Bio

Bio


Trained in the French school of Data Analysis in Montpellier, Susan Holmes has been working in non parametric multivariate statistics applied to Biology since 1985. She has taught at MIT, Harvard and was an Associate Professor of Biometry at Cornell before moving to Stanford in 1998. She teaches the Thinking Matters class: Breaking Codes and Finding patterns and likes working on big messy data sets, mostly from the areas of Immunology, Cancer Biology and Microbial Ecology. Her theoretical interests include applied probability, Graph Limit Theory and the topology of the space of Phylogenetic Trees.

Academic Appointments


Administrative Appointments


  • Professor, Member, BioX (2003 - Present)
  • Director, VIGRE program in Statistics (2005 - 2014)
  • CoDirector, Mathematical and Computational Sciences IDP (2002 - 2015)

Honors & Awards


  • Director's Transformative Research Award, NIH (2013)
  • John Henry Samter University Fellow in Undergraduate Education, Stanford (2012)
  • Fellow of the Institute of Mathematical Statistics, IMS (08/2005)

Boards, Advisory Committees, Professional Organizations


  • Science Boards, Fields Research Institute in the Mathematical Sciences (2012 - Present)
  • Member and Chair (2010-2012), Science Board, NimBioS (2007 - 2012)

Research & Scholarship

Current Research and Scholarly Interests


Our work focuses on large heterogeneous multi-layer data analyses. Whether using image analysis and segmentation for the study of cancer and immune cell interactions, or brain imaging and DNA sequence analyses for the study of dependencies between genetic and neurological dynamics, all these statistical studies have involved large complex datasets of different types where dynamics of interactions between different components of a system are the key to understanding the underlying biology.

We have generalized methods such as Principal Components Analysis (PCA) to more diverse data incorporating spatial information as well as tree dependency structures. This has proved useful in the study of drug resistant mutations in HIV and in the study of the dynamics of bacterial communities in the Human Microbiome.

The statistical bases for these nonparametric methods are computer intensive methods using optimization and Kernels and we often find useful embeddings of high dimensional data in low dimensional structures, the extreme case being finding a natural ordering in high dimensional data. More general manifolds have also proved useful in one of our current projects, joint with Xavier Pennec of INRIA-SophiaAntiolis which focuses on the uses of differential geometry in computational anatomy and image processing.

In a long term collaboration with Professor David Relman (Stanford Medical School) we are developing a multi-table toolbox of non parametric methods that enable users to normalize and visualize the multiple facets of the microbiota in the human body under different classes of perturbations. The tools developed in this project are all open source packages developed in R and provide an example of reproducible research in action.

Projects


  • Study of the dynamics of the human microbiome., Stanford University (March 1, 2013)

    We are using statistical multivariate methods we are devloping new methods for modeling and visualizing the dynamics of bacterial community networks in the human microbiome.

    Location

    United States

    Collaborators

    • David Relman, Thomas C. and Joan M. Merigan Professor and Professor of Microbiology and Immunology
  • Hierarchical Testing, Stanford University (8/1/2012)

    Develop tools for testing evokutionary signals in bacterial data.

    Location

    Stanford

    Collaborators

  • Use of Differential Geometry for Identification of Features in Spinal Images Predictive of Lower Back Pain, Stanford University and INRIA Sophia-Antipolis (1/1/2013)

    Using modern Monte Carlo Markov chain techniques to generate posterior distributions on the space of transformations on manifolds, we are discovering the geometric features predictive of back pain using high resolution imagery.

    Location

    France

  • Multivariate Data Analysis of Drug Resistance in HIV, Stanford University (9/1/2003)

    We use phylogenetic trees, networks and multivariate analyses to deompose the complexities of drug resistance in HIV.

    Location

    Stanford

    Collaborators

    • Robert Shafer, Professor (Research) of Medicine (Infectious Diseases and Geographic Medicine) and, by courtesy, of Pathology

Teaching

2013-14 Courses


Graduate and Fellowship Programs


  • Biomedical Informatics (Phd Program)

Publications

Journal Articles


  • Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLoS Comput Biology McMurdie, P. J., Holmes, S. 2014; 10 (4)
  • phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PloS one McMurdie, P. J., Holmes, S. 2013; 8 (4)

    Abstract

    the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

    View details for DOI 10.1371/journal.pone.0061217

    View details for PubMedID 23630581

  • Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS Chakerian, J., Holmes, S. 2012; 21 (3): 581-599
  • The effect of individual variation on the structure and function of interaction networks in harvester ants JOURNAL OF THE ROYAL SOCIETY INTERFACE Pinter-Wollman, N., Wollman, R., Guetz, A., Holmes, S., Gordon, D. M. 2011; 8 (64): 1562-1573

    Abstract

    Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant's interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow.

    View details for DOI 10.1098/rsif.2011.0059

    View details for Web of Science ID 000295211200003

    View details for PubMedID 21490001

  • An Interactive Java Statistical Image Segmentation System: GemIdent JOURNAL OF STATISTICAL SOFTWARE Holmes, S., Kapelner, A., Lee, P. P. 2009; 30 (10): 1-20
  • HORSESHOES IN MULTIDIMENSIONAL SCALING AND LOCAL KERNEL METHODS ANNALS OF APPLIED STATISTICS Diaconis, P., Goel, S., Holmes, S. 2008; 2 (3): 777-807

    View details for DOI 10.1214/08-AOAS165

    View details for Web of Science ID 000261057900001

  • Gene expression network analysis and applications to immunology BIOINFORMATICS Nacu, S., Critchley-Thorne, R., Lee, P., Holmes, S. 2007; 23 (7): 850-858

    Abstract

    We address the problem of using expression data and prior biological knowledge to identify differentially expressed pathways or groups of genes. Following an idea of Ideker et al. (2002), we construct a gene interaction network and search for high-scoring subnetworks. We make several improvements in terms of scoring functions and algorithms, resulting in higher speed and accuracy and easier biological interpretation. We also assign significance levels to our results, adjusted for multiple testing. Our methods are successfully applied to three human microarray data sets, related to cancer and the immune system, retrieving several known and potential pathways. The method, denoted by the acronym GXNA (Gene eXpression Network Analysis) is implemented in software that is publicly available and can be used on virtually any microarray data set.The source code and executable for the software, as well as certain supplemental materials, can be downloaded from http://stat.stanford.edu/~serban/gxna.

    View details for DOI 10.1093/bioinformatics/btm019

    View details for Web of Science ID 000246120400010

    View details for PubMedID 17267429

  • Geometry of the space of phylogenetic trees ADVANCES IN APPLIED MATHEMATICS Billera, L. J., Holmes, S. P., Vogtmann, K. 2001; 27 (4): 733-767
  • Bootstrap confidence levels for phylogenetic trees (vol 93, pg 7085, 1996) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Efron, B., Halloran, E., Holmes, S. 1996; 93 (23): 13429-13434

    Abstract

    Evolutionary trees are often estimated from DNA or RNA sequence data. How much confidence should we have in the estimated trees? In 1985, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literature. This paper concerns the use of the bootstrap in the tree problem. We show that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing. These corrections can be made by using the more elaborate bootstrap method presented here, at the expense of considerably more computation.

    View details for Web of Science ID A1996VT05400135

    View details for PubMedID 8917608

  • HIV-1 Transmission Networks in a Small World. journal of infectious diseases Pennings, P. S., Holmes, S. P., Shafer, R. W. 2014; 209 (2): 180-182

    View details for DOI 10.1093/infdis/jit525

    View details for PubMedID 24151310

  • Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage. Cell host & microbe Yan, M., Pamp, S. J., Fukuyama, J., Hwang, P. H., Cho, D., Holmes, S., Relman, D. A. 2013; 14 (6): 631-640

    Abstract

    The indigenous microbiota of the nasal cavity plays important roles in human health and disease. Patterns of spatial variation in microbiota composition may help explain Staphylococcus aureus colonization and reveal interspecies and species-host interactions. To assess the biogeography of the nasal microbiota, we sampled healthy subjects, representing both S. aureus carriers and noncarriers at three nasal sites (anterior naris, middle meatus, and sphenoethmoidal recess). Phylogenetic compositional and sparse linear discriminant analyses revealed communities that differed according to site epithelium type and S. aureus culture-based carriage status. Corynebacterium accolens and C. pseudodiphtheriticum were identified as the most important microbial community determinants of S. aureus carriage, and competitive interactions were only evident at sites with ciliated pseudostratified columnar epithelium. In vitro cocultivation experiments provided supporting evidence of interactions among these species. These results highlight spatial variation in nasal microbial communities and differences in community composition between S. aureus carriers and noncarriers.

