Oct 22
Dwight Koeberl, M.D., Ph.D., Heather Whitson, M.D., M.H.S., & Paula Tanabe, Ph.D., M.S.N.
Duke University School of Medicine and Duke School of Nursing

CHDI Seminar: Promoting Life Course and Disparities Research: The CTSA Special Populations Core

Oct 23
John Boothroyd
Stanford University, School of Medicine, Dept of Microbiology & Immunology

The Challenge of Living in a Bubble: How Toxoplasma gondii Manipulates Host Cell Cycle from Inside a Parasitophorous Vacuole.

  • October 25, 2018 12:00pm to 1:00pm

    Butterfly spots and rattlesnake tales: The evolution of novelty

    UPGG Distinguished Lecture Series

  • October 26, 2018 9:00am to 12:00pm

    An Overview of Risk Prediction and Classification in Omics Settings

    Registration Deadline: Oct. 8, 2018Location: 2240 CIEMASCost: FreeThis course has two objectives. First, it seeks to develop an understanding of risk prediction and classification in the Omics setting. Second, for researchers who plan to develop risk models, this course seeks to provide concrete steps for study design, analysis, and interpretation. To accomplish these goals, we will discuss how different aspects of a statistical model can provide measures of association or measures of predictive accuracy. This distinction is important in understanding how developing a model for association/etiology/causal inference is conceptually different from using the model to predict. We will then discuss risk models in the conventional setting: larger sample sizes with a smaller number of predictors. We will cover study design, statistical models, and performance metrics. The course seeks to develop an appreciation of challenging considerations in the field, but also seeks to provide clear steps on how to proceed. Finally, we will review areas of active research and in what direction the field is moving. After establishing foundations, we will move into the Omics realm, which is characterized by smaller samples sizes and thousands of predictors. Prediction models in Omics often use machine-learning techniques, so we will cover some common machine-learning techniques and what makes them different from more conventional models. We will review current best practices with an emphasis on estimating performance. This course will not include any hands-on coding because of time limitations, but this will be the topic of a future course. The course focuses on understanding the most important aspects of risk prediction and classification.Register

  • October 29, 2018 8:00am to November 2, 2018 12:00pm

    Introduction to Scientific Computing for Genomics

    Date: Oct. 29, 30, 31, and Nov. 2, 2018; 8 A.M. - 12 P.M. each dayRegistration Deadline: Oct. 19, 2018Instructor: Hilmar LappLocation: 2240 CIEMASCost: $200 for faculty, postdocs and staff; Free for grad studentsComputing has become an integral and indispensable part of genomic biology. This course teaches basic skills in scientific computing, with a focus on applications for genomic science, aimed at making you more productive, your computational work more reliable, and your research easier to reproduce and extend, including by your future self. The course includes introductions to (1) using Unix shell commands to efficiently find, organize, and stage data for analysis; (2) basic data types, control flows, functions, and 3rd party packages for the Python programming language commonly encountered in scientific computing; (3) using version control to manage with confidence the numerous directions research code takes from inception to publication; and (4) techniques for optimizing how your computational analyses run on a high-performance computing cluster. The format of the course is inspired by the acclaimed Software Carpentry-style bootcamps. Hence, this is a fully hands-on workshop, and students are expected to bring a laptop.Pre-requisites: "Introduction to Unix" (or equivalent experience).Register

  • October 29, 2018 11:30am to 12:30pm

    CBB Seminar: Mechanistic models of recent admixture histories

    Host: Jenny TungLocation: French 4233

  • October 30, 2018 12:30pm to 1:30pm

    Sex-specific mating shapes genetic variation in the admixed population of Cape Verde

    UPGG Tuesday Seminar SeriesHost: Jenny TungLocation: Room 147, Nanaline Duke

  • October 30, 2018 1:00pm to 5:00pm

    Fundamentals of Mass Spectrometry from Proteomic & Metabolomic Analysis

    Registration Deadline: Oct. 22, 2018Location: 2240 CIEMASCost: FreeLiquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) continues to be the key technology for the qualitative and quantitative analysis of peptides, proteins and metabolites for both basic and clinical research projects. This GCB Academy session is designed as an introduction for researchers needing to expand their knowledge of the use of LC/MS/MS-based methods for proteomics and metabolomics, and thus help researchers better understand how these technologies can help inform their research goals. Background material in basic protein/metabolite chemistries will be provided, with an emphasis on how to use the physicochemical characteristics of these biomolecules for sample preparation specifically for LC/MS/MS analyses. In addition, the fundamentals of liquid chromatography and mass spectrometry will be discussed to enable students to understand the nuances of the experimental designs required to address their specific project. Real-world examples will be used to illustrate sample preparation and analysis strategies, including basic identification projects, characterization of Post-Translational Modifications and differential expression analyses (including 'omic biomarker discovery and targeted biomarker verification).Register

