BIO 395J Genes, Genomes, and Gene Expression

Prof. Rick Russell. BIO 395J requires graduate students to develop novel approaches to problems, especially translation and entrepreneurial approaches.  It focuses on providing insights into recent work, especially from UT faculty, that has the opportunity to play out in larger contexts, and challenges them to figure out what could be done to realize these greater innovations.  It is primarily a course about biotechnology, but is largely student-led.  Assignments focus on multiple in-class presentations and numerous short writing pieces.

BIO 391 Grant Writing and Presentation Skills

Prof. Arlen Johnson, Tanya Paull. In preparation for the qualifying exam, 2^nd Year students are required to take BIO 391 Grant Writing & Presentation Skills. BIO 391 is a writing-intensive course for 2nd year Ph.D. student in the fall semester that involves writing of an NIH-style grant proposal on their own research, presentation of the proposal to the class, and practice in identifying specific aims in research areas outside their primary area. The class is taken by students in the Microbiology, Biochemistry, and Cell and Molecular Biology Programs.

BIO 394L Immunology

Prof. Ehrlich. This course provides an introduction to the immune system for graduate students without prior coursework in immunology. We will discuss innate immunity, the molecular basis of T cell and B cell antigen recognition, hematopoiesis and the development of lymphocytes, and cellular and humoral immune responses.  In addition, we will touch on immunodeficiency, autoimmunity, immunotherapy and vaccination. Graduate students will explore current primary literature on select immunological topics in greater depth.

CSE 380 Tools and Techniques of Computational Science

Prof. Schulz. Scientific and technical computing covers an increasingly wide range of disciplines. To effectively leverage available scientific/high-performance computing (HPC) hardware, the modern computational scientist must have a practical understanding of underlying HPC architecture design, operating system tools and behavior, scientific programming, compiler transformations, performance optimization, and basic software engineering and verification procedures. This course provides an introductory perspective on these topics, with the goal of enabling participants to leverage Linux workstations and supercomputers effectively for developing scientific research applications.

We begin with an introduction to the traditional mainstays of scientific and technical computing: computer architecture and hardware principles, followed by operating systems and environments. These topics will be covered in the context of computational science, so much attention will be paid to floating point arithmetic and tools for developing and managing scientific code (including source code control and build systems). We also discuss practical tips for developing effective, high-performance scientific technical applications.   This course is designed to provide practical exposure to scientific computing in order to develop a minimum research computing skillset, and as such, hands-on computer exercises and individual programming assignments are a fundamental learning component of the class. 

BIO 394L Advanced Immunology

Prof. Greg Ippolito. A survey of modern immunology with an introduction to its fundamental concepts: innate and acquired immunity, clonal selection theory, cellular and humoral components and pathways of protection, and the basics of primary immunodeficiency, autoimmunity, cancer, and prophylactic vaccination. Recent advances in the therapeutic intervention of human immunologic diseases (i.e., immunotherapy) will also be discussed.            

BIO 391P Advanced Virology

Prof. Chris Sullivan, Jackie Dudley. The goal of this course is to understand the basic principles of virology using specific examples of topical or historical interest. The principles learned from this class will allow for an understanding of all viruses- even those not yet discovered. The focus will be on concepts of viral replication and pathogenesis.

BIO 394M 1 Advanced Immunology

Prof. Lauren Ehrlich. This course provides an introduction to the immune system for graduate students without prior coursework in immunology. We will discuss innate immunity, the molecular basis of T cell and B cell antigen recognition, hematopoiesis and the development of lymphocytes, and cellular and humoral immune responses.  In addition, we will touch on immunodeficiency, autoimmunity, immunotherapy and vaccination. Graduate students will explore current primary literature on select immunological topics in greater depth.

BIO 394M Tumor Biology

Prof. Jon Huibregtse. This course covers core aspects of cancer pathology, chemotherapies, immunotherapies, epidemiology, the discovery of oncogenes and tumor suppressors, and the molecular genetics underlying the characteristic features of malignant tumors (including metastatic behavior, genomic instability, angiogenesis, cell cycle regulation, and apoptosis).  There will be a strong emphasis on the biochemical functions of cancer-related proteins and enzymes and therapeutic approaches based on our understanding of these proteins. Important experimental approaches that have influenced our current understanding of cancer will also be stressed. 

