Skip to content

Commit

Permalink
Add new publication!
Browse files Browse the repository at this point in the history
  • Loading branch information
@vlandham
vlandham committed Jan 16, 2019
1 parent 4f7288b commit 333fd6a
Show file tree
Hide file tree
Showing 2 changed files with 210 additions and 52 deletions.
236 changes: 189 additions & 47 deletions about.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,66 +7,208 @@
<div class="section">
<h2>About Me</h2>

<p>Hello There! I'm a software developer focused on using data visualization, data analysis and data science to solve problems and improve capabilities for reasoning and making decisions with data.</p>
<p>
Hello There! I'm a software developer focused on using data visualization,
data analysis and data science to solve problems and improve capabilities
for reasoning and making decisions with data.
</p>

<p>
I work at <a href="http://https://www.zymergen.com/">Zymergen</a> as a Senior Data Visualization and Data Science Engineer. I am very fortunate to be able to combine my passions for data visualization, data science, and biology to make visual solutions for biological problems.
I work at <a href="http://https://www.zymergen.com/">Zymergen</a> as a
Senior Data Visualization and Data Science Engineer. I am very fortunate to
be able to combine my passions for data visualization, data science, and
biology to make visual solutions for biological problems.
</p>

<p>
Previously, I have worked at <a href="http://bocoup.com/datavis">Bocoup</a> as part of the Data Visualization team along with <a href="http://www.ireneros.com/">Irene Ros</a>, <a href="http://clome.info/">Yannick Assogba</a> and <a href="https://peterbeshai.com/">Peter Beshai</a>.
Previously, I have worked at
<a href="http://bocoup.com/datavis">Bocoup</a> as part of the Data
Visualization team along with
<a href="http://www.ireneros.com/">Irene Ros</a>,
<a href="http://clome.info/">Yannick Assogba</a> and
<a href="https://peterbeshai.com/">Peter Beshai</a>.
</p>

<p>I've also worked for the <a href="http://nordstrom.github.io/">Nordstrom Data Lab</a> as a Data Visualization Engineer/Data Scientist. And before that, I helped analyze genomic data as a member of the <a href="http://research.stowers.org/compbio/">Bioinformatic Group</a> at the very special <a href="http://www.stowers.org/">Stowers Institute</a>.</p>
<p>Find out more about me from the links below, find me on <a href="https://twitter.com/vlandham">Twitter</a>, or drop me an email any time.</p>
<p>
I've also worked for the
<a href="http://nordstrom.github.io/">Nordstrom Data Lab</a> as a Data
Visualization Engineer/Data Scientist. And before that, I helped analyze
genomic data as a member of the
<a href="http://research.stowers.org/compbio/">Bioinformatic Group</a> at
the very special <a href="http://www.stowers.org/">Stowers Institute</a>.
</p>
<p>
Find out more about me from the links below, find me on
<a href="https://twitter.com/vlandham">Twitter</a>, or drop me an email any
time.
</p>

<h2>More Info</h2>

<ul>
<!-- <li><a class="title" href='/documents/jim_vallandingham_resume.pdf' target='_blank' rel='me'>Résumé</a></li> -->
<li><a class="title" href='http://github.com/vlandham' target='_blank' rel='me'>GitHub</a></li>
<li><a class="title" href='http://www.linkedin.com/pub/jim-vallandingham/4/417/61b' target='_blank' rel='me'>LinkedIn</a></li>
<li><a class="title" href='https://twitter.com/vlandham' target='_blank' rel='me'>Twitter</a></li>
<li><a class="title" href='/publications.html' >Publications</a></li>
<li>
<a
class="title"
href="http://github.com/vlandham"
target="_blank"
rel="me"
>GitHub</a
>
</li>
<li>
<a
class="title"
href="http://www.linkedin.com/pub/jim-vallandingham/4/417/61b"
target="_blank"
rel="me"
>LinkedIn</a
>
</li>
<li>
<a
class="title"
href="https://twitter.com/vlandham"
target="_blank"
rel="me"
>Twitter</a
>
</li>
</ul>

