Papers

Methodology

• An interactive statistical image segmentation and visualization system. (2007).
  A. Kapelner, P. Lee, and S. Holmes. Medivis 00:81-86.
• Horseshoes in Multidimensional Scaling and Kernel Methods. (2007).
  With Diaconis, P. and Goel, S.
  To appear in: Annals of Applied Statistics [PDF]
• Multivariate Analysis: The French Way. (2007).
  Holmes, S.
  Probability and Statistics: Essays in Honor of David A. Freedman, Volume 56, Lecture Notes Monograph Series, IMS, Beachwood, OH. [PDF]
• Error Distribution for Gene Expression Data. (2005).
  Holmes, S. and Purdom, E.
  Statistical Applications in Genetics and Molecular Biology BEPress 4(1) Article No. 16. http://www.bepress.com/sagmb/vol4/iss1/art16
• Sequential Monte Carlo Methods for Statistical Analysis of Tables. (2005).
  Chen, Y., Diaconis, P., Holmes, S. and Liu, J.S.
  Journal of the American Statistical Association, 100(469):109-120. [PDF]
• Stein's Method for the Bootstrap. (2004).
  Holmes S. and Reinert G.
  Stein's Method: Expository Lectures and Applications.
  IMS, Lecture Notes and Monograph Series, IMS, Beachwood, Ohio. [PDF] To order the book click here
  
• Stein's method for birth and death chains. (2004). Holmes S.
  Stein's Method: Expository Lectures and Applications.
  IMS, Lecture Notes and Monograph Series, IMS, Beachwood, Ohio. [PDF] To order the book click here
• A Bayesian peek into Feller Volume I. (2002). Diaconis, P. and Holmes, S.
  Sankhya, vol. 64(33):820-841. [PDF]
• Analysis of a Non-reversible Markov Chain Sampler. (2001).
  Diaconis P., Holmes, S. and Neal, R.
  Ann. of Appl. Probab. 10(3):726-752. ps version
• Statistical Problems involving permutations with restricted positions. (1999).
  Diaconis P. Graham, R. and Holmes S.
  Festschrift in Honor of William van Zwet.Proc. Nat. Academy Sc., 93:7085-7090.
  ps version

Immunology

• Natural variation of HIV-1 group M integrase: Implications for a new class of antiretroviral inhibitor. (2008).
  Soo-Yon Rhee, Tommy F Liu, Mark Kiuchi, Rafael Zioni, Robert J Gifford, Susan P Holmes and Robert W Shafer. Retrovirology , 5:74 doi:10.1186/1742-4690-5-74 Retrovirology Journal link
• Unusual codon bias in vinyl chloride reductase genes of dehalococcoides species. (2007).
  P. J. McMurdie, S. F. Behrens, S. Holmes, and A. M. Spormann. Appl Environ Microbiol, 73(8):2744-7.
• Gene Expression Network Analysis, and Applications to Immunology. (2007).
  Nacu, S., Critchley-Thorne, R., Lee, P., and Holmes, S. Bioinformatics (23)850-858.
  [PDF]
• Down-Regulation of the Interferon Signaling Pathway in T Lymphocytes from Patients with Metastatic Melanoma. (2007).
  Critchley-Thorne, R.J., Holmes, S.P., Lee, P., Nacu,. S., Yan, N.
  PLoS Medicine 4(5):e176 doi:10.1371/journal.pmed.0040176
  PLOS Journal Article
• Profile of Immune Cells in Axillary Lymph Nodes Predicts Disease-Free Survival in Breast Cancer. (2005).
  Kohrt, H.E., Nouri, N., Nowels, K., Johnson, D., Holmes, S., and Lee, P. PLoS Medicine 2(9):e284 doi:10.1371/journal.pmed.0020284 PLoS Medicine
• Rapid assessment of recognition efficiency and functional capacity of antigen-specific T-cell responses. (2005).
  Kohrt, H.E., Shu, C.T., Stuge, T.B., Holmes, S.P., Weber, J., Lee, P.P.
  J. Immunother. 28(4):297-305 16000947. Journal of Immunotherapy
• HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation. (2007).
  Holmes, S., Liu, T.R., Rhee, S-Y., Shafer, R.W.
  PLoS Computational Biology 3(5):e87 doi:10.1371/journal.pcbi.0030087.
  PLos Computational Biology
• Memory T cells have gene expression patterns intermediate between naive and effector. (2005).
  Holmes, S., He, M., Xu,T., Lee, P.
  PNAS 102(15): 5519-5523. PNAS article
• Gene expression diversity among Mycobacterium tuberculosis clinical isolates. (2005).
  Gao, Q., Kripke, K.E., Saldanha, A.J., Yan, W., Holmes, S. and Small, P.M.
  Microbiology 151(1):5-14. [PDF]
• Microarray Analysis Reveals Differences in Gene Expression of Circulating CD8+
  T Cells in Melanoma Patients and Healthy Donors. (2004).
  Xu, T., Shu, C.T., Purdom, E., Dang, D., Ilsley, D., Guo,Y., Weber, J., Holmes, S., and Lee, P.
  Cancer Res. 64(10):3661-3667. Link to Cancer research
• Diversity and Recognition Efficiency of T Cell Responses to Cancer. (2004).
  Stuge, T., Holmes, S., Saharan, S., Tuettenberg, A., Roederer, M., Weber.J., Lee, P.
  PLoS Medicine 1(2): e28 PLOS Journal Article

