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.

BIMS Module Schedule, 2019 - Fall 1

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.

BIMS Module Schedule, 2019 - Fall 2

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.

BIMS Module Schedule, 2020 - Spring 1

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: Sharlow and Lazo

Time: 1:30-3:30pm T, R

Prerequisites:

None.

Description:

This advanced course explores the molecular entities popular for existing and new medicines and the strategies used to validate these targets for drug design and development. We will discuss the impact of diseases on human life, the evolution of drug discovery, and the “exploitable” chemical universe. Included are case studies focusing on how specific drugs were “born” and how they facilitated new understandings about biology and disease. Prerequisite: None, but an understanding of human physiology, cell biology and signaling, and biochemistry is necessary.

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.

BIMS Module Schedule, 2020 - Spring 2

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:

Instructor: Sharlow & Lazo

Time: 1:30-3:30pm T, R

Prerequisites:

None.

Description:

This advanced course delves into the current and future technologies useful for uncovering the drugs of today and which are driving drug discovery into the future. Topics will include “dirty drugs” (or polypharmacology), pharmacogenomics, drug repurposing, theranostics, famous drug failures and drug resurrections, and advanced drug delivery systems. Prerequisite: None, but an understanding of human physiology, cell biology and signaling, and biochemistry is necessary.

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.