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Wheeler Lab Alumni

Postdoc alumni

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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

PhD student alumni

Alex Nord

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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

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Computer Science (UMontana) (2024)
Research: FPGA algorithms and software optimization for sequence alignment
Next steps: Research Scientist, University of Montana (Lucy Williams)

Walt Shands

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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

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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

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CMMB / Computational Biology (UMontana) (2023)
Research: Prophage genome annotation
Next steps: Fred Hutch (JT McCrone)

Audrey Shingleton

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Computer Science (UMontana) (2022)
Research: Improved methods for subfamily labeling in transposable elements
Next steps: Loxo

Chris Burgoyne

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Computer Science (UMontana) (2022)
Research: Algorithms for subset sum, in the context of mass spectrometry peptide analysis
Next steps: Skyfish

David Rich

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Computer Science (UMontana) (2021)
Research: Sparse dynamic programming w/ profile HMMs
Next steps: Fred Hutch (Erick Matsen)

Sarah Walling

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Computer Science (UMontana) (2020-2021)
Research: Splicing patterns of dual-coding exons

Kaitlin Carey

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Computer Science (UMontana) (2020)
Research: Adjudication of candidate genome annotations; specifically Transposable Element subfamily annotation
Next steps: Submittable

Adam Clemons

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Computer Science (UMontana) (2019)
Research: Software plagiarism
Next steps: Submittable

Angela (Gross) Breuer

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Computer Science (UMontana) (2016)
Research: Video game optimization (particle system / rendering)
Next steps: FAST Enterprises, then Epic Games

Pre-graduate researcher alumni

Katelen Tellez

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Computer Science & Psychology (2023-2023)
Research: Computational neuroscience (animal behavior)

Shifat Hossain

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Biochemistry (2022)
Research: Transposable element family redundancy detection in a phylogenetic context

Jackie Olexa

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Bio + CS (UMontana) (2021-2022)
Research: Genome annotation - regional variability in satellite repeats

Cory Emlen

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Math (UMontana) (2020-2021)
Research: Sequence annotation w/ protein interaction networks

Gilia Patterson

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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

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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

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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)

Staff alumni

Syed Zaidi

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Bioinformatician ( - 2024)
Computational analysis for microbiomes (and more)

Daphne Demekas

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Machine Learning Engineer (2023-2024)
Machine Learning for protein homology and animal tracking

Cassie Trier

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Senior Bioinformatician – (joint with Arizona Genomics Institute, 2023-2024)
Genome assembly and annotation, statistical genetics, and more

Isaac Robinson

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Software Scientist (2020-2023)
ML methods for tracking and behavior classification, infrastructure for a molecular dynamics repository.

Rudra Pokhrel

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Bioinformatician in the Bioinformatics Research Group –
Multiomics, Molecular Dynamics Simulation and Small Molecule Drug Design.

Aakash Kolekar

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Machine Learning Engineer (2023)
Data acquisition for molecular dynamics web service

Tommy Colligan

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Machine Learning Engineer (2020-2022)
Neural networks for faster and more sensitive sequence annotation

Pawan Jayaswal

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Bioinformatician – (joint with Arizona Genomics Institute) (2023)
Genome assembly and annotation

George Lesica

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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

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Data Scientist (2020-2022)
Event classification in sound files
Next steps: PhD student at University of Washington

Natalia Sizochenko

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Bioinformatician (2021)
Use of multi-omic data to improve metagenome annotation

Stavi Tennenbaum

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Junior Bioinformatician (2020-2021)
Pseudogene annotation
Next steps: PhD student at Princeton


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