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Wheeler Lab Folks

Travis Wheeler


Chief Suggestion Officer and Manuscript Bottleneck
Email | Personal Page | Curriculum Vitae | Google Scholar profile | ORCID iD icon

University of Arizona
Department of Pharmacy Practice & Science
   Computer Science, School of Information
   Applied Mathematics, Statistics and Data Science
   Genetics, Bio5

Editorial Board Member - Mobile DNA

Research: Computational genomics, Computational drug discovery, Machine Learning

Support staff

Erin Chaballa


Administrative Assistant – Email

Research staff

Jack Roddy


Senior Software Scientist – Email | Personal Page

Jack of all trades, master of some
(including sequence annotation and visualization)

Clément Goubert


Senior Bioinformatician – Email | Personal Page

Transposable elements, evolution, splicing, and all things genomics

Ken Youens-Clark


Senior Software Scientist – Email | Personal Page

Software and web/cloud services

Genevieve Krause


Software Scientist – Email | Personal Page

Sequence annotation with profile HMMs; frameshift model for protein-coding DNA.

George Glidden


Software Scientist – Email | Personal Page

Peptide and modification identification in Mass Spectrometry; animal tracking.

Terrill Yuhas


Senior Data Architect – Email | Personal Page
(Joint with Bonnie LaFleur)

Building data systems for precision medicine research

Ethan Ward


Full Stack Developer – Email | Personal Page

Full stack web development on multiple projects

David Jurkowitz


Junior Bioinformatician – Email | Personal Page

Protein binding pocket prediction

UA Health Sciences Bioinformatics Group (UAHS-BIG)

Syed Zaidi


Bioinformatician – Email | Personal Page

Computational analysis for microbiomes (and more)

Noor Subah


Bioinformatician – Email | Personal Page

Transcriptomics, flow cytometry, differential splicing (and more)

PhD students

Alex Nord


PhD candidate, CMMB / Computational Biology (UMontana) (2017-) – Email | Personal Page

Research: Improved read mapping; splice sites in translated sequence alignment

BA, Philosophy, Reed College
MS, Computer Science, University of Montana

Tim Anderson


PhD candidate, Computer Science (UMontana) (2017-) – Email | Personal Page

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 candidate, Computer Science (UMontana, NIH-NIAID) (2017-) – Email | Personal Page

Research: Models for repetitive biological sequences; adaptive element detection in sequence data

BS, Biochemistry, University of Montana

Anna Marbut


PhD candidate, Computer Science (DIS) (UMontana) (2019-) – Email | Personal Page

Research: Language representation (ML and NLP)

BA, Linguistics, Reed College
MA, Business Analytics, University of Montana

Jeremiah Gaiser


PhD student, School of Information (2023-) – Email | Personal Page
Previously: Undergraduate researcher, Biochemistry, (2017-2020); Biochem PhD in Wheeler lab at UMontana (2020-2023)

Research: Protein-drug biding affinity prediction

BS, Computational Biochemistry, University of Montana

Neha Sontakke


PhD student, Computer Science (2021-) – Email | Personal Page

Research: Protein interactions: computational annotation and functional prediction

BS, Computer Engineering, Pune Institute of Computer Technology

Masters students

Max Copeland


MS student, Computer Science (UMontana) (2022-) – Email | Personal Page

Research: Petascale genomics in the cloud

BS, Physics, University of Missouri

Sadaf Raoufi


MS student, Computer Science (2022-) – Email | Personal Page

Research: Computational precision medicine

BS, Computer Engineering, Qom University of Technology, Iran

Patricia Woo


MS student, Business Analytics (2024-) – Email | Personal Page

Research: Computational drug screening

Bachelors and Masters, Pharmacy, Chinese University of Hong Kong, HK

Undergraduate students

Peniella Irakoze


Undergraduate researcher, Microbiology (2023-) – Email | Personal Page

Research: Genomics (splicing oddities, transposons)

Zach Keyes


Undergraduate researcher, School of Information (2024-) – Email | Personal Page

Research: Alignment-free sequence comparison

Regular Collaborators

Arian Smit (Institute for Systems Biology)

Robert Hubley (Institute for Systems Biology)

Amit Roy (Rocky Mountain Labs, NIH)

Vishwesh Venkatraman (Norwegian University of Science and Technology)

Jason McDermott (Pacific Northwest National Laboratory)

Nathan Insel (Wilfrid Laurier University)

Jason Karnes (University of Arizona)

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

Grad student alumni

Conner Copeland


MS student, CMMB / Computational Biology (UMontana) (2020-2023)
Undergraduate researcher (joint with Pat Secor), Computer Science (2017-2020)
Research: Prophage genome annotation

David Geller-McGrath


PhD candidate at Woods Hole Oceanographic Institution and Massachusetts Institute of Technology (2021-2023)
(Primary advisor: Virginia Edgcomb; co-advised on extended project with Jason McDermott)
Research: Filling gaps in observed metabolic pathways

Audrey Shingleton


MS student, Computer Science (2020-)
Research: Improved methods for subfamily labeling in transposable elements
Next steps: Loxo

Chris Burgoyne


MS student, Computer Science (2021-)
Research: Algorithms for subset sum, in the context of mass spectrometry peptide analysis
Next steps: Skyfish

David Rich


MS student, Computer Science (2018-2021)
BS, Business Administration, University of Montana
Research: Sparse dynamic programming w/ profile HMMs
Next steps: Bioinformatician in Erick Matsen’s lab (Fred Hutch)

Sarah Walling


MS student, Computer Science (2019-2021)
BS, Computer Science, University of Montana
Research: Splicing patterns of dual-coding exons

Kaitlin Carey


MS student, Computer Science (2017-2020)
BS, Biochemistry, University of Montana
Research: Adjudication of candidate genome annotations; specifically Transposable Element subfamily annotation
Next steps: Submittable

Adam Clemons


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

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

Angela (Gross) Breuer


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

Pre-graduate researcher alumni

Katelen Tellez


Undergraduate researcher, Computer Science & Psychology (2023-2023) –

Research: Computational neuroscience (animal behavior)

Shifat Hossain


Undergraduate researcher, Biocemistry (2022-2022) –
Research: Transposable element family redundancy detection in a phylogenetic context

Jackie Olexa


Undergraduate researcher, Bio + CS (2021-2022)

Research: Genome annotation - regional variability in satellite repeats

Cory Emlen


Undergraduate researcher, Math (2020-2021)
Research: Sequence annotation w/ protein interaction networks

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)

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

Staff alumni

Daphne Demekas


Machine Learning Engineer –
Machine Learning for protein homology and animal tracking

Cassie Trier


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

Isaac Robinson


Software Scientist –
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
Data acquisition for molecular dynamics web service

Tommy Colligan


Machine Learning Engineer –
Neural networks for faster and more sensitive sequence annotation

Pawan Jayaswal


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

George Lesica


Senior Software Scientist
Master of web services, workflows and cloud computing, testing and automation, etc.
Next steps: Senior Developer at OnX Maps

Kayla Irish


Data Scientist –
Event classification in sound files
Next steps: PhD student at University of Washington

Natalia Sizochenko


Use of multi-omic data to improve metagenome annotation

Stavi Tennenbaum


Junior Bioinformatician
Pseudogene annotation
Next steps: PhD student at Princeton

Sean Rice


Software Developer – (Reported to Robert Hubley at the Institute for Systems Biology)
RepeatMasker pipeline
Next steps: Consumer Direct Care Network

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