BIMS Modules
BIMS students have the flexibility to choose from over 40, six-weeks, modular courses focused on a wide array of topics in biomedical sciences. In these higher-level courses, our expectation is that the students will apply the tools that they have learned in the core course to synthesize and integrate the most current knowledge in the field.
Following is the schedule for the Fall 1 (Sept 3-Oct 16) for 2019. Below there is a list of each course, to find out more about that course, click on that courses tab.
Key: Monday- (M), Tuesday- (T), Wednesday- (W), Thursday- (R), Friday- (F)
Note: Some courses may occur for the entire semester.
Credits: 2
Instructor: Bushweller
Time: 10:30am-12:30pm – T,R
Prerequisites
Magnetic Resonance Spectroscopy of Macromolecules I
Description
Exploration of magnetic resonance spectroscopy as it is applied to biopolymers. The first module will cover principles of nuclear magnetic resonance (NMR) will be covered, including basic principles, homonuclear and heteronuclear NMR methods.
Credits: 2
Instructor: Nakamoto
Time: 3:30-5pm – T, R
Prerequisites
BIOP 8201/8301, Biophysical Principles
Description
The course will provide in-depth assessment of the structure and function of biological membranes and membrane proteins. Emphasis will be placed on biophysical and approaches. The primary literature will be the main source of reading. The course will run as a colloquium with the instructors introducing a different topic at each session and students presenting relevant papers.
Credits: 2
Instructor: Casanova, Halme
Time: 9am-12 pm T – Section 1
9am-12 pm W – Section 2
Prerequisites
Instructor permission; identified research problem and substantial knowledge of background literature
Description
The ability to effectively communicate scientific concepts and justify proposed experiments are essential skills for biomedical researchers. The goals of this course are for trainees to learn and practice effective scientific proposal writing. The course will provide students with extensive peer and faculty mentoring in a workshop format as they each prepare an NIH NRSA-style fellowship application.
Credits: 2
Instructor: Rutkowski, Melanie
Time: 9-11am – R
Prerequisites:
MICR 8200: Building Blocks of the Immune System and MICR 8203: Integration and Diversification of the Immune System or equivalent permission.
Description
The module will cover in depth selected contemporary topics in molecular and cellular immunology. Sessions are discussion-based and facilitated by faculty. Students will learn how to critically evaluate primary literature and to clearly present scientific information. Prerequisite: MICR 8200: Building Blocks of the Immune System and MICR 8202: Integration and Diversification of the Immune System or equivalent.permission.
Credits: 2
Instructor: Criss, Rekosh
Time: 1:30-3 pm – M,W
Prerequisites
Core Course and Molecular Principles of Bacteriology and Virology
Description
The class provides a comprehensive study of pathogenic microbes and their unique and conserved mechanisms of virulence.
Credits: 2
Instructor: Cliffe, Anna
Time: 1:00pm-2:30pm T
Prerequisites
MICR 8400 or equivalent, or consent of the course organizers
Description
This year’s focus will be the current topics on virus-host cell interactions
This module will cover recent topics from papers published in the past 12 months. Sessions will be based on published primary literature and will consist of discussions facilitated by the faculty with student participation heavily encouraged. Students will learn how to critically evaluate the primary literature and to clearly present scientific information. Topics will be focused primarily on host detection and defense mechanisms, and how viruses overcome these mechanisms to promote replication.
Session will consist of two journal articles/session. Each student enrolled in the course will present. Students are also required to write a short summary of the papers and discussion, which will be due prior to the following class
Credits: 2
Instructor: Luckey
Time: 1-3pm, R, Full Semester
Location: MR6 Rm 3501
Prerequisites
None.
Description
A series of joint lectures by basic and clinical scientists that focuses on the clinical context of a specific biomedical problem and the contemporary research that has resulted in major advances and treatment of the disease. Note: Students may take part II before part I of this course.
Credits: 2
Instructor: Bullock
Time: 9-10:30 am – M and 11 am-12:30 pm -R
Prerequisites
MICR 8200: Building Blocks of the Immune System, MICR 8203: Integration and Diversification of the Immune System, and MICR 8040: Fundamentals in Cancer Biology
Description
This module will allow students to gain comprehensive understanding of the extensive interactions between the immune system and neoplasia. The course will focus on discussion of contemporary literature, and will require students to have a strong knowledge of innate and adaptive immunity.
