Stephen Schaffner

26PUBLICATIONS
361CO-AUTHORS
Microbial taxonomyGenomicsHost-parasite interactionsMedical virologyComputational linguistics
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Publications (26)

|Sep 16, 2026
Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy.

|Apr 16, 2025
Towards an open analysis ecosystem for Plasmodium genomic epidemiology.

Shazia Ruybal-Pesántez, Jorge Amaya-Romero, Sophie Bérubé

|Apr 08, 2025
JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.

Ivan Specht, Gage K Moreno, Taylor Brock-Fisher

|Mar 17, 2025
JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.

Ivan Specht, Gage K Moreno, Taylor Brock-Fisher

|Dec 14, 2024
Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.

Lydia A Krasilnikova, Christopher H Tomkins-Tinch, Alton C Gayton

|Nov 23, 2024
MalKinID: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent.

Wesley Wong, Lea Wang, Stephen F Schaffner

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Frequent Collaborators

15 joint publications

Danny Park

14 joint publications

Pardis C Sabeti

12 joint publications

Bronwyn McInnis

10 joint publications

Katherine Siddle