Trees

• Bootstrapping Phylogenies. (2003). Holmes S.
  Statistical Science 18(2):241-255. [PDF] or [Euclid Link]
• Statistics for Phylogenetic Trees. (2002). Holmes, S.
  Theoretical Population Biology 63:17-32. [PDF]
• Geometry of the Space of Phylogenetic Trees. (2001).
  Billera, L.J., Holmes, S., and Vogtmann, K.
  Advances in Applied Mathematics 27(4):733-767.
  [PDF] ps version
• Phylogenies: An Overview. (1999).
  Holmes S.
  IMA series, Statistics and Genetics, 112:81-119 (ed. Halloran and Geisser), Springer Verlag, NY.
  ps version
• Matchings and Phylogenies. (1998).
  Diaconis P. and Holmes, S.
  Proc. Nat. Acad. Sciences, 95(25):14600-14602. PNAS link
• Bootstrap Confidence Levels for Phylogenetic Trees. (1996).
  Efron B., Halloran E., and Holmes S.
  Proc. Natl. Acad. Sci. USA. 93:13429. PNAS link

Ant Networks

• Forager activation and food availability in harvester ants. (2006)
  R. Schafer, S. Holmes, and D. Gordon. Animal Behaviour
• The Short-term Regulation of Foraging in Harvester Ants. (2008)
  With Gordon, D. Holmes, S., and Nacu, S. Behavioral Ecology 19(1):217-222; doi:10.1093/beheco/arm125
• How Site Fidelity Leads to Individual Differences in the Foraging Activity of Harvester Ants.
  With Beverly, B., McLendon, H., Nacu, S., Holmes, S., and Gordon, D. In Revision.

Physics

• Visualising Data. (2006). Holmes, S.
  Proceedings of Statistical Problems in Particle Physics, Astrophysics and Cosmology, Phystat, Oxford. [PDF]
• Constraints on Yukawa-type deviations from Newtonian gravity at 20 microns. (2005).
  Smullin, S. J., Geraci, A. A., Weld, D. M., Chiaverini, J., Holmes, S., Kapitulnik, A.
  Physical Review D, 72:122001. Sciatation link
• Dynamical Bias in the Coin Toss. (2007).
  Diaconis, P., Holmes, S. and Montgomery, R. SIAM Review archive 49(2):211-235.
  [PDF]