course will take a hands-on computational approach, teaching students the statistical programming language R. In addition to teaching the fundamentals of data analysis, we will emphasize several key concepts of efficient computer programming that students can use in a variety of other areas outside of data analysis. More Info
Offered in:BIOL 609 Advanced Data Analysis for Biology +
Description:
This course will cover the advanced statistical modeling techniques needed for students investigating complex biological systems. The course aims to have students focus on thinking about the biological processes that they are studying in their research and how to translate them into statistical models of realistic complexity. This includes models that deal with autocorrelation, mixed models, multivariate Structural Equation Models with latent variables, and more. We will also emphasize Bayesian inferential techniques, as they have proven to be powerful and flexible in a wide variety of situations. They are also often philosophically aligned with scientists goals, perhaps more often than frequentist techniques. The course will take a hands-on computational approach, allowing students to first approach concepts theoretically, and then implement them in the programming language R. More Info
Offered in:BIOL 611 Epigenetics +
Description:
How does the environment inside and outside an organism impact gene expression and cellular behavior? The answer, to some degree, is epigenetic regulation: the regulation of gene expression by chromosomal modifications, rather than by altering the genetic code directly. In this graduate-level course we will start to answer this question in move detail, and in the context of development by studying the regulation and role of specific epigenetic mechanisms in patterning and tissue specification during embroyogenesis, regeneration, and disease. More Info
Offered in:- TBA
BIOL 612 Advanced Cell Biology +
Description:
The analysis of gene transfer and expression at the cellular level, including the nature of metabolic systems and the factors governing their regulation. More Info
Offered in:- TBA
BIOL 617 Biostatistics and Experimental Design Lab +
Description:
This lab will cover the practical application of statistical programming for data analysis in biology. As BIOL 607 itself focuses on the conceptual material surrounding experimental design, observational survey design, and the fundamentals of the analytic techniques required to analyze said experiments and surveys, this lab will focus instead on implementation of those technique. This lab is intended to be taken along with BIOL 607, to allow students to spend time developing mastery of programming and data analytic skills. It will stress computational techniques for how to deal with modern complex data sets, efficient computation, big data, and algorithmic approaches to likelihood and Bayesian statistical problems. See the lecture and lab website at http://biol607.github.io for more. More Info
Offered in:BIOL 625 Genomics and Biotechnology +
Description:
This course provides an overview of genomics and covers topics such as mapping genomes, acquiring genomes and annotating genomes. Students will critically assess the genome projects from various organisms. Special emphasis will be given to technologies that contribute to and stem from the advances in genome sciences, including principles of sequencing, computational tools for gene annotation, functional genomic tolls for systems genetics, and technologies for massively parallel analyses of gene function. The applications of these techniques to various areas of biology will also be presented. More Info
Offered in:BIOL 634 Methods in Phylogenetics and Macroevolutionary Analysis +
Description:
Evolutionary biology is unique in the biological sciences because it is, to a large extent, a historical discipline. In the absence of direct paleontological data one of the best resources we have for studying evolutionary history over very long timescales I phylogenetic biology. In the first part of this course, students will survey the theory and application of modern phylogeny inferences. In the second part of this course, students will learn the important theory and practical methods of phylogenetic comparative biology - the use of inferred trees in evolutionary inferences. This course will consist of a combined weekly lecture & computer lab; regular computer exercises; and two independent projects in which the students may use their own dataset or one obtained from an online data repository. More Info
Offered in:- TBA
BIOL 635 Population Genetics and Diversity +
Description:
A quantitative approach to the concept of populations and the evolutionary forces affecting them. The course analyzes the interactions among forces and the resulting dynamics of population structure. Toward the end of the semester, the course shifts its primary emphasis from lecture to discussion in order to cover current topics in population genetics. Topics include the theory and application of tools necessary for assaying genetic variation in natural populations, DNA fingerprinting in forensics, the evolution of sex, and the genetics of rare and endangered species. More Info
Offered in:BIOL 637 Climate Change: Mechanisms and Biological Impacts +
BIOL 638 Advanced Ecology +
Description:
Concepts of population and community ecology. Topics covered may include population dynamics, life history strategies, theory of r- and K-selection, competition, predation, community organization, and species diversity. Particular emphasis is placed on the relationship between theoretical and empirical ecology. A weekly tutorial provides the opportunity for greater discussion of material covered in lecture. Emphasis changes from year to year. More Info
Offered in:BIOL 639 Conservation Biology +
Description:
The principles of conservation biology are drawn from such various subdisciplines of biology as ecology, genetics, evolution, and biogeography. The course begins with an analysis of the distribution of biodiversity, proceeds to examine the patterns of biodiversity loss at all levels, from genes to ecosystems, and finishes with a discussion of the causes, consequences, and solutions of the crisis. Topics include assessment and monitoring of species diversity, conservation genetics, the theory of island biogeography, habitat loss and forest fragmentation, human impacts on biodiversity, the design of nature reserves, economic valuation of biodiversity, and sustainable use of biodiversity. More Info
