Olga Botvinnik

Doctoral Student
Prof. Gene Yeo's Laboratory
Bioinformatics and Systems Biology Program
University of California, San Diego

Publications
LinkedIn Resume
Twitter

Loading,

% complete

In preparation

Botvinnik OB*, Kim W*, Tamayo P, Abazeed M, Mesirov JP. Exploring the Landscape of Genomic Abnormalities using Functional Profiles of Oncogenic Pathway Activation and Dependency. *These authors contributed equally to this work

Birger C, Botvinnik OB, Tamayo P, Mesirov JP. Single-sample GSEA compares gene set enrichment of multi-sample experiments.

Published/submitted

Goncearenco A, Grynberg P,Botvinnik OB, Macintyre G, Abeel T. Highlights from the 8th ISCB Student Council Symposium, Long Beach, California, USA, July 13 2012. BMC Bioinformatics (2012) [PDF]

Botvinnik OB, Lopez-Diaz F, Lee W, Pourmand N. Single-cell analysis of taxol resistance in breast cancer. Intelligent Systems for Molecular Biology. Long Beach, California, USA (2012)

Wood KC, Konieczkowski DJ, Johannessen CM, Boehm JS, Tamayo P, Botvinnik OB, Mesirov JP, Hahn WC, Root D.E, Garraway LA, Sabatini DM. Miniaturized functional screening reveals genetic modifiers of therapeutic response in melanoma. Science Signaling (2012) [PDF]

Galili N, Tamayo P, Botvinnik OB, Mesirov JP, Brown G, Raza A. Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome. J Hematology and Oncology (2012) [PDF]

Botvinnik OB, Tamayo P, Mesirov JP. Discovery of novel candidate oncogenic activators with REVEALER. Intelligent Systems for Molecular Biology. Vienna, Austria (2011) [PDF]

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Pena-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) [PDF]

Info

Info

Profile
- Olga Botvinnik
  
  Bioinformatics Researcher at UC San Diego
  
  Biotechnology | Greater San Diego Area, US
  
  Summary
  
  Double majored in Biological Engineering and Mathematics at MIT.
  
  Research interests: single-cell sequencing, genomics, cancer.
  
  Specialties: Hidden markov models (HMMs), Gene Set Enrichment Analysis (GSEA), machine-learning algorithms, information theory, image analysis, graph theory, newtork analysis, clustering. Programming Languages: Java, C, Python/BioPython, Perl, R/Bioconductor, MATLAB, and LaTeX. Graphic Design: Adobe Illustrator, Photoshop, OmniGraffle Pro.
  
  Experience
  - 2012 - Present
    Bioinformatics Researcher / UC San Diego
  - Nov 2010 - Present
    Bioinformatics Research Technician / Broad Institute
    
    Developed REVEALER, an iterative algorithm to discover new associations between binary mutation/copy number data and functional readouts such as expression or drug sensitivity.
  - Sept 2011 - Jun 2012
    Graduate Researcher / UC Santa Cruz
  - Jan 2010 - Jun 2010
    Researcher / MIT Department of Brain and Cognitive Sciences
    
    Analyzed neuron segmentations of electron microscopy images of rabbit retina inner plexiform layer slices and elucidated patters in interneuron size, shape, and orientation.
  - Dec 2008 - Dec 2009
    Computational Biology Researcher / MIT CSAIL
    
    Using graph theory to model regulatory networks of the yeast genome, and Kirchhoff's circuit laws to model deletions in the network. Researching strain-specific essentiality of genes.
  - Jun 2008 - Aug 2008
    Summer Student, Eddy Lab / Howard Hughes Medical Institute
    
    Computational Biology Internship. Developed first-ever model representing content of large protein databases using Machine-Learning Algorithms. Code written in Python and C, incorporated into HMMER 3.0 release (Eddy Lab Software)
  - Jun 2007 - Aug 2007
    Researcher, Bulyk Lab / Harvard Medical School
    
    Helped create a database of high-resolution mouse transcription factor binding motifs. Resulted in publication in Cell journal.
  Education
  - 2012 - 2016
    
    University of California, San Diego
    
    Doctor of Philosophy (PhD) in Bioinformatics and Systems Biology
  - 2011 - 2012
    
    University of California, Santa Cruz
    
    M.S. in Bioinformatics
    Activities: Professional Development Program
  - 2006 - 2010
    
    Massachusetts Institute of Technology
    
    S.B., S.B. in Mathematics, Biological Engineering
    Activities: DanceTroupe, Kappa Alpha Theta, Baker House Executive Committee, UPOP, Gordon-MIT Engineering Leadership Program
  - 2002 - 2006
    
    South Eugene High School
    
    International Baccalaureate Diploma
  Additional Information
  - Websites:
    
    Personal Website, Blog
Tweets

Tweets

Profile
- @ctitusbrown Thanks for sharing!
  
