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Postdoctoral researcher

 
Open Postdoc Position – Computational Math and Biology – Krishnan Lab, MSU

Connecting gene networks to plant morphology using topological data analysis and machine learning

 

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, and machine learning (ML) to analyze and connect gene networks to plant morphology. 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, Dan Chitwood, Elizabeth Munch, and Arjun Krishnan 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.

The postdoc 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 TDA to plant morphology and gene networks, with the long-term goal of predictively modeling each from the other using ML 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.

 

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.

 

Qualifications

  1. PhD with a strong background in mathematics, network biology, computational biology, computer science, machine learning, or other closely related fields.

  2. Programming experience (Python) + version control (e.g. Git); Bonus: experience w/ high-performance computing.

  3. Good communication skills, willingness to collaborate openly, give/take constructive feedback, and, overall sustain a friendly & fun group culture.

 

Apply | Find out more

If you have questions or want to chat about this position, please write to me.
To apply, please respond to this online posting.

 

Scientific programmer

 

We are looking for a coding ninja to join the Krishnan Lab as a scientific programmer. We extensively develop/apply computational approaches to analyze and visualize large-scale biological data.

The programmer is expected to contribute most of the code that goes into our analytical pipelines (that utilize high-performance clusters) and production-ready web-servers. They are expected to maintain high standards for code documentation, clarity, efficiency, and maintainability. In addition to maintaining these standards in their own code, they should set high expectations for other lab members and share her/his expertise to improve the code that all members of the lab are writing.

 

What will you get

  • Work on big data / machine learning / data science applied to important problems in biomedicine, supported by ample computational resources. 

  • Mentor me, trainees, and students to inculcate high standards of writing and maintaining code.

  • Publish first-authored papers on creative tools and pipelines, publish/maintain open-source software projects, and present in scientific meetings/conferences.

  • A vibrant, supportive environment: A bunch of really smart and fun colleagues; Office in a fancy newly built space and quiet workspaces when needed.

  • Beautiful campus; Low cost-of-living.

  • Guidance & support: In addition to being your expert partner, my primary responsibility is to help your personal and professional growth. You will always find in me an audience to discuss opportunities/challenges and a strong advocate for your interests.

 

Qualifications

  1. Excellent programming skills in Python, R, and/or C++.

  2. Experience in web development: Django, SQL, HTML5, CSS, and JavaScript.

  3. It is plus if you have experience with a) High-performance cluster computing, b) Distributed task queue, c) RESTful web services, d) Docker containers.

  4. Have high coding standards for writing efficient, clear, well-documented, version-controlled code.

  5. Good communication skills, willingness to collaborate openly, give/take constructive feedback, and sustain a friendly and fun lab culture.

 

Apply | Find out more

If you have questions or want to chat about this position, please write to me.

To apply, send me an email with your CV, highlighting your released software, reusable packages &/or code repositories (GitHub or Bitbucket), and names & contact information for three references.

 

Graduate students

 

Currently, we are only accepting applications from folks who have their own funding. If you're an undergraduate student and would like to apply for a graduate fellowship to work in our group, please send us an email. We are happy to explore the fit and – if we mutually agree to proceed – work with you in preparing your fellowship proposal.

We are looking for talented and motivated individuals to join the Krishnan Lab as graduate students. If you're interested, please apply to one of the graduate programs we are affiliated with: 1) Computational Mathematics, Science and Engineering, 2) BioMolecular Sciences, and 3) Neuroscience. You will be a great fit if you have a background in bioinformatics, computational biology, genetics, statistics, computer science, machine learning, or other closely related fields. Having programming experience in Python, R, and/or C++ is another huge plus.

In addition to these technical qualifications, we are looking for someone with a growth mindset – embracing challenges, putting in persistent effort, and giving/taking constructive feedback – all of which will set you up for high levels of achievement in your graduate journey.

 

What will you get

  • Our goal is to help our students to develop both an expertise with the computational methods for data-intensive science and a strong understanding of one or more biological application areas.

  • We are committed to providing extensive research training through group meetings, individual meetings, peer-to-peer support, collaborative research, journal clubs, technical workshops, and national/international conferences.

  • Our students will get to work with a bunch of really smart and fun colleagues in a friendly and supportive environment.

  • In addition to being your scientific mentor, my primary responsibility is to help your personal and professional growth. You will always find in me an audience to discuss opportunities/challenges and a strong advocate for your interests.

 

Find out more​

If you are already at MSU, please e-mail me to set up a time to discuss your interest.

If you are elsewhere and interested in joining the lab, please send me an e-mail with your CV and a cover letter that (briefly, in three paragraphs):

  • summarizes your preparation (academics, work experience),

  • describes highlights: particularly tough courses you took, research experience in an academic/industrial setting, any publications you have co-authored, etc.,

  • explains what you know of our work (which papers, by us and others, you've read that are relevant to the Krishnan lab).

We'll pick up a serious communication from there.

 

Undergrad / High school students

 

We welcome undergraduate and high school students to join our lab and we are happy to train them in many aspects of data-intensive biology. We have high expectations for their level of commitment to research and we are keen on incorporating their contributions into co-authored papers in conferences/journals.

As an undergraduate / high school student, if you are interested in discussing research opportunities, please send me an e-mail to set up a time to talk.

 

Visiting scientists

 

We welcome visiting scientists to come and collaborate with our lab to work on any number of projects in data-intensive biology. If you have a burning question or an interesting idea, we would be glad to share our space, experience, and resources with you to develop your project and execute it. Having your own funding would be the easiest way to make this happen. There are some funding sources that you can apply to (e.g. CoB). Please send me an email to discuss the opportunity.

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