Statistics Department

VIGRE

Methodology   Genomics   Microbiome Studies   Immunology/Cancer   Trees   Ant Networks   Physics

Methodology
  • Diaconis, P., Holmes, S. & Shahashahani, M. (2011).
    Sampling from a Manifold. To appear: Festchrift for Joe Eaton [PDF]
  • Diaconis, P., Fulman, J. & Holmes, S. (2011).
    Analysis of Casino Shelf Shuffling Machines. arXiv:1107.2961v1 [PDF] submitted
  • De la Cruz, O. & Holmes, S. (2010).
    The Duality Diagram in Data Analysis: Examples of Modern Applications Annals of Applied Statistics
  • Chakerian, J. & Holmes, S. (2010).
    Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees, technical report, Stanford University. arXiv 1006.1015 To appear in JCGS
  • Bhattacharya, R. & Holmes, S. (2010).
    An Exposition of Götze's Estimation of the Rate of Convergence in the  Multivariate Central Limit Theorem, technical report, Stanford University arXiv pdf,
    Chapter 7: An Application of Stein's Method. In Bhattacharya, R.N. & Rao, R.R. (Eds.), Normal Approximation and Asymptotic Expansions (p. 260). Philadelphia, Pennsylvania: SIAM, 2010. ISBN13: 9780898718973
  • Holmes, S., Kapelner, A. & Lee, P.P. (2009).
    An interactive JAVA statistical image segmentation system: GemIdent.
    Journal of Statistical Software, 30(10). [PDF]
  • Diaconis, P., Goel, S. & Holmes, S. (2008).
    Horseshoes in Multidimensional Scaling and Kernel Methods.
    Annals of Applied Statistics 2(3):777-807. [PDF]
  • Holmes, S. (2007).
    Multivariate Analysis: The French Way.
    Probability and Statistics: Essays in Honor of David A. Freedman, Volume 2, pp219-233
    IMS Lecture Notes - Monograph Series, IMS, Beachwood, OH. [PDF]
  • Chen, Y., Diaconis, P., Holmes, S. & Liu, J.S. (2005).
    Sequential Monte Carlo Methods for Statistical Analysis of Tables.
    Journal of the American Statistical Association, 100(469):109-120. [PDF]
  • Holmes, S. & Reinert, G. (2004).
    Stein's Method for the Bootstrap.
    in Stein's Method: Expository Lectures and Applications.
    IMS Lecture Notes - Monograph Series, IMS, Beachwood, Ohio. [PDF]
    To order the book click here
  • Stein, C., Diaconis, P., Holmes, S. & Reinert, G. (2004).
    Use of Exchangeable Pairs in the Analysis of Simulations.
    in Stein's Method: Expository Lectures and Applications,
    IMS Lecture Notes - Monograph Series, IMS, Beachwood, Ohio. [PDF]
    To order the book click here
  • Holmes, S. (2004).
    Stein's method for birth and death chains.
    Stein's Method: Expository Lectures and Applications,
    IMS Lecture Notes - Monograph Series, IMS, Beachwood, Ohio. [PDF]
    To order the book click here doi:10.1214/lnms/1196283799
  • Diaconis, P. & Holmes, S. (2002).
    A Bayesian peek into Feller volume I.
    Sankhyā Series A, 64(3):820-841. [PDF]
  • Diaconis, P., Holmes, S. & Neal, R. (2001).
    Analysis of a Non-reversible Markov Chain Sampler.
    Ann. of Appl. Probab., 10(3):726-752. ps version doi:10.1214/aoap/1019487508
  • Diaconis, P. Graham, R. & Holmes, S. (1999).
    Statistical Problems involving permutations with restricted positions.
    Festschrift in Honor of William van Zwet, University of Leiden, March 23-26, 1999
    (Beachwood, OH: Institute of Mathematical Statistics, 2001), 195-222. ps version