<h2>Projects</h2>
<p>Apart from my <a href="http://vallandingham.me/vis/">visualizations</a> and <a href="http://vallandingham.me/">tutorials</a>, I've worked on a number of interesting projects, large and small. Here are just a few of them.</p>
<div class="project span-7 last">
<a class="title" href="http://learntextvis.github.io/textkit/">textkit</a>
<p>Command line tool for working and analyzing text. Provides much of the power of a package like <a href="http://www.nltk.org/">nltk</a>, but without having to know how to program!</p>
</div>
<div class="project span-7 last">
<a class="title" href="http://learnjsdata.com/">Learn JS Data</a>
<p>A teaching resource for understanding basic data manipulation tools in Javascript. Got data and need to work with it online? LearnJSData can teach you what to do!</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/vlandham/illuminati">Illuminati</a>
<p>System that completely automates the execution and control of the <a href="http://www.illumina.com/software/genome_analyzer_software.ilmn">CASAVA</a> genomic aligment software from Illumina.</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/vlandham/hastie">Hastie</a>
<p>Built on top of <a href="https://jekyllrb.com/">Jekyll</a>, this tool provided a way to centralize and distribute analysis and research done by bioinformaticians.</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/metalhelix/pipette">Pipette</a>
<p>A tool to facilitate the creation of pipelines for processing and analyzing genomic data. Included pipelines for SNP calling and annotation using <a href="https://software.broadinstitute.org/gatk/">GATK</a></p>
</div>
<div class="project prepend-1 span-7">
<a class="title" href="http://github.com/beardy/lincoln_client">Lincoln</a>
<p>Network monitoring with style. Won first place in <a href="http://www.perceptivesoftware.com/">Perceptive</a> sponsored application development competition. Client written in Ruby on Rails with graphing capabilities from <a href="http://teethgrinder.co.uk/open-flash-chart/">open flash charts</a>.</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/vlandham/blertr">Blertr</a>
<p>Alerts for long running bash terminal commands. A fun but useful tool that will email you automatically when a long running script or command has completed. Can also notify user through Growl or Twitter</p>
</div>
<div class="project span-7 prepend-1">
<a class="title" href="https://github.com/vlandham/greenword">Greenword</a>
<p>Academic research tool for discovering cultural differences through language. Used at Kansas University to share between students in Costa Rica and America. Written in Rails. </p>
</div>
<div class="project span-7" last>
<a class="title" href="http://github.com/vlandham/minds_eye">Mind's Eye</a>
<p>The start of a face recognition project. Comes in two parts: <a href="http://github.com/vlandham/minds_eye">Mind's Eye</a> - the UI for capturing test data. Implemented in Rails. And <a href="http://github.com/vlandham/minds_eye_forest">Mind's Eye Forest</a> - the detection algorithm written in Ruby and <a href="http://www.r-project.org/">R</a>.</p>
</div>
<h2>Publications</h2>

<ul>
<li>
<a class="title" href="https://www.ncbi.nlm.nih.gov/pubmed/30484125"
>Systematic investigation of CRISPR-Cas9 configurations for flexible and
efficient genome editing in Corynebacterium glutamicum NRRL-B11474.</a
>
</li>

<li>
<a class="title" href="http://www.ncbi.nlm.nih.gov/pubmed/24684930"
>The DEAD Box Helicase RDE-12 Promotes Amplification of RNAi in
Cytoplasmic Foci in C. elegans.</a
>
</li>

<li>
<a
class="title"
href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635348/"
>Evaluation of Whole Transcriptome Amplification Methods by RNA-Seq.</a
>
</li>

<li>
<a
class="title"
href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630707/"
>Gene Expression Profiling of Picogram Amounts of Mouse Universal
Reference RNA Amplified Using the Miltenyi Biotec μMACS SuperAmp
Technology.</a
>
</li>

<li>
<a
class="title"
href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337458/"
>The RDE-10/RDE-11 complex triggers RNAi-induced mRNA degradation by
association with target mRNA in <i>C. elegans</i></a
>
</li>
</ul>