  Jun 20, 13 from web in reply to ctitusbrown Reply, Retweet, Favorite
- RT @ctitusbrown: @olgabot has posted all of her graduate fellowship apps text: http://t.co/a8UwBsZJtf
  
  Jun 20, 13 from web Reply, Retweet, Favorite
- Just made my first @everlane purchase! If you wanna buy stuff and give me credit, use this link https://t.co/BdutPAAWne :)
  
  Jun 19, 13 from web Reply, Retweet, Favorite
- Paper by Crick, Brenner et al first postulating that three DNA bases (or multiples of three!) code for amino acids http://t.co/OJH01qPsXc
  
  Jun 18, 13 from web Reply, Retweet, Favorite
- RT @BioMickWatson: RT @DrLabRatOry @drchriscole “Some scientists work so hard there is no time left for serious thinking.” - Francis Crick
  
  Jun 17, 13 from web Reply, Retweet, Favorite
- RT @philogeny: #GmailTeX is fantastic for math equations in gmail...why have I just now discovered it? http://t.co/LYR3TVDOJb
  
  Jun 03, 13 from web Reply, Retweet, Favorite
- The R script that will change your life - If you use the R programming language, you probably know how much... http://t.co/ntaC6UagUn
  
  May 03, 13 from Tumblr Reply, Retweet, Favorite
- How to fail (and sometimes win) at graduate fellowships - The title of this post is rather tongue-in-cheek,... http://t.co/gtUgzqC2nh
  
  Apr 28, 13 from Tumblr Reply, Retweet, Favorite
- Beautiful boxplots and sassy small multiples - Last week, I posted about implementing design principles in... http://t.co/QjnxwwI4mE
  
  Apr 22, 13 from Tumblr Reply, Retweet, Favorite
- In India, 'no frills' hospitals offer $800 heart surgery - nerdneha: Using pre-fabricated buildings,... http://t.co/JuU8XjIdbX
  
  Apr 22, 13 from Tumblr Reply, Retweet, Favorite
- @janfoosh haha :) How you doin? Miss you and your silliness <3 <3
  
  Apr 20, 13 from Tweet Button in reply to janfoosh Reply, Retweet, Favorite
- Can we please stop talking about what a good kid this bomber was? Cause uh... Clearly he's not.
  
  Apr 19, 13 from Twitter for Android Reply, Retweet, Favorite
- RT @YourAnonNews: Wanna know who else was identified by photograph? A rapist in #Halifax. #OpJustice4Rehtaeh
  
  Apr 19, 13 from web Reply, Retweet, Favorite
- RT @peteyMIT: The green building right now. cc @bostonglobe @MITnews http://t.co/qx5TuJoC1X
  
  Apr 16, 13 from web Reply, Retweet, Favorite
- My thoughts and best wishes go out to those at the Boston Marathon finish line.
  
  Apr 15, 13 from Twitter for Android Reply, Retweet, Favorite
- make sure the kids are actually siblings #kual
  
  Apr 12, 13 from web Reply, Retweet, Favorite
- Pumped for this talk #kual
  
  Apr 12, 13 from web Reply, Retweet, Favorite
- Implementing graphic design principles in Python's matplotlib - Tired of ugly 2d histograms and bar charts... http://t.co/yJvlo5Fbnr
  
  Apr 11, 13 from Tumblr Reply, Retweet, Favorite
- RT @omarabudayyeh: Provocative words: 1) What are the most important problems in your field. 2) Are you working on them? 3) Why not? - R ...
  
  Apr 04, 13 from web Reply, Retweet, Favorite
- @gosubha You should do it!!
  
  Mar 31, 13 from web in reply to gosubha Reply, Retweet, Favorite