  • November 6, 2018 12:30pm to 1:30pm

    UPGG Tuesday Seminar Series

    Host: Jenny TungLocation: Room 147, Nanaline Duke

  • November 7, 2018 12:00pm to 1:30pm

    NSF Convergence Workshop

    Location: Holsti-Anderson Assembly Room (Rubenstein 153)Growing Convergence Research is one of NSF's 10 Big Ideas and focuses on centering research around a complex societal problem that involves multiple disciplines. This workshop will focus on ways in which faculty can demonstrate convergence research, as it is becoming more and more of an expected requirement in NSF research proposals.Lunch providedRegistration Required

  • November 8, 2018 9:00am to 1:00pm

    RNA-Seq Analysis

    Limited to 12 participantsRegistration Deadline: Oct. 29, 2018Location: Old Chem 101Cost: $50 for faculty, postdocs and staff; Free for grad studentsThis 4-hour tutorial will provide you with a better understanding of the data processing and analysis methods that are used in RNA-seq analysis. We will cover topics such as data quality control, normalization, and calling differentially expressed genes. We will provide hands-on experience that will allow you to go back to your lab and work with your own data.Pre-requisites: "Introduction to Unix" and "Introduction to Scientific Computing for Genomics" (or equivalent experience).Register

  • November 8, 2018 1:00pm to 5:00pm

    Experimental Design: Get the Most Out of Your Proteome

    Registration Deadline: Oct. 29, 2018Location: 100 North BuildingCost: FreeThis course will provide an in-depth overview of experimental design, focusing on proteomic analysis of protein post-translational modifications (PTMs) and protein expression in (but not limited to) mammalian cells, tissues and biofluids. Topics will be aimed at getting maximum biological information from your samples. We will discuss methods for enriching subproteomes and PTMs; best practices for insuring sample integrity and avoiding common contaminants that will be carried downstream; and how to be aware of additional factors that might influence reproducibility across biological replicates. In addition, we will discuss where discovery-based or targeted proteomic analyses may be most appropriate. Feel free to bring specific questions about your favorite proteins, model systems, or biological matrices. Prerequisite: Fundamentals of Mass Spectrometry for Proteomic and Metabolomic Analyses, encouraged, but not required.Register

