Bioinformatics Courses
BINF 5964. Projects for Professionals. (0 Hours)
Offers students an applied project setting in which to apply their curricular learning. Working with a sponsor, students refine an applied research topic, perform research, develop recommendations that are shared with a partner sponsor, and create a plan for implementing their recommendations. Seeks to benefit students with a curriculum that supports the development of key business communication skills, project and client management skills, and frameworks for business analysis. Offers students an opportunity to learn from sponsor feedback, review 'lessons learned,' and incorporate suggestions from this review to improve and further develop their career development and professional plan. May be repeated twice.
BINF 5976. Directed Study. (1-4 Hours)
Offers independent work under the direction of members of the department on a chosen topic. Course content depends on instructor. May be repeated twice.
BINF 6200. Bioinformatics Programming. (4 Hours)
Focuses on the fundamental programming skills required in the bioinformatics industry. Focuses on Python and R as the main programming language used. Topics include string operations, file manipulation, regular expressions, object-oriented programming, data structures, testing, program design, and implementation. Includes substantial out-of-classroom assignments.
BINF 6201. Introduction to Bioinformatics Using RNA Sequencing. (4 Hours)
Introduces RNA-Seq, a commonly used method for analyzing gene expression. Offers students an opportunity to obtain hands-on experience processing and analyzing high-throughput sequencing data, as well as exposure to NGS and RNA-Seq processes, applications, and terminology.
BINF 6250. Algorithmic Foundations in Bioinformatics. (3 Hours)
Explores algorithmic principles in the context of bioinformatics. Through a dynamic and comprehensive journey encompassing sequence alignment, genome assembly, phylogenetics, hidden Markov models, and predictive analyses in protein and RNA structures, delves into the core techniques essential for deciphering biological data. Uses lectures, hands-on sessions, and case studies to offer students an opportunity to obtain a rich understanding of how algorithms drive insights into evolutionary relationships, genetic patterns, and molecular structures.
Prerequisite(s): BINF 6200 with a minimum grade of C- or BINF 6200 with a minimum grade of C-
BINF 6308. Bioinformatics Computational Methods 1. (4 Hours)
Offers the first semester of a two-semester sequence on the use of computers in bioinformatics research. Offers students an opportunity to work with current methods and computational algorithms used in contemporary sequence analysis. Teaches practical skills necessary to manage and mine the vast biological information being generated and housed in public databases. Emphasizes the use of Python as the primary computer language and requires students to learn and understand basic computer logic and syntax, including an introduction to scalars, arrays, hashes, decision statements, loops, subroutines, references, and regular expressions. A focus on fundamental skills, including the command line interface found in the Linux operating system, is designed to prepare students for second-semester applications.
BINF 6309. Bioinformatics Computational Methods 2. (4 Hours)
Designed to build upon the core topics covered in BINF 6308, i.e., use of the computer as a tool for bioinformatics research. Builds upon the Python language fundamentals covered during the first semester but requires students to apply these fundamentals to a semester-long project. The project includes protein family analysis, multiple sequence analysis, phylogeny, and protein structure analysis. Additionally, students have an opportunity to learn to build, load, connect, and query custom MySQL databases, and parse command line flags.
Prerequisite(s): BINF 6308 with a minimum grade of C- or BINF 6308 with a minimum grade of C- or BIOL 6308 with a minimum grade of C-
BINF 6310. Introduction to Computational Methods in Bioinformatics. (4 Hours)
Focuses on the core bioinformatics skill set and knowledge base necessary to conduct exploratory data analysis of large-scale biological data. Offers students an opportunity to work with the latest computational approaches in the context of real-world data and to obtain practical skills necessary to access, manage, and mine the vast biological information housed in public repositories. Presents core computational skills. Introduces DevOps concepts including version control, using Linux, as well as introductory CLI Logic and syntax related to pipeline development. Reviews basic molecular biology concepts and techniques necessary for contemporary bioinformatics analytical approaches. Examines similarities and differences among applications of next-generation sequencing and third-generation sequencing platforms. Covers sequence similarity analysis methods and related biological file formats.