<h2>Projects</h2>
<p>
Apart from my <a href="http://vallandingham.me/vis/">visualizations</a> and
<a href="http://vallandingham.me/">tutorials</a>, I've worked on a number of
interesting projects, large and small. Here are just a few of them.
</p>
<div class="project span-7 last">
<a class="title" href="http://learntextvis.github.io/textkit/">textkit</a>
<p>
Command line tool for working and analyzing text. Provides much of the
power of a package like <a href="http://www.nltk.org/">nltk</a>, but
without having to know how to program!
</p>
</div>
<div class="project span-7 last">
<a class="title" href="http://learnjsdata.com/">Learn JS Data</a>
<p>
A teaching resource for understanding basic data manipulation tools in
Javascript. Got data and need to work with it online? LearnJSData can
teach you what to do!
</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/vlandham/illuminati"
>Illuminati</a
>
<p>
System that completely automates the execution and control of the
<a href="http://www.illumina.com/software/genome_analyzer_software.ilmn"
>CASAVA</a
>
genomic aligment software from Illumina.
</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/vlandham/hastie">Hastie</a>
<p>
Built on top of <a href="https://jekyllrb.com/">Jekyll</a>, this tool
provided a way to centralize and distribute analysis and research done by
bioinformaticians.
</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/metalhelix/pipette">Pipette</a>
<p>
A tool to facilitate the creation of pipelines for processing and
analyzing genomic data. Included pipelines for SNP calling and annotation
using <a href="https://software.broadinstitute.org/gatk/">GATK</a>
</p>
</div>
<div class="project prepend-1 span-7">
<a class="title" href="http://github.com/beardy/lincoln_client">Lincoln</a>
<p>
Network monitoring with style. Won first place in
<a href="http://www.perceptivesoftware.com/">Perceptive</a> sponsored
application development competition. Client written in Ruby on Rails with
graphing capabilities from
<a href="http://teethgrinder.co.uk/open-flash-chart/">open flash charts</a
>.
</p>
</div>
<div class="project span-7 last">
<a class="title" href="https://github.com/vlandham/blertr">Blertr</a>
<p>
Alerts for long running bash terminal commands. A fun but useful tool that
will email you automatically when a long running script or command has
completed. Can also notify user through Growl or Twitter
</p>
</div>
<div class="project span-7 prepend-1">
<a class="title" href="https://github.com/vlandham/greenword">Greenword</a>
<p>
Academic research tool for discovering cultural differences through
language. Used at Kansas University to share between students in Costa
Rica and America. Written in Rails.
</p>
</div>
<div class="project span-7" last>
<a class="title" href="http://github.com/vlandham/minds_eye">Mind's Eye</a>
<p>
The start of a face recognition project. Comes in two parts:
<a href="http://github.com/vlandham/minds_eye">Mind's Eye</a> - the UI for
capturing test data. Implemented in Rails. And
<a href="http://github.com/vlandham/minds_eye_forest"
>Mind's Eye Forest</a
>
- the detection algorithm written in Ruby and
<a href="http://www.r-project.org/">R</a>.
</p>
</div>
</div>
26 changes: 21 additions & 5 deletions publications.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,28 @@

<p>Here are the few publications I have been privileged to be a part of</p>

<a class="title" href="http://www.ncbi.nlm.nih.gov/pubmed/24684930?ordinalpos=1&itool=EntrezSystem2.P">The DEAD Box Helicase RDE-12 Promotes Amplification of RNAi in Cytoplasmic Foci in C. elegans.</a><br/>
<a class="title" href="https://www.ncbi.nlm.nih.gov/pubmed/30484125"
>Systematic investigation of CRISPR-Cas9 configurations for flexible and
efficient genome editing in Corynebacterium glutamicum NRRL-B11474.</a
><br />

<a class="title" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635348/">Evaluation of Whole Transcriptome Amplification Methods by RNA-Seq</a><br/>
<a
class="title"
href="http://www.ncbi.nlm.nih.gov/pubmed/24684930?ordinalpos=1&itool=EntrezSystem2.P"
>The DEAD Box Helicase RDE-12 Promotes Amplification of RNAi in Cytoplasmic
Foci in C. elegans.</a
><br />

<a class="title" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630707/">Gene Expression Profiling of Picogram Amounts of Mouse Universal Reference RNA Amplified Using the Miltenyi Biotec μMACS SuperAmp Technology</a><br/>

<a class="title" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337458/">The RDE-10/RDE-11 complex triggers RNAi-induced mRNA degradation by association with target mRNA in <i>C. elegans</i></a><br/>
<a class="title" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635348/"
>Evaluation of Whole Transcriptome Amplification Methods by RNA-Seq</a
><br />

<a class="title" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630707/"
>Gene Expression Profiling of Picogram Amounts of Mouse Universal Reference
RNA Amplified Using the Miltenyi Biotec μMACS SuperAmp Technology</a
><br />

<a class="title" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337458/"
>The RDE-10/RDE-11 complex triggers RNAi-induced mRNA degradation by
association with target mRNA in <i>C. elegans</i></a
><br />

0 comments on commit 333fd6a

Please sign in to comment.