Home | People | Contact

Wheeler Lab Folks

Travis Wheeler

-

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

University of Arizona
  Department of Pharmacy Practice & Science
  Computer Science (Affiliate)
  Genetics Graduate Program (Affiliate)
  Statistics and Data Science Graduate Program (Affiliate)
  School of Information (Affiliate)
  Applied Mathematics (Affiliate)
  Bio5 (Affiliate)

Director of UAHS Bioinformatics Group

Editorial Board Member - Mobile DNA

Research: Computational genomics, 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)

Genevieve Krause

-

Software Scientist – Email | Personal Page

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

Clément Goubert

-

Senior Bioinformatician – Email | Personal Page

Transposable elements, evolution, splicing, and all things genomics

Daphne Demekas

-

Machine Learning Engineer – Email | Personal Page

Machine Learning for protein homology and drug binding prediction

George Glidden

-

Software Scientist – Email | Personal Page

Peptide and modification identification in Mass Spectrometry

Terrill Yuhas

-

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

Building data systems for precision medicine research

Cassie Trier

-

Senior Bioinformatician – Email | Personal Page
(joint with Arizona Genomics Institute)

Genome assembly and annotation, statistical genetics, and more

Ethan Ward

-

Web Developer – Email | Personal Page

Full stack web development on multiple projects

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
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 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

Undergraduate students

David Jurkowitz

-

Undergraduate researcher, Biochemistry (2022-) – Email | Personal Page

Research: Protein binding pocket prediction

Peniella Irakoze

-

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

Research: Genomics (splicing oddities, transposons)

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

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

-

Bioinformatician
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


Home | People | Contact