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
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
Senior Software Engineer – Email
Jack of all trades, Master of some
Alex Nord
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
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
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
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
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
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
MS student, Computer Science (2016-) – Email
Research: Pseudogene detection; frameshift model for sequence alignment.
BS, Environmental Studies, Prescott College
Kaitlin Carey
MS student, Computer Science (2017-) – Email
Research: Adjudication of candidate annotations; specifically Transposable Element subfamily annotation
BS, Biochemistry, University of Montana
Jack Roddy
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
MS student (previously undergraduate researcher), Computer Science (2019-) – Email
Research: Expression patterns of dual-coding exons
BS, Computer Science, University of Montana
David Rich
MS student, Computer Science (2018-) – Email
Research: Pruned dynamic programming w/ profile HMMs
BS, Business Administration, University of Montana
Isaac Robinson
Undergraduate researcher (joint with Nathan Insel), Computer Science (2019-) – Email
Research: Tracking and behavior classification in rodent videos
George Glidden-Handgis
Undergraduate researcher (joint with Rocky Mountain Labs), Computer Science (2020-) – Email
Research: Machine learning methods for cell culture image segmentation
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