Statistics Department

Methodology   Genomics   Microbiome Studies   Immunology   Trees   Ant Networks   Physics

Methodology
  • Holmes, S. (2017) Statistical Proof? The problem of irreproducibility. Bulletin of the American Mathematics Society, October 2017.
    [Journal link]
  • Kris Sankaran and Susan Holmes (2017)
    Interactive Visualization of Hierarchically Structured Data
    Paper: [ JCGS link ] [ preprint ] Software: [ On github ] Video [ Youtube ]
  • Lan Huong Nguyen and Susan Holmes (2017)
    Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations. BMC Bioinformatics, August, 2017. [BMC journal link]
  • Julia Fukuyama , Laurie Rumker , Kris Sankaran , Pratheepa Jeganathan, Les Dethlefsen, David A. Relman , Susan P. Holmes (2017)
    Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
    PLOS Computational Biology, August 2017. [Plos Comp Bio Link]
  • Ren, B., Bacallado, S., Favaro, S., Holmes, S. and Trippa, L., (2017).
    Bayesian Nonparametric Ordination for the Analysis of Microbial Communities. JASA, [Journal link], earlier arXiv preprint
    arXiv:1601.05156. [PDF file]
  • Miolane, N, Holmes, SP, Pennec, X.
    Template shape estimation: correcting an asymptotic bias.
    arXiv:1610.01502 (2016). [PDF file]
    to appear in SIAM Imaging Science, 2017.
  • Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP.
    Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Research. 2016;5. Link to journal
    Github repo
  • Bacallado, S , Diaconis, P and Holmes, S (2015).
    De Finetti Priors using Markov chain Monte Carlo computations. Statistics and Computing, published May 2015,
    [PDF file]
  • Sankaran, K and Holmes, S (2014).
    structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data Journal of Statistical Software, Vol. 59, Issue 13, Sep 2014
    JSS link
  • Josse, J. and Holmes, S. (2014).
    Measures of dependence between random vectors and tests of independence: A survey.
     arXiv:1307.7383 [PDF]
  • McMurdie, PJ and Holmes, S (2013).
    Waste not, want not: Why Rarefying Microbiome Data is Inadmissible.
    PLOS Computational Biology, Methods Section.
  • Diaconis, P., Holmes, S.P. & Shahashahani, M. (2013).
    Sampling from a Manifold. To appear: Festchrift for Joe Eaton, IMS, G. Jones and X. Shen, Eds, [revised PDF] Full volume
  • Diaconis, P., Fulman, J. & Holmes, S.P. (2013).
    Analysis of Casino Shelf Shuffling Machines.
    arXiv:1107.2961v1 [PDF]
    Annals of Applied Probability,Volume 23, Number 4 (2013), 1692-1720.
  • 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 .
  • 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 [PDF]
  • 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)
    Using 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
  • Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han A.W., Johnson, A.J. & Holmes, S.P. (2016) DADA2: High-resolution sample inference from Illumina amplicon data. ,
    Nature Methods, vol. 13, 581, May 23. Nature Methods Journal Link
    bioRxiv link
  • Sahoo, MK, Lefterova,MI., Yamamoto, F and Waggoner,JJ, Chou,S ,Holmes,SP , Anderson, MW and Pinsky, BA (2013) Detection of Cytomegalovirus Drug Resistance Mutations by Next-Generation Sequencing Journal of Clinical Microbiology , online ahead of print, Aug 23, 2013. Journal abstract
  • 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
  • Anastassia Gorvitovskaia, Susan P Holmes, Susan M. Huse (2016)
    Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle
    Microbiome, April, 2016, 4:16, DOI: 10.1186/s40168-016-0160-7
    [article]
  • Bik, EM, Costello, EK Switzer, AD Callahan, BJ, Holmes, SP, Wells, RS, Carlin, KP, Jensen, ED, Venn-Watson,S & Relman,DA (2016)
    Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea
    Nature Communications 7, Article number: 10516 doi:10.1038/ncomms10516
    [pdf article]
  • DB DiGiulio, BJ Callahan, PJ McMurdie, EK Costello, DJ Lyell, A Robaczewska, CL Sun, DSA Goltsman, RJ Wong, G Shaw, DK Stevenson,
    SP Holmes, and DA Relman
    Temporal and spatial variation of the human microbiota during pregnancy PNAS 2015 ; published ahead of print August 17, 2015, doi:10.1073/pnas.1502875112
    [Journal PDF with Supplementary]
    [Reproducible Research: Rmd files and RData]
    [Permanent url link: Stanford Digital Repository]
  • McMurdie, P.J. & Holmes, S.P. (2014)
    Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking Bioinformatics, 2014, [Journal open-access link]
  • Yan, M. , Pamp, S., Fukuyama, J., Hwang, P., Cho, D-Y, Holmes, S. and Relman, DA. (2013)
    Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage
    Cell Host and Microbe, Vol 14, pp 631--640. [Journal Abstract]
  • Purna C. Kashyap, Angela Marcobal, Luke K. Ursell, Samuel A. Smits, Erica D. Sonnenburg, Elizabeth K. Costello, Steven K. Higginbottom, Steven E. Domino, Susan P. Holmes, David A. Relman, Rob Knight, Jeffrey I. Gordon, and Justin L. Sonnenburg (2013)
    Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota
    PNAS; published ahead of print September 23, 2013, doi:10.1073/pnas.1306070110 [Journal Link]
  • 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 and HIV
  • Alison F Feder, Soo-Yon Rhee, Susan P Holmes, Robert W Shafer, Dmitri A Petrov and Pleuni S Pennings. (2016)
    More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1
    [PDF file] [Youtube Video Explaining Results by Alison Feder]
  • Strauss-Albee, Dara M., Julia Fukuyama, Emily C. Liang, Yi Yao, Justin A. Jarrell, Alison L. Drake, John Kinuthia , Ruth R. Montgomery, Grace John-Stewart, Susan Holmes and Catherine A. Blish Human NK cell repertoire diversity reflects immune experience and correlates with viral susceptibility. Science translational medicine 7, no. 297 (2015): 297ra115-297ra115. Link to Journal
  • Alexander W. Kay, Julia Fukuyama, Natali Aziz, Cornelia L. Dekker, Sally Mackey, Gary E. Swan, Mark M. Davis, Susan Holmes, and Catherine A. Blish Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy PNAS 2014 ; published ahead of print September 22, 2014, doi:10.1073/pnas.1416569111 Link to PDF at PNAS
  • 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
  • Pleuni S. Pennings, Susan P. Holmes and Robert W. Shafer (2013)
    HIV-1 Transmission Networks in a Small World ,
    Journ. Infectious Diseases
    Journal Link
  • 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 Phylogenetic 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., Bala, A., Merrell, A., Queirolo, J., Stumpe, M.C., Holmes, S., Gordon, D.M.
    Harvester ants use interactions to regulate forager activation and availability.
    Animal Behaviour volume 86, issue 1, year 2013, pp. 197 - 207
  • 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/rs066 [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