research.html

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<h2>Lab Interests</h2>

<p>

The lab interests are diverse, yet there is a common goal: we seek to
intertwingle computation with experiment in order to improve our
understanding of biology.  We intersect with a number of fields, both
new and old, including developmental biology, molecular biology,
bioinformatics, regulatory genomics, metagenomics, and next-generation
sequencing data.

<p>

If you're interested in more detail, see
CTB's <a href='downloads/2013-research.pdf'>research statement (Oct
2013)</a> and <a href='downloads/2013-teaching.pdf'>teaching statement
(Oct 2013)</a>.

<p>

Below, we've made several <a href='#papers'>papers and submission
cover letters</a>, as well as <a href='#grants'>submitted grants</a>,
available.  The full list of papers for CTB is available via
<a href="http://scholar.google.com/citations?user=O4rYanMAAAAJ&hl=en">Google
Scholar</a>, and you can also see his <a href='https://github.com/ctb/resume/blob/master/full-CV.pdf?raw=true'>full CV (Oct 2013)</a>.

<p>

<A name='papers'>
<h4>Papers and cover letters</h4>
<ul>
<li><A href='http://arxiv.org/abs/1309.2975'>arXiv paper: These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure</a>, submitted to PLoS One.</li>
<p>
Authors: Qingpeng Zhang, Jason Pell, Rosangela Canino-Koning, Adina Chuang Howe, C. Titus Brown</a>.
<p>
<p>
<li> <a href='http://arxiv.org/abs/1212.2832'>arXiv paper: Assembling large, complex environmental metagenomes</a></li>
<p>
Authors:Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah G. Tringe, James M. Tiedje, C. Titus Brown
<p>
<li> <a href='http://arxiv.org/abs/1203.4802'>arXiv paper: A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data</a>, submitted to PLoS One; see <a href='downloads/2012-diginorm-plos-cover-letter.pdf'>cover letter</a>, too.</li>
<p>
Authors: C. Titus Brown, Adina Howe, Qingpeng Zhang, Alexis B. Pyrkosz, Timothy H. Brown.
<p>
<li> <A href='http://arxiv.org/abs/1112.4193'>arXiv: Scaling metagenome sequence assembly with probabilistic de Bruijn graphs</a></li>
<p>
Authors: Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe,
James M. Tiedje, C. Titus Brown.
<p>
My first senior author paper!!
<p>
Submitted to PNAS on Dec 28th, 2011 (<a href='downloads/2011-kmer-percolation-pnas-cover-letter.pdf'>cover letter</a>) and accepted in July, 2012.
</ul>

<a name='grants'>
<h4>Grant proposals:</h4>
<ul>
<li> <a href='downloads/2014-moore-ddd-preapp.pdf'>2014 / Pre-application</a> to <a href='http://moore.org/programs/science/data-driven-discovery/ddd-investigators'>Moore Foundation Data Driven Discovery Investigator program</a>
<p>
<li> <a href='downloads/2013-chick-genome-improvement.pdf'>2013 / Improving the Chick Genome Sequence</a></li>
<P>
A collaborative proposal to the USDA led by Wes Warren at WUSTL, with Hans Cheng, Jerry Dodgson, and myself participating, focused on improving the current chick genome assembly.  (Funded.)
<p>
<li> <a href='downloads/2012-nih-ngs-r25-FINAL.pdf'>2012 / Next-gen course, NIH R25</a> </li>
<p>
A renewal request for <a href='http://bioinformatics.msu.edu/ngs-summer-course-2013'>our summer course</a> on next-gen sequence analysis; see the initial proposal, from 2010, below.  This one is way better :)  (Funded.)
<p>
<li> 2012 / <A href='http://www.nsf.gov/pubs/2012/nsf12101/nsf12101.jsp?WT.mc_id=USNSF_25&WT.mc_ev=click'>NSF Office of Cyberinfrastructure</a> proposal, <a href='downloads/2012-beacon-education-suppl-pub.pdf'>Materials and Workshops for Cyberinfrastructure Education in Biology</a> supplement to <a href='http://www.beacon-center.org/'>BEACON</a>.  (funded)
<p>
<li> 2012 / <A href='http://www.nsf.gov/pubs/2011/nsf11690/nsf11690.htm'>NSF CAREER</a> proposal, <a href='downloads/2012-career-nsf-final.pdf'>Assembling Extremely Large Metagenomes</a>
<p>
<li> 2012 / <a href='http://www.nsf.gov/pubs/2012/nsf12499/nsf12499.htm'>NSF BIGDATA</a> proposal, <a href='downloads/2012-bigdata-nsf.pdf'>Low-memory Streaming Prefilters for Biological Sequencing Data</a>
<p>
<li> 2012 / <a href='downloads/2012-moorefund.pdf'>Moore Foundation proposal on marine metagenomics</a>
<li> <a href='downloads/2011-nsf-career.pdf'>2011 / NSF CAREER proposal: "Scaling and Improving de Bruijn graph assembly"</a></li>
<p>
My (rejected) grant proposal to work on de Bruijn graph
filtering/breakdown approaches for de novo assembly.
<p>
<li> <a href='downloads/2011-reappointment.pdf'>2011 / Reappointment</a></li>
<p>
"Dear MSU, please do not fire me.  I will be good, I promise."  A writeup
of what I have accomplished and what I hope to accomplish as a professor, and
why MSU should keep me around.
<p>
(They believed me; I'm hired through 2015.)
<p>
<li> <a href='downloads/2010-ngs-course-nih-r25.pdf'>2010 / Next-gen course, NIH R25</a> </li>
<p>
Our (accepted) grant proposal to support <A href='http://bioinformatics.msu.edu/ngs-summer-course-2011'>our summer course</a> on next-gen sequence analysis.
<p>
<li> <a href='downloads/2009-usda-vertex.pdf'>2009 / Web tools for next-gen sequence analysis</a></li>
<p>
Our (accepted) grant proposal to build an easy-to-use Web interface for
next-gen sequence analysis. (USDA NIFA)
<p>
<li> <a href='downloads/cartwheel-nih-sep2007-short.pdf'>2007 / Cartwheel</a> </li>
<p>
A (rejected) grant
proposal on the need for easy-to-use Web interfaces for comparative sequence
analysis.  (NIH R01)
</ul>

<a name='oldstuff'>
<h4>Miscellany:</h4>
<ul>
<li> See
CTB's <a href='downloads/2006-research-statement.pdf'>research
statement</a>
and <a href='downloads/2006-teaching-statement.pdf'>teaching
statement</a> from his 2006 applications.
</ul>

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