    View details for DOI 10.1016/j.chom.2013.11.005

    View details for PubMedID 24331461

  • Detection of cytomegalovirus drug resistance mutations by next-generation sequencing. Journal of clinical microbiology Sahoo, M. K., Lefterova, M. I., Yamamoto, F., Waggoner, J. J., Chou, S., Holmes, S. P., Anderson, M. W., Pinsky, B. A. 2013; 51 (11): 3700-3710

    Abstract

    Antiviral therapy for cytomegalovirus (CMV) plays an important role in the clinical management of solid organ and hematopoietic stem cell transplant recipients. However, CMV antiviral therapy can be complicated by drug resistance associated with mutations in the phosphotransferase UL97 and the DNA polymerase UL54. We have developed an amplicon-based high-throughput sequencing strategy for detecting CMV drug resistance mutations in clinical plasma specimens using a microfluidics PCR platform for multiplexed library preparation and a benchtop next-generation sequencing instrument. Plasmid clones of the UL97 and UL54 genes were used to demonstrate the low overall empirical error rate of the assay (0.189%) and to develop a statistical algorithm for identifying authentic low-abundance variants. The ability of the assay to detect resistance mutations was tested with mixes of wild-type and mutant plasmids, as well as clinical CMV isolates and plasma samples that were known to contain mutations that confer resistance. Finally, 48 clinical plasma specimens with a range of viral loads (394 to 2,191,011 copies/ml plasma) were sequenced using multiplexing of up to 24 specimens per run. This led to the identification of seven resistance mutations, three of which were present in <20% of the sequenced population. Thus, this assay offers more sensitive detection of minor variants and a higher multiplexing capacity than current methods for the genotypic detection of CMV drug resistance mutations.

    View details for DOI 10.1128/JCM.01605-13

    View details for PubMedID 23985916

  • Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kashyap, P. C., Marcobal, A., Ursell, L. K., Smits, S. A., Sonnenburg, E. D., Costello, E. K., Higginbottom, S. K., Domino, S. E., Holmes, S. P., Relman, D. A., Knight, R., Gordon, J. I., Sonnenburg, J. L. 2013; 110 (42): 17059-17064

    Abstract

    We investigate how host mucus glycan composition interacts with dietary carbohydrate content to influence the composition and expressed functions of a human gut community. The humanized gnotobiotic mice mimic humans with a nonsecretor phenotype due to knockout of their α1-2 fucosyltransferase (Fut2) gene. The fecal microbiota of Fut2(-) mice that lack fucosylated host glycans show decreased alpha diversity relative to Fut2(+) mice and exhibit significant differences in community composition. A glucose-rich plant polysaccharide-deficient (PD) diet exerted a strong effect on the microbiota membership but eliminated the effect of Fut2 genotype. Additionally fecal metabolites predicted host genotype in mice on a polysaccharide-rich standard diet but not on a PD diet. A more detailed mechanistic analysis of these interactions involved colonization of gnotobiotic Fut2(+) and Fut2(-) mice with Bacteroides thetaiotaomicron, a prominent member of the human gut microbiota known to adaptively forage host mucosal glycans when dietary polysaccharides are absent. Within Fut2(-) mice, the B. thetaiotaomicron fucose catabolic pathway was markedly down-regulated, whereas BT4241-4247, an operon responsive to terminal β-galactose, the precursor that accumulates in the Fut2(-) mice, was significantly up-regulated. These changes in B. thetaiotaomicron gene expression were only evident in mice fed a PD diet, wherein B. thetaiotaomicron relies on host mucus consumption. Furthermore, up-regulation of the BT4241-4247 operon was also seen in humanized Fut2(-) mice. Together, these data demonstrate that differences in host genotype that affect the carbohydrate landscape of the distal gut interact with diet to alter the composition and function of resident microbes in a diet-dependent manner.

    View details for DOI 10.1073/pnas.1306070110

    View details for Web of Science ID 000325634200076

    View details for PubMedID 24062455

  • Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1 ANTIMICROBIAL AGENTS AND CHEMOTHERAPY Varghese, V., Mitsuya, Y., Fessel, W. J., Liu, T. F., Melikian, G. L., Katzenstein, D. A., Schiffer, C. A., Holmes, S. P., Shafer, R. W. 2013; 57 (9): 4290-4299
  • ANALYSIS OF CASINO SHELF SHUFFLING MACHINES ANNALS OF APPLIED PROBABILITY Diaconis, P., Fulman, J., Holmes, S. 2013; 23 (4): 1692-1720

    View details for DOI 10.1214/12-AAP884

    View details for Web of Science ID 000321678200014

  • Harvester ants use interactions to regulate forager activation and availability ANIMAL BEHAVIOUR Pinter-Wollman, N., Bala, A., Merrell, A., Queirolo, J., Stumpe, M. C., Holmes, S., Gordon, D. M. 2013; 86 (1): 197-207
  • Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line Stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out Stavudine. journal of infectious diseases Tang, M. W., Rhee, S., Bertagnolio, S., Ford, N., Holmes, S., Sigaloff, K. C., Hamers, R. L., de Wit, T. F., Fleury, H. J., Kanki, P. J., Ruxrungtham, K., Hawkins, C. A., Wallis, C. L., Stevens, W., van Zyl, G. U., Manosuthi, W., Hosseinipour, M. C., Ngo-Giang-Huong, N., Belec, L., Peeters, M., Aghokeng, A., Bunupuradah, T., Burda, S., Cane, P., Cappelli, G., Charpentier, C., Dagnra, A. Y., Deshpande, A. K., El-Katib, Z., Eshleman, S. H., Fokam, J., Gody, J., Katzenstein, D., Koyalta, D. D., Kumwenda, J. J., Lallemant, M., Lynen, L., Marconi, V. C., Margot, N. A., Moussa, S., Ndung'u, T., Nyambi, P. N., Orrell, C., Schapiro, J. M., Schuurman, R., Sirivichayakul, S., Smith, D., Zolfo, M., Jordan, M. R., Shafer, R. W. 2013; 207: S70-7

    Abstract

    Background The World Health Organization Antiretroviral Treatment Guidelines recommend phasing-out stavudine because of its risk of long-term toxicity. There are two mutational pathways of stavudine resistance with different implications for zidovudine and tenofovir cross-resistance, the primary candidates for replacing stavudine. However, because resistance testing is rarely available in resource-limited settings, it is critical to identify the cross-resistance patterns associated with first-line stavudine failure. Methods We analyzed HIV-1 resistance mutations following first-line stavudine failure from 35 publications comprising 1,825 individuals. We also assessed the influence of concomitant nevirapine vs. efavirenz, therapy duration, and HIV-1 subtype on the proportions of mutations associated with zidovudine vs. tenofovir cross-resistance. Results Mutations with preferential zidovudine activity, K65R or K70E, occurred in 5.3% of individuals. Mutations with preferential tenofovir activity, ?two thymidine analog mutations (TAMs) or Q151M, occurred in 22% of individuals. Nevirapine increased the risk of TAMs, K65R, and Q151M. Longer therapy increased the risk of TAMs and Q151M but not K65R. Subtype C and CRF01_AE increased the risk of K65R, but only CRF01_AE increased the risk of K65R without Q151M. Conclusions Regardless of concomitant nevirapine vs. efavirenz, therapy duration, or subtype, tenofovir was more likely than zidovudine to retain antiviral activity following first-line d4T therapy.

    View details for DOI 10.1093/infdis/jit114

    View details for PubMedID 23687292

  • Interval Graph Limits ANNALS OF COMBINATORICS Diaconis, P., Holmes, S., Janson, S. 2013; 17 (1): 27-52
  • Low-Level Persistence of Drug Resistance Mutations in Hepatitis B Virus-Infected Subjects with a Past History of Lamivudine Treatment ANTIMICROBIAL AGENTS AND CHEMOTHERAPY Margeridon-Thermet, S., Svarovskaia, E. S., Babrzadeh, F., Martin, R., Liu, T. F., Pacold, M., Reuman, E. C., Holmes, S. P., Borroto-Esoda, K., Shafer, R. W. 2013; 57 (1): 343-349

    Abstract

    We sought to determine the prevalence of hepatitis B virus (HBV) lamivudine (LAM)-resistant minority variants in subjects who once received LAM but had discontinued it prior to virus sampling. We performed direct PCR Sanger sequencing and ultradeep pyrosequencing (UDPS) of HBV reverse transcriptase (RT) of plasma viruses from 45 LAM-naive subjects and 46 LAM-experienced subjects who had discontinued LAM a median of 24 months earlier. UDPS was performed to a depth of ?3,000 reads per nucleotide. Minority variants were defined as differences from the Sanger sequence present in ?0.5% of UDPS reads in a sample. Sanger sequencing identified ?1 LAM resistance mutations (rtL80I/V, rtM204I, and rtA181T) in samples from 5 (11%) of 46 LAM-experienced and none of 45 LAM-naive subjects (0%; P = 0.06). UDPS detected ?1 LAM resistance mutations (rtL80I/V, rtV173L, rtL180M, rtA181T, and rtM204I/V) in 10 (22%) of the 46 LAM-experienced subjects, including 5 in whom LAM resistance mutations were not identified by Sanger sequencing. Overall, LAM resistance mutations were more likely to be present in LAM-experienced (10/46, 22%) than LAM-naive subjects (0/45, 0%; P = 0.001). The median time since LAM discontinuation was 12.8 months in the 10 subjects with a LAM resistance mutation compared to 30.5 months in the 36 LAM-experienced subjects without a LAM resistance mutation (P < 0.001). The likelihood of detecting a LAM resistance mutation was significantly increased using UDPS compared to Sanger sequencing and was inversely associated with the time since LAM discontinuation.

