“2019 R for Bioinformatics" Workshop – USC Libraries Bioinformatics

The USC Libraries Bioinformatics Service is pleased to present the 2019 R for Bioinformatics workshop. Knowing how to use R is a valuable skillset as numerous open access and cutting-edge tools for various genomic data analyses are written in R.  This full-day workshop is aimed at training participants to achieve basic competency in using R for simple bioinformatics tasks, which will form the foundation for other more specialized and advanced R analysis packages. This is a beginner workshop and no prior R knowledge is required.

Topics Covered 
• Introduction to R and learning R for bioinformatics
• Using RStudio – an integrated development environment for R
• The general context and concepts of R programming
• Commonly used functions for wrangling bioinformatics data
• Practical examples of wrangling bioinformatics data
• Visualization – creating plots using R
• Bioinformatics Package Repositories: CRAN and Bioconductor

The workshops will be conducted at both UPC and HSC. You will be required to bring your own laptops.

UPC:      9am to 4.30pm, Wednesday, October 30th, 2019
Learning Center, Wilson Dental Library (DEN21) 

HSC:      9am to 4.30pm, Tuesday, November 19th, 2019  
Computer Classroom (2nd Level), Norris Medical Library

Limited to 20 participants per workshop. Due to high demand, please register only if you are sure you would be able to attend. Attendance will be checked and no-shows may be subjected to restriction of future bioinformatics services.

Please register at:
https://usc.qualtrics.com/jfe/form/SV_835wUPfkfMXvY1L

Also, we understand that the demand and popularity of R workshops is extremely high and many of you may not be successful in your registration. We have specially packaged last year’s R workshop into a series of online videos where you can learn the same R workshop contents at your own pace. The videos and training materials are available at https://libguides.usc.edu/c.php?g=913498.

Overcoming Research Anxiety: A Mindful Approach to Literature Review Searching

Presented by Kevin Klipfel, Instructional Design & Assessment Librarian, and Elizabeth Galoozis, Head of Information Literacy

This workshop will discuss psychological strategies for approaching literature reviews, such as adopting a process-oriented “growth” mindset toward research, as well as several practical search techniques that will help you feel confident both getting started with your research and knowing when your literature review is complete. Though this workshop is intended for graduate students, all are welcome.

In-person: Thursday, November 7, 3:30-4:30, Leavey Library 113J: More information and RSVP
Online: Tuesday, November 19, 3:00, 4:00: More information and RSVP

Using Zotero to Organize Your Research

At this workshop, get an introduction to, and hands-on practice using, the free, open-source software Zotero, which can help you organize and cite sources. Zotero is particularly good at capturing web content and for creating group and public "libraries" of sources. Bring a laptop or tablet that you normally use for research.

Presented by Elizabeth Galoozis, Head of Information Literacy, USC Libraries

In-person:
• Tuesday, October 22, 12:00-1:00, Leavey Library 113H: More information and RSVP
• Thursday, November 21, 12:30-1:30, VKC Library B40E - Multi-Media Room: More information and RSVP

Online:
• Tuesday, October 29, 2:00-3:00: More information and RSVP
• Monday, November 18, 3:30-4:30: More information and RSVP

HEB Seminar | Dr. Lindsey Schier

HEB Seminar Schier by uscbiscgrad on Scribd

QCB Colloquium | Dr. Jill Gallaher

Dr. Jill Gallaher
Research Scientist, Moffit Cancer Center
Google Scholar Profile

Systemic dynamics of multiple metastases during adaptive therapy

Tuesday, October 15
2 PM
RRI 101

Abstract: Although metastatic disease is thought to be responsible for about 90% of cancer deaths, there has been relatively little improvement in the understanding and treatment of cancer at this advanced stage. Increasingly, data point toward intra- and inter-tumor heterogeneity as a major driver of treatment failure in metastatic cancer. We have recently shown that disseminated disease may be better managed using evolutionary-designed maintenance therapies as opposed to maximum tolerated dose, treat-to-kill strategies. Adaptive therapy is one such evolutionary treatment strategy that exploits sensitive and resistant cell competition; a lower dose is given to a shrinking tumor and a higher dose to a growing tumor. From clinical and pre-clinical data, we are learning how the total tumor burden (for example, PSA in prostate cancer) can be used to control disease using this strategy, but details on how multiple distinct heterogeneous metastatic lesions contribute to systemic measures of burden are not fully understood or well documented. We use an off-lattice agent-based computational model to simulate different treatment schedules of an anti-proliferative drug applied systemically to multiple individual micro-metastases. We assume that there is a tradeoff between fast proliferation and drug resistance, and use the total tumor burden from all metastases to make treatment decisions for adaptive therapy. We simulate how intra- and inter- tumor heterogeneity and seeding dynamics affect the best treatment strategy between a maximum continuous dose or an adaptive therapy schedule. When adaptive therapy is optimal, we investigate how tumor composition and number of metastases change the treatment cycling times and indicate future treatment failure. We examine how using different biomarkers that only measure a subset of the tumor phenotypes versus the total tumor burden affect the dose schedule and overall disease control. With these trends in mind, we aim to identify which which patients are best suited for an adaptive therapy strategy, and for those that qualify, identify metrics to assess ongoing treatment response.

