Statistics Department

VIGRE

Methodology   Genomics   Microbiome Studies   Immunology/Cancer   Trees   Ant Networks   Physics

Methodology
  • Diaconis, P., Fulman, J. & Holmes, S.P. (2013).
    Analysis of Casino Shelf Shuffling Machines. arXiv:1107.2961v1 [PDF].
    Annals of Applied Probability.
  • Chakerian, J. & Holmes, S.P. (2012).
    Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees, JCGS, 21(3):581-599.
    [Link to Journal] or arXiv 1006.1015 .
  • Diaconis, P., Holmes, S.P. & Shahashahani, M. (2012).
    Sampling from a Manifold. To appear: Festchrift for Joe Eaton [revised PDF]
  • De la Cruz, O. & Holmes, S.P. (2010).
    The Duality Diagram in Data Analysis: Examples of Modern Applications Annals of Applied Statistics 2011 Dec;5(4):2266-2277. PMID: 22282721
  • Bhattacharya, R. & Holmes, S.P. (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 SIAM link
  • Holmes, S.P., Kapelner, A. & Lee, PP. (2009).
    An interactive JAVA statistical image segmentation system: GemIdent.
    Journal of Statistical Software, 30(10).
    [Link to Journal] or [Local PDF]
  • Diaconis, P., Goel, S. & Holmes, S.P. (2008).
    Horseshoes in Multidimensional Scaling and Kernel Methods.
    Annals of Applied Statistics 2(3):777-807. [PDF]
  • Holmes, S.P. (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.P. & 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.P. & 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.P. & 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.P. (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.P. (2002).
    A Bayesian peek into Feller volume I.
    Sankhyā Series A, 64(3):820-841. [PDF]
  • Diaconis, P., Holmes, S.P. & 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.P. (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
  • Holmes, S. P. (1989)
    Unsing the bootstrap and the RV coefficient in the multivariate context
    Invited Paper, Data Analysis, Learning Symbolic and Numeric Knowledge, Edited by E. Diday, INRIA, Nova Sciences. [PDF version]

Genomics and Metagenomics
  • Rosen, M.J., Callahan, B.J., Fisher, D.S. & Holmes, S.P. (2012) Denoising PCR-Amplified Metagenome Data,
    BMC Bioinformatics, 13 (1) 283. BMC Bioinformatics Journal Link
  • Doherty, K.M., Nakka, P., King, B.M., Rhee, S-Y., Holmes, S.P., Shafer, R.W. & Radhakrishnan, M.L. (2011).
    A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes BMC Bioinformatics 12:477 PMID:22172090
  • McMurdie, P.J., Hug, L.A., Edwards, E.A., Holmes, S.P., & 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.P. & 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.P. & 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.J., Behrens, S., Müller, J., Göke, J., Ritalahti, K., Wagner, R., Goltsman, E., Lapidus, A., Holmes, S.P., 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.P., 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.P., 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.P. & 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
  • Rhee, S-Y., Liu, T.F. , Holmes, S.P. & 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.P., & 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.P. & 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.P. (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
  • McMurdie, P.J. & Holmes, S.P. (2013)
    phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLOS ONE, April 22, 2013, [Journal Link]
  • Holmes, S.P. & McMurdie, P.J. (2012).
    Statistical Analysis Challenges in the Microbiome. NAS-IOM: The Social Biology of Microbial Communities forum on Microbial Threats.
  • Fukuyama, J., McMurdie, P.J., Dethfelsen, L., Relman, D. and Holmes, S.P. (2012).
    Comparisons of Distance Methods for Combining Covariates and Abundances in Microbiome Studies DPCOA PSB 2012, PDF
  • McMurdie, P.J. and Holmes, S.P. (2012)
    PHYLOSEQ: A Bioconductor package for handling and analysis of highthroughput phylogenetic sequence data Phyloseq PSB 2012, PDF
  • Aronov, P., Luo, F., Plummer, N., Quan, Z., Susan Holmes, Hostetter, T. & Meyer, T.W. (2011).
    Colonic Contributions to Uremic Solutes, J Am Soc Nephrol. 2011 Sep;22(9):1769-76. Epub 2011 Jul 22.
  • Holmes, S.P., Alekseyenko, A., Timme, A., Nelson, T., Pasricha, P.J. & Spormann, A.M. (2011).
    Visualization and Statistical Comparisons of Microbial Communities using R packages on Phylochip Data, PSB 2011, PDF
  • Nelson, T.A., Holmes, S.P., Alekseyenko, A., Shenoy, M., DeSantis, T., Wu, C., Anderson, G.L., Sonnenburg, J., Pasricha, P.J. & Spormann, A.M. (2010).
    Phylochip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity. Neurogastroenterology & Motility , 23(2): 169 e42.

