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
|