Credits: 2
Instructor: Creutz
Time: 9-10:30 am – M,W,F
Prerequisites
PHY 8040 and 8041: Physiology A & B recommended
Description
The course will cover the major classes of therapeutically relevant drugs, and how they work at the molecular and cellular levels. The major topics include: general principles, chemical mediators, drugs affecting major organ systems and chemotherapy of infectious and malignant disease.
Following is the schedule for the Fall 2 (Oct 21-Dec 10) for 2019. Below there is a list of each course, to find out more about that course, click on that courses tab.
Key: Monday- (M), Tuesday- (T), Wednesday- (W), Thursday- (R), Friday- (F)
Note: Some courses may occur for the entire Fall semester.
Credits: 2
Instructor: Bushweller
Time: 10:30-12:30pm, T, R
Prerequisites
BIOP 8030, Magnetic Resonance Spectroscopy of Macromolecules I
Description
The course offers in depth coverage of theory and practical applications of electron microscopy methods in structure determination of biological macromolecules and their complexes. Topics : the history of electron microscopy, imaging and scattering, electron diffraction, CTF and new technologies.
Credits: 2
Instructor: Nakamoto
Time:3:30-5pm T,R
Prerequisites
BIOP 8130, Structure-Function of Biological Membranes
Description
The course will provide in-depth assessment of the structural biology of membrane proteins. Emphasis will be placed on the methodologies of solving membrane protein structure. The primary literature will be the main source of reading. The course will run as a colloquium with the instructors introducing a different topic at each session and students presenting relevant papers. The students will create a grant proposal for the final project.
Credits: 2
Instructor: Casanova, Halme
Time: 9am-12 pm T – Section 1
9am-12 pm W – Section 2
Prerequisites
MICR 8040 and MICR 8044
Description
This course will cover contemporary topics relevant to the detection and treatment of solid tumors and hematopoietic cancers. These include, but are not limited to, clinical trials, metabolism and cancer, cancer stem cells, cancer biomarkers, systems and networks in cancer. Students will attend organ-based tumor boards, which expose the students to the team-based approach for individualizing treatments that is practiced in the UVA Cancer Center. Prerequisite: Fundamentals in Cancer Biology
Credits: 2
Instructor: Purow/Gioeli
Time: 10:30am-12pm T,R
Prerequisites
MICR 8040 and MICR 8044
Description
This course will cover contemporary topics relevant to the detection and treatment of solid tumors and hematopoietic cancers. These include, but are not limited to, clinical trials, metabolism and cancer, cancer stem cells, cancer biomarkers, systems and networks in cancer. Students will attend organ-based tumor boards, which expose the students to the team-based approach for individualizing treatments that is practiced in the UVA Cancer Center. Prerequisite: Fundamentals in Cancer Biology
Credits: 2
Instructor: Rutkowski, Melanie
Time: 9-11am, R, *All Semester
Prerequisites
MICR 8200: Building Blocks of the Immune System and MICR 8203: Integration and Diversification of the Immune System or equivalent permission.
Description
The module will cover in depth selected contemporary topics in molecular and cellular immunology. Sessions are discussion-based and facilitated by faculty. Students will learn how to critically evaluate primary literature and to clearly present scientific information. Prerequisite: MICR 8200: Building Blocks of the Immune System and MICR 8202: Integration and Diversification of the Immune System or equivalent.permission.
Credits: 2 Class Limit: 15
Instructor: Derre, Isabelle
Time: 1:30-3:30pm W
Prerequisites
MICR 8401: Microbial Pathogenesis
Description
This course will discuss the grant process including applications for federal and foundation grants, proposal writing and submissions, and grant reviews. A research proposal (based loosely on guidelines for NIH postdoctoral fellowship grant application) on a selected topic in Microbial Pathogenesis will be developed by each student (or student teams).