Prerequisite(s): BINF 6200 (may be taken concurrently) with a minimum grade of C- or BINF 6200 (may be taken concurrently) with a minimum grade of C- or DS 2500 with a minimum grade of C-
BINF 6400. Genomics in Bioinformatics. (4 Hours)
Introduces the field of genomics. With the completion of the Human Genome Project several years ago, there has been an explosion of genetic data collected. Focuses on the bioinformatics tools necessary to analyze large-scale genomic data. Covers topics such as phylogenetic trees, molecular evolution, gene expression profiling, heterogeneous genomic data, as well as next-generation sequencing (NGS) data.
Prerequisite(s): ((BINF 6200 with a minimum grade of C- or BINF 6200 with a minimum grade of C- ); (BINF 6310 with a minimum grade of C- or BINF 6310 with a minimum grade of C- )) or ((BINF 6308 with a minimum grade of C- or BINF 6308 with a minimum grade of C- ); (BINF 6309 with a minimum grade of C- or BINF 6309 with a minimum grade of C- ))
BINF 6420. Omics in Bioinformatics. (4 Hours)
Focuses on some of the omics, other than genomics and proteomics, in relation to the bioinformatic tools that exist to analyze data. Provides a brief background on each field of study and then focuses on the current bioinformatics tools used. Topics include transcriptomics (transcription and gene expression), metabolomics (metabolism), glycomics (carbohydrates), lipomics (lipids), and phenomics (phenotypic data). Does not cover genomics and proteomics.
Prerequisite(s): ((BINF 6310 with a minimum grade of C- or BINF 6310 with a minimum grade of C- ); (BINF 6200 with a minimum grade of C- or BINF 6200 with a minimum grade of C- )) or ((BINF 6308 with a minimum grade of C- or BINF 6308 with a minimum grade of C- ); (BINF 6309 with a minimum grade of C- or BINF 6309 with a minimum grade of C- ))
BINF 6430. Transcriptomics in Bioinformatics. (4 Hours)
Introduces the study of the complete RNA transcriptome, otherwise known as “transcriptomics.” Covers the molecular genetics that underlie RNA and its various sequencing protocols (e.g., RNA-seq, ATAC-seq, and scRNA-seq), data preprocessing, transcriptome assembly, differential gene expression, and gene set enrichment analysis. Throughout the course and in collaboration with our academic partners, students take part in experiential learning by processing and analyzing various real-world RNA-seq datasets, including bulk RNA and single-cell sequencing.
Prerequisite(s): ((BINF 6310 with a minimum grade of C- or BINF 6310 with a minimum grade of C- ); (BINF 6200 with a minimum grade of C- or BINF 6200 with a minimum grade of C- )) or ((BINF 6308 with a minimum grade of C- or BINF 6308 with a minimum grade of C- ); (BINF 6309 with a minimum grade of C- or BINF 6309 with a minimum grade of C- ))
BINF 6500. Professional Development for Co-op. (0 Hours)
Introduces the cooperative education program. Offers students an opportunity to develop job-search and career-management skills; to assess their workplace skills, interests, and values and to discuss how they impact personal career choices; to prepare a professional resumé; and to learn proper interviewing techniques. Explores career paths, choices, professional behaviors, work culture, and career decision making.
BINF 6900. Pre–Co-op Experience. (0 Hours)
Offers students an opportunity to gain necessary skills and practical experience in order to prepare for graduate co-op.
BINF 6954. Co-op Work Experience - Half-Time. (0 Hours)
Provides eligible students with an opportunity for work experience. May be repeated without limit.
BINF 6962. Elective. (1-4 Hours)
Offers elective credit for courses taken at other academic institutions. May be repeated without limit.
BINF 6964. Co-op Work Experience. (0 Hours)
Provides eligible students with an opportunity for work experience. May be repeated without limit.
BINF 6965. Co-op Work Experience Abroad. (0 Hours)
Offers eligible students an opportunity for work experience abroad. May be repeated without limit.
BINF 7700. Bioinformatics Research Directions. (4 Hours)
Delves into the foundations of research planning and implementation in bioinformatics. Offers students an opportunity to learn experimental design and organization of the research process, as well as to develop the skills and techniques for writing, communication, and presentation of research work. Students work with a faculty member to design and conduct a short research project in the faculty member’s area of research, present to different audiences, and construct a proposal for continuing their research.
Prerequisite(s): (BINF 6200 with a minimum grade of C- or BINF 6200 with a minimum grade of C- ); (BINF 6310 with a minimum grade of C- or BINF 6310 with a minimum grade of C- ); MATH 7340 with a minimum grade of C-
Biology Courses
BIOL 5100. Biology Colloquium. (1 Hour)
Offers a series of colloquia in biological research by invited experts on current topics. May be repeated without limit.
