Sunday, April 22, 2018

2018 INTD 500 Course Announcement

USC Annenberg Graduate Fellowship Research and Creative Project Symposium

Phi Beta Kappa Alumni Awards

The graduate school is delighted to announce that the nomination site for the Phi Beta Kappa Alumni Awards is now open. The scholarship recognizes international students pursuing graduate degrees in the U.S. Recipients of the PBK award must be about to begin the final year of their program and be seeking a degree that is considered “terminal” in their field (i.e. PhD).

Two awards, in the amount of $2,000 will be given to graduate students at USC.

Students should complete the attached Phi Beta Kappa Alumni Awards application and upload it here by Friday, May 4, 2018.

One letter of reference from the student’s faculty advisor should be sent to the graduate school via email at by Friday, May 4, 2018.

Please note, to upload PDF files to this site, Google requires that you be signed into Drive. All USC students have access to Google Drive. You can access Google Drive by going to and entering your USC NetID and password. For more information see the ITS website:

Sunday, April 15, 2018

CBIO Colloquium | 4/16/2018

Haris Vikalo
University of Texas at Austin
Research Profile

Efficient Algorithms for Haplotype Assembly and Viral Quasispecies Reconstruction

Monday April 16
2:00 PM
RRI 101

Abstract: We study two applications of high-throughput DNA sequencing: haplotype assembly and viral quasispecies reconstruction. These NP-hard tasks are rendered challenging by sequencing errors and limited lengths of sequencing reads. We present a framework that casts haplotype assembly as the problem of decomposing a tensor of sequencing reads into a product of two factors -- one that reveals haplotype information and another one that encodes origin of the reads. The performance and convergence properties of a proposed tensor factorization method are analyzed and, in doing so, guarantees on the achievable minimum error correction scores and correct phasing rate are established. We then extend this framework and utilize it to reconstruct viral quasispecies characterized by uneven frequencies of their components. This is accomplished by successively inferring strains in a quasispecies in order from the most to the least abundant one; every time a strain is inferred, sequencing reads generated from that strain are removed from the dataset. Extensive benchmarking studies on synthetic and experimental data demonstrate efficacy of the proposed methods. Finally, after noting a connection between single individual haplotyping and the task of deciphering coded messages in communication systems, we employ information-theoretic tools to study fundamental limits of performance of haplotype assembly algorithms.

NBIO Seminar | 4/16/2018

Sunday, April 8, 2018

AmeriCorps Watershed Stewards Program accepting applications for Year 25

The AmeriCorps Watershed Stewards Program (WSP) is seeking Member applicants for 
Service Year 25 (October 1st, 2018 – August 9th, 2019)!

Application Due: June 29th, 2018.

Join a team of 48 committed individuals throughout California engaged in watershed protection, community outreach and education, and restoration projects! Spend 10 ½ months working alongside natural resource professionals with one of WSP’s 25 Placement Sites.

WSP Program Overview:
For 24 years, the AmeriCorps Watershed Stewards Program (WSP) has been engaged in comprehensive, community-based, watershed restoration and education throughout coastal California. The primary focus of WSP is to assist communities and organizations with habitat restoration for salmonids (Chinook salmon, Coho salmon and Steelhead trout) in order to rehabilitate these threatened and endangered species to healthy and historic populations. Additionally, WSP provides watershed education and outreach in high-needs communities throughout the state, engages WSP Members in volunteer recruitment efforts to increase the capacity and reach of partner organizations, and helps Members develop into the next generation of natural resource professionals.

Each year, WSP places approximately 48 Members with natural resource organization Placement Sites throughout California to work collaboratively for a 10 ½ month service term. Members serve under the guidance and mentorship of resource professionals in collaboration with local landowners, public agencies, and private industry to assess, monitor, and enhance watersheds. WSP’s diverse Placement Sites include federal, state, county, tribal, and non-profit agencies and organizations. Each Placement Site engages between one and two Members in all the service activity areas, while each site's overall strategy, emphasis, effort, and timing of service activities varies. For more specific information about each WSP Placement Site, please refer to the WSP website:

WSP fosters inclusion, inspires innovation, and encourages respect by embracing the diverse talents, perspectives, and backgrounds of all applicants. Each of us brings to the table a lifetime of experiences and knowledge. Each of us is different and adds value to the organization because of these differences. WSP seeks applicants that represent the racial, gender, cultural, and socio-economic diversity of American society.

During their service, Members participate in a wide array of activities, including:
Regular watershed recovery and protection work with their Placement Site
Teaching the Wonders of Watersheds (WOW!) curriculum in elementary schools
Engaging their service community in watershed outreach
Creating and implementing their own Watershed Awareness Project (WAP), and recruiting community volunteers
Training and professional development opportunities

Qualifications for Applicants:
High school diploma
25 credits of college-level science OR 6 months of relevant experience in fisheries/habitat restoration, invasive removal, instream structure installation, etc.
Interest and experience in natural resources management and environmental education
Possess or be willing to obtain a California Driver's License
Clean driving record (no more than 2 points)
US Citizen or Lawful Permanent Resident Alien

Preferred Skills and Qualities for Members:
Willingness and desire to learn
Effective communication skills
Good basis of relative skills and experiences
Willingness to relocate to Placement Site community

Benefits Include:
Opportunity to make a difference in a Californian community
A monthly living stipend: $1,780
An Education Award of approximately $5,920 upon successful completion of the 10 ½ month service term
Hands-on training opportunities
Uniform and field gear provided
Opportunities to see some of the most beautiful places in California
Mentorship from a natural resources professional and networking opportunities
No-cost medical insurance
Student loan forbearance on eligible loans
Valuable work experience for your future

How to Apply to WSP:
Look under the member applicant tab on the WSP website
Watch the Recruitment Video at
Send the following to by June 29th, 2018.
o Year 25 WSP Application, available under the MEMBER APPLICANTS tab on the WSP website
o Cover letter
o One-page resume
o Two signed letters of recommendation (can be submitted on your behalf) to email above

Contact Information:
If you have any questions about the AmeriCorps Watershed Stewards Program or how to apply, please contact the WSP Recruiters, Jody Weseman (805) 542-8461 or Greg Poulton (707)725-8601.

[Bioinformatics Lunch Series] Key Considerations for NGS Experimental Design, April 18 2018

The USC Libraries Bioinformatics Service is pleased to present a four-workshop series on next generation sequencing (NGS) studies, addressing key issues from experiment design to functional interpretation of NGS results. 

NGS Workshop #1-- “Key Considerations for NGS Experimental Design” 

With a primary focus on RNA-Seq experiments, this workshop covers the following topics:
Proper number of replicates
Optimal sequencing depth
Appropriate read type and length
Quick points on designing single-cell RNA-Seq, ChIP-Seq, and DNA-Seq experiments
Find the right sequencing service providers

Time                Noon - 1 pm, Wednesday, April 18th
1. Health Science Campus
West Conference Room, Norris Medical Library
2. University Park Campus (via livestreaming)
Learning Center, Wilson Dental Library (DEN21)

Lunch will be provided at both locations.  Link to the livestreaming for private viewing is also available.  

Sign up is mandatory:

Stay tuned for the announcement of upcoming NGS study workshops:
#2 (May 4th)—Analyzing RNA-Seq data with Partek Flow
#3 (May 15th)—Making sense of RNA-Seq data Part 1—Downstream effect analysis (pathways, diseases etc.)
#4 (June 7th)—Making sense of RNA-Seq data Part 2—Upstream regulation analysis (transcription factors etc.)
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.

USC Libraries Bioinformatics Service