Credits: 2
Instructor: Cliffe, Anna
Time: 1-2:30pm T
Prerequisites
MICR 8400 or equivalent, or consent of the course organizers
Description
This year’s focus will be the current topics on virus-host cell interactions
This module will cover recent topics from papers published in the past 12 months. Sessions will be based on published primary literature and will consist of discussions facilitated by the faculty with student participation heavily encouraged. Students will learn how to critically evaluate the primary literature and to clearly present scientific information. Topics will be focused primarily on host detection and defense mechanisms, and how viruses overcome these mechanisms to promote replication.
Session will consist of two journal articles/session. Each student enrolled in the course will present. Students are also required to write a short summary of the papers and discussion, which will be due prior to the following class.
Credits: 2
Instructor: Harris, Tajie
Time: 1:30-3:30pm, T
Prerequisites
None.
Description
This course will explore how reciprocal crosstalk between the central nervous system (CNS) and the immune system contributes to health and disease. Attention will be paid to highlight how immune responses contribute to neurological disorders such as multiple sclerosis, stroke, Alzheimers disease, depression, anxiety, and autism.
Credits: 2
Instructor: John Luckey
Time: 1-3pm R
Prerequisites
None.
Description
A series of joint lectures by basic and clinical scientists that focuses on the clinical context of a specific biomedical problem and the contemporary research that has resulted in major advances and treatment of the disease. Note: Students may take part II before part I of this course.
Credits: 2
Instructor: Carl Creutz
Time: 9 – 10:30 M,W,F
Prerequisites
Prerequisite: PHY 8040 & 8041: Physiology A & B recommended, PHAR 8100: Introduction to Pharmacology or permission of instructor
Description
The course will cover the major classes of therapeutically relevant drugs, and how they work at the molecular and cellular levels. The major topics include: general principles, chemical mediators, drugs affecting the central nervous system.
Following is the schedule for the Spring 1 (Feb 10-Mar 24) for 2020. Below there is a list of each course, to find out more about that course, click on that courses tab.
Key: Monday- (M), Tuesday- (T), Wednesday- (W), Thursday- (R), Friday- (F)
Note: Some courses may occur for the entire semester.
Credits: 1
Instructor: Jean Eby
Time: 3:30-5pm T
Prerequisites:
None.
Description:
Beginning in 1989, the National Institutes of Health introduced a requirement that institutions provide a program of instruction in the responsible conduct of research (NIH Guide for Grants and Contracts, Volume 18, Number 45, 1989). This was later expanded to require that all fellows on NIH training grants should receive instruction in the responsible conduct of research. The requirement does not specify a particular format or curriculum. However, recommendations are made that several areas should be covered in the instruction: conflict of interest, responsible authorship, policies for handling misconduct, policies regarding the use of human and animal subjects, and data management. This course is designed to help student consider each of these areas and therein formulate an understanding of responsible conduct in research.
Credits:
Instructor: Farber
Time: 1-2pm W *All Semester
Prerequisites:
None.
Description:
Each week, a UVA faculty member or guest lecturer will summarize current work in their area of research. The emphasis in these lectures will be on high-throughput genomic and bio-informatic approaches to elucidating the mechanisms of pathogenesis in human disease and disease models.
Credits: 3
Instructor: Farber
Time: 8:30-9:45am MW, all semester
Prerequisites:
BIOL 3010 or BIOL 4210 or instructor consent
Description:
The course will cover human genetics and genomics, including the human/mammalian genome variation, determination of genomic variation on phenotype and disease risk, mapping and characterizing genetic variants on phenotype, determining the putative impact of genetic variants on gene expression (transcriptomics, epigenomics), the promise and implications of genome science on precision medicine and the ethical, legal & social implications.
(Crosslisted with PHS 5705 and BIOC 5705)
Credits: 2
Instructor: Marieke Jones and David Martin
Time: 9-10:30am T, R
Prerequisites:
None.
Description:
The course format will include: lecture, web-based learning, group discussions, and practical laboratory exercises with stats software. Students will learn the basics of typical study designs and practical use of common statistical methods. Students will apply learning to reinforce skills and achieve practical competence in: identification of design and statistical resources, experimental design, evaluation of results, and data interpretation.
