Thursday, September 29, 2016

Thesis Center Information Sessions - Oct. 5 and 12

I will be hosting Thesis Center information Sessions for students who are submitting their thesis or dissertation. The sessions will be about 50 minutes long. Advisors and faculty are welcome and encouraged to attend.

There will be one session on University Park Campus, and one session on Health Sciences Campus:
     UPC: WEDNESDAY, OCTOBER 5TH, in THH 202 at 12:00 PM
     HSC: WEDNESDAY, OCTOBER 12TH , in MCH 156 at 12:00 PM

Topics will include important information for both students and advisors, such as:
·         Thesis Center navigation
·         submission deadlines
·         required documentation
·         Finalizing publishing information with the USC Digital Library

There will be an opportunity for questions following the presentation. These dates and times will also be listed in myGradSchool for reference. Hope to see you there!

Fight On!

Samuel Mantell
Academic Services Coordinator
The Graduate School
Office of the Provost
University of Southern California
3601 Trousdale Pkwy, STU 301N
Los Angeles, CA 90089-1695
(213) 740-9033

Help save the endangered turtles of Sulawesi!


I'm a graduate student in IEB and have been working on a project to save endangered turtles in Indonesia. We are in the middle of a fundraising campaign.

~ Andrea Currylow

Tuesday, September 27, 2016

CLC Genomics Workbench On-Site Training at USC, September 30

This is the only on-site training on CLCbio Genomics Workbench in next 12 months, don’t miss it!

Starting the week of Oct. 3, 2016, we will offer free access of the CLC Genomics Workbench Software, along with the Microbial Genomics Module and the Genome Finishing Module, to all USC users.

To help USC researchers get started with this software, QIAGEN will provide an one-day on-site training.  Please follow the link below to register for the online training.

CLC Genomics Workbench On-site Training at USC

Date and Time:       10 am to 4 pm, Friday September 30, 2016
Location:                   Aresty Auditorium, Health Science Campus
Lunch will be provided

Training Agenda

10-11 am—Introduction to the CLC Genomics Workbench

Overview of Application: Reqsequencing, RNA-seq, Small RNA, Epigenomics, De Novo Assembly, Microbial and Metagenomics
Preprocessing of Data
Incorporation of MetaData
Building a workflow/pipeline
Installation and setting up reference database(s)

11am-noon—DNA-seq, ChIP-seq, and Bisulfite-seq Pipelines

Map reads to reference
Indels and structural variants
Local realignment
Variant determination
Annotate, filter and compare variants
Histone ChIP-seq and bisulfite sequencing

Noon to 1 pm—Lunch will be provided

1:00 pm-2:30 pm—Microbial Module Tools and Metagenomics Pipelines

Microbiome Analysis: Explore the taxonomic and functional composition of Microbial communities
Analyze 16S rRNA or other amplicon data.
From raw reads to interactive visualization in four steps.
De novo or reference based OTU-clustering
Supports common OTU Databases Greengenes, Silva, and UNITE.
Analyze and browse micro biome composition at different taxonomic levels and in the context of metadata.

Whole metagenome function analysis: Functional Profiling of Microbiomes
Assemble whole metagenome datasets
Functional profiling
Stacked bar charts, area charts and zoomable sunburst diagrams to explore and compare the functional composition of metagenomic samples, or sample groups.

Typing and whole genome based analysis of microbial isolates
Confirm the identity of pathogens, or starter cultures.
Establish an association between an outbreak and its source.
Monitor pathogens outbreaks.
Manage samples, meta-information and results all from a convenient Analysis Dashboard.

2:30 pm-3:30 pm—De Novo Assembly and Genome Finishing Tools and Pipelines

Use reads to assemble an estimate of genome regions
Support for a variety of data formats, including both short and long reads, and mixing of paired reads
Assess quality of assembly/QC
Automate scaffolding, contig joining, and the ordering of contigs relative to each other or to a closely related reference genome

Let us know if you have any questions.

Yibu Chen and Meng Li
Bioinformatics Service Program
Norris Medical Library
University of Southern California
323-442-3309 (Yibu)
323-442-3447 (Meng)

Hertz Foundation Fellowship

Eligible: Domestic PhD students, i.e. U.S. Citizens and Permanent Residents

Friday, September 23, 2016

Dr. Steven Finkel awarded ASM award

*Photo credit: Mark Berndt, USC Trojan Family Magazine

USC Professor Steven Finkel has been selected to receive the William A. Hinton Research Training Award for 2017. This award honors outstanding contributions toward fostering the research training of underrepresented minorities in microbiology. It is given in memory of William A. Hinton, a physician-research scientist and one of the first African-Americans to join the ASM. This award is also associated with an award lecture at the 2017 Microbe meeting in New Orleans.

Job Posting | Social Media Specialist

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Thursday, September 22, 2016

University Staff Club Scholarship

Following this announcement is the flyer, application, and instructions for the University Staff Club Scholarship. The deadline to apply is Monday, October 3rd by 3:00 pm PST.

Criteria: All students who preferably, have an undergraduate degree from USC, (but not limited to) and are currently enrolled in a USC graduate program are eligible for one of the twenty five (25) $1000 scholarships. Criteria for selection include: financial need, academic record, activities, service, and future goals.

If you have any questions about the scholarship, please e-mail them to

Insight Fellows Programs

Now accepting applications for January 2017 Insight Fellowships!

600+ Insight alumni are now data scientists and data engineers at Facebook, LinkedIn, The New York Times, Apple, Airbnb, Netflix, Memorial Sloan Kettering Cancer Center, Uber, Seven Bridges Genomics, Twitter, Bloomberg, NBC, Microsoft, and 200+ other top companies.

