Folks in the Wheeler lab
I’m lucky to have a great group of people working together on a broad range of projects (in a pretty great place to live!)
Travis Wheeler (aka the big boss)
Principal Investigator – Email | Personal Page | Curriculum Vitae | Google Scholar profile
Department of Computer Science
Research: Computational genomics, Machine Learning
Research staff
George Lesica
Senior Software Engineer – Email | Personal Page
Jack of all trades, Master of some
Sean Rice
Guest Software Developer – Email | Personal Page
Projects: RepeatMasker pipeline
Reports to Robert Hubley at the Institute for Systems Biology; caucuses with the Wheeler lab
PhD students
Alex Nord
PhD candidate, CMMB (Computational Biology) (2015-) – Email | Personal Page
Research: Splice sites in translated sequence alignment; multiple sequence alignment
BA, Philosophy, Reed College
MS, Computer Science, University of Montana
Tim Anderson
PhD candidate, Computer Science (DIS) (2017-) – Email | Personal Page
Research: FPGA algorithms for sequence alignment; optimized FM index; Custom data logging systems
BS, Music, University of Montana
MS, Computer Science, University of Montana
Daniel Olson
PhD student, Computer Science (2017-) – Email | Personal Page
Previously: Undergraduate researcher (2016-2017)
Research: Models for repetitive biological sequences; adaptive element detection in sequence data
BS, Biochemistry, University of Montana
Anna Marbut
PhD student, Computer Science (DIS) (2019-) – Email | Personal Page
Research: Recommendation engines (ML and NLP)
BA, Linguistics, Reed College
MA, Business Analytics, University of Montana
Conner Copeland
PhD student, CMMB (Computational Biology) (2020-) – Email | Personal Page
Previously: Undergraduate researcher (joint with Pat Secor), Computer Science (2017-2020)
Research: Prophage genome annotation
BS, Computational Biochemistry, University of Montana
Jeremiah Gaiser
PhD student, CMMB (Computational Biology) (2020-) – Email | Personal Page
Previously: Undergraduate researcher, Biochemistry, (2017-2020)
Research: Viral genome annotation w/ sequencing error
BS, Computational Biochemistry, University of Montana
Masters students
Genevieve Krause
MS student, Computer Science (2016-) – Email | Personal Page
Research: Pseudogene detection; frameshift model for sequence alignment.
BS, Environmental Studies, Prescott College
Kaitlin Carey
MS student, Computer Science (2017-) – Email | Personal Page
Research: Adjudication of candidate annotations; specifically Transposable Element subfamily annotation
BS, Biochemistry, University of Montana
David Rich
MS student, Computer Science (2018-) – Email | Personal Page
Research: Pruned dynamic programming w/ profile HMMs
BS, Business Administration, University of Montana
Jack Roddy
MS student, Computer Science (2019-) – Email | Personal Page
Previously: Undergraduate researcher, Computer Science, (2018-2019)
Research: Sequence Alignment - homologous overextension; Dfam infrastructure
BS, Computer Science, University of Montana
Sarah Walling
MS student, Computer Science (2019-) – Email | Personal Page
Previously: Undergraduate researcher, Computer Science, (2018-2019)
Research: Expression patterns of dual-coding exons
BS, Computer Science, University of Montana
Audrey Shingleton
MS student, Computer Science (2020-) – Email | Personal Page
Research: Sequence annotation, especially transposable elements
BS, Applied and Computational Math Sciences, University of Washington
Undergraduate students
Isaac Robinson
Undergraduate researcher, Computer Science (2019-) – Email | Personal Page
(joint with Nathan Insel)
Research: Tracking and behavior classification in rodent videos
George Glidden-Handgis
Undergraduate researcher, Computer Science (2020-) – Email | Personal Page
(joint with Rocky Mountain Labs)
Research: Machine learning methods for cell culture image segmentation, beetle song classification
Lab Alumni
Dylan Wichman
Student - Billings Central High School, (2019-2020) Research: Machine learning approaches to wildfire risk prediction
Next steps: Louisiana State Universty
Adam Clemons
MS student, Computer Science, (2017-2019)
BS, Computer Science, University of Montana
Research: Software plagiarism
Next steps: Submittable
Joyce Liu
Student - Sentinel High School (Missoula), (2016-2018)
Research: Sequence alignment guide trees and quality assessment
Next steps: Columbia Universty (Hillman lab)
Gilia Patterson
Undergraduate / post-baccalaureate researcher, Biology / Math, (2015-2017)
Research: Transposable element annotation
Next steps: Masters in Statistics at Oregon State University; PhD program at UOregon (Kern Lab)
Michel Wan Der Maas Soares
Undergraduate researcher, Computer Science (2015-2017)
Summer intern at NERSC (LBNL)
Completed degree at Universidade Federal de Lavras (Brazil)
Research: Fast phylogeny inference
Next steps: Data Science Analyst @ Accenture
Angela Gross
Masters student, Computer Science (2015-2016)
Research: Video game optimization (particle system / rendering)
Next steps: FAST Enterprises
Bill Arndt
Postdoctoral Fellow (joint with Kjiersten Fagnan at JGI/NERSC), (2015-2016)
BS, PhD, Computer Science, University of South Carolina
Research: HPC optimization of bioinformatics applications
Next steps: Computer Systems Engineer at NERSC
Walt Shands
BS, MS, Computer Science, Columbia University
MBA, Santa Clara University
Research: Translated search in HMMER, (2014-2016)
Next steps: Software Developer, Genomics Institute at UC Santa Cruz
Regular Collaborators
Arian Smit (Institute for Systems Biology)
Robert Hubley (Institute for Systems Biology)
Pat Secor (University of Montana)
Amit Roy (Rocky Mountain Labs, NIH NIAID)