Credits: 2
Instructor: Lynch
Time: 1:30-2:45pm W, F
Prerequisites:
None.
Description:
The Translational Science Course is designed to prepare graduate students to engage in cutting-edge basic science discovery; understand proof-of-concept research and industrial designed experiments; innovate and invent; create valuable intellectual properties; optimize patent enablements and claims; interact with regulatory agencies; champion entrepreneurship and commercialization activities; and enhance societal impact of basic research.
Credits:2
Instructor: Smith
Time: 10:30am-12:00pm T, R
Prerequisites:
Description:
The Chromatin course modules are designed to provide students with an in-depth understanding of chromatin structure and function. In Chromatin I, the focus will be on chromatin structure and organization, nucleosome and chromatin remodeling factors, and the multiple histone modifying enzymes that regulate DNA-templated cellular functions such as transcription, DNA replication, and repair.
Credits:
Instructor: Nakamoto
Time: 9:30-10:45am T, R
Prerequisites:
BIOP 8020, Macromolecular Crystallography I
Description:
The course offers in depth coverage of theory and practical applications of X-ray diffraction methods to crystals of biological macromolecules and their complexes. Topics of the second module will cover phase determination, electron density interpretation, refinement, and model validation. Case studies will be presented by the students.
Credits: 2
Instructor: Dudley
Time: 1:30-3pm T, R
Prerequisites:
BIMS 6000 (CCIB)
Description:
This course examines the molecular basis of cancer and how environmental and hereditary factors cooperate to elicit the transformed phenotype and promote cancer progression. It is team taught by both basic scientists and clinical faculty, providing students with an introduction to clinical presentation, progression, and outcomes; genetic/cellular/tissue drivers of oncogenesis and metastasis; and therapeutic challenges for the treatment of cancer.
Credits: 2
Instructor: Bender, Ewald
Time: 10:30am – 12pm M, W, F
Prerequisites:
Previous Immunology class or permission of the instructor
Description:
This module will cover the different components of the adaptive and innate arms of the immune system with a focus on development and molecular pathways regulating these processes.
Credits: 1
Instructor: Mann
Time: 3 – 4:30pm R
Prerequisites:
None.
Description:
The course will cover the science and policies governing the study of select agents, and emerging infectious diseases. Topics will include, but are not limited to pathogen characteristics, regulatory requirements, recognition and detection of intentional and natural outbreaks, emergency preparedness and interfaces with public health.
Credits: 6
Instructor: Kucenas Deppman, Condron Patel, and Gaultier Scott
Time:8-10 am M, T, W, R, F
Prerequisites:
None.
Description:
This advanced course introduces critical areas in neuroscience. In 3 sections, it covers: Molecular, Cellular, & Dev Neuroscience, Systems & Circuits, & Behavior & Disease. Will explore: nervous sys development, basic principles of neurobio, membrane & action potential, ion channels, synaptic transmission & modulation, brain structures, sensory & motor circuits, neurological disease, animal models used to study them & the clinical context.
Credits: 2
Instructor: Luckey
Time:1-3pm W
Prerequisites:
None.
Description:
This is a series of joint lectures by basic and clinical scientists that focuses on the clinical context of a specific biomedical problem and the contemporary research that has resulted in major advances and treatment of the disease. Note: Students may take part II before part I of this course. This is a series of joint lectures by basic and clinical scientists that focuses on the clinical context of a specific biomedical problem and the contemporary research that has resulted in major advances and treatment of the disease.
Credits:2
Instructor: Harris
Time: 8:00-11:0am T
Prerequisites:
Instructor Permission.
Description:
This course will help students learn to effectively communicate scientific concepts and proposals in the field of Pharmacology. Trainees will practice effective science writing and will participate in extensive peer and faculty workshop sessions as they prepare materials for their Advancement to Candidacy Exam or for an NIH NRSA-style fellowship application.
Credits: 2
Instructor: Sonkusare
Time: 8:30-10:00am M, W, F
Prerequisites:
None.
Description:
The course will integrate background cellular and molecular knowledge into organ systems and whole animal, function. It is intended to provide the ability to integrate knowledge at the molecular level into function, the foundation of translational-based research. The physiology to be covered will include the nervous system, metabolism and endocrine systems.
