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Wheeler Lab Folks

zoom meeting 2021 breakout room 2018 picnic 2021

Travis Wheeler

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

Department of Computer 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)

George Lesica

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Senior Software Scientist – Email | Personal Page | Schedule

George of all trades, master of some2 (some2 != some1)
(including web services, testing and automation, optimization)

Genevieve Krause

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Software Scientist – Email | Personal Page

Projects: 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)

Tracking and behavior classification in rodent videos;

Kayla Irish

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Data Scientist – Email | Personal Page

Event classification in sounds files; behavior labeling in videos (rodents)

PhD students

Alex Nord

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PhD candidate, CMMB / Computational Biology (2015-) – 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: Recommendation engines (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

Audrey Shingleton

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MS student, Computer Science (2020-) – Email | Personal Page

Research: Improved methods for subfamily labeling in transposable elements

BS, Applied and Computational Math Sciences, University of Washington

Chris Burgoyne

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MS student, Computer Science (2021-) – Email | Personal Page

Research: Algorithms for subset sum, in the context of mass spectrometry peptide analysis

PhD, Environmental Science, University of Johannesburg

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

Jackie Olexa

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Undergraduate researcher, Bio + CS (2021-) – Email | Personal Page

Research: Genome annotation - regional variability in satellite repeats

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

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

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

Natalia Sizochenko

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Bioinformatician
Research: Using multi-omic data to improve metagenome annotation

Stavi Tennenbaum

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Junior Bioinformatician
Research: 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)

Projects: RepeatMasker pipeline
Next steps: Consumer Direct Care Network


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