Wheeler Lab Alumni
Postdoc alumni
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
PhD student alumni
Alex Nord
CMMB / Computational Biology (UMontana) (2024)
Research: Improved read mapping; splice sites in
translated sequence alignment
Next steps:
Assistant Professor, College of Wooster (Ohio)
Tim Anderson
Computer Science (UMontana) (2024)
Research:
FPGA algorithms and software optimization for sequence alignment
Next steps: Research Scientist, University of Montana
(Lucy Williams)
Walt Shands
Computer Science (UMontana) (2014-2016)
Research: Translated search in HMMER
Next
steps: Software Developer, Genomics Institute at UC Santa
Cruz
Masters student alumni
Sadaf Raoufi
MS student, Computer Science (2022-2025)
Research: Computational precision medicine
Next steps: PhD student, North Carolina State
(Bioinformatics)
Patricia Woo
MS student, Business Analytics (2024-2025)
Research: Computational drug screening
Max Copeland
MS student, Computer Science (UMontana) (2022-2025)
Research: Petascale data handling in the cloud
Next steps: Amazon
Conner Copeland
CMMB / Computational Biology (UMontana) (2023)
Research: Prophage genome annotation
Next
steps: Fred Hutch (JT McCrone)
Audrey Shingleton
Computer Science (UMontana) (2022) Research:
Improved methods for subfamily labeling in transposable elements
Next steps: Loxo
Chris Burgoyne
Computer Science (UMontana) (2022) Research:
Algorithms for subset sum, in the context of mass spectrometry peptide
analysis
Next steps: Skyfish
David Rich
Computer Science (UMontana) (2021)
Research:
Sparse dynamic programming w/ profile HMMs
Next
steps: Fred Hutch (Erick Matsen)
Sarah Walling
Computer Science (UMontana) (2020-2021)
Research: Splicing patterns of dual-coding exons
Kaitlin Carey
Computer Science (UMontana) (2020)
Research:
Adjudication of candidate genome annotations; specifically Transposable
Element subfamily annotation
Next steps:
Submittable
Adam Clemons
Computer Science (UMontana) (2019)
Research:
Software plagiarism
Next steps: Submittable
Angela (Gross) Breuer
Computer Science (UMontana) (2016)
Research:
Video game optimization (particle system / rendering)
Next
steps: FAST Enterprises, then Epic Games
Visiting students
Rita Ann Roessner
PhD Student, Institut des Biomolécules Max Mousseron (IBMM)
Wheeler Lab summer visitor (2024)
Research: Graph
Neural Networks for GPCR interaction modeling
Pre-graduate researcher alumni
Zach Keyes
Undergraduate
School of Information (2024)
Research: Alignment-free sequence comparison
Peniella Irakoze
Undergraduate
Microbiology (2023-2024)
Research: Genomics (bacterialtransposons)
Next steps: PhD student, UC Irvine (Genetics,
Epigenetics and Genomics)
Katelen Tellez
Undergraduate
Computer Science & Psychology (2023-2023)
Research: Computational neuroscience (animal
behavior)
Shifat Hossain
Undergraduate
Biochemistry (2022)
Research: Transposable element family redundancy
detection in a phylogenetic context
Jackie Olexa
Undergraduate
Bio + CS (UMontana) (2021-2022)
Research: Genome annotation - regional variability in
satellite repeats
Next steps: Wildlife Biology in
Good Lab @ UM, then Masters at Kansas State (Hope Lab)
Cory Emlen
Undergraduate
Math (UMontana) (2020-2021)
Research: Sequence annotation w/ protein interaction
networks
Gilia Patterson
Undergraduate
Biology / Math (UMontana) (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
Computer Science (UMontana) (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
Dylan Wichman
Student - Billings Central High School (2019-2020)
Research: Machine learning approaches to wildfire risk
prediction
Next steps: Louisiana State
Universty
Joyce Liu
Student - Sentinel High School (Missoula) (2016-2018)
Research: Sequence alignment guide trees and quality
assessment
Next steps: Columbia Universty (Hillman
lab), then PhD at University of Washington (Bioengineering)
Staff alumni
David Jurkowitz
Junior Bioinformatician (2023-2025)
Research:
Protein binding pocket prediction
Next steps: PhD
student, University of Virginia (Biomedical Sciences)
Erin Chaballa
Administrative Assistant (2022-2025)
Ethan Ward
Full Stack Developer (2023-2025)
Research: Web
development on MDRepo, PanDB, and miscellaneous
Syed Zaidi
Bioinformatician (2022-2024)
Research:
Computational analysis for microbiomes (and more)
Next
steps: Data Scientist, MD Anderson Cancer Center
Daphne Demekas
Machine Learning Engineer (2023-2024)
Research:
Machine Learning for protein homology and animal tracking
Cassie Trier
Senior Bioinformatician – (joint with Arizona Genomics Institute,
2023-2024)
Research: Genome assembly and
annotation, statistical genetics, and more
Next
steps: Bioinformatics Researcher at Oslo University
Hospital
Rudra Pokhrel
Bioinformatician in the Bioinformatics Research Group –
Research: Multiomics, Molecular Dynamics Simulation and
Small Molecule Drug Design.
Next steps:
Computational Scientist, University of Arizona Cancer Center
Aakash Kolekar
Machine Learning Engineer (2023)
Research: Data
acquisition for molecular dynamics web service
Next
steps: Amazon
Tommy Colligan
Machine Learning Engineer (2020-2022)
Research:
Neural networks for faster and more sensitive sequence annotation
Next steps: Scientific Software Developer, NASA
Pawan Jayaswal
Bioinformatician – (joint with Arizona Genomics Institute)
(2023)
Research: Genome assembly and
annotation
George Lesica
Senior Software Scientist (2019-2022) Research:
Master of web services, workflows and cloud computing, testing and
automation, etc.
Next steps: Senior Developer at
OnX Maps
Kayla Irish
Data Scientist (2020-2022)
Event classification in sound
files
Next steps: PhD student at University of
Washington (Statistics)
Natalia Sizochenko
Bioinformatician (2021)
Use of multi-omic data to improve
metagenome annotation
Stavi Tennenbaum
Junior Bioinformatician (2020-2021)
Pseudogene annotation
Next steps: PhD student, Princeton (Ecology and
Evolutionary Biology)