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letter and cv


{\Large Toby Dylan Hocking} & nationality: American &
phone: +33 1 39 63 54 99
email: toby.hocking AT & birth: 17 March 1984& 
web: \url{}

\subsection*{Publications, posters, talks}
\item ``Sustainable package development using documentation generation,'' talk 21 October 2010 for semin-r, the Paris R user group.
\href{\%3Adoi\%2F10.1371\%2Fjournal.pone.0011913}{Gautier M, {\bf Hocking~TD}, Foulley JL.
A Bayesian Outlier Criterion to Detect SNPs under Selection in Large
Data Sets, \emph{PLoS ONE} 5(8): e11913 (2010).}
\item ``Visualizing
multivariate data using lattice and direct labels,'' talk 15 October
2009 for semin-r, the Paris R user group.
\item Sublogo dendrograms:
visualizing correlation in biological sequence motifs, poster
presented at
\href{}{useR! 2009}.
\item \href{}{Doyon~Y, McCammon~JM, Miller~JC, Faraji~F, Ngo~C,
Katibah~GE, Amora~R, {\bf Hocking~TD}, Zhang~L, \mbox{Rebar~EJ}, Gregory~PD,
Urnov~FD, Amacher~SL. Heritable targeted gene disruption in zebrafish
using designed zinc-finger nucleases, \emph{Nature~Biotechnology}
26, 702-708 (2008).

\subsection*{Professional and research experience} \label{profexp}

\newcommand{\job}[4]{\item[#1, #2]\hrulefill\ #3 \\ #4}

\job{Free software developer}{,}{since November 2007}{
  - \href{}{Django-dataplot} for
  statistical graphics on a web site using R, Python, and
- \href{}{GPSDB}, a Python
  program for making websites for GPS data, and visualizing them using
  Google Maps.\\
- \href{}{inlinedocs} R package for documentation generation based on comments in R code.\\
- \href{}{directlabels} R package for automatic direct labeling of multicolor plots.\\
- \href{}{nicholsonppp} R package for fitting a Bayesian model of evolution.\\
- \href{}{sublogo} R package for plotting sublogo dendrograms, for visualizing biological sequence alignment data.\\
- \href{}{Patched the R interpreter} to support named capture in regular expressions using the PCRE library.

\job{Research assistant}{Sangamo BioSciences, Richmond, CA}{June 2006
-- August 2008}{
  Performed biochemical assays to determine sequence specificity of
  DNA-binding proteins.  \\ 
  Designed protein linkers for optimal
  nuclease activity and specificity. \\ 
  Deployed an internal web
  database for visualizing and comparing proteins and experiments.

\job{General manager}{Open Computing Facility, Berkeley, CA}{October 2005 -- May 2006}{
Managed finances, personnel, and public relations for this student computer
center of over 10,000 users.  \\
Installed and maintained software packages and helped users with
technical difficulties.


\subsection*{Programming skills}
Fortran, C, C++, Perl, Python, regular expressions, Emacs-Lisp, R,
SAS, HTML, SQL, PHP, CSS, \LaTeX, Subversion, Mercurial, Debian
systems administration.

\subsection*{Language skills: English (mother tongue), French (fluent)}

\item[Ecole Normale Sup\'erieure, Paris, France, October 2009 -- 2012]
Doctoral research in statistical learning applied to computer vision
and bioinformatics with advisors Francis Bach and Jean-Philippe Vert.
\item[Pierre and Marie Curie University, Paris, France, September
2009] Masters of statistics with internship at INRA in
\href{}{Bayesian statistics
applied to models of domestic animal evolution} with advisors Mathieu
Gautier and Jean-Louis Foulley.
\item[UC Berkeley, Spring 2006] Bachelors in molecular and cell
  biology and statistics. Honors thesis with advisor Terry Speed on
  chromosomal copy number analysis using SNP microarrays.

Playing saxophone and clarinet (since 1994), playing soccer (since 2006),
bicycle riding and touring (since 2007).

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