Rhee, Soo-Yon, Liu, Tommy F, Kiuchi, Mark, Zioni, Rafael, Gifford, Robert J, Holmes, Susan P, ...
Abstract HIV-1 integrase is the third enzymatic target of antiretroviral (ARV) therapy. However, few data have been published on the distribution of naturally occurring amino acid variation in this...
Ning Yan, Serban Nacu, Jeffrey Weber, Susan P. Holmes, Peter P. Lee
BackgroundDysfunction of the immune system has been documented in many types of cancers. The precise nature and molecular basis of immune dysfunction in the cancer state are not well defined.Methods...
HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation (2007)
Soo-Yon Rhee, Tommy F. Liu, Susan P. Holmes, Robert W. Shafer
Despite the high degree of HIV-1 protease and reverse transcriptase (RT) mutation in the setting of antiretroviral therapy, the spectrum of possible virus variants appears to be limited by patterns...
Error Distribution for Gene Expression Data (2005)
Purdom, Elizabeth, Holmes, Susan P
We present a new instance of Laplace's second Law of Errors and show how it can be used in the analysis of data from microarray experiments. This error distribution is shown to fit microarray...
Error Distribution for Gene Expression Data (2005)
Purdom, Elizabeth, Holmes, Susan P
We present a new instance of Laplace's second Law of Errors and show how it can be used in the analysis of data from microarray experiments. This error distribution is shown to fit microarray...
Error Distribution for Gene Expression Data (2005)
Purdom, Elizabeth, Holmes, Susan P
We present a new instance of Laplace's second Law of Errors and show how it can be used in the analysis of data from microarray experiments. This error distribution is shown to fit microarray...
Error Distribution for Gene Expression Data (2005)
Purdom, Elizabeth, Holmes, Susan P
We present a new instance of Laplace's second Law of Errors and show how it can be used in the analysis of data from microarray experiments. This error distribution is shown to fit microarray...
Diversity and Recognition Efficiency of T Cell Responses to Cancer (2004)
Tor B. Stuge, Susan P. Holmes, Sahdev Saharan, Andrea Tuettenberg, Mario Roederer, Jeffrey S. Weber, ...
State-of-the art analysis of patients' response to melanoma vaccines yields lessons about cancer vaccines and rationale vaccine design in general.
Diversity and Recognition Efficiency of T Cell Responses to Cancer (2004)
Tor B. Stuge, Susan P. Holmes, Sahdev Saharan, Andrea Tuettenberg, Mario Roederer, Jeffrey S. Weber, ...
Background Melanoma patients vaccinated with tumor-associated antigens frequently develop measurable peptide-specific CD8+ T cell responses; however, such responses often do not confer clinical...
Sequential Monte Carlo Methods for Statistical Analysis of (2004)
Yuguo Chen, Persi Diaconis, Susan P. Holmes, Jun S. Liu
We describe a sequential importance sampling (SIS) procedure for analyzing two-way zero-one or contingency tables with fixed marginal sums. An essential feature of the new method is that it samples...
Random Walks on Trees and Matchings (2002)
Persi Diaconis, Susan P. Holmes
We give sharp rates of convergence for a natural Markov chain on the space of phylogenetic trees and dually for the natural random walk on the set of perfect matchings in the complete graph on 2n...
Geometry of the Space of Phylogenetic Trees (2001)
Louis J. Billera, Susan P. Holmes, Karen Vogtmann
ields to graphically represent various types of hierarchical relationships, including evolutionary relationships between species, divergent patterns between subpopulations and evolutionary...
Geometry of the Space of Phylogenetic Trees (2000)
Louis J. Billera, Susan P. Holmes, Karen Vogtmann
We consider a continuous space which models the set of all phylogenetic trees having a fixed set of leaves. This space has a natural metric of nonpositive curvature, giving a way of measuring...
Matchings and phylogenetic trees
Diaconis, Persi W., Holmes, Susan P.
This paper presents a natural coordinate system for phylogenetic trees using a correspondence with the set of perfect matchings in the complete graph. This correspondence produces a distance between...
Diversity and Recognition Efficiency of T Cell Responses to Cancer
Stuge, Tor B, Holmes, Susan P, Saharan, Sahdev, Tuettenberg, Andrea, Roederer, Mario, Weber, Jeffrey S, ...
State-of-the art analysis of patients' response to melanoma vaccines yields lessons about cancer vaccines and rationale vaccine design in general
Matchings and phylogenetic trees
Diaconis, Persi W., Holmes, Susan P.
This paper presents a natural coordinate system for phylogenetic trees using a correspondence with the set of perfect matchings in the complete graph. This correspondence produces a distance between...
Diversity and Recognition Efficiency of T Cell Responses to Cancer
Stuge, Tor B, Holmes, Susan P, Saharan, Sahdev, Tuettenberg, Andrea, Roederer, Mario, Weber, Jeffrey S, ...
State-of-the art analysis of patients' response to melanoma vaccines yields lessons about cancer vaccines and rationale vaccine design in general
HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation
Rhee, Soo-Yon, Liu, Tommy F, Holmes, Susan P, Shafer, Robert W
Despite the high degree of HIV-1 protease and reverse transcriptase (RT) mutation in the setting of antiretroviral therapy, the spectrum of possible virus variants appears to be limited by patterns...
Critchley-Thorne, Rebecca J, Yan, Ning, Nacu, Serban, Weber, Jeffrey, Holmes, Susan P, Lee, Peter P
Prompted by altered expression patterns of interferon-responsive genes in T and B cells, Peter Lee and colleagues find that lymphocytes from melanoma patients have defects in interferon signaling.
Rhee, Soo-Yon, Liu, Tommy F, Kiuchi, Mark, Zioni, Rafael, Gifford, Robert J, Holmes, Susan P, ...
HIV-1 integrase is the third enzymatic target of antiretroviral (ARV) therapy. However, few data have been published on the distribution of naturally occurring amino acid variation in this enzyme. We...