Immunology/Cancer
  • Yu H, Simons DL, Segall I, Carcamo-Cavazos V, Schwartz EJ, Yan N, Zuckerman NS, Dirbas FM,Johnson DL, Holmes, SP and Lee PP (2012) 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 7(12): e51239. doi:10.1371/journal.pone.0051239 Link to Journal Article
  • Leitner, A., Joachimiak, L.A., Bracher, A., Monkemeyer, L., Walzthoeni, T., Chen, B., Pechmann, S., Holmes, S.P.,Cong, Y., Ma, B., Ludtke, S., Chiu, W., Hartl, F., Aebersold, R. & Frydman, J. (2012). The Molecular Architectureof the Eukaryotic Chaperonin TRiC/CCT, Structure 20(5):814-825.
  • 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.P., Lee, P.P. (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 PMID: 20811638
  • Shahriar, R., Rhee, S-Y., Liu, T.F., Fessel, W.J., Scarsella, A., Towner, W., Holmes, S.P., 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.P. & Lee, PP. (2009).
    Impaired interferon signaling is a common immune defect in human cancer, PNAS 106(22):9010-9015.
  • Nacu, S., Critchley-Thorne, R., Lee, PP., & Holmes, S.P. (2007).
    Gene Expression Network Analysis and Applications to Immunology,
    Bioinformatics 23(7):850-858. [PDF] PMID:17267429
  • Critchley-Thorne, R.J., Holmes, S.P., Lee, PP., 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. PLOS Journal Article doi:10.1371/journal.pmed.0040176 PMID:17488182
  • Kohrt, H.E., Nouri, N., Nowels, K., Johnson, D., Holmes, S.P. & Lee, PP. (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 PMID:16124834
  • Kohrt, H.E., Shu, C.T., Stuge, T.B., Holmes, S.P., Weber, J., Lee, PP. (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.P., He, M., Xu,T., & Lee, PP. (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.P. & 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.P. & Lee, PP. (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.P., Saharan, S., Tuettenberg, A., Roederer, M., Weber.J., & Lee, PP. (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.P. (2013).
    Interval Graph Limits. Annals of Combinatorics 2013, Volume 17, Issue 1, pp 27-52.
    Journal Link     or arXiv: arXiv:1102.2841v1
  • Guetz, A. & Holmes, S.P. (2010).
    Adaptive importance sampling for network growth models, Annals of Operations Research,
    http://dx.doi.org/10.1007/s10479-010-0685-2.
  • Holmes, S.P., 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.P. (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.P. (2003).
    Bootstrapping Phylogentic Trees: Theory and Methods,
    Statistical Science, 18(2):241-255. [PDF] or [Euclid Link] doi:10.1214/ss/1063994979
  • Holmes, S.P. (2002).
    Statistics for Phylogenetic Trees,
    Theoretical Population Biology, 63(1):17-32. [PDF]
  • Billera, L.J., Holmes, S.P. & Vogtmann, K. (2001).
    Geometry of the Space of Phylogenetic Trees,
    Advances in Applied Mathematics, 27(4):733-767.
    [PDF] ps version
  • Holmes, S.P. (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.P. (1998).
    Matchings and Phylogenies, Proc. Natl. Acad. Sciences, 95(25):14600-14602. PNAS link
  • Efron, B., Halloran, E. & Holmes, S.P. (1996).
    Bootstrap Confidence Levels for Phylogenetic Trees,
    Proc. Natl. Acad. Sci. USA, 93(14):7085-7090. PNAS link

Ant Networks
  • Pinter-Wollman, N. ,Gordon, DM and Holmes, S.P. (2012) Nest site and weather affect the personality of harvester ant colonies Behavioral Ecology (2012) 23(5): 1022-1029, doi:10.1093/beheco/ars066 [link to journal]
  • Pinter-Wollman, N., Wollman, R., Guetz, A., Holmes, S.P., & Gordon D.M. (2011).
    The effect of individual variation on the structure and function of interaction networks in harvester ants, J. R. Soc. Interface, April 13, 2011, 8: 15621573. link to article doi: 10.1098/rsif.2011.0059
  • Gordon, D.M., Guetz, A., Greene, M.J. & Holmes, S.P. (2011).
    Colony variation in the collective regulation of foraging by harvester ants, Behavioral Ecology, February 2011. doi:10.1093/beheco/arq218
  • Beverly, B., McLendon, H., Nacu, S., Holmes, S.P. & Gordon, D.M. (2009).
    How Site Fidelity Leads to Individual Differences in the Foraging Activity of Harvester Ants,
    Behavioral Ecology, 20(3):633-638. doi:10.1093/beheco/arp041
  • Gordon, D.M., Holmes, S.P., & Nacu, S. (2008).
    The Short-term Regulation of Foraging in Harvester Ants,
    Behavioral Ecology 19(1):217-222. doi:10.1093/beheco/arm125
  • Schafer, R., Holmes, S.P., & Gordon, D.M. (2006).
    Forager activation and food availability in harvester ants,
    Animal Behaviour, 71(4):815-822. doi:10.1016/j.anbehav.2005.05.024 [PDF].

Physics
  • Diaconis, P., Holmes, S.P. & Montgomery, R. (2007).
    Dynamical Bias in the Coin Toss, SIAM Review 49(2):211-235.
    [PDF]
  • Holmes, S.P. (2006).
    Visualising for Physicists
    Proceedings of PHYSTAT 2005. Statistical Problems in Particle Physics, Astrophysics and Cosmology, Phystat, Oxford. Imperial College Press, 197-207. [PDF]
  • Smullin, S. J., Geraci, A. A., Weld, D. M., Chiaverini, J., Holmes, S.P., & Kapitulnik, A. (2005).
    Constraints on Yukawa-type deviations from Newtonian gravity at 20 microns,
    Physical Review D 72(12):2001(20). APS: Physical Review D

  © 2011 Susan Holmes