    View details for DOI 10.1128/AAC.01601-12

    View details for Web of Science ID 000312958400044

    View details for PubMedID 23114756

  • Advancing Our Understanding of the Human Microbiome Using QIIME. Methods in enzymology Navas-Molina, J. A., Peralta-Sánchez, J. M., González, A., McMurdie, P. J., Vázquez-Baeza, Y., Xu, Z., Ursell, L. K., Lauber, C., Zhou, H., Song, S. J., Huntley, J., Ackermann, G. L., Berg-Lyons, D., Holmes, S., Caporaso, J. G., Knight, R. 2013; 531: 371-444

    Abstract

    High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.

    View details for DOI 10.1016/B978-0-12-407863-5.00019-8

    View details for PubMedID 24060131

  • PRC2/EED-EZH2 Complex Is Up-Regulated in Breast Cancer Lymph Node Metastasis Compared to Primary Tumor and Correlates with Tumor Proliferation In Situ PLOS ONE Yu, H., Simons, D. L., Segall, I., Carcamo-Cavazos, V., Schwartz, E. J., Yan, N., Zuckerman, N. S., Dirbas, F. M., Johnson, D. L., Holmes, S. P., Lee, P. P. 2012; 7 (12)

    Abstract

    Lymph node metastasis is a key event in the progression of breast cancer. Therefore it is important to understand the underlying mechanisms which facilitate regional lymph node metastatic progression.We performed gene expression profiling of purified tumor cells from human breast tumor and lymph node metastasis. By microarray network analysis, we found an increased expression of polycomb repression complex 2 (PRC2) core subunits EED and EZH2 in lymph node metastatic tumor cells over primary tumor cells which were validated through real-time PCR. Additionally, immunohistochemical (IHC) staining and quantitative image analysis of whole tissue sections showed a significant increase of EZH2 expressing tumor cells in lymph nodes over paired primary breast tumors, which strongly correlated with tumor cell proliferation in situ. We further explored the mechanisms of PRC2 gene up-regulation in metastatic tumor cells and found up-regulation of E2F genes, MYC targets and down-regulation of tumor suppressor gene E-cadherin targets in lymph node metastasis through GSEA analyses. Using IHC, the expression of potential EZH2 target, E-cadherin was examined in paired primary/lymph node samples and was found to be significantly decreased in lymph node metastases over paired primary tumors.This study identified an over expression of the epigenetic silencing complex PRC2/EED-EZH2 in breast cancer lymph node metastasis as compared to primary tumor and its positive association with tumor cell proliferation in situ. Concurrently, PRC2 target protein E-cadherin was significant decreased in lymph node metastases, suggesting PRC2 promotes epithelial mesenchymal transition (EMT) in lymph node metastatic process through repression of E-cadherin. These results indicate that epigenetic regulation mediated by PRC2 proteins may provide additional advantage for the outgrowth of metastatic tumor cells in lymph nodes. This opens up epigenetic drug development possibilities for the treatment and prevention of lymph node metastasis in breast cancer.

    View details for DOI 10.1371/journal.pone.0051239

    View details for Web of Science ID 000312201900057

    View details for PubMedID 23251464

  • Denoising PCR-amplified metagenome data BMC BIOINFORMATICS Rosen, M. J., Callahan, B. J., Fisher, D. S., Holmes, S. P. 2012; 13

    Abstract

    PCR amplification and high-throughput sequencing theoretically enable the characterization of the finest-scale diversity in natural microbial and viral populations, but each of these methods introduces random errors that are difficult to distinguish from genuine biological diversity. Several approaches have been proposed to denoise these data but lack either speed or accuracy.We introduce a new denoising algorithm that we call DADA (Divisive Amplicon Denoising Algorithm). Without training data, DADA infers both the sample genotypes and error parameters that produced a metagenome data set. We demonstrate performance on control data sequenced on Roche's 454 platform, and compare the results to the most accurate denoising software currently available, AmpliconNoise.DADA is more accurate and over an order of magnitude faster than AmpliconNoise. It eliminates the need for training data to establish error parameters, fully utilizes sequence-abundance information, and enables inclusion of context-dependent PCR error rates. It should be readily extensible to other sequencing platforms such as Illumina.

    View details for DOI 10.1186/1471-2105-13-283

    View details for Web of Science ID 000314687600001

    View details for PubMedID 23113967

  • Nest site and weather affect the personality of harvester ant colonies BEHAVIORAL ECOLOGY Pinter-Wollman, N., Gordon, D. M., Holmes, S. 2012; 23 (5): 1022-1029

    Abstract

    Environmental conditions and physical constraints both influence an animal's behavior. We investigate whether behavioral variation among colonies of the black harvester ant, Messor andrei, remains consistent across foraging and disturbance situations and ask whether consistent colony behavior is affected by nest site and weather. We examined variation among colonies in responsiveness to food baits and to disturbance, measured as a change in numbers of active ants, and in the speed with which colonies retrieved food and removed debris. Colonies differed consistently, across foraging and disturbance situations, in both responsiveness and speed. Increased activity in response to food was associated with a smaller decrease in response to alarm. Speed of retrieving food was correlated with speed of removing debris. In all colonies, speed was greater in dry conditions, reducing the amount of time ants spent outside the nest. While a colony occupied a certain nest site, its responsiveness was consistent in both foraging and disturbance situations, suggesting that nest structure influences colony personality.

    View details for DOI 10.1093/beheco/ars066

    View details for Web of Science ID 000308228200017

    View details for PubMedID 22936841

  • The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT STRUCTURE Leitner, A., Joachimiak, L. A., Bracher, A., Moenkemeyer, L., Walzthoeni, T., Chen, B., Pechmann, S., Holmes, S., Cong, Y., Ma, B., Ludtke, S., Chiu, W., Hartl, F. U., Aebersold, R., Frydman, J. 2012; 20 (5): 814-825

    Abstract

    TRiC/CCT is a highly conserved and essential chaperonin that uses ATP cycling to facilitate folding of approximately 10% of the eukaryotic proteome. This 1 MDa hetero-oligomeric complex consists of two stacked rings of eight paralogous subunits each. Previously proposed TRiC models differ substantially in their subunit arrangements and ring register. Here, we integrate chemical crosslinking, mass spectrometry, and combinatorial modeling to reveal the definitive subunit arrangement of TRiC. In vivo disulfide mapping provided additional validation for the crosslinking-derived arrangement as the definitive TRiC topology. This subunit arrangement allowed the refinement of a structural model using existing X-ray diffraction data. The structure described here explains all available crosslink experiments, provides a rationale for previously unexplained structural features, and reveals a surprising asymmetry of charges within the chaperonin folding chamber.

    View details for DOI 10.1016/j.str.2012.03.007

    View details for Web of Science ID 000304214400008

    View details for PubMedID 22503819

  • Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing McMurdie, P. J., Holmes, S. 2012: 235-246

    Abstract

    We present a detailed description of a new Bioconductor package, phyloseq, for integrated data and analysis of taxonomically-clustered phylogenetic sequencing data in conjunction with related data types. The phyloseq package integrates abundance data, phylogenetic information and covariates so that exploratory transformations, plots, and confirmatory testing and diagnostic plots can be carried out seamlessly. The package is built following the S4 object-oriented framework of the R language so that once the data have been input the user can easily transform, plot and analyze the data. We present some examples that highlight the methods and the ease with which we can leverage existing packages.

    View details for PubMedID 22174279

  • Comparisons of distance methods for combining covariates and abundances in microbiome studies. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Fukuyama, J., McMurdie, P. J., Dethlefsen, L., Relman, D. A., Holmes, S. 2012: 213-224

    Abstract

    This article compares different methods for combining abundance data, phylogenetic trees and clinical covariates in a nonparametric setting. In particular we study the output from the principal coordinates analysis on UNIFRAC and WEIGHTED UNIFRAC distances and the output from a double principal coordinate analyses DPCOA using distances computed on the phylogenetic tree. We also present power comparisons for some of the standard tests of phylogenetic signal between different types of samples. These methods are compared both on simulated and real data sets. Our study shows that DPCoA is less robust to outliers, and more robust to small noisy fluctuations around zero.

