Contact Information:

I have (sadly) departed the Holmes Lab in September 2007 for the Bioinformatics PhD program at UCSC. My new web presence is here.

Publications:

• 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.

• 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.

Posters:

• Skinner ME, Uzilov AV, Mungall CJ, Stein LD, Holmes I. AJAX GBrowse: Community Genome Annotation Made Easy. (TODO: link to Biology of Genomes 2007 version from BiologyOfGenomes2007GenomeWikiPoster)

• Bendana YR, Uzilov AV, Holmes I. ISMB 2006: Prediction of RNA and Protein Secondary Structure using Xrate.

• Uzilov AV, Mathews DH. ISMB 2005: Predicting Non-Coding RNA Genes in Genome Sequences.

Past projects:

• Twelve Fly Screen
  • Screening 12 Drosophila species for structurally conserved RNAs.

• AJAX GBrowse
  • Writing server-side Perl code to pre-render images, render on-the-fly, or some such combination.
  • Writing the new client-side GUI in JavaScript.
  • Coordinating the open-source development effort.

• Maintaining the Babylon Cluster and being the sys admin of the lab in general.

• 12-fly ncRNA multiple alignments
  • multiple alignments of computationally predicted fruitfly ncRNAs

• Transferring ncRNA annotations from Drosophila melanogaster to the other 11 flies^? (on hiatus)

Background:

Andrew Uzilov triumphantly joined the Holmes lab in September 2005, after surviving a brutal 3.5-year tour of duty as an undergraduate at the University of Rochester, located in scenic upstate New York known for its lovely white winters and snowy, gentle 30+ mph breezes.

He escaped with a B.S. in Biochemistry, a B.A. in Computer Science, and only two toes lost to frostbite.

Previously, he has done research for the lab of Dr. David H. Mathews in computational detection of non-coding RNA in genome sequences on the basis of folding free energy minimization.

Currently, he intends to do research at the Holmes lab with a similar goal - computational modeling of non-coding RNA - but using evolutionary/probabilistic methods. But even more currently, he is a system administrator and programmer for the lab, laying down the foundation for a bigger and brighter future.

See also:

• Andrew Uzilov Links
• silly notes to self

• Set ALLOWTOPICCHANGE = Andrew Uzilov