NEU 382T Principles of Neuroscience I

Prof. Darrin Barger. Principles of Neuroscience I, II: The Principles of Neuroscience course is a two-semester graduate course beginning with molecular and cellular neuroscience and ending with human studies of learning and memory. Although most entering graduate students have taken introductory course(s) in neuroscience, these lectures ensure that all students have a broad introduction to topics ranging from neuroanatomy, neurophysiology, molecular neuroscience, neurodevelopment, systems neuroscience, computational neuroscience, behavior, etc. The course covers the following topics, listed by semester

NEU 383C Functional Neuroanatomy

Prof. F Gonzalez-Lima. We will examine the anatomical and functional organization of the human brain, emphasizing functional aspects of various neural systems, neuroimaging and translational research topics of clinical relevance. Both a conceptual understanding of central nervous system organization and the necessary memorization of specific neural structures and pathways will be required at the levels of macroscopic (MRI) and microscopic (histology) anatomical analysis. 

BIO 388M Plant Molecular Biology

Prof. Herrin. Meets Tuesday and Thursday from 3:30 to 5 pm. In this lecture course, students will learn the molecular biology of plant systems, including the structure, expression and regulation of genes in the nucleus, chloroplasts and mitochondria. Students will demonstrate knowledge and thinking ability by examination, and a research paper, which is due at the end of the semester. The prerequisite is graduate standing.

BIO 395 Laboratory Studies in Molecular Biology

Prof. Mehdy. Meets Mon or Wed sections, each section 11am-noon lecture and 1-6 pm lab. Explores molecular biology methods, experimental design, and analyses applicable to both research and fields such as healthcare, biotechnology, and forensics, while conducting novel research experiments. For graduate students, this course will provide in-depth experience with real time PCR, RNA and protein purifications, subcellular fractionation, Western blotting, cloning, DNA sequencing and analyses. Graduate students complete an additional project that provide skills of interest to the student beyond those taught in class, in consultation with the instructor.

BCH 394 Structure and Dynamics of Protein and Nucleic Acids

Prof. Ken Johnson. The structure and function of proteins and nucleic acids will be presented. Students will learn the tools they need to understand and evaluate structure and measure function through kinetic and equilibrium methods. Students are expected to have a basic knowledge of protein and nucleic acid structure at the introductory biochemistry level.

BIO 395M Advanced Microbiology

Prof. Ian Molineaux. Prokaryotic and lower eukaryote genome organization; control of gene/operon/regulon expression; chromosome replication and its control; signal transduction; protein trafficking; organelle assembly; the cell cycle and its control; developmental processes; cell to cell communication; and DNA polymorphisms and adaption.

BIO 394 1 Advanced Immunology

Prof. Greg Ippolito

BIO 395H Cellular Systems: From Biology to Disease and Back Again

Prof. Jon Wallingford. Mechanisms of growth control, cell regulation, mitosis, cell signaling, protein targeting, and the integration of these processes in various cellular processes. Three lecture hours a week for one semester. Prerequisite: Graduate standing

MOL 395F Genetics, Genomics and Epigenetics

Prof. Kyle Miller. Basic principles of Mendelian and molecular genetics, and an exploration of the genetic toolbox using examples of analytic methods and modern manipulations; focus on the genetic analysis of model organisms. Use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. Three lecture hours a week for one semester. Prerequisite: Graduate standing. An introductory course in genetics, such as Biology 325, is strongly recommended.

BIO 382K Introduction to Bio for Data Science

Prof. Johann Hofmann. An introduction to modern biology for students with quantitative backgrounds. The course includes a survey of modern biology and also introduces modern statistical approaches, bioinformatics analyses, and computational approaches fundamental to "big data" and other life sciences in contexts students are likely to encounter in their own research.

BCH 394P Bioinformatics

Prof. Edward Marcotte. The course covers typical data, data analysis, and algorithms encountered in computational biology. Topics will include introductory probability and statistics, basics of programming, protein and nucleic acid sequence analysis, genome sequencing and assembly, synthetic biology, analysis of large-scale gene expression data, data clustering, biological pattern recognition, and biological networks.

