• Name: Yuri Bendana
• Email: ybendana at gmail com

About Me

After starting out as a control systems and software engineer, I enrolled in the UC Berkeley/UCSF Joint Graduate Group in Bioengineering in 2004. I was a member of the HolmesLab from February 2006 to June 2007.

My research interests are broadly in computational biology, more specifically in applying statistical machine learning methods to biological data, especially at the molecular and cellular level. I am also interested in systems biology analysis/simulation, synthetic biology design, and bioinformatic visualization tools.

Projects

• Prediction of non-coding RNA genes in the Drosophila genome. See TwelveFlyScan, TwelveFlyScreen, FruitflyBioinformaticsResources, XratePipeline.
• RATON

Publications

• Bendana YR, Holmes IH.  Colorstock, SScolor, Raton: RNA alignment visualization tools.  Bioinformatics. 2008 Feb 15;24(4):579-80. doi: 10.1093/bioinformatics/btm635. Epub 2008 Jan 24.
• 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 Oct 3;7:428.

Presentations

• ISMB2006

Comp Bio Links

• RNA engineering
• JournalClub, FruitflyRiboClub, CompbioConferences
• Tools
  • DART sw library: XgramSoftware, XgramFormat
  • FreeSoftware, GffTools, StockholmTools
  • JBrowse
  • HowToUseSunGridEngine, TroubleShooting
• HowMuchTrainingDataDoINeed
• MakeUseCases

Other Links

• YbLog, YbBiblio, YbToDo
• HolmesLab, LabMeeting, LabTravel, Biowiki CVS
• BioE131, Teaching.BioE131-F05, BioE190B
• Grad School: How To, PHD, The Snail's Pace
• Concepts: Parse
• Manuals:
  • Lab: BubblePlots
  • Unix: UnixMnl, CvsManual, MakeMnl, OSXStuff, PythonMnl
  • Computational sw: OctaveMnl, RprojMnl
• Safari bookshelf
  • Perl: Learning Perl, Intermediate Perl, Advanced Perl
  • Python: Python in a Nutshell, Python Cookbook, Learning Python, Programming Python
  • Java: Java in a Nutshell
  • DB: MySQL in a Nutshell
  • Web: HTML: The Definitive Guide, Javascript: The Definitive Guide, CSS: The Definitive Guide, Dynamic HTML: The Definitive Reference, Web Design in a Nutshell, Ajax Design Patterns
  • Mac OS X: Mac OS X in a Nutshell, Running Mac OS X, Mac OS X: The Missing Manual, Mac OS X for Unix Geeks
  • Linux: Linux in a Nutshell, Learning Red Hat Linux and Fedora, Learning the bash shell, Running Linux

Archive

• YbXgramPaper
• MercatorPerl, NonCodingRNADatasets, NonCodingRNAAnnotationTransfer, EightFlyScan, FlyNcRna
• BendanaChaoTemmeGraduateProject