Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. - Robert W. Shafer; Derek Stevenson; Bryan Chan (Nucleic Acids Res., 1999)

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. - Robert W. Shafer; Duane R. Jung; Bradley J. Betts; Yinong Xi; Matthew J. Gonzales (Nucleic Acids Res., 2000)

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs. - Rami Kantor; Rhoderick Machekano; Matthew J. Gonzales; Kathryn Dupnik; Jonathan M. Schapiro; Robert W. Shafer (Nucleic Acids Res., 2001)

Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). - Matthew J. Gonzales; Jonathan M. Dugan; Robert W. Shafer (Bioinform., 2002)

Human immunodeficiency virus reverse transcriptase and protease sequence database. - Soo-Yon Rhee; Matthew J. Gonzales; Rami Kantor; Bradley J. Betts; Jaideep Ravela; Robert W. Shafer (Nucleic Acids Res., 2003)

Prediction of HIV Mutation Changes based on Treatment History. - Ray S. Lin; Soo-Yon Rhee; Robert W. Shafer; Amar K. Das (AMIA, 2006)

HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. - Soo-Yon Rhee; Tommy F. Liu; Susan P. Holmes; Robert W. Shafer (PLoS Comput. Biol., 2007)

Viral Population Estimation Using Pyrosequencing. - Nicholas Eriksson; Lior Pachter; Yumi Mitsuya; Soo-Yon Rhee; Chunlin Wang; Baback Gharizadeh; Mostafa Ronaghi; Robert W. Shafer; Niko Beerenwinkel (PLoS Comput. Biol., 2008)

The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. - Robert J. Gifford; Tommy F. Liu; Soo-Yon Rhee; Mark Kiuchi; Stéphane Hué; Deenan Pillay; Robert W. Shafer (Bioinform., 2009)

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. - Elizabeth C. Reuman; Severine Margeridon-Thermet; Harrison B. Caudill; Tommy F. Liu; Katyna Borroto-Esoda; Evguenia S. Svarovskaia; Susan P. Holmes; Robert W. Shafer (Bioinform., 2010)

Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. - Kristof Theys; Koen Deforche; Gertjan Beheydt; Yves Moreau; Kristel Van Laethem; Philippe Lemey; Ricardo Camacho; Soo-Yon Rhee; Robert W. Shafer; Eric Van Wijngaerden; Anne-Mieke Vandamme (BMC Bioinform., 2010)

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. - Kathleen M. Doherty; Priyanka Nakka; Bracken M. King; Soo-Yon Rhee; Susan P. Holmes; Robert W. Shafer; Mala L. Radhakrishnan (BMC Bioinform., 2011)

NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. - Philip L. Tzou; Xiaoqiu Huang 001; Robert W. Shafer (BMC Bioinform., 2017)