Elizabeth Munch writes:
We have recently gotten word of funding 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, in MSU CMSE and Math
- Arjun Krishnan in MSU CMSE and BMB
- Beronda Montgomery in MSU BMB and MMG
- Aman Husbands in OSU MG
- Dan Chitwood in MSU CMSE and Horticulture
The official job posting is here: https://careers.msu.edu/cw/en-us/job/503667/research-associatefixed-term
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!
Job no: 654988
Work type: Faculty/Academic Staff
Major Administrative Unit / College: College Of Natural Science
Department: Biochemistry & Molecular Biology Cns 10032098
Location: East Lansing
Categories: Full Time (90-100%), Fixed Term Academic Staff, Research/Scientific, Non-Union
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 Professors Beronda Montgomery, Arjun 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.
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.
Doctorate -Math, Network Biology, Computation Biology
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.
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.
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, 2020 Eastern Daylight Time
Applications close: Nov 2, 2020 Eastern Standard Time