    View details for PubMedID 22174277

  • A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes BMC BIOINFORMATICS Doherty, K. M., Nakka, P., King, B. M., Rhee, S., Holmes, S. P., Shafer, R. W., Radhakrishnan, M. L. 2011; 12

    Abstract

    Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to arise within the population. Understanding the phenotypic and genotypic patterns responsible for multi-PI resistance is necessary for developing PIs that are active against clinically-relevant PI-resistant HIV-1 variants.In this work, we use globally optimal integer programming-based clustering techniques to elucidate multi-PI phenotypic resistance patterns using a data set of 398 HIV-1 protease sequences that have each been phenotyped for susceptibility toward the nine clinically-approved HIV-1 PIs. We validate the information content of the clusters by evaluating their ability to predict the level of decreased susceptibility to each of the available PIs using a cross validation procedure. We demonstrate the finding that as a result of phenotypic cross resistance, the considered clinical HIV-1 protease isolates are confined to ~6% or less of the clinically-relevant phenotypic space. Clustering and feature selection methods are used to find representative sequences and mutations for major resistance phenotypes to elucidate their genotypic signatures. We show that phenotypic similarity does not imply genotypic similarity, that different PI-resistance mutation patterns can give rise to HIV-1 isolates with similar phenotypic profiles.Rather than characterizing HIV-1 susceptibility toward each PI individually, our study offers a unique perspective on the phenomenon of PI class resistance by uncovering major multidrug-resistant phenotypic patterns and their often diverse genotypic determinants, providing a methodology that can be applied to understand clinically-relevant phenotypic patterns to aid in the design of novel inhibitors that target other rapidly evolving molecular targets as well.

    View details for DOI 10.1186/1471-2105-12-477

    View details for Web of Science ID 000301382000001

    View details for PubMedID 22172090

  • THE DUALITY DIAGRAM IN DATA ANALYSIS: EXAMPLES OF MODERN APPLICATIONS ANNALS OF APPLIED STATISTICS De la Cruz, O., Holmes, S. 2011; 5 (4): 2266-2277

    View details for DOI 10.1214/10-AOAS408

    View details for Web of Science ID 000300382800002

  • Adaptive importance sampling for network growth models ANNALS OF OPERATIONS RESEARCH Guetz, A. N., Holmes, S. P. 2011; 189 (1): 187-203
  • Colonic Contribution to Uremic Solutes JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY Aronov, P. A., Luo, F. J., Plummer, N. S., Quan, Z., Holmes, S., Hostetter, T. H., Meyer, T. W. 2011; 22 (9): 1769-1776

    Abstract

    Microbes in the colon produce compounds, normally excreted by the kidneys, which are potential uremic toxins. Although p-cresol sulfate and indoxyl sulfate are well studied examples, few other compounds are known. Here, we compared plasma from hemodialysis patients with and without colons to identify and further characterize colon-derived uremic solutes. HPLC confirmed the colonic origin of p-cresol sulfate and indoxyl sulfate, but levels of hippurate, methylamine, and dimethylamine were not significantly lower in patients without colons. High-resolution mass spectrometry detected more than 1000 features in predialysis plasma samples. Hierarchical clustering based on these features clearly separated dialysis patients with and without colons. Compared with patients with colons, we identified more than 30 individual features in patients without colons that were either absent or present in lower concentration. Almost all of these features were more prominent in plasma from dialysis patients than normal subjects, suggesting that they represented uremic solutes. We used a panel of indole and phenyl standards to identify five colon-derived uremic solutes: ?-phenylacetyl-l-glutamine, 5-hydroxyindole, indoxyl glucuronide, p-cresol sulfate, and indoxyl sulfate. However, compounds with accurate mass values matching most of the colon-derived solutes could not be found in standard metabolomic databases. These results suggest that colonic microbes may produce an important portion of uremic solutes, most of which remain unidentified.

    View details for DOI 10.1681/ASN.2010121220

    View details for Web of Science ID 000295705800024

    View details for PubMedID 21784895

  • Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides BMC GENOMICS McMurdie, P. J., Hug, L. A., Edwards, E. A., Holmes, S., Spormann, A. M. 2011; 12

    Abstract

    Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene, ssrA.We targeted conserved positions in available genomic islands to amplify and sequence four additional vcrABC -containing genomic islands from previously-unsequenced vinyl chloride respiring Dehalococcoides enrichments. We identified a total of 31 ssrA-specific genomic islands from Dehalococcoides genomic data, accounting for 47 reductive dehalogenase homologous genes and many other non-core genes. Sixteen of these genomic islands contain a syntenic module of integration-associated genes located adjacent to the predicted site of integration, and among these islands, eight contain vcrABC as genetic 'cargo'. These eight vcrABC -containing genomic islands are syntenic across their ~12 kbp length, but have two phylogenetically discordant segments that unambiguously differentiate the integration module from the vcrABC cargo. Using available Dehalococcoides phylogenomic data we estimate that these ssrA-specific genomic islands are at least as old as the Dehalococcoides group itself, which in turn is much older than human civilization.The vcrABC -containing genomic islands are a recently-acquired subset of a diverse collection of ssrA-specific mobile elements that are a major contributor to strain-level diversity in Dehalococcoides, and may have been throughout its evolution. The high similarity between vcrABC sequences is quantitatively consistent with recent horizontal acquisition driven by ~100 years of industrial pollution with chlorinated ethenes.

    View details for DOI 10.1186/1471-2164-12-287

    View details for Web of Science ID 000293280200001

    View details for PubMedID 21635780

  • Colony variation in the collective regulation of foraging by harvester ants BEHAVIORAL ECOLOGY Gordon, D. M., Guetz, A., Greene, M. J., Holmes, S. 2011; 22 (2): 429-435

    Abstract

    This study investigates variation in collective behavior in a natural population of colonies of the harvester ant, Pogonomyrmex barbatus. Harvester ant colonies regulate foraging activity to adjust to current food availability; the rate at which inactive foragers leave the nest on the next trip depends on the rate at which successful foragers return with food. This study investigates differences among colonies in foraging activity and how these differences are associated with variation among colonies in the regulation of foraging. Colonies differ in the baseline rate at which patrollers leave the nest, without stimulation from returning ants. This baseline rate predicts a colony's foraging activity, suggesting there is a colony-specific activity level that influences how quickly any ant leaves the nest. When a colony's foraging activity is high, the colony is more likely to regulate foraging. Moreover, colonies differ in the propensity to adjust the rate of outgoing foragers to the rate of forager return. Naturally occurring variation in the regulation of foraging may lead to variation in colony survival and reproductive success.

    View details for DOI 10.1093/beheco/arq218

    View details for Web of Science ID 000289299500033

    View details for PubMedID 22479133

  • PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity NEUROGASTROENTEROLOGY AND MOTILITY Nelson, T. A., Holmes, S., ALEKSEYENKO, A. V., Shenoy, M., DeSantis, T., Wu, C. H., Andersen, G. L., Winston, J., Sonnenburg, J., Pasricha, P. J., Spormann, A. 2011; 23 (2)

    Abstract

    Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease.Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS.Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species.The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.

    View details for DOI 10.1111/j.1365-2982.2010.01637.x

    View details for Web of Science ID 000286211600017

    View details for PubMedID 21129126

  • Visualization and statistical comparisons of microbial communities using R packages on Phylochip data. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Holmes, S., Alekseyenko, A., Timme, A., Nelson, T., Pasricha, P. J., Spormann, A. 2011: 142-153

    Abstract

    This article explains the statistical and computational methodology used to analyze species abundances collected using the LNBL Phylochip in a study of Irritable Bowel Syndrome (IBS) in rats. Some tools already available for the analysis of ordinary microarray data are useful in this type of statistical analysis. For instance in correcting for multiple testing we use Family Wise Error rate control and step-down tests (available in the multtest package). Once the most significant species are chosen we use the hypergeometric tests familiar for testing GO categories to test specific phyla and families. We provide examples of normalization, multivariate projections, batch effect detection and integration of phylogenetic covariation, as well as tree equalization and robustification methods.

    View details for PubMedID 21121042

  • A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads BIOINFORMATICS Reuman, E. C., Margeridon-Thermet, S., Caudill, H. B., Liu, T., Borroto-Esoda, K., Svarovskaia, E. S., Holmes, S. P., Shafer, R. W. 2010; 26 (23): 2929-2932

    Abstract

    G ? A hypermutation is an innate antiviral defense mechanism, mediated by host enzymes, which leads to the mutational impairment of viruses. Sensitive and specific identification of host-mediated G ? A hypermutation is a novel sequence analysis challenge, particularly for viral deep sequencing studies. For example, two of the most common hepatitis B virus (HBV) reverse transcriptase (RT) drug-resistance mutations, A181T and M204I, arise from G ? A changes and are routinely detected as low-abundance variants in nearly all HBV deep sequencing samples.We developed a classification model using measures of G ? A excess and predicted indicators of lethal mutation and applied this model to 325 920 unique deep sequencing reads from plasma virus samples from 45 drug treatment-naïve HBV-infected individuals. The 2.9% of sequence reads that were classified as hypermutated by our model included most of the reads with A181T and/or M204I, indicating the usefulness of this model for distinguishing viral adaptive changes from host-mediated viral editing.Source code and sequence data are available at http://hivdb.stanford.edu/pages/resources.html.ereuman@stanfordalumni.orgSupplementary data are available at Bioinformatics online.

