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Eren, Kemal, et al. "Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons." PLoS computational biology 14.12 (2018): e1006498

Shank, Stephen D., Steven Weaver, and Sergei L. Kosakovsky Pond. "phylotree. js-a JavaScript library for application development and interactive data visualization in phylogenetics." BMC bioinformatics 19.1 (2018): 276.

Kosakovsky Pond, Sergei L, Steven Weaver, Andrew J Leigh Brown, and Joel O Wertheim. 2018. “HIV-TRACE (Transmission Cluster Engine): A Tool for Large Scale Molecular Epidemiology of Hiv-1 and Other Rapidly Evolving Pathogens.” Molecular Biology and Evolution 35 (7). Oxford University Press: 1812–9.

Weaver, Steven, Stephen D Shank, Stephanie J Spielman, Michael Li, Spencer V Muse, and Sergei L Kosakovsky Pond. 2018. “Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes.” Molecular Biology and Evolution. Oxford University Press, msx335.

Laird Smith, Melissa, Ben Murrell, Kemal Eren, Caroline Ignacio, Elise Landais, Steven Weaver, Pham Phung, et al. 2016. “Rapid Sequencing of Complete Env Genes from Primary Hiv-1 Samples.” Virus Evolution 2 (2). Oxford University Press: vew018.

Murrell, Ben, Steven Weaver, Martin D Smith, Joel O Wertheim, Sasha Murrell, Anthony Aylward, Kemal Eren, et al. 2015. “Gene-Wide Identification of Episodic Selection.” Molecular Biology and Evolution 32 (5). Oxford University Press: 1365–71.

Smith, Martin D, Joel O Wertheim, Steven Weaver, Ben Murrell, Konrad Scheffler, and Sergei L Kosakovsky Pond. 2015. “Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection.” Molecular Biology and Evolution 32 (5). Oxford University Press: 1342–53.

Hepler, N Lance, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Davey M Smith, and Sergei L Kosakovsky Pond. 2014. “IDEPI: Rapid Prediction of Hiv-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform.” PLoS Computational Biology 10 (9). Public Library of Science: e1003842.

Young, JA, DA Mote, MA Martinez, JE Rodriguez-Mueller, S Weaver, DM Smith, DD Richman, SJ Little, and SL Kosakovsky Pond. n.d. “OCCAMS: An Open Source Clinical Content Analysis and Management System. Applications for Hiv Primary Infection Research.”