Home | People | Contact

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)


Home | People | Contact