BIOL 5301. Clinical Embryology. (4 Hours)
Designed to familiarize students with core biological processes associated with fertilization and early embryogenesis in humans, with an emphasis on clinical relevance. Covers fundamental aspects of female fertility and embryo development, including hormonal control of ovarian follicle growth and ovulation, fertilization, preimplantation embryonic development, implantation, and postimplantation embryonic development through gastrulation. Examines current parameters for determining egg and embryo quality. Additionally, discusses evolving stem-cell-based strategies for the treatment of female reproductive failure.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5306. Biological Clocks. (4 Hours)
Examines the expression of endogenously generated twenty-four-hour (circadian) rhythms in eukaryotic life, emphasizing theoretical foundations as well as current research strategies for understanding how biological clocks work. Presents analytic principles essential for understanding biological rhythmicity in any organism at any level of organization. Emphasizes strategies used to understand the concrete mechanisms underlying biological rhythmicity.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5535. Expanding Frontiers: Vector-Borne Diseases. (4 Hours)
Explores the biology of vectors and vector-borne infectious diseases. The World Health Organization estimates that about one-fifth of all infectious diseases are caused by vector-borne diseases. Vectors discussed include mosquitoes; ticks; Plasmodium; trypanosomes; Lyme disease-causing bacteria; and arboviruses such as dengue, yellow fever, West Nile, and Zika. Examines the development, metabolism, behavior, and symbiotic relationships—including the vector-host-pathogen relationships—through a student-generated literature review and a research proposal. Thoroughly reviews treatments and prevention strategies ranging from vaccination, pre- and postexposure prophylaxis, antimicrobial intervention, management of sequelae, and vector-control strategies. Discusses each topic from the perspective of historical and modern research.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5539. Advances in Genome Editing. (4 Hours)
Analyzes the scientific literature to investigate the rapidly changing field of genome editing and identify the implications for biological sciences. Explores developments in genome editing along with the clinical and experimental applications of these tools. Life sciences have been revolutionized by the emergence of technologies that enable precise alterations in DNA sequences, cells, model organisms, and even humans.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5541. Endocrinology. (4 Hours)
Explores the endocrine regulation of physiological systems, emphasizing current research. Lectures provide background, followed by analysis of primary literature and case studies. Topics include growth, reproduction, nutrient utilization, stress, and environmental endocrine disruption. Emphasizes humans but includes material on other animals, including invertebrates.
Prerequisite(s): BIOL 2319 with a minimum grade of D- or BIOL 2323 with a minimum grade of D- or BIOL 3405 with a minimum grade of D- or BIOL 3611 with a minimum grade of D- or BIOL 4707 with a minimum grade of D- or graduate program admission
BIOL 5543. Stem Cells and Regeneration. (4 Hours)
Explores the biological basis of embryonic, adult, and induced pluripotent stem cells toward an understanding of their roles in development, homeostasis, and regeneration, as well as their therapeutic potential. The study of stem cells is a rapidly advancing area in biology and biomedicine. Although the biological basis of stem cells is a major focus, the course aims to put this knowledge into a biomedical context.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5549. Inventions in Microbial Biotechnology. (4 Hours)
Offers readings and seminar-style discussion from the current literature on important inventions and practical applications in biotechnology, with a focus on microbiome and antibiotic discovery, emphasizing new concepts.
BIOL 5573. Medical Microbiology. (4 Hours)
Emphasizes host-parasite interactions: virulence, toxins, natural flora, and immunological responses; characteristics of the common bacterial, rickettsial, and protozoal infections in humans; and epidemiology, pathology, vaccines, and chemotherapy.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5581. Biological Imaging. (4 Hours)
Illustrates imaging principles and techniques and their application to biological problems. Topics vary and may include microscopic and macroscopic approaches in areas such as cellular and neurobiology, ecology, and biochemistry.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5583. Immunology. (4 Hours)
Provides an overview of the structure and function of genes, proteins, and cells involved in the generation of the immune response. Emphasis is on molecular immunology and immunogenetics.