Genomics and Metagenomics
  • McMurdie, P., Hug, L.A., Edwards, E.A., Holmes, S., & Spormann, A.M. (2011).
    Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides BMC Genomics, 12(287):1471-2164. PMID: 21635780 PMCID: PMC3146451
  • Reuman, E.C., Margeridon-Thermet, S.,Caudill, H.B., Liu, T., Borroto-Esoda, K., Svarovskaia, E.S., Holmes, S. & Shafer, R.W. (2010).
    A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. Bioinformatics, Dec 1;26(23):2929-32. Epub 2010 Oct 11.
  • Reuman, E.C., Rhee, S.Y., Holmes, S. & Shafer, R.W. (2010).
    Constrained Patterns of Covariation and Clustering of Non-Nucleoside RT Inhibitor HIV-1 Resistance Mutations, J Antimicrob Chemother., 65(7):1477-85.
  • McMurdie, P., Behrens, S., Müller, J., Göke, J., Ritalahti, K., Wagner, R., Goltsman, E., Lapidus, A., Holmes, S., Löffler, F. & Spormann, A.M. (2009).
    Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genetics 5(11):e1000714 [PDF]
  • Margeridon-Thermet, S., Shulman, N.S., Ahmed, A., Shahriar, R., Liu,T., Wang, C., Holmes, S., Babrzadeh, F., Gharizadeh, B., Hanczaruk, B., Simen, B.B., Egholm, M., & Shafer, R.W. (2009).
    Ultra-deep pyrosequencing of hepatitis B Virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naïve patients.
    J Infect Dis. 2009 May 1; 199(9):1275-85. PMID: 19301976 [PubMed - in process] PubMed link
  • Mitsuya Y., Varghese V., Wang, C., Liu, T.F., Holmes, S., Jayakumar P., Gharizadeh B., Ronaghi M., Klein D., Fessel W.J. & Shafer R.W. (2008).
    Minority human immunodeficiency virus type 1 variants in antiretroviral-naïve persons with reverse transcriptase codon 215 revertant mutations.
    J Virol. 2008 Nov 82(21):10747-55. PMCID: PMC2573178
  • Rhee, S-Y., Liu, T.F., Kiuchi, M., Zioni R., Gifford, R.J., Holmes, S. & Shafer, R.W. (2008).
    Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitor.
    Retrovirology, 5:74. doi:10.1186/1742-4690-5-74 Retrovirology Journal link
  • Holmes, S., Liu, T.F., Rhee, S-Y., & Shafer, R.W. (2008).
    HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation.
    PLoS Computational Biology 3(5):e87. doi:10.1371/journal.pcbi.0030087.
    PLos Computational Biology
  • Narayanan, S., Gagneux, S. , Hari, L. , Tsolaki, A., Rajasekhar, S., Narayanan, S.N., Small, P., Holmes, S., & DeRiemer, K. (2007).
    Genomic interrogation of ancestral Mycobacterium tuberculosis from south India.
    Infect., Genet. and Evol. 8(4):474-483. doi:10.1016/j.meegid.2007.09.007
  • McMurdie, P.J., Behrens, S.F., Holmes, S. & Spormann, A.M. (2007).
    Unusual codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides species.
    Appl. Environ. Microbiol., 73(8):2744-7. AEM link doi:10.1128/AEM.02768-06
  • Purdom, E., & Holmes, S. (2005).
    Error Distribution for Gene Expression Data, Statistical Applications in Genetics and Molecular Biology, 4(1) Article 16.
    [PDF] DOI: 10.2202/1544-6115.1070 Available at: http://www.bepress.com/sagmb/vol4/iss1/art16