    View details for DOI 10.1093/bioinformatics/btq570

    View details for Web of Science ID 000284430900001

    View details for PubMedID 20937597

  • Quantitative, Architectural Analysis of Immune Cell Subsets in Tumor-Draining Lymph Nodes from Breast Cancer Patients and Healthy Lymph Nodes PLOS ONE Setiadi, A. F., Ray, N. C., Kohrt, H. E., Kapelner, A., Carcamo-Cavazos, V., Levic, E. B., Yadegarynia, S., van der Loos, C. M., Schwartz, E. J., Holmes, S., Lee, P. P. 2010; 5 (8)

    Abstract

    To date, pathological examination of specimens remains largely qualitative. Quantitative measures of tissue spatial features are generally not captured. To gain additional mechanistic and prognostic insights, a need for quantitative architectural analysis arises in studying immune cell-cancer interactions within the tumor microenvironment and tumor-draining lymph nodes (TDLNs).We present a novel, quantitative image analysis approach incorporating 1) multi-color tissue staining, 2) high-resolution, automated whole-section imaging, 3) custom image analysis software that identifies cell types and locations, and 4) spatial statistical analysis. As a proof of concept, we applied this approach to study the architectural patterns of T and B cells within tumor-draining lymph nodes from breast cancer patients versus healthy lymph nodes. We found that the spatial grouping patterns of T and B cells differed between healthy and breast cancer lymph nodes, and this could be attributed to the lack of B cell localization in the extrafollicular region of the TDLNs.Our integrative approach has made quantitative analysis of complex visual data possible. Our results highlight spatial alterations of immune cells within lymph nodes from breast cancer patients as an independent variable from numerical changes. This opens up new areas of investigations in research and medicine. Future application of this approach will lead to a better understanding of immune changes in the tumor microenvironment and TDLNs, and how they affect clinical outcomes.

    View details for DOI 10.1371/journal.pone.0012420

    View details for Web of Science ID 000281234700034

    View details for PubMedID 20811638

  • Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY Reuman, E. C., Rhee, S., Holmes, S. P., Shafer, R. W. 2010; 65 (7): 1477-1485

    Abstract

    We characterized pairwise and higher order patterns of non-nucleoside reverse transcriptase inhibitor (NNRTI)-selected mutations because multiple mutations are usually required for clinically significant resistance to second-generation NNRTIs.We analysed viruses from 13 039 individuals with sequences containing at least one of 52 published NNRTI-selected mutations, including 1133 viruses from individuals who received efavirenz but no other NNRTI and 1510 viruses from individuals who received nevirapine but no other NNRTI. Of the 17 reported etravirine resistance-associated mutations (RAMs), Y181C/I/V, L100I, K101P and M230L were considered major based on published in vitro susceptibility data.Efavirenz preferentially selected for 16 mutations, including L100I (14% versus 0.1%, P < 0.001), K101P (3.3% versus 0.4%, P < 0.001) and M230L (2.8% versus 1.3%, P = 0.004), whereas nevirapine preferentially selected for 12 mutations, including Y181C/I/V (48% versus 6.9%, P < 0.001). Twenty-nine pairs of NNRTI-selected mutations covaried significantly, including Y181C with seven other mutations (A98G, K101E/H, V108I, G190A/S and H221Y), L100I with K103N, and K101P with K103S. Two pairs (Y181C + V179F and Y181C + G190S) were predicted to confer >10-fold decreased etravirine susceptibility. Seventeen percent of sequences had three or more NNRTI-selected mutations, mostly in clusters of covarying mutations. Many clusters had Y181C plus a non-major etravirine RAM; few had more than one major etravirine RAM.Although major etravirine RAMs rarely occur in combination, 2 of 29 pairs of covarying mutations were associated with >10-fold decreased etravirine susceptibility. Viruses with three or more NNRTI-selected mutations often contained Y181C in combination with one or more minor etravirine RAMs; however, phenotypic and clinical correlates for most of these higher order combinations have not been published.

    View details for DOI 10.1093/jac/dkq140

    View details for Web of Science ID 000279926500027

    View details for PubMedID 20462946

  • Nonpolymorphic Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Treatment-Selected Mutations ANTIMICROBIAL AGENTS AND CHEMOTHERAPY Shahriar, R., Rhee, S., Liu, T. F., Fessel, W. J., Scarsella, A., Towner, W., Holmes, S. P., Zolopa, A. R., Shafer, R. W. 2009; 53 (11): 4869-4878

    Abstract

    The spectrum of human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT) mutations selected by antiretroviral (ARV) drugs requires ongoing reassessment as ARV treatment patterns evolve and increasing numbers of protease and RT sequences of different viral subtypes are published. Accordingly, we compared the prevalences of protease and RT mutations in HIV-1 group M sequences from individuals with and without a history of previous treatment with protease inhibitors (PIs) or RT inhibitors (RTIs). Mutations in protease sequences from 26,888 individuals and in RT sequences from 25,695 individuals were classified according to whether they were nonpolymorphic in untreated individuals and whether their prevalence increased fivefold with ARV therapy. This analysis showed that 88 PI-selected and 122 RTI-selected nonpolymorphic mutations had a prevalence that was fivefold higher in individuals receiving ARVs than in ARV-naïve individuals. This was an increase of 47% and 77%, respectively, compared with the 60 PI- and 69 RTI-selected mutations identified in a similar analysis that we published in 2005 using subtype B sequences obtained from one-fourth as many individuals. In conclusion, many nonpolymorphic mutations in protease and RT are under ARV selection pressure. The spectrum of treatment-selected mutations is changing as data for more individuals are collected, treatment exposures change, and the number of available sequences from non-subtype B viruses increases.

    View details for DOI 10.1128/AAC.00592-09

    View details for Web of Science ID 000270881200040

    View details for PubMedID 19721070

  • Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides PLOS GENETICS McMurdie, P. J., Behrens, S. F., Mueller, J. A., Goeke, J., Ritalahti, K. M., Wagner, R., Goltsman, E., Lapidus, A., Holmes, S., Loeffler, F. E., Spormann, A. M. 2009; 5 (11)

    Abstract

    Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.

    View details for DOI 10.1371/journal.pgen.1000714

    View details for Web of Science ID 000272419500010

    View details for PubMedID 19893622

  • Impaired interferon signaling is a common immune defect in human cancer PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Critchley-Thorne, R. J., Simons, D. L., Yan, N., Miyahira, A. K., Dirbas, F. M., Johnson, D. L., Swetter, S. M., Carlson, R. W., Fisher, G. A., Koong, A., Holmes, S., Lee, P. P. 2009; 106 (22): 9010-9015

    Abstract

    Immune dysfunction develops in patients with many cancer types and may contribute to tumor progression and failure of immunotherapy. Mechanisms underlying cancer-associated immune dysfunction are not fully understood. Efficient IFN signaling is critical to lymphocyte function; animals rendered deficient in IFN signaling develop cancer at higher rates. We hypothesized that altered IFN signaling may be a key mechanism of immune dysfunction common to cancer. To address this, we assessed the functional responses to IFN in peripheral blood lymphocytes from patients with 3 major cancers: breast cancer, melanoma, and gastrointestinal cancer. Type-I IFN (IFN-alpha)-induced signaling was reduced in T cells and B cells from all 3 cancer-patient groups compared to healthy controls. Type-II IFN (IFN-gamma)-induced signaling was reduced in B cells from all 3 cancer patient groups, but not in T cells or natural killer cells. Impaired-IFN signaling was equally evident in stage II, III, and IV breast cancer patients, and downstream functional defects in T cell activation were identified. Taken together, these findings indicate that defects in lymphocyte IFN signaling arise in patients with breast cancer, melanoma, and gastrointestinal cancer, and these defects may represent a common cancer-associated mechanism of immune dysfunction.

    View details for DOI 10.1073/pnas.0901329106

    View details for Web of Science ID 000266580500043

    View details for PubMedID 19451644

  • How site fidelity leads to individual differences in the foraging activity of harvester ants BEHAVIORAL ECOLOGY Beverly, B. D., McLendon, H., Nacu, S., Holmes, S., Gordon, D. M. 2009; 20 (3): 633-638
  • Ultra-Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse-Transcriptase Inhibitor (NRTI)-Treated Patients and NRTI-Naive Patients JOURNAL OF INFECTIOUS DISEASES Margeridon-Thermet, S., Shulman, N. S., Ahmed, A., Shahriar, R., Liu, T., Wang, C., Holmes, S. P., Babrzadeh, F., Gharizadeh, B., Hanczaruk, B., Simen, B. B., Egholm, M., Shafer, R. W. 2009; 199 (9): 1275-1285

    Abstract

    The dynamics of emerging nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI) resistance in hepatitis B virus (HBV) are not well understood because standard dideoxynucleotide direct polymerase chain reaction (PCR) sequencing assays detect drug-resistance mutations only after they have become dominant. To obtain insight into NRTI resistance, we used a new sequencing technology to characterize the spectrum of low-prevalence NRTI-resistance mutations in HBV obtained from 20 plasma samples from 11 NRTI-treated patients and 17 plasma samples from 17 NRTI-naive patients, by using standard direct PCR sequencing and ultra-deep pyrosequencing (UDPS). UDPS detected drug-resistance mutations that were not detected by PCR in 10 samples from 5 NRTI-treated patients, including the lamivudine-resistance mutation V173L (in 5 samples), the entecavir-resistance mutations T184S (in 2 samples) and S202G (in 1 sample), the adefovir-resistance mutation N236T (in 1 sample), and the lamivudine and adefovir-resistance mutations V173L, L180M, A181T, and M204V (in 1 sample). G-to-A hypermutation mediated by the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like family of cytidine deaminases was estimated to be present in 0.6% of reverse-transcriptase genes. Genotype A coinfection was detected by UDPS in each of 3 patients in whom genotype G virus was detected by direct PCR sequencing. UDPS detected low-prevalence HBV variants with NRTI-resistance mutations, G-to-A hypermutation, and low-level dual genotype infection with a sensitivity not previously possible.