Prerequisite(s): BIOL 2323 with a minimum grade of D- or BIOL 3611 with a minimum grade of D- or graduate program admission
BIOL 5585. Evolution. (4 Hours)
Discusses history of evolutionary theory and lines of evidence. Emphasis is on mechanisms of speciation. Introduces and discusses current evolutionary topics.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5587. Comparative Neurobiology. (4 Hours)
Presents a cellular approach to structure and function of the nervous system. Topics include neuronal anatomy, phylogeny of nervous systems, electrophysiology of membrane conductances, synaptic transmission, integration in nerve cells, neuronal networks, sensory systems, motor systems, sensory-motor integration, development and regeneration of neuronal connectivity, and fundamentals of neurotechnology for biomedics. Focuses on the development of these concepts from the primary research literature. A term project involves the design of a simple nervous system for a hypothetical animal.
Attribute(s): NUpath Creative Express/Innov
BIOL 5591. Advanced Genomics. (4 Hours)
Intended for those familiar with the basics of genetics, molecular and cellular biology, and biochemistry, all of which are required to appreciate the beauty, power, and importance of modern genomic approaches. Introduces the latest sequencing methods, array technology, genomic databases, whole genome analysis, functional genomics, and more.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5593. Cell and Molecular Biology of Aging. (4 Hours)
Covers the recent scientific discoveries that have transformed our understanding of the process of aging. Examines in-depth the current understanding of the molecular mechanisms that control life span in model organisms, including yeast, worms, flies, and mice. Discusses dietary interventions and pharmacological approaches that extend the life span and delay the onset of age-related diseases. Covers potential applications of the new science of aging to improve human health. Requires students to read, discuss, present, and report on primary research papers from the literature.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
Attribute(s): NUpath Writing Intensive
BIOL 5595. Cell and Molecular Neuroscience. (4 Hours)
Combines molecular biology, cell biology, pharmacology, and genetics to address the fundamental molecular properties of neurons and neuronal networks. At its core, the principles that govern the communication between cells of the nervous system are determined by their molecular components. The molecular landscape defines the individual properties of a neuron and the function of neuronal networks as a whole. Focuses on neuronal signaling through the function of ion channels and receptors, supramolecular mechanisms like synaptic transmission and axonal transport, and the molecular mechanisms that underlie biological networks and neural coding of information. Uses the fundamental understanding of molecular networks as a framework to explore the mechanisms that underlie neurological diseases and disorders. Discusses current treatments and therapies that rely on modulating neuronal signaling through molecular interactions.
Prerequisite(s): (BIOL 2301 with a minimum grade of D- ; (PSYC 3458 with a minimum grade of D- or BIOL 3405 with a minimum grade of D- )) or graduate program admission
BIOL 5597. Immunotherapies of Cancer and Infectious Disease. (4 Hours)
Describes the basic principles and the current promises and disappointments with immunotherapies of cancer. Provides a historical overview of the main barriers between tumors and antitumor killer cells. The unifying focus of the lectures is the role of immunological and physiological negative regulators, i.e., “brakes” of anti-tumor immune response. A significant part of the course is dedicated to the retrospective evaluation of the last three decades of the immunological and biochemical studies that culminated in identification of the “chief of tumor defense operations,” i.e., a hypoxia-adenosinergic pathway in the tumor microenvironment.
Prerequisite(s): BIOL 2301 with a minimum grade of D- or graduate program admission
BIOL 5601. Multidisciplinary Approaches in Motor Control. (4 Hours)
Studies the field of human motor control, or motor neuroscience. Offers students an opportunity to obtain a fundamental understanding of the processes underlying the acquisition and control of sensorimotor behavior. The systems approach connects a variety of disciplines ranging from neurophysiology, to engineering, to neurorehabilitation. Reviews a selection of approaches with emphasis on motor learning. Focuses on early behavioral approaches, more recent neurophysiological and imaging approaches, and rehabilitation. Discusses selected representative papers, including seminal historical papers and more recent studies reflecting the current discussion in the field.
Prerequisite(s): (BIOL 2301 with a minimum grade of D- ; (PSYC 3458 with a minimum grade of D- or BIOL 3405 with a minimum grade of D- )) or graduate program admission
BIOL 5821. Cell and Gene Therapies. (4 Hours)
Presents a comprehensive overview of the most recent clinical approaches in treating previously known incurable diseases. Focuses on an introduction to cell and gene therapy, how gene therapies are developed to treat some rare and genetic diseases, different modalities of in vivo and ex vivo gene therapy (cell therapy), the delivery of genetic materials to the cells, limitations, and more. Offers students an opportunity to learn about CAR T-cell therapy, different types of viruses (AAVs and retroviruses), nanoparticles, CRISPR-Cas9, RNA interference(RNAi), and many more tools in this fast-paced field.