Microbiome Studies

Immunology/Cancer

  • Setiadi, A.F., Ray, N.C., Kohrt, H.E., Kapelner, A., Carcamo-Cavazos, V., Levic, E., Yadegarynia, S., van der Loos, C., Schwartz, E., Holmes, S., Lee, .PP. (2010).
    Quantitative, Architectural Analysis of Immune Cell Subsets in Tumor-Draining Lymph Nodes from Breast Cancer Patients and Healthy Lymph Nodes
    PLoS ONE 5(8): e12420. doi:10.1371/journal.pone.0012420
    PLOS ONE Journal Article
  • Shahriar, R., Rhee, S.-Y., Liu, T.F., Fessel, W.J., Scarsella, A., Towner, W., Holmes, S., Zolopa, A.R., & Shafer, R.W. (2009).
    Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations. Antimicrob. Agents Chemother., 53(11):4869-78.
  • Critchley-Thorne, R., 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).
    Impaired interferon signaling is a common immune defect in human cancer, PNAS 106(22):9010-9015.
  • Nacu, S., Critchley-Thorne, R., Lee, P., & Holmes, S. (2007).
    Gene Expression Network Analysis and Applications to Immunology,
    Bioinformatics 23(7):850-858.
    [PDF]
  • Critchley-Thorne, R.J., Holmes, S., Lee, P., Nacu,. S., & Yan, N. (2007).
    Down-Regulation of the Interferon Signaling Pathway in T Lymphocytes from Patients with Metastatic Melanoma,
    PLoS Medicine 4(5):e176. doi:10.1371/journal.pmed.0040176
    PLOS Journal Article
  • Kohrt, H.E., Nouri, N., Nowels, K., Johnson, D., Holmes, S. & Lee, P. (2005).
    Profile of Immune Cells in Axillary Lymph Nodes Predicts Disease-Free Survival in Breast Cancer,
    PLoS Medicine 2(9):e284. doi:10.1371/journal.pmed.0020284 PLoS Medicine
  • Kohrt, H.E., Shu, C.T., Stuge, T.B., Holmes, S., Weber, J., Lee, P.P. (2005).
    Rapid assessment of recognition efficiency and functional capacity of antigen-specific T-cell responses,
    J. Immunother. 28(4):297-305 16000947. Journal of Immunotherapy
  • Holmes, S., He, M., Xu,T., & Lee, P.P. (2005).
    Memory T cells have gene expression patterns intermediate between naïve and effector,
    PNAS 102(15): 5519-5523. PNAS article
  • Gao, Q., Kripke, K.E., Saldanha, A.J., Yan, W., Holmes, S. & Small, P.M. (2005).
    Gene expression diversity among Mycobacterium tuberculosis clinical isolates,
    Microbiology 151(1):5-14. [PDF] doi 10.1099/mic.0.27539-0
  • Xu, T., Shu, C.T., Purdom, E., Dang, D., Ilsley, D., Guo,Y., Weber, J., Holmes, S. & Lee, P.P. (2004).
    Microarray Analysis Reveals Differences in Gene Expression of Circulating CD8+
    T Cells in Melanoma Patients and Healthy Donors    ,
    Cancer Res. 64(10):3661-3667. Link to Cancer research
  • Stuge, T., Holmes, S., Saharan, S., Tuettenberg, A., Roederer, M., Weber.J., & Lee, P. (2004).
    Diversity and Recognition Efficiency of T Cell Responses to Cancer,
    PLoS Medicine 1(2): e28 PLOS Journal Article

Trees & Networks

  • Diaconis, P., Janson, S., & Holmes, S. (2011).
    Interval Graph Limits. To appear: Annals of Combinatorics.     arXiv:1102.2841v1
  • Guetz, A. & Holmes, S. (2010).
    Adaptive importance sampling for network growth models, Annals of Operations Research,
    http://dx.doi.org/10.1007/s10479-010-0685-2.
  • Holmes, S., Diaconis, P. & Janson, S. (2008).
    Threshold Graph Limits and Random Threshold Graphs, Internet Mathematics, 5(3):267-320.
    arXiv:0908.2448v1 [math.CO] [PDF],
  • Holmes, S. (2007).
    Statistical Approach to Tests Involving Phylogenies,
    In O. Gascuel. (ed.), Mathematics of Evolution and Phylogeny,
    Edited by Oxford University Press, USA. [PDF]
  • Holmes, S. (2003).
    Bootstrapping Phylogentic Trees: Theory and Methods,
    Statistical Science, 18(2):241-255. [PDF] or [Euclid Link] doi:10.1214/ss/1063994979
  • Holmes, S. (2002).
    Statistics for Phylogenetic Trees,
    Theoretical Population Biology, 63(1):17-32. [PDF]
  • Billera, L.J., Holmes, S. & Vogtmann, K. (2001).
    Geometry of the Space of Phylogenetic Trees,
    Advances in Applied Mathematics, 27(4):733-767.
    [PDF] ps version
  • Holmes, S. (1999).
    Phylogenies: An Overview,
    IMA series, Statistics and Genetics, 112:81-119 (ed. Halloran and Geisser), Springer Verlag, NY.
    ps version
  • Diaconis, P. & Holmes, S. (1998).
    Matchings and Phylogenies, Proc. Natl. Acad. Sciences, 95(25):14600-14602. PNAS link
  • Efron, B., Halloran, E. & Holmes, S. (1996).
    Bootstrap Confidence Levels for Phylogenetic Trees,
    Proc. Natl. Acad. Sci. USA, 93(14):7085-7090. PNAS link

Ant Networks

Physics

  © 2011 Susan Holmes