Offered in:- TBA
BIOL 646 Disease Ecology +
Description:
This graduate lecture course will focus on current ecological theory in disease ecology. Ecological and evolutionary topics discussed in class will partially represent student interests and may include core microbiome analysis, evolution of symbiosis, comparative germ-free and gnotobiotic studies, historical contingency and co-infection in symbiont establishment, host development and colonization resistance, immunomics, or host immunity vs environmental determinants of symbiotic communities. This lecture course will be taught alongside the optional data analysis lab course, BIOL 647. Students can sign up for either course separately or both together. More Info
Offered in:- TBA
BIOL 647 Data Analysis for Disease Ecology +
Description:
Next-generation sequencing data are becoming an integral part of disease ecology. For targeted amplicon sequencing to transcriptomics and metagenomics, these robust datasets can transform our understanding of host-pathogen interactions in complex environments. In particular, microbiomes are increasingly being studied for their symbiotic relationships with hosts, influence on host-pathogen dynamics, and their role in ecosystem processes. Analysis of these data requires the use of a suite of bioinformatics pipelines and analysis tools. In this workshop style class students will gain hands-on experience with next generation datasets. The focus will be on analysis of microbiome data, but can be applied in broader contexts to other data from next-generation sequencing from targeted amplicon sequencing to shotgun transcriptomics and metagenomics. Special topics will range from calculation and analysis of alpha and beta diversity to co-occurrence analysis, and from differential abundance analysis to complex multivariate statistics for time series data. Students will be given the opportunity to work with their own data as well as instructor-provided tutorial data and gain experience with QIIME2, R as well as other command line tools. This lab will be taught alongside the optional graduate seminar BIOL 646. Students can sign up for either course separately or both together. More Info
Offered in:- TBA
BIOL 649 Responsible Conduct of Research +
Description:
The overall goals of this course are to: a) sensitize students to and stimulate their interest in ethical issues that arise in biomedical and biological research; b) introduce students to best practices, guidelines and expectations, and available resources regarding the responsible conduct of science; and c) foster critical thinking skills as applied to ethical decision making in research. Topics include bias and objectivity in research, authorship and peer review, competing interests in research, research data and intellectual property, scientific record keeping, and mentor-mentee relationships. More Info
Offered in:BIOL 650 Scientific Communication +
Description:
Required of all master's and doctoral students; usually taken in the second year. The course covers the storage and retrieval of scientific information (including searching of computerized data bases), the design of tables, figures, and other graphics, the writing of technical reports and papers, and the preparation of posters and publications. Writing, oral presentations and other assignments, and attendance at the weekly departmental seminar, are required. More Info
Offered in:BIOL 652 Biological Diversity and Evolution +
Description:
This course is an inquiry into the origin and evolution of patterns of biological diversity. It begins with an overview of the biogeochemical history of the Earth, theories of origin of life, diversification of metazoans during the Panerozoic, and the nature and causes of periodic mass extinction events. Biological diversity is considered at molecular, population, and community levels. More Info
Offered in:BIOL 653 Current Literature in Biology +
Description:
A series of one-credit seminar courses focusing on subfields of environmental biology, to help students develop the habit of keeping up with recent developments through reading scientific journals. The seminars also provide a forum for oral presentations where students can get comment and critique on their scientific progress. Students must take a minimum of five seminars, for a total of five credits. This course is part of the required core in both the Environmental Sciences/Environmental Biology and MCOB PhD tracks. More Info
Offered in:BIOL 654 Sustainability Science: Environment, Economy and Equity +
Description:
Sustainability science is an emerging field combining tools from biology, ecology, evolution, economics and sociology (as well as political science, history and philosophy) to address complex problems of society's relationship with the natural world and natural resources. This course gives an overview of key issues in sustainability science, including oncoming climate change, economic globalization, population growth and movement, biodiversity loss and homogenization, fossil fuel use and alternative energy sources. It models a 'problem-based' approach to scientific research, in contrast to a more traditional 'tool-based' approach. It explicitly explores the interface between research and a policy action. Drawing on our own research and that of others, we focus particularly on the relationships among ecosystem services, economics, and equity across social groups, gender, and geography. At the end of the semester, UMB will hold an inter-departmental, public mini-symposium featuring 3-4 eminent speakers on sustainability science , along with opportunities for student interaction. More Info
Offered in:- TBA
BIOL 664 Bioinformatics for Molecular Biologists +
Description:
