Category Archives: News

Professor Wheeler Awarded Junior Investigator Grant

The Wheeler lab has been awarded the CBSD COBRE Junior Investigator project grant to develop “methods for fast bio-sequence comparison with profile hidden Markov models”. The grant will provide $450K in funding over three years, supporting research by two graduate students and several undergraduate researchers.
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Annual CS Picnic!

The end-of-spring-picnic is always a hit. This year was no exception. Burgers, hot dogs, cake, pie, potato salad, all the fixins, conversations and team sports! Now we just have to get through finals.

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Students Present at UMCUR

Michael Kinsey and Greg McMann presented at this year’s University of Montana Conference on Undergraduate Research. Their presentation was entitled “Integrating Cellular Percolation Fire Spread into an Existing Landscape Model” and it described their work with the US Forest Service on the open source software used by the USFS for land management operations.


Great job, and best of luck to these two graduating seniors!

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Professor Wheeler Awarded NIH Grant

Professor Travis Wheeler has been awarded a grant from the National Institute of General Medical Sciences (a division of the National Institutes of Health) to develop “Improved protein-DNA models for translated sequence search with profile Hidden Markov models”. The grant is for $426K over three years, beginning April 1, 2017.

Fast and sensitive sequence database search is fundamental to modern molecular biology. The funded research will improve the accuracy of annotation of protein-coding content in sequenced genomes and metagenomic datasets. The research builds on established sequence database search software that employs probabilistic models to increase sensitivity through greater statistical power and ability to better model family complexity. The probabilistic models are called profile hidden Markov models (profile HMMs), and the software is HMMER.

Dr. Wheeler’s group will develop new models that account for frameshifting mutations or errors that obscure the protein-coding nature of sequence, and for splice sites that break genes or domains into distant fragments on the genome. Through a combination of new algorithms and application of existing approaches, these models will be fast enough to use for large-scale annotation, such as in the EMBL European Bioinformatics Institute’s  Metagenomics Portal.

For questions about this project or to get involved, contact Travis Wheeler (

Anonymous Donor provides scholarships for Montana CS students

We gratefully acknowledge an Anonymous Donor who has provided for the continuation of the J.R. Scholarship for Montana Computer Scientists, with a $200,000 gift that will support five $10,000 scholarships per year for four years (AY 2018-2022).

Eligibility requirements:

  • Montana high school graduates who will major in Computer Science at the University of Montana.
  • Recipients must demonstrate service and/or volunteerism in their community.
  • Of the five scholarships awarded annually, the preference is for one award to be made to a graduate of a Ravalli County high school. If there are no qualified Ravalli County high school graduates then another qualifying Montana high school graduate may be selected.

For further details about this and other scholarships for UM CS students, please visit our scholarships page.

Grad students Kyle Handy and Andre Gillan present research at international conference

20161209_095142MS students Kyle Handy and Andre Gillan recently presented research conducted in the Computational Mass Spectrometry lab at the University of Montana at the 2016 Biotechnology and Bioinformatics Symposium (BIOT) held at Brigham Young University in Provo, UT 8-9 Dec. BIOT is an annual peer reviewed bioinformatics conference attended by researchers from around the world.

Kyle Handy presented a novel software package for mass spectrometry signal segmentation, the first program ever created to solve this type of problem. Andre Gillan’s presentation presented a new parser for mass spectrometry data that outperformed all existing parsers. Handy and Gillan were accompanied by their advisor, Dr. Rob Smith, director of the Computational Mass Spectrometry lab at the University of Montana.

Gianforte Family Foundation Supports Growth of UM Computer Science

The Gianforte Family Foundation once again has shown its dedication to supporting education and job creation in Montana, pledging $290,000 to the University of Montana’s Department of Computer Science. The two-year gift will help the department grow its enrollment capacity, ultimately graduating more computer science majors and minors for careers in Montana’s growing technology sector.

The generous gift will underwrite two new lecturers, allowing our department to expand sections of its introductory computing classes and create two new foundational courses. The department’s goal is to double the number of computer science majors and minors during the next five years.

The first lecturer, Trish Duce, was hired over the summer and started teaching this fall. A second will join for the 2017-18 academic year. In addition to the lecturer positions, the gift supports Assistant Professor Rob Smith‘s efforts to work with local businesses to develop internship opportunities and help students attain them.

In Montana and nationwide, high-tech jobs go unfilled because there aren’t enough graduates with computer science training. In addition, more and more careers use computing in their respective fields. To address this, UM’s computer science department worked with the Gianforte Family Foundation to develop a plan to increase enrollment and grow course offerings by creating courses that show the relevance of computing in other disciplines. These new offerings allow for a cross-disciplinary computer science minor and provide students with a broader skill-set for today’s technological workplace.

“Computer science is a growing and needed field,” said Andrew Ware, professor and chair of the Department of Computer Science. “By building our department, we can help more students find high-paying jobs and fill a need in the state’s economy.”

“Computing is increasingly important across many academic disciplines and careers,” said Greg Gianforte, foundation board member. “We’re excited to work with the University of Montana to help expand cross-disciplinary computer science courses for all students on campus, and to help connect these students with good jobs in Montana.”

(text is largely reproduced from a UM news release: link to original)