    View details for DOI 10.1086/597808

    View details for Web of Science ID 000265035500007

    View details for PubMedID 19301976

  • Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations JOURNAL OF VIROLOGY Mitsuya, Y., Varghese, V., Wang, C., Liu, T. F., Holmes, S. P., Jayakumar, P., Gharizadeh, B., Ronaghi, M., Klein, D., Fessel, W. J., Shafer, R. W. 2008; 82 (21): 10747-10755

    Abstract

    T215 revertant mutations such as T215C/D/E/S that evolve from the nucleoside reverse transcriptase (RT) inhibitor mutations T215Y/F have been found in about 3% of human immunodeficiency virus type 1 (HIV-1) isolates from newly diagnosed HIV-1-infected persons. We used a newly developed sequencing method-ultradeep pyrosequencing (UDPS; 454 Life Sciences)--to determine the frequency with which T215Y/F or other RT inhibitor resistance mutations could be detected as minority variants in samples from untreated persons that contain T215 revertants ("revertant" samples) compared with samples from untreated persons that lack such revertants ("control" samples). Among the 22 revertant and 29 control samples, UDPS detected a mean of 3.8 and 4.8 additional RT amino acid mutations, respectively. In 6 of 22 (27%) revertant samples and in 4 of 29 control samples (14%; P = 0.4), UDPS detected one or more RT inhibitor resistance mutations. T215Y or T215F was not detected in any of the revertant or control samples; however, 4 of 22 revertant samples had one or more T215 revertants that were detected by UDPS but not by direct PCR sequencing. The failure to detect viruses with T215Y/F in the 22 revertant samples in this study may result from the overwhelming replacement of transmitted T215Y variants by the more fit T215 revertants or from the primary transmission of a T215 revertant in a subset of persons with T215 revertants.

    View details for DOI 10.1128/JVI.01827-07

    View details for Web of Science ID 000260109600041

    View details for PubMedID 18715933

  • Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitors RETROVIROLOGY Rhee, S., Liu, T. F., Kiuchi, M., Zioni, R., Gifford, R. J., Holmes, S. P., Shafer, R. W. 2008; 5

    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 enzyme. We therefore characterized the distribution of integrase variants among more than 1,800 published group M HIV-1 isolates from more than 1,500 integrase inhibitor (INI)-naïve individuals. Polymorphism rates equal or above 0.5% were found for 34% of the central core domain positions, 42% of the C-terminal domain positions, and 50% of the N-terminal domain positions. Among 727 ARV-naïve individuals in whom the complete pol gene was sequenced, integrase displayed significantly decreased inter- and intra-subtype diversity and a lower Shannon's entropy than protease or RT. All primary INI-resistance mutations with the exception of E157Q--which was present in 1.1% of sequences--were nonpolymorphic. Several accessory INI-resistance mutations including L74M, T97A, V151I, G163R, and S230N were also polymorphic with polymorphism rates ranging between 0.5% to 2.0%.

    View details for DOI 10.1186/1742-4690-5-74

    View details for Web of Science ID 000259485200001

    View details for PubMedID 18687142

  • Genomic interrogation of ancestral Mycobacterium tuberculosis from south India INFECTION GENETICS AND EVOLUTION Narayanan, S., Gagneux, S., Hari, L., Tsolaki, A. G., Rajasekhar, S., Narayanan, P. R., Small, P. M., Holmes, S., DeRiemer, K. 2008; 8 (4): 474-483

    Abstract

    Mycobacterium tuberculosis is a very important global pathogen. One quarter of the world's TB cases occur in India. The tuberculosis strains isolated from south Indian patients exhibit certain phenotypic characteristics like low virulence in guinea-pigs, resistance to isoniazid, thiophene-2-carboxylic acid hydrazide (TCH) and para-amino salicylic acid (PAS), and enhanced susceptibility to H2O2. Besides this, a large percentage of the isolates harbor only a single copy of IS 6110 which makes these strains distinct. Hence, we have studied the genotypic characteristics of these strains by using advanced techniques like Deletion Micro array, deletion PCR, allelic discrimination RT-PCR using several lineage specific markers and KatG G1388T (non-synonymous) polymorphism along with spoligotyping. The analysis of 1215 tuberculosis patient isolates from south India revealed that 85.2% belonged to the ancestral lineage of M. tuberculosis. Comparative whole-genome hybridization identified six new genomic regions within this lineage that were variably deleted.

    View details for DOI 10.1016/j.meegid.2007.09.007

    View details for Web of Science ID 000257001400012

    View details for PubMedID 18024233

  • The short-term regulation of foraging in harvester ants BEHAVIORAL ECOLOGY Gordon, D. M., Holmes, S., Nacu, S. 2008; 19 (1): 217-222
  • Dynamical bias in the coin toss SIAM REVIEW Diaconis, P., Holmes, S., Montgomery, R. 2007; 49 (2): 211-235
  • HIV-1 subtype B protease and reverse transcriptase amino acid covariation PLOS COMPUTATIONAL BIOLOGY Rhee, S., Liu, T. F., Holmes, S. P., Shafer, R. W. 2007; 3 (5): 836-843

    Abstract

    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 of amino acid covariation. We analyzed patterns of amino acid covariation in protease and RT sequences from more than 7,000 persons infected with HIV-1 subtype B viruses obtained from the Stanford HIV Drug Resistance Database (http://hivdb.stanford.edu). In addition, we examined the relationship between conditional probabilities associated with a pair of mutations and the order in which those mutations developed in viruses for which longitudinal sequence data were available. Patterns of RT covariation were dominated by the distinct clustering of Type I and Type II thymidine analog mutations and the Q151M-associated mutations. Patterns of protease covariation were dominated by the clustering of nelfinavir-associated mutations (D30N and N88D), two main groups of protease inhibitor (PI)-resistance mutations associated either with V82A or L90M, and a tight cluster of mutations associated with decreased susceptibility to amprenavir and the most recently approved PI darunavir. Different patterns of covariation were frequently observed for different mutations at the same position including the RT mutations T69D versus T69N, L74V versus L74I, V75I versus V75M, T215F versus T215Y, and K219Q/E versus K219N/R, and the protease mutations M46I versus M46L, I54V versus I54M/L, and N88D versus N88S. Sequence data from persons with correlated mutations in whom earlier sequences were available confirmed that the conditional probabilities associated with correlated mutation pairs could be used to predict the order in which the mutations were likely to have developed. Whereas accessory nucleoside RT inhibitor-resistance mutations nearly always follow primary nucleoside RT inhibitor-resistance mutations, accessory PI-resistance mutations often preceded primary PI-resistance mutations.

    View details for DOI 10.1371/journal.pcbi.0030087

    View details for Web of Science ID 000249105100007

    View details for PubMedID 17500586

  • Down-regulation of the interferon signaling pathway in T lymphocytes from patients with metastatic melanoma PLOS MEDICINE Critchley-Thorne, R. J., Yan, N., Nacu, S., Weber, J., Holmes, S. P., Lee, P. P. 2007; 4 (5): 897-911

    Abstract

    Dysfunction 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.To gain insights into the molecular mechanisms of immune dysfunction in cancer, gene expression profiles of pure sorted peripheral blood lymphocytes from 12 patients with melanoma were compared to 12 healthy controls. Of 25 significantly altered genes in T cells and B cells from melanoma patients, 17 are interferon (IFN)-stimulated genes. These microarray findings were further confirmed by quantitative PCR and functional responses to IFNs. The median percentage of lymphocytes that phosphorylate STAT1 in response to interferon-alpha was significantly reduced (Delta = 16.8%; 95% confidence interval, 0.98% to 33.35%) in melanoma patients (n = 9) compared to healthy controls (n = 9) in Phosflow analysis. The Phosflow results also identified two subgroups of patients with melanoma: IFN-responsive (33%) and low-IFN-response (66%). The defect in IFN signaling in the melanoma patient group as a whole was partially overcome at the level of expression of IFN-stimulated genes by prolonged stimulation with the high concentration of IFN-alpha that is achievable only in IFN therapy used in melanoma. The lowest responders to IFN-alpha in the Phosflow assay also showed the lowest gene expression in response to IFN-alpha. Finally, T cells from low-IFN-response patients exhibited functional abnormalities, including decreased expression of activation markers CD69, CD25, and CD71; TH1 cytokines interleukin-2, IFN-gamma, and tumor necrosis factor alpha, and reduced survival following stimulation with anti-CD3/CD28 antibodies compared to controls.Defects in interferon signaling represent novel, dominant mechanisms of immune dysfunction in cancer. These findings may be used to design therapies to counteract immune dysfunction in melanoma and to improve cancer immunotherapy.

