Events

Sep 19
Lisa Tucker-Kellogg
Center for Computational Biology and Program in Cancer and Stem Cell Biology -- Duke - NUS Medical school

Evolution of Drug-Resistance in Cancer: Computational Modeling of Combination Treatment and the Dynamics of Cellular Subpopulations

Sep 20
John Rawls, Helen Binns, Catherine Lozupone, Curtis Huttenhower
Duke University, Northwestern University, University of Colorado, Harvard T.H. Chan School of Public Heatlh

Pediatric Obesity Microbiome and Metabolism Mini-Symposium

  • September 20, 2018 12:00pm to 1:00pm

    UPGG Distinguished Lecture Series

  • September 24, 2018 8:30am to 10:00am

    Children's Health & Discovery Initiative: Shining Evolutionary Light on Human Sleep and Health

    Location: Trent Semans Center, Room 3025 (Classroom 3)Charles Nunn is Professor of Evolutionary Anthropology and Global Health at Duke University, and Director of the Triangle Center for Evolutionary Medicine (TriCEM). Charlie uses evolutionary approaches to understand and improve human and animal health. He and his research group investigate the ecology of infectious disease, the evolution of sleep, and the links between ecology, evolution and global health. They investigate these topics using phylogenetic methods, mathematical modeling, and fieldwork in Madagascar, Kenya and other locations. He is the author of Infectious Diseases of Primates: Behavior, Ecology and Evolution and The Comparative Approach in Evolutionary Anthropology and Biology.Children’s Health & Discovery Initiative: “Great Minds Think for Kids” Seminar and Brainstorming Series The goal of the Children’s Health & Discovery initiative (CHDI) is to foster multidisciplinary and innovative research that will positively impact childhood and lifelong health. As part of our goal of fostering multidisciplinary collaborations, the CHDI is holding seminar/brainstorming sessions, which we’ve termed “Great Minds Think for Kids”. These sessions will include a 40-minute research-in-progress talk from a guest speaker, followed by a 40-minute brainstorming/group discussion session led by the guest speaker and a member of the CHDI scientific leadership.

  • September 24, 2018 11:30am to 12:30pm

    Bottom-up Assembly of Microbial Communities: Modeling, Analysis and Engineering

    Host: Lingchong YouLocation: 4233 French

  • September 25, 2018 5:00pm

    Genetic dissection of trait variation between long-diverged species

    Host: Paul MagweneLocation: Room 147, Nanaline Duke

  • October 1, 2018 11:30am to 12:30pm

    Computational Biology Seminar

    Host: Yuning ZhangLocation: 4233 French

  • October 2, 2018 12:00pm to 1:00pm

    New approaches to probe computations in neural circuits using single-neuron perturbations

    Location: Bryan Research 103Dr. Harvey will present new worked aimed at identifying computations performed in local neuronal populations. They have developed a method based on two-photon imaging and two-photon optogenetics to measure the causal, functional connectivity in a population of neurons with characterized activity patterns and tuning. We call this method influence mapping - a measure of how one neuron's spiking causally affects spiking in its neighbors. They have applied this method in mouse V1 to reveal new functional relationships between tuned neurons. He will also discuss applications of influence mapping to the study of computations for flexible sensorimotor decision-making.

  • October 2, 2018 12:30pm to 1:30pm

    UPGG Tuesday Seminar Series

    Host: Jorn CoersLocation: Room 147, Nanaline Duke

  • October 2, 2018 1:00pm to 5:00pm

    Introduction to DNA Sequencing Technologies

    Registration Deadline: Sept. 24Location: 2240 CIEMASCost: FreeDuring the past decade, a new generation of high-throughput DNA sequencers has transformed biomedical and biotechnology research. These new technologies have fostered the development of a wide range of applications to basic and clinical research, including SNP discovery, transcriptome profiling, genome sequencing, and epigenetics. The goal of this introductory course is to teach the basic principles of next generation sequencing technology (NGS) and to present an overview of various library preparations and their applications. Advantages and limitations of various methods will be discussed and compared across technologies/platforms (Illumina, PacBio, Oxford Nanopore, Ion Torrent). This course will also provide an introduction to primary data analysis and data quality assessment steps. Attendees will become familiar with NGS technology terms and fundamentals, NGS data format and quality, and will acquire a better understanding of how to choose a suitable NGS sequencing method or instrument for their study.Register

  • October 9, 2018 12:30pm to 1:30pm

    UPGG Tuesday Seminar Series

    Host: Ryan BaughLocation: Room 147, Nanaline Duke

  • October 10, 2018 12:00pm to 1:00pm

    Systems genomics and gene networks in neuro- developmental and neurodegenerative disorders

    Location: Bryan Research 103Advances in genetics and genomics have begun to deliver on their promise to expand our understanding of nervous system function in health and disease. One of the interesting challenges that perhaps paradoxically has emerged from these successes is an understanding of the profound genetic heterogeneity and complexity of most nervous system disorders. For example in Autism Spectrum Disorder (ASD), over a hundred of probable risk loci have been identified, none of which account for more than 1% of cases. This has led to what we consider to be a central question highly relevant to precision health approaches: will we have to treat each rare genetic form as a unique condition, or will there be convergence on a smaller number of shared pathways? I will highlight advances in the genetics of ASD and discuss integrative genomic approaches such as genome-wide transcriptional profiling that inform this important issue and that do suggest a substantial level of convergence. These studies provide a quantitative framework for functional investigation of disease mechanisms with a goal of accelerating therapeutic development.

  • October 15, 2018 11:30am to 12:30pm

    Understanding Familial Cardiomyopathies from the Ground Up

    Host: Debraj GhoseLocation: French 4233

  • October 16, 2018 12:30pm to 1:30pm

    UPGG Tuesday Seminar Series

    Host: Purushothama Rao TataLocation: Room 147, Nanaline Duke

  • October 22, 2018 11:30am to 12:30pm

    Adaptive priors for estimating effect sizes with sequence count data

    Host: Greg WrayLocation: 4233 French

  • October 23, 2018 12:30pm to 1:30pm

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

    Host: Joe HeitmanLocation: Room 147, Nanaline Duke

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

    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

    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 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 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

    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

    UPGG Distinguished Lecture Series

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

    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

    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

    Computational Biology 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 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