  • November 8, 2018 4:00pm to 7:00pm

    Second Annual Invented at Duke Celebration

    Duke OLV and Duke I&E’s #InventedatDuke Celebration is an opportunity to meet with University researchers commercializing technologies generated by the more than $1 billion in research conducted annually at Duke.Join us and discover how Duke has been innovating this year. Connect with Alumni, entrepreneurs, CEOs, and investors while exploring our featured innovators as they show off their inventions and novel ideas.This event will honor this past year's Duke faculty, staff, and student innovators whose research and ideas have the potential to improve and save lives.After drinks and hors d'oeuvres, we will hear special remarks around 5:30 from this year's guest speaker Nathan Kundtz, CEO of Kymeta, a company spun out of the David Smith labs at Pratt Engineering. Learn more about KymetaIf you are an inventor, researcher, licensee, investor, entrepreneur or someone interested in partnering with Duke, we hope you’ll join us for our 2nd Annual #InventedAtDuke Celebration.CHECK OUT LAST YEAR’S EVENTRSVP**Please note: We will have shuttles running continuously from the Washington Duke/JB Duke to Penn Pavilion from 4-7:30pm. Starting at 6pm, we will have shuttles running to the Chesterfield for Pratt's BOV cocktail party until 7:30pm**Featured InnovatorsCereius aims to improve the lives and survival of patients facing solid tumor brain metastasis through the use of personalized and highly targeted radiotherapy. Mike Zalutsky (Radiology) and Kim Blackwell (Medicine)CEO: Ed Field (Duke Alumni and President of BioLabs, North Carolina)TRPblue is a therapeutics company developing a unique, dual acting inhibitor that targets transient receptor potential (TRP) cation channels TRPV4 and TRPA1. TRPblue has developed small molecule antagonists that preferentially attenuate signaling of these calcium-permeable channels with proven efficacy in several acute pain and chemical denervation nerve-pain models. These inhibitors have also demonstrated anti-pruritic, anti-fibrotic and anti-inflammatory activity in relevant preclinical models. The team will develop a topically applied, highly tolerated go-to dermatology therapeutic.Inventors: Wolfgang Liedtke (Neorology)Management: Barney KoszalkaEric Benner, Assistant Professor of Pediatrics, will feature his myelin, proteins and phospholipids mixture that forms a whitish insulating sheath around many nerve fibers, repair technology which uses oxysterols to promote myelin repair for white matter damage.Duke Health Video of Dr. Benner: Robotics have invented a specialized processor for generating safe robot motion plans in microseconds, enabling robots to function in unstructured, collaborative workspaces, reacting to other movements as soon as they are perceived. Dan Sorin, George Konidaris (Electrical & Computer Engineering)CEO: Peter Howard (Four startups, two IPOs, one strategic exit in robotics)Zephyr Mobility is a Pratt School of Engineering student startup building a new way to transfer disabled patients in and out of hospital beds.Inventor: Sam Fox (Pratt Grad)Funding from DIHIFacebook page: Story:, Teaching Assignment Management System is a software application developed at the School of Nursing that helps predict teaching efforts needed for university courses and assign faculty to those courses. This has been recently licensed to George Washington and University of IllinoisInventors:  David Bowersox/David Parrish (Nursing)Management: Michael EvansSchool of Nursing News: Review: Lotion is the developer of antiperspirant solutions for all the neglected, sweaty areas of the body:  Hands, feet, and soon, far more. Our mission is simple: Stop the sweat, no matter where you sweat, why you sweat, or how you sweat.  Founded by then-UNC sophomore David Spratte and Duke sophomore Kasper Kubica in 2014, Carpe has grown into a top-selling brand on Amazon and reached millions of Americans with its nationwide presence at CVS.Inventors:  Kasper Kubica (Duke Grad)I&E Video: Water Marc Deshusses, professor of civil and environmental engineering at Duke University, is working on a project funded by the Gates Foundation to "Reinvent the Toilet." His supercritical water oxidation technology has been implemented into a prototype on campus, which Deshusses hopes will mark the beginning of a sanitation revolution for millions of people around the world.Inventor:  Marc DeshussesDuke Video:

  • November 9, 2018 1:00pm to 4:00pm

    Proteomic Data Analysis: Strategies and Software Solutions

    Registration Deadline: Oct. 30, 2018Location: 2240 CIEMASCost: FreeLiquid chromatography coupled with mass spectrometry (LC/MS) is a versatile tool for the qualitative and quantitative characterization of peptides, proteins and metabolites for both basic and clinical research projects. One of the most important considerations in being able to translate LC-MS datasets into meaningful biological observations is to effectively use open source software packages and/or online resources geared toward LC-MS based datasets.  This GCB Academy session is designed as a complement to GCB Academy course “Fundamentals of Mass Spectrometry for Proteomic and Metabolomic Analyses” (Nov. 7) and GCB Academy course “Experimental Design: Get the most your of your proteome” (Nov. 8) and is intended for users of the Proteomics and Metabolomics Shared Resource who have or plan on generating LC/MS based Proteomic Datasets with the Shared Resource. This first portion of the course will focus on the effective use of Scaffold to characterize qualitative proteomic datasets. This will include an overview of Scaffold and features such as interpretation of spectral matches at a protein or peptide level, gene ontology classification, homology matching, spectral count data, and data export. The second portion of the course will cover common proteomic data analysis strategies from supplemental data (typically .xlsx file formats from Rosetta Elucidator) provided as part of the Shared Resource’s quantitative proteomic workflows. This will include an overview of the typical features of a quantitative data return document, various data summarization levels, calculating peptide/protein relative fold-changes and p-values, exporting data for motif analysis (PTM specific datasets), and performing Principle Component Analysis (PCA) and 2D Clustering within JMP Pro.Register

  • November 12, 2018 11:30am to 12:30pm

    CBB Seminar: Environmental ‘Omics: exploring the molecular mediators and modifiers of environmental exposures.