    View details for DOI 10.1371/journal.pmed.0040176

    View details for Web of Science ID 000246889700018

    View details for PubMedID 17488182

  • Unusual codon bias in vinyl chloride reductase genes of Dehalococcoides species APPLIED AND ENVIRONMENTAL MICROBIOLOGY McMurdie, P. J., Behrens, S. F., Holmes, S., Spormann, A. M. 2007; 73 (8): 2744-2747

    Abstract

    Vinyl chloride reductases (VC-RDase) are the key enzymes for complete microbial reductive dehalogenation of chloroethenes, including the groundwater pollutants tetrachloroethene and trichloroethene. Analysis of the codon usage of the VC-RDase genes vcrA and bvcA showed that these genes are highly unusual and are characterized by a low G+C fraction at the third position. The third position of codons in VC-RDase genes is biased toward the nucleotide T, even though available Dehalococcoides genome sequences indicate the absence of any tRNAs matching codons that end in T. The comparatively high level of abnormality in the codon usage of VC-RDase genes suggests an evolutionary history that is different from that of most other Dehalococcoides genes.

    View details for DOI 10.1128/AEM.02768-06

    View details for Web of Science ID 000246542400039

    View details for PubMedID 17308190

  • An interactive statistical image segmentation and visualization system MEDIVIZ 2007: 4TH INTERNATIONAL CONFERENCE MEDICAL INFORMATION VISUALISATION - BIOMEDICAL VISUALISATION, PROCEEDINGS Kapelner, A., Lee, P. R., Holmes, S. 2007: 81-86
  • Forager activation and food availability in harvester ants ANIMAL BEHAVIOUR Schafer, R. J., Holmes, S., Gordon, D. M. 2006; 71: 815-822
  • Constraints on Yukawa-type deviations from Newtonian gravity at 20 microns PHYSICAL REVIEW D Smullin, S. J., Geraci, A. A., Weld, D. M., Chiaverini, J., Holmes, S., Kapitulnik, A. 2005; 72 (12)
  • Profile of immune cells in axillary lymph nodes predicts disease-free survival in breast cancer PLOS MEDICINE Kohrt, H. E., Nouri, N., Nowels, K., Johnson, D., Holmes, S., Lee, P. P. 2005; 2 (9): 904-919

    Abstract

    While lymph node metastasis is among the strongest predictors of disease-free and overall survival for patients with breast cancer, the immunological nature of tumor-draining lymph nodes is often ignored, and may provide additional prognostic information on clinical outcome.We performed immunohistochemical analysis of 47 sentinel and 104 axillary (nonsentinel) nodes from 77 breast cancer patients with 5 y of follow-up to determine if alterations in CD4, CD8, and CD1a cell populations predict nodal metastasis or disease-free survival. Sentinel and axillary node CD4 and CD8 T cells were decreased in breast cancer patients compared to control nodes. CD1a dendritic cells were also diminished in sentinel and tumor-involved axillary nodes, but increased in tumor-free axillary nodes. Axillary node, but not sentinel node, CD4 T cell and dendritic cell populations were highly correlated with disease-free survival, independent of axillary metastasis. Immune profiling of ALN from a test set of 48 patients, applying CD4 T cell and CD1a dendritic cell population thresholds of CD4 > or = 7.0% and CD1a > or = 0.6%, determined from analysis of a learning set of 29 patients, provided significant risk stratification into favorable and unfavorable prognostic groups superior to clinicopathologic characteristics including tumor size, extent or size of nodal metastasis (CD4, p < 0.001 and CD1a, p < 0.001). Moreover, axillary node CD4 T cell and CD1a dendritic cell populations allowed more significant stratification of disease-free survival of patients with T1 (primary tumor size 2 cm or less) and T2 (5 cm or larger) tumors than all other patient characteristics. Finally, sentinel node immune profiles correlated primarily with the presence of infiltrating tumor cells, while axillary node immune profiles appeared largely independent of nodal metastases, raising the possibility that, within axillary lymph nodes, immune profile changes and nodal metastases represent independent processes.These findings demonstrate that the immune profile of tumor-draining lymph nodes is of novel biologic and clinical importance for patients with early stage breast cancer.

    View details for DOI 10.1371/journal.pmed.0020284

    View details for Web of Science ID 000232433600019

    View details for PubMedID 16124834

  • Rapid assessment of recognition efficiency and functional capacity of antigen-specific T-cell responses JOURNAL OF IMMUNOTHERAPY Kohrt, H. E., Shu, C. T., Stuge, T. B., Holmes, S. P., Weber, J., Lee, P. P. 2005; 28 (4): 297-305

    Abstract

    It is increasingly recognized that cells within an antigen-specific CD8 T-cell population may be diverse in recognition efficiency for target, which may significantly affect the overall efficacy of the response in clinical settings such as viral infections and cancer. CD8 T cells with seemingly identical antigen specificity, particularly those elicited by cancer vaccines, may be heterogeneous for sensitivity and recognition efficiency for the cognate peptide and functional state in vivo. Analysis of individual T-cell clones derived from an antigen-specific T-cell population would provide an accurate assessment of the overall response; however, this is time- and labor-intensive, preventing rapid and routine assessment of patient samples from clinical trials. By stimulating antigen-specific T cells that otherwise appear homogeneous on tetramer staining with graded amounts of cognate peptides, the authors show that individual cells downmodulate surface T-cell receptors (TCR) and thus lose tetramer reactivity with variable dynamics within the T-cell population. The dynamics of TCR downregulation represent an accurate assessment of an individual cell's antigen sensitivity, recognition efficiency, and relative functional state within an antigen-specific population and have direct correlation to killing capacity by chromium release as well as degranulation by CD107 mobilization. Furthermore, despite correlation of average T-cell function by all three techniques, TCR downregulation uncovered heterogeneity in T-cell responses after vaccination among patient samples directly ex vivo. When examined using this novel technique, antigen-specific T cells elicited by vaccination with heteroclitic peptides exhibited significantly different recognition efficiencies for the heteroclitic versus native peptides, translating into differences in functional responses. With advancing cancer vaccine trials, the capacity to detect and functionally characterize antigen-specific T-cell responses in detail is critical. Techniques, as presented here, that rapidly assess the overall antigen sensitivity, recognition efficiency, and functional status of patients' T-cell responses will guide future vaccine trials and immunotherapies.

    View details for Web of Science ID 000230219200004

    View details for PubMedID 16000947

  • Memory T cells have gene expression patterns intermediate between naive and effector PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Holmes, S., He, M., Xu, T., Lee, P. P. 2005; 102 (15): 5519-5523

    Abstract

    The biological basis underlying differentiation of naive (NAI) T cells into effector (EFFE) and memory (MEM) cells is incompletely understood. Furthermore, whether NAI T cells serially differentiate into EFFE and then MEM cells (linear differentiation) or whether they concurrently differentiate into either EFFE or MEM cells (parallel differentiation) remains unresolved. We isolated NAI, EFFE, and MEM CD8(+) T cell subsets from human peripheral blood and analyzed their gene expression by using microarrays. We identified 156 genes that strongly differentiate NAI, EFFE, and MEM CD8(+) T cells; these genes provide previously unrecognized markers to help identify each cell type. Using several statistical approaches to analyze and group the data (standard heat-map and hierarchical clustering, a unique circular representation, multivariate analyses based on principal components, and a clustering method based on phylogenetic parsimony analysis), we assessed the lineage relationships between these subsets and showed that MEM cells have gene expression patterns intermediate between NAI and EFFE T cells. Our analysis suggests a common differentiation pathway to an intermediate state followed by a split into EFFE or MEM cells, hence supporting the parallel differentiation model. As such, conditions under which NAI T cells are activated may determine the magnitude of both EFFE and MEM cells, which arise subsequently. A better understanding of these conditions may be very useful in the design of future vaccine strategies to maximize MEM cell generation.

