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Wheeler Lab Folks

Travis Wheeler

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Chief Suggestion Officer and Manuscript Bottleneck
Email | Personal Page | Curriculum Vitae | Google Scholar profile

Department of Pharmacy Practice & Science (and others)

Research: Computational genomics, Machine Learning

Research staff

Jack Roddy

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Senior Software Scientist – Email | Personal Page

Jack of all trades, master of some1
(including sequence annotation and visualization)

Genevieve Krause

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Software Scientist – Email | Personal Page

Sequence annotation with profile HMMs; frameshift model for protein-coding DNA.

Tommy Colligan

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Machine Learning Engineer – Email | Personal Page

Neural networks for faster and more sensitive sequence annotation

Isaac Robinson

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Software Scientist – Email | Personal Page
(joint with Nathan Insel)

ML methods for tracking and behavior classification, sequence database search

Kayla Irish

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Data Scientist – Email | Personal Page
Event classification in sound files

Cosimo Gonnelli

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Data Scientist – Email | Personal Page
(joint with Nathan Insel)

Behavior classification in rodent videos

PhD students

Alex Nord

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PhD candidate, CMMB / Computational Biology (2017-) – Email | Personal Page

Research: Improved read mapping; splice sites in translated sequence alignment

BA, Philosophy, Reed College
MS, Computer Science, University of Montana

Tim Anderson

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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

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PhD student, Computer Science (NIH-NIAID) (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

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PhD student, Computer Science (DIS) (2019-) – Email | Personal Page

Research: Language representation (ML and NLP)

BA, Linguistics, Reed College
MA, Business Analytics, University of Montana

Conner Copeland

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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

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PhD student, Biochem / Computational Biology (NIH-NIAID) (2020-) – Email | Personal Page
Previously: Undergraduate researcher, Biochemistry, (2017-2020)

Research: Representation of small molecules

BS, Computational Biochemistry, University of Montana

Masters students

Max Copeland

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MS student, Computer Science (2022-) – Email | Personal Page

Research: Petascale genomics in the cloud

BS, Physics, University of Missouri

Undergraduate students

David Jurkowitz

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Undergraduate researcher, Biocemistry (2022-) – Email | Personal Page

Research: Protein binding pocket prediction

Regular Collaborators

Arian Smit (Institute for Systems Biology)

Robert Hubley (Institute for Systems Biology)

Pat Secor (University of Montana)

Doug Brinkerhoff (University of Montana)

Amit Roy (Rocky Mountain Labs, NIH)

Jason McDermott (Pacific Northwest National Laboratory)

Lab Alumni

Postdoc alumni

Bill Arndt

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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

Grad student alumni

Audrey Shingleton

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MS student, Computer Science (2020-)
Research: Improved methods for subfamily labeling in transposable elements
Next steps: Loxo

Chris Burgoyne

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MS student, Computer Science (2021-)
Research: Algorithms for subset sum, in the context of mass spectrometry peptide analysis
Next steps: Skyfish

David Rich

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MS student, Computer Science (2018-2021)
BS, Business Administration, University of Montana
Research: Sparse dynamic programming w/ profile HMMs
Next steps: Bioinformatician in Erick Matsen’s lab (Fred Hutch)

Sarah Walling

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MS student, Computer Science (2019-2021)
BS, Computer Science, University of Montana
Research: Splicing patterns of dual-coding exons

Kaitlin Carey

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MS student, Computer Science (2017-2020)
BS, Biochemistry, University of Montana
Research: Adjudication of candidate genome annotations; specifically Transposable Element subfamily annotation
Next steps: Submittable

Adam Clemons

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MS student, Computer Science, (2017-2019)
BS, Computer Science, University of Montana
Research: Software plagiarism
Next steps: Submittable

Walt Shands

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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

Angela Gross

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Masters student, Computer Science (2015-2016)
Research: Video game optimization (particle system / rendering)
Next steps: FAST Enterprises

Pre-graduate researcher alumni

Jackie Olexa

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Undergraduate researcher, Bio + CS (2021-2022)

Research: Genome annotation - regional variability in satellite repeats

Cory Emlen

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Undergraduate researcher, Math (2020-2021)
Research: Sequence annotation w/ protein interaction networks

Dylan Wichman

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Student - Billings Central High School, (2019-2020)
Research: Machine learning approaches to wildfire risk prediction
Next steps: Louisiana State Universty

Joyce Liu

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Student - Sentinel High School (Missoula), (2016-2018)
Research: Sequence alignment guide trees and quality assessment
Next steps: Columbia Universty (Hillman lab)

Gilia Patterson

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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

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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

Staff alumni

George Lesica

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Senior Software Scientist
Master of web services, workflows and cloud computing, testing and automation, etc.
Next steps: Senior Developer at OnX Maps

Natalia Sizochenko

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Bioinformatician
Use of multi-omic data to improve metagenome annotation

Stavi Tennenbaum

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Junior Bioinformatician
Pseudogene annotation
Next steps: PhD student at Princeton

Sean Rice

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Software Developer – (Reported to Robert Hubley at the Institute for Systems Biology)
RepeatMasker pipeline
Next steps: Consumer Direct Care Network


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