CSE 383M Statistics and Discrete Methods of Computational Science

Prof. Chandrajit Bajaj. This course covers the computational mathematical foundations of data sciences, machine learning and statistical inference analysis. The foundational topics and techniques span  the geometry of high dimensional spaces (vector, Banach and Hilbert ), low discrepancy and incoherent sampling and recovery of sparse and almost sparse signals,  spectral methods for learning, low-rank approximations, and low-dimensional embeddings, kernelized and sparse versions of PCA, CCA, ICA, SVM, LDA, statistical parametric and non-parametric estimation, latent variable models, primal-dual-proximal optimization and the geometry of deep learning.  Issues of measurement errors, noise and outliers are central to bounding the precision, bias, variance. The geometric insight and characterization gained provide the structural basis for designing and improving existing approximation algorithms problems with better accuracy / speed tradeoffs.

SDS 385 Computational Biology and Bioinformatics

Prof. Claus Wilke. Computational-based data sorting and data transformation, Three lecture hours and one laboratory hour per week. Prerequisite: Statistics and Data Sciences 328M (or Statistics and Scientific Computation 328M).

BCH 387D Physical Methods in Biochemistry and Molecular Biology

Prof. Jason McLellan. Theory of physical methods used in biochemistry and molecular biology, with a strong emphasis on macromolecular structure determination by X-ray crystallography and cryo-electron microscopy. Other topics include surface plasmon resonance, isothermal titration calorimetry, and biolayer interferometry.

PGS 384L Biochemical and Molecular Toxicology

Prof. Karen Vasquez. The overall objective of this course in Biochemical and Molecular Toxicology is to highlight important cellular mechanisms, at the biochemical and molecular levels, which are activated in response to environmental toxicant exposure, and their disease relevance. Understanding the mechanistic basis underlying the disruption of these cellular pathways by toxicants that leads to the pathogenesis of disease is a unifying concept for each of the units of this course. Successful completion of this course will prepare graduate students with a foundation of knowledge that will strengthen their ability for critical thinking and performance of laboratory research in mechanistic toxicology.  

BIO 381K Cellular and Molecular Bases of Neural Development

Prof. Seema Agarwala

Scope: The course will provide an in-depth look at the cellular and molecular bases of neural development. We will examine how a three-dimensionally correct neural tube is formed and regionalized into the forebrain, midbrain, hindbrain and spinal cord. Emphasis will be given to the mechanisms that govern the acquisition of neuronal identity, the formation of neuronal circuits and synapses, and synaptic reorganization. Developmental and congenital diseases and therapies (e.g. stem cell-based therapy, gene therapy) will be discussed as relevant. 

Format: In addition to lectures, the course emphasizes analysis and presentation of primary literature and is writing intensive. Assigned papers are discussed in class followed by in-class and take-home writing assignments with feedback from the instructor as well as peers. 

3 lecture hours per semester.

BIO 381P Advanced Plant Physiology

Prof. Greg Clark. Utilizing recently published discoveries, the course aims to convey an up-to-date knowledge of important information and concepts in the broad field of plant physiology. Course will highlight aspects of plant growth, development, cell signaling, and stress responses that are very similar to these processes in animals, but will also illustrate unique aspects of plants that are fascinating and exemplify the diversity of life strategies on earth. Course should help students develop critical thinking skills in evaluating current literature, data interpretation, and methods for solving key questions in the field.

BIO 394M Genomics

Prof. Jeff Chen. This course will cover a broad field of modern genetics and genomics in a variety of model organisms including yeast, fly, worm, plant, animal and human; state-of-art DNA sequencing technologies and strategies; genome size evolution; transposable elements; chromosomal view of genome; aneuploidy and polyploidy; genetic and physical mapping, comparative genomics; quantitative trait loci analysis; genome-wide association studies; mitochondrial and chloroplast DNA; transcriptome analysis; with an emphasis on understanding the regulation and function of complex genomes, including epigenomics and epigenetic phenomena; DNA methylation; chromatin structure and function; X-chromosome inactivation; genomic imprinting; RNA interference and microRNAs; CRISPR and gene-editing; hybrid vigor; animal cloning and genetically modified organisms (GMOs).

