New grant

My colleague Indika Kahanda and I were awarded a new NSF grant this summer entitled Collaborative Research: Innovation: Pioneering New Approaches to Explore Pangenomic Space at Scale.  We are looking for a postdoc for the project so please email either one of us if you believe you are qualified and potentially interested.

Research Experience for Teachers and REU

A plug for two programs that are happening at MSU this coming summer:  The first is a new Research Experience for Teachers (RET) site.  See this article for more information.  Myself and a couple colleagues from computer science will host one of the projects.  The second summer program is our continuing Research Experience for Undergraduates (REU) program entitled Research and Development of Algorithms in a Software Factory.  This is the second year of the site; we had great projects last summer and I am looking forward to working with the next group of students this coming summer.  If you are an undergraduate student (or a teacher), please feel free to contact me about either program.

Faculty Affairs

I am chairing the faculty affairs committee this year, having served on the committee for a few years now.  This is one of the more interesting university committees in my opinion.  Our tasks are to provide feedback to faculty senate and the joint academic governance steering committee on current issues that are being discussed by the faculty and administration.  We also provide faculty peer evaluations of sabbatical applications…both interesting topics.

Pan-genomics paper in BCB

Our paper Exploring Frequented Regions in Pan-Genomic Graphs was accepted to the ACM BCB conference in Boston in August.  Looking forward to it.  Congrats to my co-authors Alan Cleary, Thiruvarangan Ramaraj, Joanne Mudge and Indika Kahanda.  Alan is going to give the talk.  (Thanks also to Brittany Fasy for making this figure from the paper.)

Update: Our paper won the Best Student Paper award!

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My student Sean Yaw successfully defended his PhD this April.  His thesis was entitled “Scheduling for Optimized Network Resource Utilization #SmartGrid #Cloud.”  Sean currently doing a postdoc at Los Alamos National Lab, working on applied optimization problems for carbon sequestration.

Congratulations as well to my students Daniel Salinas for passing his PhD comprehensive exam and Mohammadbagher Parsa Gharamaleki for passing his M.Sc. defense.

NSF REU site

News has been a little slow around these parts but my colleague Clem Izurieta and I recently received NSF funding to host an Research Experience for Undergraduates (REU) site at MSU, starting this summer.  Eight students from across the country will converge on Bozeman to work on a variety of projects for 10 weeks.  I will likely supervise one project on computational biology (pangenomics).  More information can be found here:

Semester finishing up, Summer coming up

Well another semester is nearly over.  I’ve enjoyed teaching our CSCI 532 (Graduate Algorithms) class again this spring (17 students).  My student Alan Cleary and collaborators Joann Mudge and Thiru Ramaraj at NCGR in Santa Fe just got word our two posters submissions were accepted to the Los Alamos Sequencing, Finishing, and Analysis in the Future Meeting 2016,, so I will be down in New Mexico at the beginning of June for that.  Other summer activities include writing some proposals with various collaborators and working on a variety of papers in varying states of completion (hope to submit one or two Infocom papers on recent networking and scheduling work).