Robert W. Shafer

Kathleen M. Doherty, Priyanka Nakka, Bracken M. King, Soo-Yon Rhee, Susan P. Holmes, Robert W. Shafer, Mala L. Radhakrishnan: A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinformatics 12: 477 (2011)

Elizabeth C. Reuman, Severine Margeridon-Thermet, Harrison B. Caudill, Tommy F. Liu, Katyna Borroto-Esoda, Evguenia S. Svarovskaia, Susan P. Holmes, Robert W. Shafer: A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. Bioinformatics 26(23): 2929-2932 (2010)

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: Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. BMC Bioinformatics 11: 409 (2010)

Robert J. Gifford, Tommy F. Liu, Soo-Yon Rhee, Mark Kiuchi, Stephane Hue, Deenan Pillay, Robert W. Shafer: The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics 25(9): 1197-1198 (2009)

Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel: Viral Population Estimation Using Pyrosequencing. PLoS Computational Biology 4(5) (2008)

Soo-Yon Rhee, Tommy F. Liu, Susan P. Holmes, Robert W. Shafer: HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. PLoS Computational Biology 3(5) (2007)

Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, Robert W. Shafer: Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Research 31(1): 298-303 (2003)

Matthew J. Gonzales, Jonathan M. Dugan, Robert W. Shafer: Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). Bioinformatics 18(6): 886-887 (2002)

Rami Kantor, Rhoderick Machekano, Matthew J. Gonzales, Kathryn Dupnik, Jonathan M. Schapiro, Robert W. Shafer: Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs. Nucleic Acids Research 29(1): 296-299 (2001)

Robert W. Shafer, Duane R. Jung, Bradley J. Betts, Yinong Xi, Matthew J. Gonzales: Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. Nucleic Acids Research 28(1): 346-348 (2000)

Robert W. Shafer, Derek Stevenson, Bryan Chan: Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database. Nucleic Acids Research 27(1): 348-352 (1999)