    View details for DOI 10.1073/pnas.0501437102

    View details for Web of Science ID 000228376600042

    View details for PubMedID 15809420

  • Sequential Monte Carlo methods for statistical analysis of tables JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION Chen, Y. G., Diaconis, P., Holmes, S. R., Liu, J. S. 2005; 100 (469): 109-120
  • Error distribution for gene expression data STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY Purdom, E., Holmes, S. P. 2005; 4

    Abstract

    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 expression data much better than a normal distribution. The use of this distribution in a parametric bootstrap leads to more powerful tests as we show that the t-test is conservative in this setting. We propose a biological explanations for this distribution based on the Pareto distribution of the variables used to compute the log ratios.

    View details for Web of Science ID 000238478100022

    View details for PubMedID 16646833

  • Gene expression diversity among Mycobacterium tuberculosis clinical isolates MICROBIOLOGY-SGM Gao, Q., Kripke, K. E., Saldanha, A. J., Yan, W. H., Holmes, S., Small, P. M. 2005; 151: 5-14

    Abstract

    Intraspecies genetic diversity has been demonstrated to be important in the pathogenesis and epidemiology of several pathogens, such as HIV, influenza, Helicobacter and Salmonella. It is also important to consider strain-to-strain variation when identifying drug targets and vaccine antigens and developing tools for molecular diagnostics. Here, the authors present a description of the variability in gene expression patterns among ten clinical isolates of Mycobacterium tuberculosis, plus the laboratory strains H37Rv and H37Ra, growing in liquid culture. They identified 527 genes (15 % of those tested) that are variably expressed among the isolates studied. The remaining genes were divided into three categories based on their expression levels: unexpressed (38 %), low to undetectable expression (31 %) and consistently expressed (16 %). The expression categories were compared with functional categories and three biologically interesting gene lists: genes that are deleted among clinical isolates, T-cell antigens and essential genes. There were significant associations between expression variability and the classification of genes as T-cell antigens, involved in lipid metabolism, PE/PPE, insertion sequences and phages, and deleted among clinical isolates. This survey of mRNA expression among clinical isolates of M. tuberculosis demonstrates that genes with important functions can vary in their expression levels between strains grown under identical conditions.

    View details for Web of Science ID 000226352800002

    View details for PubMedID 15632420

  • Diversity and recognition efficiency of T cell responses to cancer PLOS MEDICINE Stuge, T. B., Holmes, S. P., Saharan, S., Tuettenberg, A., Roederer, M., Weber, J. S., Lee, P. P. 2004; 1 (2): 149-160

    Abstract

    Melanoma patients vaccinated with tumor-associated antigens frequently develop measurable peptide-specific CD8+ T cell responses; however, such responses often do not confer clinical benefit. Understanding why vaccine-elicited responses are beneficial in some patients but not in others will be important to improve targeted cancer immunotherapies.We analyzed peptide-specific CD8+ T cell responses in detail, by generating and characterizing over 200 cytotoxic T lymphocyte clones derived from T cell responses to heteroclitic peptide vaccination, and compared these responses to endogenous anti-tumor T cell responses elicited naturally (a heteroclitic peptide is a modification of a native peptide sequence involving substitution of an amino acid at an anchor residue to enhance the immunogenicity of the peptide). We found that vaccine-elicited T cells are diverse in T cell receptor variable chain beta expression and exhibit a different recognition profile for heteroclitic versus native peptide. In particular, vaccine-elicited T cells respond to native peptide with predominantly low recognition efficiency--a measure of the sensitivity of a T cell to different cognate peptide concentrations for stimulation--and, as a result, are inefficient in tumor lysis. In contrast, endogenous tumor-associated-antigen-specific T cells show a predominantly high recognition efficiency for native peptide and efficiently lyse tumor targets.These results suggest that factors that shape the peptide-specific T cell repertoire after vaccination may be different from those that affect the endogenous response. Furthermore, our findings suggest that current heteroclitic peptide vaccination protocols drive expansion of peptide-specific T cells with a diverse range of recognition efficiencies, a significant proportion of which are unable to respond to melanoma cells. Therefore, it is critical that the recognition efficiency of vaccine-elicited T cells be measured, with the goal of advancing those modalities that elicit T cells with the greatest potential of tumor reactivity.

    View details for DOI 10.1371/journal.pmed.0010028

    View details for Web of Science ID 000227378800015

    View details for PubMedID 15578105

  • Microarray analysis reveals differences in gene expression of circulating CD8+ T cells in melanoma patients and healthy donors CANCER RESEARCH Xu, T., Shu, C. T., Purdom, E., Dang, D., Ilsley, D., Guo, Y., Weber, J., Holmes, S. P., Lee, P. P. 2004; 64 (10): 3661-3667

    Abstract

    Circulating T cells from many cancer patients are known to be dysfunctional and undergo spontaneous apoptosis. We used microarray technology to determine whether gene expression differences exist in T cells from melanoma patients versus healthy subjects, which may underlie these abnormalities. To maximize the resolution of our data, we sort purified CD8(+) subsets and amplified the extracted RNA for microarray analysis. These analyses show subtle but statistically significant expression differences for 10 genes in T cells from melanoma patients versus healthy controls, which were additionally confirmed by quantitative real-time PCR analysis. Whereas none of these genes are members of the classical apoptosis pathways, several may be linked to apoptosis. To additionally investigate the significance of these 10 genes, we combined them into a classifier and found that they provide a much better discrimination between melanoma and healthy T cells as compared with a classifier built uniquely with classical apoptosis-related genes. These results suggest the possible engagement of an alternative apoptosis pathway in circulating T cells from cancer patients.

    View details for Web of Science ID 000221419100043

    View details for PubMedID 15150126

  • Bootstrapping phylogenetic trees: Theory and methods STATISTICAL SCIENCE Holmes, S. 2003; 18 (2): 241-255
  • Statistics for phylogenetic trees THEORETICAL POPULATION BIOLOGY Holmes, S. 2003; 63 (1): 17-32

    Abstract

    This paper poses the problem of estimating and validating phylogenetic trees in statistical terms. The problem is hard enough to warrant several tacks: we reason by analogy to rounding real numbers, and dealing with ranking data. These are both cases where, as in phylogeny the parameters of interest are not real numbers. Then we pose the problem in geometrical terms, using distances and measures on a natural space of trees. We do not solve the problems of inference on tree space, but suggest some coherent ways of tackling them.

    View details for Web of Science ID 000180151400002

    View details for PubMedID 12464492

  • A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes AMERICAN JOURNAL OF HUMAN GENETICS Cruciani, F., Santolamazza, P., Shen, P. D., Macaulay, V., Moral, P., Olckers, A., Modiano, D., Holmes, S., Destro-Bisol, G., Coia, V., Wallace, D. C., Oefner, P. J., Torroni, A., Cavalli-Sforza, L. L., Scozzari, R., Underhill, P. A. 2002; 70 (5): 1197-1214

    Abstract

    The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (PhiST=0.342), which appears to be partially related to the geography (PhiCT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (PhiST=0.332) and geographic (PhiCT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo-speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon.

    View details for Web of Science ID 000175012400010

    View details for PubMedID 11910562

  • Statistical problems involving permutations with restricted positions STATE OF THE ART IN PROBABILITY AND STATISTICS: FESTSCHRIFT FOR WILLEM R VAN ZWET Diaconis, P., Graham, R., Holmes, S. P. 2001; 36: 195-222
  • Analysis of a nonreversible Markov chain sampler ANNALS OF APPLIED PROBABILITY Diaconis, P., Holmes, S., Neal, R. M. 2000; 10 (3): 726-752
  • Matchings and phylogenetic trees PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Diaconis, P. W., Holmes, S. P. 1998; 95 (25): 14600-14602

    Abstract

    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 phylogenetic trees, and a way of enumerating all trees in a minimal step order. It is useful in randomized algorithms because it enables moves on the space of trees that make random optimization strategies "mix" quickly. It also promises a generalization to intermediary trees when data are not decisive as to their choice of tree, and a new way of constructing Bayesian priors on tree space.

    View details for Web of Science ID 000077436700005

    View details for PubMedID 9843935

  • The next linear collider test accelerator's rf pulse compression and transmission systems PROCEEDINGS OF THE 1997 PARTICLE ACCELERATOR CONFERENCE, VOLS 1-3 Tantawi, S. G., Adolphsen, C., Holmes, S., LAVINE, T., Loewen, R. J., Nantista, C., Pearson, C., Pope, R., Rifkin, J., Ruth, R. D., Vlieks, A. E. 1998: 3192-3194
  • Are there still things to do in Bayesian statistics? PROBABILITY, DYNAMICS AND CAUSALITY Diaconis, P., Holmes, S. 1997: 5-18
  • GRAY CODES FOR RANDOMIZATION PROCEDURES STATISTICS AND COMPUTING Diaconis, P., Holmes, S. 1994; 4 (4): 287-302

Books and Book Chapters


  • Sampling from a Manifold Festchrift for Joe Eaton Diaconis, P., Holmes, S., Shahshahani, M. IMS. 2013
  • Stein's method: expository lectures and applications Institute of Mathematical Statistics Lecture Notes—Monograph Series. edited by Diaconis, P., Holmes, S. Inst. Math. Statist. . 2004

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