    Host: Debraj GhoseLocation: French 4233

  • November 13, 2018 12:30pm to 1:30pm

    Neuronal Cilia in Feeding Behavior and Obesity

    UPGG Tuesday Seminar SeriesHost: Sarah GoetzLocation: Room 147, Nanaline Duke

  • November 13, 2018 1:00pm to November 14, 2018 5:00pm

    Strategies for Metabolomic Data Collection, Analysis & Interpretation

    Registration Deadline: Nov. 5, 2018Location: 2240 CIEMASCost: FreeMetabolomics has emerged as a powerful approach for characterization of molecular systems and also development of biomarkers for disease progression or diagnosis. Broadly, metabolomics is the characterization of small molecules by mass spectrometry and can include both "unbiased" or non-targeted techniques, as well as "targeted" methods. A common misconception in the use of metabolomics is that non-targeted metabolomics can capture the majority of metabolites in any sample type; however, unlike proteomics, metabolomic analysis of any sort is inherently biased based simply on the type of solvent extraction used to isolate the metabolites. Given these complexities, the most important aspect for a successful metabolomics study is deciding which technique to use and understanding the data each approach will likely be able to provide. In this introductory course, we will utilize case studies to discuss the critical differences in targeted and non-targeted metabolomics and an investigator might choose one over another. For non-targeted metabolomics, the course will cover current methods for identification and quantification using publicly available tools as well as methods for analysis of high dimensional datasets. For targeted metabolomics, the course will cover methods for accurate quantification, how to enable longitudinal translation of metabolomics assays, and tools focused on targeted pathway mapping.Register

  • November 15, 2018 9:00am to 1:00pm

    Single-cell RNA-Seq

    Limited to 12 participantsRegistration Deadline: Nov. 5, 2018Location: 101 ChemCost: $50 for faculty, postdocs and staff; Free for grad studentsThis 4-hour hands-on tutorial will provide you with experience working with data from a single-cell RNA-Seq experiment. We will cover quality control, filtering, normalization, clustering, differential expression and mark identification analysis.Pre-requisites: Must have previously taken the GCB Academy “RNA-Seq Analysis” course.Register

  • November 15, 2018 12:00pm to 1:00pm

    Epigenomics of neuronal diversity and connectivity in the brain

    UPGG Distinguished Lecture Series

  • November 19, 2018 11:30am to 12:30pm

    CBB Seminar: Expanding the structural biology toolbox with high-resolution cryo-electron microscopy.

    Host: Paul MagweneLocation: 4233 French

  • November 20, 2018 12:30pm to 1:30pm

    Copy number variation in vertebrate evolution and human disease

    UPGG Tuesday Seminar SeriesHost: Joseph HeitmanLocation: Room 147, Nanaline Duke

  • November 26, 2018 11:30am to 12:30pm

    CBB Seminar: Finding copy number variants relevant to vertebrate evolution and human disease

    Host: Paul MagweneLocation: 4233 French 

  • November 27, 2018 12:30pm to 1:30pm

    Moving beyond microbiome-wide associations to identifying causal microbes

    UPGG Tuesday Seminar SeriesHost: John RawlsLocation: Room 147, Nanaline Duke

  • December 3, 2018 11:30am to 12:30pm

    CBB Seminar

    Host: Bruce DonaldLocation: French 4233

  • December 4, 2018 12:30pm to 1:30pm

    UPGG Tuesday Seminar Series

    UPGG Tuesday Seminar SeriesHost: Jeffrey BourgeoisLocation: Room 147, Nanaline Duke

  • December 7, 2018 9:00am to 10:30am

    Introduction to Biobanking

    Registration Deadline: Nov. 27, 2018Location: 2240 CIEMASCost: FreeThis seminar will offer an introductory overview of key considerations and best practices in establishing and maintaining clinical biospecimen collections for genomic and precision medicine research. Topics covered will include:  basic concepts in biobank and cohort research; role of standardization, harmonization, and quality control; maintaining unique sample identification and robust chain-of-custody tracking; need for secure information and inventory management systems for samples and data; important considerations in repository design; and an overview of biobanking resources at Duke and beyond.Register

  • December 10, 2018 11:30am to 12:30pm

    CBB Seminar: Measuring, manipulating and modeling chromatic regulation of neuronal gene expression

    Host: Paul MagweneLocation: 4233 French

  • December 14, 2018 8:00am to 10:00am

    Refresher on Medical Genetics and Genome Medicine

    Registration Deadline: Dec. 4, 2018Location: DMP2W91Cost: FreeCourse summary: This 90-minute course will provide attendees with an overview of general principles of genetics, genomics and molecular biology, and clinical applications and technologies currently used in clinical practice. In particular, the course will provide an overview of genomics, genome-wide association studies and other large initiatives and a range of testing technologies for diagnosis and treatment. Introduction of new technologies such as liquid biopsies will also be briefly discussed. Continuing education credits will be available.Register