The research of molecular biologists is facilitated by the numerous bioinformatics tools available on the Internet. The topics include DNA and protein sequence databases, sequence alignment, searching databases, gene structure, protein-function prediction, molecular evolution and whole genome sequences. The laboratory emphasizes hands-on experience and problem solving, and how to avoid being misled by errors in databases and improper use of computer programs. More Info
Offered in:- TBA
BIOL 672 Directed Readings in Biology +
Description:
This course provides selected readings in advanced areas of biology with guidance and regular discussion. More Info
Offered in:BIOL 673 Directed Readings +
Description:
This course provides selected readings in advanced areas of biology with guidance and regular discussion. More Info
Offered in:- TBA
BIOL 674 Cell Signaling +
Description:
This course will systematically investigate cell communication mechanisms, with an emphasis on developmental examples of cell signaling. General properties of signaling cascades will be discussed, followed by specific examples of conserved signaling pathways, such as Notch, Wnt, Hedgehog, TGF/BMP, JAK/STAT, nuclear receptors; and receptor tyrosine kinases (RTKs). Normal and aberrant receptor signaling will be examined using experimental evidence obtained in model genetic organisms. Implications of disrupting cell communication pathways in human disease will be discussed. The course will emphasize readings from the current literature. Upon completion of this course, students will have a solid understanding of the molecular mechanisms and control principles of cellular communication in normal and pathological conditions. More Info
Offered in:BIOL 676 Advanced Molecular Biology Lecture +
Description:
A lecture-only course covering the same material as BIOL 675; no lab work is required. More Info
Offered in:BIOL 677 Advanced Eukaryotic Genetics +
Description:
A broad spectrum of readings in plant, animal, and fungal genetics on such topics as segregation distortion, the control of sex determination, modes of asexual reproduction, inheritance of cytoplasmic genomes, self-incompatibility systems, transposable elements, and genetic mapping. More Info
Offered in:BIOL 680L Physical Biochemistry +
Description:
This course serves as an introduction to analytical methods and instrumentation available to the interdisciplinary scientist. While no course can be comprehensive in this field, this course will examine a broad base of analytical methods through introductory theory and will highlight applications and recent developments in these methods through current primary literature. More Info
Offered in:BIOL 681 Network Biology +
Description:
This graduate course introduces the students to an emerging field of Network Biology. The course covers general properties of biological networks, and continues with an in-depth treatment of the properties of the transcriptional, metabolic, protein-protein interaction, and signaling networks. Special emphasis is given to the technical advances in collection and analysis of high throughput data and to the associated information repositories. Reading assignments are largely based on the current literature in the field, through two texts will be recommended as additional resources. Exercises in a computer lab will give students hands-on experience with biological network analysis. More Info
Offered in:BIOL 682 GENOME STABILITY: DNA DAMAGE AND REPAIR +
Description:
This course will cover major causes (endogenous and exogenous) of DNA damage in cells, different types of DNA damage, and DNA damage repair pathways in prokaryotic and eukaryotic organisms. We will go over the DNA damage repair pathways that the cell uses, including cell cycle/DNA damage checkpoints, to repair damaged DNA upon exposure to exogenous DNA damage or endogenous DNA damage during natural developmental processes. We will also study how chromatin modification and epigenetics regulates DNA damage repair. CRISPR/Cas9 technology that is based on homologous and non-homologous DNA damage repair will also be covered. Cells have evolved a multitude of mechanisms to recognize and repair different kinds of DNA damage (stalled replication forks, DNA double-strand breaks, DNA mismatches, abasic sites, damaged nucleotides, etc) to preserve genome stability. DNA damage contributes to aging and in higher eukaryotes, such as humans, defective responses to DNA damage can cause genome instability and mutation overload, resulting in a number of diseases. These include cancers, neurodegenerative diseases, developmental syndromes, and many more. In this course, we will also learn how different model systems (including yeast, drosophila, zebra fish, mice and human cells) are studied in the laboratory to answer questions concerning DNA damage and genomic instability. More Info
Offered in:BIOL 691 Seminar in Developmental Biology +
BIOL 693 Seminar in Neurobiology +
Description:
Discussion of current literature in neuropharmacology and drug and behavior interactions. Combination of lectures and student presentations. More Info
Offered in:- TBA
BIOL 694 Research Experimentation in Biology +
Description:
This independent study provides students with sustained experience in a research laboratory. Each student pursues a specific research project, which may originate in a public or private sector laboratory or at the University. Each student's project should involve the student in ideas and laboratory skills and should permit the student to produce work of publishable quality. More Info
Offered in:BIOL 697 Special Topics in Biology +
BIOL 698 Projects in Biology +
Description:
A substantial written report based on library research or an original project such as curriculum design, design of teaching aids and exercises, or critique of a book or theory. No more than 6 credits of this course may be applied to the master's degree. More Info
Offered in:BIOL 699 Thesis Research +
Description:
Substantial laboratory or field research resulting in a master's thesis. More Info
Offered in:BIOL 899 Dissertation Research +
Description:
These are course credits for research conducted under the supervision of members of the faculty within the Biology Department and leading to the presentation of a doctoral dissertation within one of the PhD programs housed within the Biology department. More Info
Offered in: