Statistics Department
VIGRE
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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
-
Fukuyama,J. , McMurdie, PJ, Dethfelsen, L., Relman, D. and Holmes, SP
(2012)
Comparisons of Distance Methods for Combining
Covariates and Abundances in Microbiome Studies
DPCOA PSB 2012, PDF
-
McMurdie, PJ and Holmes, SP
(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., 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., 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
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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
-
Pinter-Wollman, N., Wollman, R., Guetz, A., Holmes, S., & Gordon D.M. (2010).
The effect of individual variation on the structure and function of
interaction networks in harvester ants, Journal of the Royal Society Interface, April 13, 2011. link
to article doi: 10.1098/rsif.2011.0059
- Gordon, D.M., Guetz, A., Greene, M.J. & Holmes,
S. (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. & 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., & 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., & 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. & 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). APS: Physical
Review D
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