Credits:2
Instructor: Isakson
Time: 2-3pm W, R, F
Prerequisites:
PHY 8040
Description:
The class covers the broad range of vascular biology from the basic science to clinical implications. The class integrates new methods in the field and relationships to heart function.
Following is the schedule for the Spring 2 (Mar 25 – May 8) for 2020. Below there is a list of each course, to find out more about that course, click on that courses tab.
Key: Monday- (M), Tuesday- (T), Wednesday- (W), Thursday- (R), Friday- (F)
Note: Some courses may occur for the entire semester.
Credits: 1
Instructor: Jean Eby
Time: 3:30-5pm T
Prerequisites:
None.
Description:
Beginning in 1989, the National Institutes of Health introduced a requirement that institutions provide a program of instruction in the responsible conduct of research (NIH Guide for Grants and Contracts, Volume 18, Number 45, 1989). This was later expanded to require that all fellows on NIH training grants should receive instruction in the responsible conduct of research. The requirement does not specify a particular format or curriculum. However, recommendations are made that several areas should be covered in the instruction: conflict of interest, responsible authorship, policies for handling misconduct, policies regarding the use of human and animal subjects, and data management. This course is designed to help student consider each of these areas and therein formulate an understanding of responsible conduct in research.
Credits:
Instructor: Farber
Time: 1-2pm W *All Semester
Prerequisites:
None.
Description:
Each week, a UVA faculty member or guest lecturer will summarize current work in their area of research. The emphasis in these lectures will be on high-throughput genomic and bio-informatic approaches to elucidating the mechanisms of pathogenesis in human disease and disease models.
Credits: 3
Instructor: Farber
Time: 8:30-9:45am MW, all semester
Prerequisites:
BIOL 3010 or BIOL 4210 or instructor consent
Description:
The course will cover human genetics and genomics, including the human/mammalian genome variation, determination of genomic variation on phenotype and disease risk, mapping and characterizing genetic variants on phenotype, determining the putative impact of genetic variants on gene expression (transcriptomics, epigenomics), the promise and implications of genome science on precision medicine and the ethical, legal & social implications.
(Crosslisted with PHS 5705 and BIOC 5705)
Credits: 2
Instructor: Marieke Jones and David Martin
Time: 9-10:30am T, R
Prerequisites:
None.
Description:
This course introduces methods, tools, and software for reproducibly managing, manipulating, analyzing, and visualizing large-scale biomedical data. Specifically, the course introduces the R statistical computing environment and packages for manipulating and visualizing high-dimensional data, covers strategies for reproducible research, and culminates with analysis of data from a real RNA-seq experiment using R and Bioconductor packages.
Credits:2
Instructor: Smith
Time: 10:30am-12:00pm T, R
Prerequisites:
Description:
The Chromatin course modules are designed to provide students with an in-depth understanding of chromatin structure and function. Chromatin II will focus on the functional aspects of chromatin organization and regulation. The course will meet two days a week, with time split between faculty presentations that introduce a topic and provide key information, and more interactive sessions that will involve discussions of primary literature.
Credits: 2
Instructor: Bekiranov
Time: MWF 3:00-3:50
Prerequisites:
Description:
BIOC 8145 provides the statistical and programming background as well as introduction to software tools that enable analysis of functional genomics data sets. The course will focus on identifying single nucleotide and structural variants from genomic data, gene expression changes from RNA-seq and PRO-seq data, factors that regulate gene expression including transcription factors (TFs), histone modifications and chromatin state from ChIP-seq and ATAC-seq data and cellular composition and single cell gene expression from scRNAs-seq. Students will learn UNIX basics, statistics associated with each analysis approach, programming in R, and analysis of RNA-seq, PRO-seq, scRNA-seq, ChIP-seq and ATAC-seq data using R/Bioconductor and UNIX-based software tools. Students will also learn how to perform TF DNA motif and GO/pathway enrichment analysis.
