A Brief Introduction to the Phylogentics Analysis Library V1.5. - Matthew Goode; Korbinian Strimmer; Alexei J. Drummond; Ed Buckler; Allen G. Rodrigo (APBC, 2004)

Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1. - Peter L. Meintjes; Allen G. Rodrigo (J. Bioinform. Comput. Biol., 2005)

SQUINT: a multiple alignment program and editor. - Matthew Goode; Allen G. Rodrigo (Bioinform., 2007)

A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels. - Steven H. Wu; Michael A. Black; Robyn A. North; Kelly R. Atkinson; Allen G. Rodrigo (PLoS Comput. Biol., 2009)

A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels. - Steven H. Wu; Michael A. Black; Robyn A. North; Allen G. Rodrigo (BMC Bioinform., 2012)

Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals. - Steven H. Wu; Allen G. Rodrigo (BMC Bioinform., 2015)

Neutral Models of Microbiome Evolution. - Qinglong Zeng; Jeet Sukumaran; Steven H. Wu; Allen G. Rodrigo (PLoS Comput. Biol., 2015)

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations. - Thomas K. F. Wong; Louis Ranjard; Yu Lin 001; Allen G. Rodrigo (BMC Bioinform., 2018)

Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage. - Louis Ranjard; Thomas K. F. Wong; Allen G. Rodrigo (BMC Bioinform., 2019)

Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage. - Louis Ranjard; Thomas K. F. Wong; Allen G. Rodrigo (BMC Bioinform., 2020)

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes. - Thomas K. F. Wong; Teng Li; Louis Ranjard; Steven H. Wu; Jeet Sukumaran; Allen G. Rodrigo (PLoS Comput. Biol., 2021)

ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data. - Weiling Li; Raunaq Malhotra; Steven H. Wu; Manjari Jha; Allen G. Rodrigo; Mary Poss; Raj Acharya (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data. - Teng Li; Yiran Zou; Xianghan Li; Thomas K. F. Wong; Allen G. Rodrigo (BMC Bioinform., 2024)

Extending the Hegselmann-Krause Model of Opinion Dynamics to include AI Oracles. - Allen G. Rodrigo (CoRR, 2025)