Andrew Uzilov Member of the Lowe Lab Graduate Student (Sept 2007 - Mar 2013) Bioinformatics PhD Program University of California, Santa Cruz

Background

I graduated from the University of Rochester (B.S. in Biochemistry, B.A. in Computer Science, both 2005), where I worked for Dave Mathews as an undergraduate. Then I spent two years bumming around Ian Holmes' lab at UC Berkeley.

I earned my PhD advised by Todd Lowe in the Lowe lab in March 2013. My latest whereabouts are likely to be found on my LinkedIn page.

Links to elsewhere

• The definitive FragSeq page.
• Resources for my BME110 Computational RNA lectures are here.
• Resources for my BME205 Introduction to Python lectures are here.
• Check out my wedding website, lovingly hand-made.
• Some really old, random pictures.

Research interests

• High-throughput sequencing of transcriptomes (RNA-Seq).
• RNA structure (computational prediction and experimental determination).
• Non-coding/functional RNA discovery and genomic annotation.
• RNA engineering.

Papers

1. Underwood JG*, Uzilov AV*, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nature Methods 7, 995–1001 (2010).
   • Starred (*) authors contributed equally to this work.
   • Covered by a "News and Views" story by Eric Westhof and Pascale Romby, Nature Methods 7, 965–967 (2010).
   • A CBSE news story about FragSeq.
2. Bradley RK, Uzilov AV, Skinner ME, Bendaña YR, Barquist L, Holmes I. Evolutionary modeling and prediction of non-coding RNAs in Drosophila. PLoS One (2009) 4(8):e6478.
3. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Research (2009) 19:1630-1638.
   • Mentioned in Research Highlights in Nature Biotechnology (2009) 27:734.
   • See the live demo.
4. Klosterman PS, Uzilov AV, Bendana YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I. XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics (2006) 7:428.
5. Uzilov AV, Keegan JM, Mathews DH. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinformatics (2006) 7:173.

Affiliations

I...

• ...pursued a PhD in the Bioinformatics program (BINF)
• ...which is offered through the Department of Biomolecular Engineering (BME)
• ...which is part of the Baskin School of Engineering (SOE or BSOE), formerly known as Computer Science and Engineering (CSE)
• ...which is a school of the University of California, Santa Cruz (UCSC)
• ...which is part of the University of California state university system (UC)

I was also a National Science Foundation Graduate Research Fellowship Program (NSF GRFP) fellow during 2009 - 2012. Here is the BSOE news article.