No textbook is required for the course partly because of rapid advances in genomics, epigenetics and personalized medicine. The course materials will depend on lecture notes and selected journal articles, as a transition for most students from a textbook-based to knowledge-acquired learning process. Students are encouraged to read literatures and participate in interactive discussions in the classroom, as well as to work in small groups on developing creative ideas to solve an important biological phenomenon using genomic and epigenetic approaches and techniques learned in the class. Two take-home exams will be given, one prior to the spring break and another within or before the final exam week. Biweekly commentaries on a cutting-edge research article are graded, so are the group proposal and presentation near the end of the semester. Finally, attendance and participation in the classroom, office hour, and journal club discussions will be counted as part of grades.

NEU 380E Vision Systems

Prof. Wilson Geisler. This course presents an introduction to the physiology, psychophysics and computational aspects of vision. A fundamental premise of the course is that theoretical and applied research in computational vision provides insights that are useful for understanding biological vision. Conversely, physiological and psychophysical studies of human and other biological visual systems provide important clues for the development of computational vision systems. Thus, the course will proceed by analyzing biological vision systems from an engineering/information-theoretic perspective. Although the exact content of the course will vary from year to year, the topics covered will include a large subset of the following: extraction and representation of visual information in biological and machine systems; natural scene statistics, computational theories of vision; anatomy, physiology and psychophysics of the primate (human) visual system; image processing; pattern detection and identification; stereo vision; motion perception; surface and object perception; color vision. The course will include reviews of linear systems analysis, information theory, Bayesian statistical decision theory and other relevant mathematical topics.

NEU 383T Principles of Neuroscience II

Prof. Darrin Barger. Principles of Neuroscience I, II: The Principles of Neuroscience course is a two-semester graduate course beginning with molecular and cellular neuroscience and ending with human studies of learning and memory. Although most entering graduate students have taken introductory course(s) in neuroscience, these lectures ensure that all students have a broad introduction to topics ranging from neuroanatomy, neurophysiology, molecular neuroscience, neurodevelopment, systems neuroscience, computational neuroscience, behavior, etc. The course covers the following topics, listed by semester

PSY/NEU 394P 1 Current Topics in Behavioral Neuroscience

Prof. Theresa Jones. This graduate seminar is focused on recent and ongoing research in neural plasticity and behavior. Class meetings emphasize student presentations and discussions of primary research articles. Topics include neural plasticity mechanisms of recovery from brain damage, learning and memory, stress, development, aging, neurological disorders and addiction. 

NEU 394P 3 Neurobiology of Learning and Memory

Prof. F Gonzalez-Lima. In this graduate seminar we will discuss the neuroanatomical systems and metabolic processes functionally related to basic forms of learning and memory in humans and experimental mammals and how they relate to neurocognitive and mental disorders.  We will focus on the neurocognitive effects of transcranial lasers. Readings will include ongoing research on cognitive enhancement interventions with lasers and journal articles of assigned research topics.

BIO 387J Plant Anatomy

Prof. Bradbury. Meets: TTH 11-12:30, must also be registered for BIO 187L. Provides a survey of the tissue organization and cellular details of the main parts of plants, with emphasis on development and function. Plant organization, structure, and reproduction will also be considered from an adaptive perspective, integrating both ecological and evolutionary aspects of plant history. Through the completion of the lecture and lab, student participation will also promote learning, critical thinking, microscopy skills, and laboratory techniques.

BIO 187L Plant Anatomy Lab

Prof. Bradbury. Meets TTH 1-2pm, must also be registered for BIO 387J. Provides a survey of the tissue organization and cellular details of the main parts of plants, with emphasis on development and function. Plant organization, structure, and reproduction will also be considered from an adaptive perspective, integrating both ecological and evolutionary aspects of plant history. Through the completion of the lecture and lab, student participation will also promote learning, critical thinking, microscopy skills, and laboratory techniques.

BIO 395 Laboratory Studies in Molecular Biology

Prof. Mehdy. Meets Mon or Wed sections, each section 11am-noon lecture and 1-6 pm lab. Explores molecular biology methods, experimental design, and analyses applicable to both research and fields such as healthcare, biotechnology, and forensics, while conducting novel research experiments. For graduate students, this course will provide in-depth experience with real time PCR, RNA and protein purifications, subcellular fractionation, Western blotting, cloning, DNA sequencing and analyses. Graduate students complete an additional project that provide skills of interest to the student beyond those taught in class, in consultation with the instructor.