About the team
Six labs,
one framework.
genomeRxiv is built by plant pathologists, computer scientists, mycologists, and genomicists across Virginia Tech, UC Davis, the University of Strathclyde, Oregon State, and the USDA, united by one goal: giving every microbial genome a stable address. The work is supported by the U.S. National Science Foundation and the U.S. Department of Agriculture.
Who builds it
The institutions
Virginia Tech
The School of Plant and Environmental Sciences and the Department of Computer Science, home of the LIN framework and the genomeRxiv service.
UC Davis
Genome sketching and large-scale similarity search built on sourmash, keeping placement fast as the database grows.
University of Strathclyde
Methods for resolving closely related lineages, where the last LIN positions carry epidemiological meaning.
Oregon State University
With USDA ARS collaborators, extending genome-based classification to fungi, from the genus rank down to intraspecies variants.
Supported by the U.S. National Science Foundation and the U.S. Department of Agriculture. genomeRxiv is free software released under the GNU General Public License v3.0.
Leadership
Principal investigators
Boris A. Vinatzer
Project lead; the LIN framework and curation
Virginia Tech
Lenwood S. Heath
Computer science lead; algorithms and data model
Virginia Tech
C. Titus Brown
Genome sketching and large-scale search with sourmash
UC Davis
Leighton Pritchard
Comparative genomics and lineage resolution
University of Strathclyde
The working team
Development and curation
Reza Mazloom
Lead developer; server, website, and backend
Virginia Tech
Rituraj Sharma
Website lead; visualizations
Virginia Tech
Sehgeet Kaur
Genome and metagenome lead; genomes, metadata, and reference databases
Virginia Tech
Janet Lorv
LINgroup lead; circumscriptions, descriptions, and validation
Virginia Tech
N. Tessa Pierce-Ward
sourmash development and genome placement at scale
UC Davis
New frontiers
Beyond bacteria
The LIN framework is expanding to new kingdoms: a viral genomeRxiv and a fungal genomeRxiv are in development, applying whole-genome similarity from the genus rank down to intraspecies variants.
Mitchell Gercken
Viral genomeRxiv lead; viral taxonomy and reference databases
Virginia Tech
Jessie K. Uehling
Fungal genomeRxiv lead; mycology
Oregon State University
Niklaus J. Grünwald
Fungal genomeRxiv; plant pathogen genomics
USDA ARS
Hayden Johnson
Fungal genomeRxiv; whole-genome classification of fungal taxa
Oregon State University
Abigail (Abbi) Green
genomeRxiv project contributor
Virginia Tech
Alumni and contributors
They built the foundations
LINbase and the LIN concept grew through the work of many students and collaborators, including the authors of the founding publications.
Parul Sharma
Formerly genomics research and validation
Virginia Tech
Kassaye Belay
Formerly fungal genomeRxiv; genomics research
Virginia Tech
Contact
Talk to the team
Technical questions
Something broken, an API question, or a feature request:
linbase@vt.edu
Everything else
Collaboration, curation, and general questions:
vinatzer@vt.edu
New to genomeRxiv?
Start with what the platform does and how a LIN is assigned.