MCB Seminar | Dr. Bérénice Benayoun

Dr. Bérénice Benayoun
Assistant Professor, USC, Leonard Davis School of Gerontology
Lab Website

Genomic regulation of Vertebrate aging

Friday, October, 11
12 PM
RRI 101

Abstract: The overarching goal of the Benayoun laboratory is to understand how aging influences the epigenome, and in return, how modulation of the epigenome can influence the aging process. We want to understand how this interaction is modulated in response to environmental stimuli and in the context of specific endogenous factors, specifically sex, invertebrate organisms. Aging is accompanied by striking changes in chromatin and gene expression across cell types and species. Yet, how chromatin landscapes change with age and regulate transcription, and how epigenomic changes in turn influence aging in response to external or internal cues, is largely unknown.

Such knowledge will be critical to counteract the functional decline associated with physiological aging, and its exacerbation in age-related disease. A critical aspect of our research is the use of multiple vertebrate model organisms. The short lifespan of non-vertebrate model systems (e.g. yeasts, worms, and flies) makes their use in experimental aging research very attractive, and they have been widely used to explore genetic and environmental underpinnings of aging. However, as a result of this experimental pragmatism, our understanding of mechanisms that regulate vertebrate aging, including the role of vertebrate-specific genes, organs, and tissues (e.g. bones and blood), and physiological processes (e.g. adaptive immunity), significantly lags behind.

These considerations led us to spearhead the de novo sequencing, assembly, and annotation of the African turquoise killifish genome, the shortest-lived vertebrate that can be bred in captivity. Despite this compressed lifespan, the African turquoise killifish display all key age-related phenotypes, including age-related cognitive decline. Our work has transformed the use of this organism as a vertebrate model, and we now are able to leverage this powerful new model organism in conjunction to established traditional models to rapidly identify novel pathways regulating aging and longevity in vertebrates.

Our main cell model of study are key components of the innate immune system and the inflammatory response: macrophages, which accomplish key tasks such as phagocytosis, antigen presentation, and cytokine production. Consistently, aging is associated with increased macrophage infiltration into tissues. Macrophages have two main origins: tissue-resident macrophages differentiate from specific embryonic progenitors, whereas monocyte-derived macrophages differentiate from bone-marrow progenitors throughout life.

Resident macrophage populations exist across tissues. Because of their key role in inflammation and damage repair, macrophages are a key cell type in age-related inflammatory diseases. Specific ongoing research directions in the Benayoun lab focus on (i) identifying transcriptional and epigenomic changes with age and upon interventions which extend vertebrate longevity, (ii) dissecting transcriptional regulation changes throughout life, as well as underlying molecular mechanisms for these changes, and (iii) understanding the regulation of aspects of aging by sex, an important, yet very much understudied, factor in aging and longevity.

MEB Seminar | Dr. Alyson Santoro

Dr. Alyson Santoro
Assistant Professor, UCSB, EEMB
Lab Website

Nitrification as a window on the mesopelagic

Tuesday, October 7
12 PM
AHF 153 (Torrey Webb Room)

Abstract: The mesopelagic ocean--often called the “twilight zone”--is a critical area for the microbial processing of sinking organic matter. Our lab studies some of the most abundant members of the mesopelagic microbial community, the ammonia-oxidizing archaea and nitrite-oxidizing bacteria. Together, these organisms carry out the biogeochemical process of nitrification and are responsible for producing the vast deep ocean nitrate reservoir. They also play an underappreciated role in carbon and trace metal cycling. My talk will describe combining laboratory cultures with field rate measurements to understand the critical role of nitrifiers in the intertwined geochemical cycles of carbon, nitrogen, and trace metals in the dark ocean.