Insight Fellowship:
  * 7 week, full-time, post-graduate training Fellowship
  * Mentorship from leading industry data scientists and data engineers
  * Join an active community of Insight alumni
  * Self-directed, project-based learning with support from Insight throughout the whole process
  * Tuition-free with need-based scholarships available to help cover living costs

Insight awards three distinct Fellowships:

Data Science (New York City, Silicon Valley & remote)
Deadline: October 24th
For post-docs or PhD students who will graduate by May 2017
Apply at

Health Data Science (Boston & Silicon Valley)
Deadline: October 24th
For post-docs, MDs, MD students, or PhD students who will graduate by May 2017
Apply at

Data Engineering (New York City & Silicon Valley)
Deadline: November 3rd
For post-docs or Bachelor’s, Master’s, or PhD students who will graduate by May 2017
Apply at

Not yet ready to apply? Sign up for our Notification Lists: Data Science, Data Engineering, Health Data Science

Questions? Email us at

Wednesday, September 21, 2016

Like or Follow us NOW!

The Department of Biological Sciences has unveiled its new Facebook page and Twitter handle. All content submissions can be made to We look forward to sharing your stories and tweeting with all of you!

Fall 2016 Graduate Student Luncheons

The USC Graduate School's Vice Provost for Graduate Programs, Sally Pratt invites you to attend one of the four Fall 2016 Graduate Student Luncheons.  These events serve as an opportunity to create an inclusive community for graduate students from both the University Park Campus and the Health Science Campus. You have the opportunity to talk with the Vice Provost about a variety of graduate and professional student topics that range from Diversity, Inclusion, and Access to International Student experiences to Academic Professional Development; including your own concerns and discussion items. Vice Provost Pratt is interested in hearing your news, updates, and concerns as well as what you think the USC Graduate School does well and what it can improve upon and how.

The event is open to all USC Graduate Students, and attendance will be limited to 20 Graduate Students per luncheon. Since space is limited, please remember that your RSVP does not guarantee you a seat at the luncheon. The exact location of each luncheon will be communicated through a confirmation email sent to the first 20 students, per event, who have expressed interest in the particular meeting date.

The menu for these events consists of salads, sandwiches, beverages, and dessert.

Below are the luncheon dates, and times (lunch location TBD):

University Park Campus - Monday, October 10th – 12:00pm – 1:30pm
University Park Campus - Wednesday, October 12th – 12:00pm – 1:30pm
University Park Campus - Monday, October 17th – 12:00pm – 1:30pm
Health Science Campus - Tuesday, November 1st – 12:00pm – 1:30pm

Reserve your space today: Graduate Student Luncheon with Vice Provost Sally Pratt

Tuesday, September 20, 2016

Academic Careers Week - Sept. 26-29

More Information

Writing Your Cover Letter & CV - Monday, Sept. 26th, noon - 1:00 pm
Doheny Memorial Library (DML) 240
Putting together a cover letter and CV can be a daunting task. How will yours stand out among all the other applicants? Professor Rachel Walker from the Linguistics department and Professor Najm Meskati from the Civil and Environmental Engineering department will provide insight into what faculty look for when they review cover letters and CVs.
Lunch Provided
Instant Contact: How to Shine in 1 or 2 Minutes on your Interview Day - Tuesday, Sept. 27th, 12:30 - 1:30 pm
Doheny Memorial Library (DML) 240
On your interview day you will meet many people and only have a minute or two to explain to them your academic interests. This program will allow you to practice! An overview of a typical interviewing day will be presented. Following this, you will break into small groups, where you will have a chance to explain your research interests in a short one or two minute description. The members of your small group along with a USC faculty member will provide constructive comments on your short description.
Lunch Provided


Negotiating the Academic Job Offer - Wednesday, Sept. 28th, noon - 1:00 pm
Doheny Memorial Library (DML) 240
You’ve been made an offer! Now what? How does one go about negotiating an academic job offer? A panel including Dani Byrd, Professor of Linguistics & Executive Vice Dean of USC's Dornsife College; Andrew Goodney, Lecturer, Computer Science, Viterbi School; and Bruce Zuckerman Professor of Religion, Dornsife College will share their experiences with negotiating academic job offers.
Lunch Provided

Drafting Your Teaching Philosophy / Research Statement - Thursday, Sept. 29th, 12:30 - 1:30 pm
Doheny Memorial Library (DML) 241
How does one go about articulating a teaching philosophy and a research statement? How are these documents used by search committees? Professor Armand Tanguay, Jr. from the Viterbi School of Engineering will share his insights on crafting these two documents. Presented by Professor Mark Schroeder, Donrsife College & Professor Sandy Sawchuk, Viterbi School
Lunch Provided


Monday, September 12, 2016

The DOE Office of Science Graduate Student Research program is now accepting applications!

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 2016 Solicitation 2.  Applications are due 5:00pm ET on Monday November 21, 2016. 

Starting from 2015 Solicitation 2, the SCGSR program is open to graduate students with Permanent Resident status, in addition to U.S. Citizens, who meet all other eligibility requirements. 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 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 DOE laboratories. 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 during the award period.

The Office of Science expects to make approximately 50 awards in 2016 Solicitation 2, for project periods beginning anytime between June 1, 2017 and October 2, 2017.

Since its inception in 2014, the SCGSR program has provided support to about 160 graduate awardees from over 75 different universities to conduct thesis research at 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, and the Oak Ridge Institute of Science and Education (ORISE).

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

U.S. Department of Energy, Office of Science