Methodology

• Holmes, S.P., Kapelner, A. and 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.P. (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, 219-233
  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., and 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.
  Sankhya. vol. 64(33):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. and 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

Immunology

• McMurdie, P., Behrens, S., Müller, J., Göke, J., Ritalahti, K., Wagner, R., Goltsman, E., Lapidus, A., Holmes, S., Löffler, F. & Spormann, A. (2009). Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet vol. 5 (11) pp. e1000714 PLoS Genetics [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., Robert J Gifford, 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.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
• 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. and 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. (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. (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. and Lee, 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

• Holmes, S., Diaconis, P. and Janson, S. (2009).
  Threshold Graph Limits and Random Threshold Graphs.
  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

• Beverly, B., McLendon, H., Nacu, S., Holmes, S. & 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. and 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. and Gordon, D.M. (2006).
  Forager activation and food availability in harvester ants.
  Animal Behaviour, 71(4):815-822. [PDF]. doi:10.1016/j.anbehav.2005.05.024

Physics

• Diaconis, P., Holmes, S. & Montgomery, R. (2007).
  Dynamical Bias in the Coin Toss.
  SIAM Review 49(2):211-235.
  [PDF]
• Holmes, S. (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., & Kapitulnik, A. (2005).
  Constraints on Yukawa-type deviations from Newtonian gravity at 20 microns.
  Physical Review D 72(12):2001(20). Physical Review A link