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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!)

Current Lab Members

Travis Wheeler

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Principal Investigator – Email | Curriculum Vitae | Google Scholar profile

BS, Evolutionary Biology, University of Arizona, 1995
PhD, Computer Science, University of Arizona, 2009
Postdoctorate Sean Eddy, HHMI, Janelia Research Campus, 2009-2014

Appointments

Department of Computer Science (Associate Professor)
Cellular, Molecular, and Microbial Biology (Associated Faculty)
LBNL / Joint Genome Institute (Affiliate)

George Lesica

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Senior Software Engineer – Email

Jack of all trades, Master of some

Alex Nord

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PhD candidate, CMMB (Computational Biology) (2015-) – Email

Research: Splice sites in translated sequence alignment; multiple 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

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 (2017-) – Email
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

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
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, CMMB (Computational Biology) (2020-) – Email
Previously: Undergraduate researcher, Biochemistry, (2017-2020)

Research: Viral genome annotation w/ sequencing error

BS, Computational Biochemistry, University of Montana

Genevieve Krause

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MS student, Computer Science (2016-) – Email

Research: Pseudogene detection; frameshift model for sequence alignment.

BS, Environmental Studies, Prescott College

Kaitlin Carey

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MS student, Computer Science (2017-) – Email

Research: Adjudication of candidate annotations; specifically Transposable Element subfamily annotation

BS, Biochemistry, University of Montana

Jack Roddy

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MS student, Computer Science (2019-) – Email
Previously: Undergraduate researcher, Computer Science, (2018-2019)

Research: Sequence Alignment - homologous overextension; Dfam infrastructure

BS, Computer Science, University of Montana

Sarah Walling

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MS student (previously undergraduate researcher), Computer Science (2019-) – Email

Research: Expression patterns of dual-coding exons

BS, Computer Science, University of Montana

David Rich

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MS student, Computer Science (2018-) – Email

Research: Pruned dynamic programming w/ profile HMMs

BS, Business Administration, University of Montana

Isaac Robinson

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Undergraduate researcher (joint with Nathan Insel), Computer Science (2019-) – Email

Research: Tracking and behavior classification in rodent videos

George Glidden-Handgis

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Undergraduate researcher (joint with Rocky Mountain Labs), Computer Science (2020-) – Email

Research: Machine learning methods for cell culture image segmentation

Lab Alumni

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

Adam Clemons

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

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

Angela Gross

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

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

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


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