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
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
Masters student alumni
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
Pre-graduate researcher alumni
Katelen Tellez
Computer Science & Psychology (2023-2023)
Research: Computational neuroscience (animal
behavior)
Shifat Hossain
Biochemistry (2022)
Research: Transposable
element family redundancy detection in a phylogenetic context
Jackie Olexa
Bio + CS (UMontana) (2021-2022) Research: Genome annotation - regional variability in satellite repeats
Cory Emlen
Math (UMontana) (2020-2021)
Research: Sequence
annotation w/ protein interaction networks
Gilia Patterson
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
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)
Staff alumni
Syed Zaidi
Bioinformatician ( - 2024)
Computational analysis for
microbiomes (and more)
Daphne Demekas
Machine Learning Engineer (2023-2024)
Machine Learning for
protein homology and animal tracking
Cassie Trier
Senior Bioinformatician – (joint with Arizona Genomics Institute,
2023-2024)
Genome assembly and annotation, statistical genetics,
and more
Isaac Robinson
Software Scientist (2020-2023)
ML methods for
tracking and behavior classification, infrastructure for a molecular
dynamics repository.
Rudra Pokhrel
Bioinformatician in the Bioinformatics Research Group –
Multiomics,
Molecular Dynamics Simulation and Small Molecule Drug Design.
Aakash Kolekar
Machine Learning Engineer (2023)
Data acquisition for molecular
dynamics web service
Tommy Colligan
Machine Learning Engineer (2020-2022)
Neural networks for
faster and more sensitive sequence annotation
Pawan Jayaswal
Bioinformatician – (joint with Arizona Genomics Institute)
(2023)
Genome assembly and annotation
George Lesica
Senior Software Scientist (2019-2022) 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
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 at Princeton