BIOL 6299. Molecular Cell Biology for Biotechnology. (3 Hours)
Integrates biochemistry and molecular biology in the cellular context. Includes the organization and replication of genomes, principles and methods for genetic manipulation, the regulation of gene expression, and the structure and function of organelles. Emphasizes protein synthesis, including translation, post-translational modifications, and translocations of proteins within the cells and secretion.
BIOL 6300. Biochemistry. (4 Hours)
Studies the structure and function of biomolecules, with an emphasis on proteins; enzyme catalysis; and cellular metabolism, with an emphasis on bioenergetics and carbohydrate/lipid.
BIOL 6301. Molecular Cell Biology. (4 Hours)
Integrates biochemistry and molecular biology in the cellular context. Emphasizes the organization and replication of genomes, the regulation of gene expression, the structure and function of organelles, and the mechanisms of signal transduction.
Prerequisite(s): BIOL 6300 with a minimum grade of C-
BIOL 6303. Neurobiology and Behavior. (4 Hours)
Provides a comprehensive overview of behavioral neurobiology, emphasizing a neuroethological approach. Fosters a contemporary understanding of the historical development of the behavioral sciences, the major ethological and neurobiological concepts, and the principal mechanisms that govern behavior in animals and humans.
BIOL 6381. Ethics in Biological Research. (2 Hours)
Discusses ethical issues relevant to research in the biological sciences. Requires student presentations.
BIOL 6405. Prokaryotic Cell and Molecular Biology. (4 Hours)
Provides in-depth discussion about fundamentally important cellular processes in prokaryotic systems—such as replication, transcription, and translation—and the corresponding regulatory mechanisms. Also discusses molecular mechanisms of gene regulation and bacterial pathogenesis, using selected examples and mechanisms of prokaryotic cell signaling, and advanced and high-throughput techniques used in prokaryotic molecular and cell biology.
BIOL 6962. Elective. (1-4 Hours)
Offers elective credit for courses taken at other academic institutions. May be repeated without limit.
BIOL 7962. Elective. (1-4 Hours)
Offers elective credit for courses taken at other academic institutions. May be repeated without limit.
BIOL 7986. Research. (0 Hours)
Offers students an opportunity to conduct full-time research under faculty supervision.
BIOL 7990. Thesis. (1-4 Hours)
Offers thesis supervision by members of the department. May be repeated without limit.
BIOL 7996. Thesis Continuation - Half-Time. (0 Hours)
Offers continuing thesis supervision by members of the department.
BIOL 8420. Biological Lab Rotation 1. (4 Hours)
Offers experience in biology research in a faculty research laboratory. Intended only for students who have not yet chosen a lab in which to carry out dissertation/thesis work.
BIOL 8960. Exam Preparation—Doctoral. (0 Hours)
Offers the student the opportunity to prepare for the PhD qualifying exam under faculty supervision.
BIOL 8982. Readings. (1-4 Hours)
Offers readings from current literature on an area of interest to students and faculty. May be repeated without limit.
BIOL 8984. Research. (1-4 Hours)
Focuses on research methods and their application to a specific problem under the direction of a graduate faculty member. May be repeated without limit.
BIOL 8986. Research. (0 Hours)
Offers the student the opportunity to conduct full-time research. May be repeated without limit.
BIOL 9000. PhD Candidacy Achieved. (0 Hours)
Indicates successful completion of the doctoral comprehensive exam.
BIOL 9984. Research. (1-4 Hours)
Focuses on research methods and their application to a specific problem under the direction of a graduate faculty member. May be repeated without limit.
BIOL 9990. Dissertation Term 1. (0 Hours)
Offers theoretical and experimental research for the PhD degree.
Prerequisite(s): BIOL 9000 with a minimum grade of S
BIOL 9991. Dissertation Term 2. (0 Hours)
Offers dissertation supervision by members of the department.
Prerequisite(s): BIOL 9990 with a minimum grade of S
BIOL 9996. Dissertation Continuation. (0 Hours)
Offers dissertation supervision by members of the department.
Prerequisite(s): BIOL 9991 with a minimum grade of S or Dissertation Check with a score of REQ