Sunday, March 18, 2018

“R for Bioinformatics” Workshop Series – USC Libraries Bioinformatics

The USC Libraries Bioinformatics Service is pleased to present the “R for Bioinformatics” workshop series. Knowing how to use R is a valuable skillset, as numerous cutting-edge tools for various genomic data analysis are written in R.  This workshop series is aimed at training researchers in the varied applications of R for bioinformatics.

The first two hands-on workshops of this series are designed for those with no or little experiences in R but want to achieve basic competency in R usage. 

Workshop 1—R and Bioinformatics (4 hr)
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 manipulating bioinformatics data

Workshop 2—Bioconductor and EdgeR (4 hr)  
More commonly used functions for manipulating and visualizing bioinformatics data
Introduction to bioinformatics package repositories: CRAN and Bioconductor
Bioinformatics R Packages Case Study 1 - Using EdgeR for Differential Expression analysis.

Before you sign up:
1. Participants are required to attend BOTH workshops.
2. As seating is limited to 10 participants per workshop session, registration is mandatory and must be fulfilled.
3. Participants are required to bring their own laptops.
4. Additional sessions of both workshops may be offered in near future—register to get on the waiting list.

University Park Campus
Workshop 1:      10am to 2pm, Wednesday, March 28th, 2018
Learning Center, Wilson Dental Library (DEN21) 
Workshop 2:      10am to 2pm, Friday, April 6th, 2018
Learning Center, Wilson Dental Library (DEN21)

Health Science Campus
Workshop 1:      10am to 2pm, Tuesday, April 3rd, 2018  
                                East Conference Room (Basement Level), Norris Medical Library
Workshop 2:      10am to 2pm, Tuesday, April 10th, 2018
Computer Classroom (2nd Level), Norris Medical Library

Lunch will be provided at all sessions.  Sign up with the link below:

This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.

Please let us know if you have any questions.

Eddie Loh, Yibu Chen, and Meng Li
USC Libraries Bioinformatics Service 

Survey on female doctoral students' experiences with pregnancy and parenting

If you are a woman who is pregnant or has become a parent during your doctoral program, please consider taking our anonymous, online survey. We are exploring the supports available to women and the impact of this experience (whether pregnancy, childbirth, pregnancy loss, infertility, or adoption) on women's doctoral studies and career trajectory. This project has been approved by the IRB at Salem State University -- Approval #121517-3.

If you are willing to participate, please click on the link below. If you know someone who might be interested, please pass on the survey link to them. I am happy to answer any questions about this project.

Pursuing a Doctorate & Parenthood: Understanding the Experiences of Female Doctoral Students

Graduate Research Opportunities at DOE National Laboratories

The Department of Energy’s (DOE) Office of Science is pleased to announce that the Office of Science Graduate Student Research (SCGSR) program is now accepting applications for the 2018 Solicitation 1.  Applications are due 5:00pm Eastern Time on Tuesday, May 15, 2018.

Detailed information about the program, including eligibility requirements and access to the online application system, can be found at:

The SCGSR program supports supplemental awards to outstanding U.S. graduate students to conduct part of their graduate thesis research at a DOE national laboratory/facility in collaboration with a DOE laboratory scientist for a period of 3 to 12 consecutive months—with the goal of preparing graduate students for scientific and technical careers critically important to the DOE Office of Science mission.

The SCGSR program is open to current Ph.D. students in qualified graduate programs at accredited U.S. academic institutions, who are conducting their graduate thesis research in targeted areas of importance to the DOE Office of Science. The research opportunity is expected to advance the graduate students’ overall doctoral thesis/dissertation while providing access to the expertise, resources, and capabilities available at the host DOE laboratories/facilities. The supplemental award provides for additional, incremental costs for living and travel expenses directly associated with conducting the SCGSR research project at the DOE host laboratory/facility during the award period.

The Office of Science expects to make approximately 50 awards in 2018 Solicitation 1 cycle, for project periods beginning anytime between October 29, 2018 and March 4, 2019.

Since its inception in 2014, the SCGSR program has provided support to over 300 graduate awardees from more than 100 different universities to conduct thesis research at 17 DOE national laboratories across the nation.

The SCGSR program is sponsored and managed by the DOE Office of Science’s Office of Workforce Development for Teachers and Scientists (WDTS), in collaboration with the six Office of Science research programs offices and the DOE national laboratories/facilities, and program administration support is provided by the Oak Ridge Institute of Science and Education (ORISE).

For any questions, please contact the SCGSR Program Manager, Dr. Ping Ge, at

Molecular Biology Seminar Series

Dr. Adriana Bankston
Future of Research
Personal website

Making postdocs “less invisible” in academia

Friday, March 23, 2018
12:00 PM
RRI 101

Abstract: Future of Research (FoR) aims to champion, engage and empower early career scientists with evidence-based resources to improve the scientific research endeavor. As part of this goal, we study academic policies that affect postdocs. Postdocs make up a large portion of the biomedical workforce. However, they are typically considered the “invisible” population in academia. Lack of data on postdoc numbers, titles and pay contributes to the difficulty of devising novel, or improving existing, policies for postdocs. Our studies examined national postdoc trends in these areas. We monitored institutional postdoc salary policies as a result of labor law changes; obtained actual postdoc salaries in U.S. public institutions; and found large institutional variability in reporting postdoc numbers in an established NSF survey. Given these findings, we call for better measures to assess postdoc population trends. We hope these efforts will make postdocs a “less invisible” population, and contribute to an overall recognition of the need for increased academic transparency.

Sunday, March 4, 2018

Gold, Hovel, and Del Amo Summer Awards

Attached, you will find the announcements (with application forms) for this year's Gold, Hovel and Del Amo summer awards for continuing students. The internal deadline is Friday, March 16. Please submit your applications to Doug Burleson.

Computational Biology Open Faculty Search Seminar Series

Dr. Xuebing Wu
MIT University
Research Profile

Decoding the noncoding messages in messenger RNAs

Tuesday, March 6
3:30 PM
RRI 101

Abstract: RNA plays central roles in transmitting and regulating genetic information. While the genetic code is simple and universal, the code controlling the spatiotemporal regulation of mRNAs remains poorly understood. My research aims to understand the fundamental mechanisms of gene regulation at the RNA level by using integrated computational and experimental approaches. I will highlight my recent work that has uncovered widespread roles of RNA secondary structures in regulating human mRNA biogenesis and metabolism. In addition, I will discuss my ongoing work on the translation of noncoding sequences in mRNAs and the systematic discovery of mRNAs with protein-independent functions.