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
Applied Mathematics
(Affiliate)
School of Information (Affiliate)
Genetics
Graduate Program (Affiliate)
Research: Computational genomics, Machine Learning
Support staff
Erin Chaballa
Administrative Assistant – Email
Research staff
Clément Goubert
Senior Bioinformatician – Email | Personal Page
Transposable elements, splicing, and all things genomics
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.
Isaac Robinson
Software Scientist – Email | Personal Page
(joint with
Nathan Insel)
ML methods for tracking and behavior classification, sequence database search
George Glidden
Software Scientist – Email | Personal Page
Peptide and modification identification in Mass Spectrometry
Daphne Demekas
Machine Learning Engineer – Email | Personal Page
Machine Learning for protein homology and drug binding prediction
Terrill Yuhas
Senior Data Architect – Email
| Personal Page
Building data systems for precision medicine reseearch
PhD students
Alex Nord
PhD candidate, CMMB / Computational Biology (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 (DIS) (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 (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) (2019-) – Email | Personal Page
Research: Language representation (ML and NLP)
BA, Linguistics, Reed College
MA, Business Analytics, University
of Montana
Jeremiah Gaiser
PhD student, Biochem / Computational Biology (NIH-NIAID) (2020-) – Email | Personal Page
Previously:
Undergraduate researcher, Biochemistry, (2017-2020)
Research: Representation of small molecules
BS, Computational Biochemistry, University of Montana
David Geller-McGrath
PhD candidate at Woods Hole Oceanographic Institution and
Massachusetts Institute of Technology (2021-) – Email | Personal Page
(Joint
with Virginia Edgcomb (PI) and Jason McDermott)
Research: Filling gaps in observed metabolic pathways
Masters students
Conner Copeland
MS student, CMMB / Computational Biology (2020-) – Email | Personal Page
Previously:
Undergraduate researcher (joint with Pat Secor), Computer Science
(2017-2020)
Research: Prophage genome annotation
BS, Computational Biochemistry, University of Montana
Max Copeland
MS student, Computer Science (2022-) – Email | Personal Page
Research: Petascale genomics in the cloud
BS, Physics, University of Missouri
Sadaf Raoufi
MS student (2022-) – Email | Personal Page
Research: Multi-modal computational medicine
BS, Computer Engineering, Qom University of Technology, Iran
Undergraduate students
David Jurkowitz
Undergraduate researcher, Biocemistry (2022-) – Email | Personal Page
Research: Protein binding pocket prediction
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)
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
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
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
Tommy Colligan
Machine Learning Engineer –
Neural networks for
faster and more sensitive sequence annotation
Kayla Irish
Data Scientist –
Event classification
in sound files
Next steps: PhD student at
University of Washington
George Lesica
Senior Software Scientist
Master of web services,
workflows and cloud computing, testing and automation, etc.
Next steps: Senior Developer at OnX Maps
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