[Job-offers-cs] Postdoc opening: Applications of TDA to Plant Morphology and Gene Networks

Wed Jun 24 23:16:55 EEST 2020

-------- Forwarded Message --------

Subject: 	[SIAM-DY] Postdoc opening: Applications of TDA to Plant 
Morphology and Gene Networks
Date: 	Wed, 17 Jun 2020 20:16:58 +0000
From: 	Munch, Elizabeth <muncheli at msu.edu>
To: 	Pekka Orponen <pekka.orponen at aalto.fi>
CC: 	The Dynamical Systems SIAG mailing list <siam-dy at siam.org>

Hello everyone!

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

  * Me
    <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Felizabethmunch.com%2F__%3B!!HXCxUKc!huWgzmRPpBZUZ4UwdvwP6XHmAczIqZ2_R2qhIzvkIPngCCZs4kuaVbx00gFN6V8%24&data=01%7C01%7Cmuncheli%40msu.edu%7Caa63d617ccd14fb4a1fb08d812fa1cba%7C22177130642f41d9921174237ad5687d%7C0&sdata=TUwccPxgjL%2FxPyFxtYVxpXHMGVZTTF6HOtGylAMBagA%3D&reserved=0>,
    in MSU CMSE and Math
  * Arjun Krishnan
    <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.thekrishnanlab.org%2F__%3B!!HXCxUKc!huWgzmRPpBZUZ4UwdvwP6XHmAczIqZ2_R2qhIzvkIPngCCZs4kuaVbx0o5rkm00%24&data=01%7C01%7Cmuncheli%40msu.edu%7Caa63d617ccd14fb4a1fb08d812fa1cba%7C22177130642f41d9921174237ad5687d%7C0&sdata=082OHpLJJOzZmiDwcggrNpRZwe5RLhgFRDO9VutTGRc%3D&reserved=0>in
    MSU CMSE and BMB
  * Beronda Montgomery
    <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprl.natsci.msu.edu%2Fpeople%2Ffaculty%2Fberonda-montgomery%2F&data=01%7C01%7Cmuncheli%40msu.edu%7Caa63d617ccd14fb4a1fb08d812fa1cba%7C22177130642f41d9921174237ad5687d%7C0&sdata=LKF69FDXMywfWBgV7uMaGXZaa22V1s30WOUVkj%2FcSGc%3D&reserved=0> in
    MSU BMB and MMG
  * Aman Husbands
    <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmolgen.osu.edu%2Fpeople%2Fhusbands.6__%3B!!HXCxUKc!huWgzmRPpBZUZ4UwdvwP6XHmAczIqZ2_R2qhIzvkIPngCCZs4kuaVbx0b-Agex4%24&data=01%7C01%7Cmuncheli%40msu.edu%7Caa63d617ccd14fb4a1fb08d812fa1cba%7C22177130642f41d9921174237ad5687d%7C0&sdata=j4MC1tvgLEfbWKr%2BPXb47Zd6GRdmgEZ3LanPpAWlxVE%3D&reserved=0> in
    OSU MG
  * Dan Chitwood
    <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcmse.msu.edu%2Fdirectory%2Ffaculty%2Fdan-chitwood%2F&data=01%7C01%7Cmuncheli%40msu.edu%7Caa63d617ccd14fb4a1fb08d812fa1cba%7C22177130642f41d9921174237ad5687d%7C0&sdata=p7njH4Cm3mn3FDtJZSY342lbPbC%2Bw8a6AkNeXysXNyA%3D&reserved=0>in
    MSU CMSE and Horticulture

The official job posting is here: 
https://careers.msu.edu/cw/en-us/job/503667/research-associatefixed-term 
<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcareers.msu.edu%2Fcw%2Fen-us%2Fjob%2F503667%2Fresearch-associatefixed-term&data=01%7C01%7Cmuncheli%40msu.edu%7Caa63d617ccd14fb4a1fb08d812fa1cba%7C22177130642f41d9921174237ad5687d%7C0&sdata=mi9q3gFZJOmsqI6i65AL4itmtFsOpo1H726FnAFwzTM%3D&reserved=0>
The relevant information is copied below.

I would be happy to answer any questions you might have, so please feel 
free to get in touch!

Best,
Liz

--------------------------------------------------------

*Job no:*654988
*Work type:*Faculty/Academic Staff
*Major Administrative Unit / College:*College Of Natural Science
*Department:*Biochemistry & Molecular Biology Cns 10032098
*Salary:*48671.00
*Location:*East Lansing
*Categories:*Full Time (90-100%), Fixed Term Academic Staff, 
Research/Scientific, Non-Union

      Position Summary

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.

The project is based at Michigan State University between the 
laboratories of ProfessorsBerondaMontgomery,ArjunKrishnan, 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.

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.

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.

      Required Degree

Doctorate -Math, Network Biology, Computation Biology

      Minimum Requirements

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.

      Desired Qualifications

Programming experience in Python, R, and/or C++ with version control 
(Git), and experience with high-performance cluster computing.

      Required Application Materials

A CV, 2) A statement of your research interests (≤ 500 words), and 3) 
Names & contact information for three references.

      Website

https://bmb.natsci.msu.edu/

      MSU Statement

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.

*Advertised:*Jun 16, 2020Eastern Daylight Time
*Applications close:*Nov 2, 2020Eastern Standard Time

---

*Elizabeth Munch, PhD*
Assistant Professor
Dept of Computational Mathematics, Science, and Engineering
Dept of Mathematics
Michigan State University
Office: 517-432-0619
elizabethmunch.com 
<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Felizabethmunch.com%2F&data=01%7C01%7Cmuncheli%40msu.edu%7Caa63d617ccd14fb4a1fb08d812fa1cba%7C22177130642f41d9921174237ad5687d%7C0&sdata=vxp47IlASxnkOvsDoUk51SHAUM1FvTEYoZmITFN3YTw%3D&reserved=0>

-- 

<elizabethmunch.com>

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