Credits: 2
Instructor: Nakamoto
Time: 9:30-10:45am T, R
Prerequisites:
BIMS 6000 (CCIB)
Description:
This course will introduce students to some of the physical and chemical underpinnings of molecular biophysics. Physical principles will be discussed and related to how they govern biological systems and how they enable important biophysical techniques. Topics: Equilibrium thermodynamics: mean behavior of ensembles at equilibrium, and Biological fluctuations: deviations from the mean
Credits: 2
Instructor: Lu
Time: 10am -12pm T, R
Prerequisites:
BIMS 6000 (CCIB)
Description:
This module will cover topics not discussed in the Core Course and provide depth to topics covered in less detail. These will include, but are not limited to membrane biogenesis and trafficking, cytoskeleton dynamics and regulation, cell adhesion and motility, cell polarity, cell cycle control and regulation. The course will be primarily literature-based and emphasis will be placed on model systems, experimental design and data interpretation.
Credits: 2
Instructor: Gioeli
Time: 1:30-3pm T, R
Prerequisites:
MICR 8040
Description:
This course is a follow-up to Fundamentals in Cancer Biology. It examines hormonal regulation and signal transduction pathways in breast cancer and leukemia/lymphoma. Clinical and basic science faculty again team up to provide students with a comprehensive view of clinical aspects (early detection, diagnosis, epidemiology, prognosis, treatment, and prevention) and experimental strategies that reveal basic mechanisms underlying these diseases.
Credits: 2
Instructor: Bender/ Ewald
Time: 10:30am-12pm M, W, F
Prerequisites:
Building Blocks of the Immune System
Description:
This module will cover how the diverse components of the immune system are integrated and how this integration influences further maturation and differentiation of elements of the immune system under physiological and patho-physiological conditions. This will include responses to different types of pathogens.
Credits: 2
Instructor: Criss, Rekosh
Time: 1-3pm M, W, F
Prerequisites:
BIMS 6000 (CCIB)
Description:
This foundational module will cover fundamentals of the biology of bacteria and viruses. Bacteriology topics to be discussed include bacterial physiology, genetics, and gene regulation, and how these and other features impact drug discovery and pathogenesis. Virology topics to be discussed include virus structure and assembly, viral replication, viral genetic regulation, virus/immune interactions, and applications of viruses in 21st century.
Credits: 2
Instructor: Lu/ Deppman
Time: 1-3pm M, W, F
Prerequisites:
None.
Description:
This course will provide the strong foundation in signal transduction in developing neurons. Upon completion of this course, students will understand signal transduction in neural development and beyond. This will be a combination of lecture and discussion of classic and contemporary literature.
Credits: 2
Instructor: Zhu, Stometta
Time: 9-11am W, F
Prerequisites:
None.
Description:
We will highlight mechanisms that allow the nervous system to produce complex behaviors. Using a bottom-up approach beginning with classical descriptions of ion channels & the mathematical models used to understand their gating properties. We describe how neurons communicate via chemical and electrical synapses. Finally, we describe how the specific connections among neurons enable structures in the brain to carry out complex tasks.
Credits: 2
Instructor: Luckey
Time: 1-3pm W
Prerequisites:
None.
Description:
This is a series of joint lectures by basic and clinical scientists that focuses on the clinical context of a specific biomedical problem and the contemporary research that has resulted in major advances and treatment of the disease. Note: Students may take part II before part I of this course. This is a series of joint lectures by basic and clinical scientists that focuses on the clinical context of a specific biomedical problem and the contemporary research that has resulted in major advances and treatment of the disease
Credits: 2
Instructor: Sonkusare
Time: 8:30-10:00 M, W, F
Prerequisites:
PHY 8040 or permission of instructor
Description:
The course will integrate background cellular and molecular knowledge into organ systems and whole animal, function. It is intended to provide the ability to integrate knowledge at the molecular level into function the foundation of translational-based research. Specifically, the physiology to be covered will include the heart, vasculature, kidney, GI, and muscle.
Credits: 2
Instructor: Isakson
Time: 2-3pm W, R, F
Prerequisites:
PHY 8040 and PHY 8052
Description:
The class covers the broad range of vascular biology from the basic sciences to the clinical implications. In addition, the class integrates new methods in the field and relationships to heart function.
BIMS Master Course schedule for 2019-2020. Please notice tabs across the top of the document.