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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">Subject:
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<td>[SIAM-DY] Postdoc opening: Applications of TDA to Plant
Morphology and Gene Networks</td>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">Date: </th>
<td>Wed, 17 Jun 2020 20:16:58 +0000</td>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">From: </th>
<td>Munch, Elizabeth <a class="moz-txt-link-rfc2396E" href="mailto:muncheli@msu.edu"><muncheli@msu.edu></a></td>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">To: </th>
<td>Pekka Orponen <a class="moz-txt-link-rfc2396E" href="mailto:pekka.orponen@aalto.fi"><pekka.orponen@aalto.fi></a></td>
</tr>
<tr>
<th valign="BASELINE" nowrap="nowrap" align="RIGHT">CC: </th>
<td>The Dynamical Systems SIAG mailing list
<a class="moz-txt-link-rfc2396E" href="mailto:siam-dy@siam.org"><siam-dy@siam.org></a></td>
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Hello everyone!</div>
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We invite applicants for a postdoc position here at MSU to study
plant morphology and gene networks through the lens of
topological data analysis. The successful candidate will be
housed in the Dept of Biochemistry and Molecular Biology, but
the project includes collaborators from multiple departments
including</div>
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MSU CMSE and BMB</li>
<li><a
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MSU CMSE and Horticulture</li>
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The official job posting is here:<a
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The relevant information is copied below.</div>
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I would be happy to answer any questions you might have, so
please feel free to get in touch!</div>
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Best,</div>
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Liz</div>
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Of Natural Science</span><br>
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10032098</span><br>
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font-weight: bold; box-sizing: border-box; color: rgb(34, 34,
34); background-color: rgb(249, 249, 247);">Salary:</b><span
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sans-serif, serif, EmojiFont; color: rgb(34, 34, 34);
background-color: rgb(249, 249, 247);"><span style="margin:
0px"></span>48671.00</span><br>
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"Helvetica Neue", Helvetica, Arial, sans-serif;
font-weight: bold; box-sizing: border-box; color: rgb(34, 34,
34); background-color: rgb(249, 249, 247);">Location:</b><span
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Neue", Helvetica, Arial, sans-serif, serif, EmojiFont;
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background-color: rgb(249, 249, 247);">East Lansing</span><br>
<b style="font-size: 14px; font-family: "Open Sans",
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34); background-color: rgb(249, 249, 247);">Categories:</b><span
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Neue", Helvetica, Arial, sans-serif, serif, EmojiFont;
box-sizing: border-box; color: rgb(34, 34, 34);
background-color: rgb(249, 249, 247);">Full Time (90-100%),
Fixed Term Academic Staff, Research/Scientific, Non-Union</span><br>
<p style="font-size: 14px; font-family: "Open Sans",
"Helvetica Neue", Helvetica, Arial, sans-serif;
margin: 0px 0px 10.5px; box-sizing: border-box; color: rgb(34,
34, 34); background-color: rgb(249, 249, 247);">
</p>
<div style="margin: 0px; font-size: 14px; font-family:
"Open Sans", "Helvetica Neue", Helvetica,
Arial, sans-serif, serif, EmojiFont; box-sizing: border-box;
color: rgb(34, 34, 34); background-color: rgb(249, 249, 247);">
<h3 style="margin-top: 21px; margin-bottom: 10.5px; font-size:
26px; font-family: Raleway, "Helvetica Neue",
Helvetica, Arial, sans-serif; line-height: 1.4; box-sizing:
border-box">
Position Summary</h3>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">All
data has shape, and embedded within all shapes is data that
can be extracted. Shapes can be obvious and apparent to the
eye, like the morphology of plants. Or, shapes can be more
abstract, like that of a gene expression network. We are
seeking an individual passionate about applying Topological
Data Analysis (TDA), a mathematical method that measures
shape, to the plant sciences. The successful candidate will
be a pioneer, applying state-of-the-art data science
techniques and mathematical approaches to the analysis of
intensive datasets and predictive modeling.</p>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">The
project is based at Michigan State University between the
laboratories of Professors<span></span><span style="margin:
0px">Beronda</span><span></span>Montgomery,<span></span><span
style="margin: 0px">Arjun</span><span></span>Krishnan,
Elizabeth Munch, and Dan Chitwood together with collaborator
Aman Husbands (Ohio State University). The postdoc will work
with all five PIs, who offer complementary scientific and
mathematical expertise. Between the PIs, the candidate will
have access to expertise including Topological Data
Analysis, network biology, machine learning approaches,
bioinformatics, molecular biology, and plant growth and
development. The PIs are committed to the career development
of the candidate who will be mentored in line with their
professional goals.</p>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">We
live in extraordinary times during the COVID-19 pandemic.
