Bioinformatics and Computational Biology of Gene Regulation

photo of genome chart.

Students will participate in a USDA-funded project to identify and characterize gene regulatory sequences throughout the genomes of 50 or more insects of agricultural and biomedical importance.

Project is Not Currently Available

The project mentor is no longer accepting student inquires, because this project is currently at full capacity. 

Project description

Our laboratory studies gene regulation and genome evolution using a mixture of computational and experimental methods. We are interested in motivated students who are comfortable using command-line based software running on Linux and working with large data sets. While extensive coding skills are not required, minimal coding ability in Python, R, or a similar language is preferable. Students will participate in a USDA-funded project to identify and characterize gene regulatory sequences throughout the genomes of 50 or more insects of agricultural and biomedical importance, helping to develop and use computational approaches to discover, describe, and disseminate information about these important genomic elements.

Project outcome

The specific outcomes of this project will be identified by the faculty mentor at the beginning of your collaboration. 

Project details

Timing, eligibility and other details
Length of commitment Semester or longer; longer commitments preferred
Start time Anytime
Level of collaboration Individual student project
Benefits Academic Credit, Volunteer
Who is eligible Students with basic command-line Linux skills and familiarity with R or Python. Interest/background in genetics/genomics preferred.
Support Funding is available after the completion of the preparation badge. See below.

Project mentor

Marc Halfon

Professor

Biochemistry

B3-307 COEBLS, Jacobs School of Medicine and Biomedical Sciences

Phone: (716) 829-3126

Email: mshalfon@buffalo.edu

Preparation

To engage with this project, you will work through a series of Project-Based Collaboration digital badges to guide your experience. These badges will:

  1. Guide you in setting your goals and intentions as well as gaining additional context,
  2. Enhance your collaboration with your mentor/partner,
  3. Support your reflection and help you integrate your learning with your academic and professional goals.

All students who wish to participate in a project on the Project Portal must first complete the Project Preparation Digital Badge. First, contact the project mentor to discuss availability and after you’ve received approval, you can start the Project Preparation Digital Badge.

Preparation guidance

Once you have registered for the Project Preparation Digital Badge, you will receive further instructions related to the activities you will need to complete. In addition, you will also complete the following preparation activities for this particular project:

  • Students should demonstrate comfort with the Unix/Linux command line and familiarity in simple coding skills, preferably using Python or R. If students have not completed CSE115/116, proof of necessary skills should be provided. 
  • Interested students should review the attached paper. If the methods described therein appear too difficult, this will not be an appropriate project. It is OK if not all of the scientific details make sense, as long as the methods fall within the student's skill set.