The circumstances of employment, including start date,
possibility of remote work, and access to on-campus
resources, will be discussed with the candidate to
accommodate their health, well-being, and success on the
project.</p>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">The
post-doc will lead data analysis efforts in: 1) creating and
processing plant growth time lapse images from 3D X-ray
Computed Tomography (CT) data, 2) processing corresponding
gene expression time series data using RNA-Seq and
constructing gene networks, and 3) applying Topological Data
Analysis (TDA) to plant morphology and gene networks, with
the long-term goal of predictively modeling each from the
other using machine learning approaches. This project will
focus on the model plant Arabidopsis, utilizing accessions
with contrasting developmental stability and leaf
morphology, as well as differing light regimens that elicit
plastic changes in plant growth and gene expression.</p>
<h3 style="margin-top: 21px; margin-bottom: 10.5px; font-size:
26px; font-family: Raleway, "Helvetica Neue",
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border-box">
Required Degree</h3>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">Doctorate
-Math, Network Biology, Computation Biology</p>
<h3 style="margin-top: 21px; margin-bottom: 10.5px; font-size:
26px; font-family: Raleway, "Helvetica Neue",
Helvetica, Arial, sans-serif; line-height: 1.4; box-sizing:
border-box">
Minimum Requirements</h3>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">A
PhD with a strong background in mathematics, network
biology, computational biology, computer science, machine
learning, or other closely related fields. Good
communication skills, willingness to collaborate openly,
give/take constructive feedback, and sustain a friendly and
collegial workplace environment.</p>
<h3 style="margin-top: 21px; margin-bottom: 10.5px; font-size:
26px; font-family: Raleway, "Helvetica Neue",
Helvetica, Arial, sans-serif; line-height: 1.4; box-sizing:
border-box">
Desired Qualifications</h3>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">Programming
experience in Python, R, and/or C++ with version control
(Git), and experience with high-performance cluster
computing.</p>
<h3 style="margin-top: 21px; margin-bottom: 10.5px; font-size:
26px; font-family: Raleway, "Helvetica Neue",
Helvetica, Arial, sans-serif; line-height: 1.4; box-sizing:
border-box">
Required Application Materials</h3>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">A
CV, 2) A statement of your research interests ( 500 words),
and 3) Names & contact information for three references.</p>
<h3 style="margin-top: 21px; margin-bottom: 10.5px; font-size:
26px; font-family: Raleway, "Helvetica Neue",
Helvetica, Arial, sans-serif; line-height: 1.4; box-sizing:
border-box">
Website</h3>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box"><a class="moz-txt-link-freetext" href="https://bmb.natsci.msu.edu/">https://bmb.natsci.msu.edu/</a></p>
<h3 style="margin-top: 21px; margin-bottom: 10.5px; font-size:
26px; font-family: Raleway, "Helvetica Neue",
Helvetica, Arial, sans-serif; line-height: 1.4; box-sizing:
border-box">
MSU Statement</h3>
<p style="margin: 0px 0px 10.5px; box-sizing: border-box">Michigan
State University has been advancing the common good with
uncommon will for more than 160 years. One of the top
research universities in the world, MSU pushes the
boundaries of discovery and forges enduring partnerships to
solve the most pressing global challenges while providing
life-changing opportunities to a diverse and inclusive
academic community through more than 200 programs of study
in 17 degree-granting colleges.</p>
</div>
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<b style="font-weight: bold; box-sizing: border-box">Advertised:</b><span
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<p style="font-size: 11pt; margin-top: 0px; margin-bottom:
0px"><span style="margin: 0px; font-family: Arial,
Helvetica, sans-serif, serif, EmojiFont"><b>Elizabeth
Munch, PhD</b></span><br>
<span style="margin: 0px; font-family: Arial, Helvetica,
sans-serif, serif, EmojiFont">Assistant Professor</span><br>
<span style="margin: 0px; font-family: Arial, Helvetica,
sans-serif, serif, EmojiFont">Dept of Computational
Mathematics, Science, and Engineering</span><br>
<span style="margin: 0px; font-family: Arial, Helvetica,
sans-serif, serif, EmojiFont">Dept of Mathematics</span><br>
<span style="margin: 0px; font-family: Arial, Helvetica,
sans-serif, serif, EmojiFont">Michigan State
University</span><br>
<span style="margin: 0px; font-family: Arial, Helvetica,
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