PhD and Master thesis

• Bootsma, M. C. J. (2005) Mathematical studies of the dynamics of antibiotic resistance Ph.D. thesis (Utrecht Univ., Utrecht, The Netherlands). pdf
  
• M.C.J. Bootsma. The influence of impurities on equilibrium crystal shapes. Master's thesis, Utrecht University, 2001. pdf

Articles

• M.C.J.Bootsma, O.Diekmann, and M.J.M. Bonten. Controlling methicillin-resistant Staphylococcus aureus: Quantifying the effects of interventions and rapid diagnostic testing (2006). Proc. Natl. Acad. Sci. USA 103, 5620-5625 Article (pdf), Supplementary material
  
• Marc J.M. Bonten, Jan Kluytmans, Anne Marie de Smet, Martin Bootsma, and Arno Hoes. Correspondence: Selective decontamination of digestive tract in intensive care. Lancet, 362:2118-2119, 2003. pdf
  
• H. Grundmann and M. Bootsma. Predicting the success of preventive measures in infection control using mathematical models. Nederlands Tijdschrift Voor Medische Microbiologie, 12:14-16, 2005. pdf
  
• S. Nijssen, M.C.J. Bootsma, and M.J.M. Bonten. Potential confounding in evaluating infection control interventions in hospital settings: changing antibiotic prescription. Clinical Infectious Diseases, 43:616-623, 2006. pdf
• M. C. J. Bootsma and O. Diekmann. Comment on "linking population level models with growing networks: A class of epidemic models". Phys. Rev. E, 74:018101, 2006. pdf
• M.C.J. Bootsma, Bonten, M.J.M. and Nijssen, A.C. Fluit, and O. Diekmann. An algorithm to estimate the importance of bacterial acquisition routes in hospital settings. Am J Epidemiol, 2007; doi: 10.1093/aje/kwm149 pdf Preprint
• M.C.J. Bootsma, N.M. Ferguson. The effect of public health measures on the 1918 influenza pandemic in US cities. Proc. Natl. Acad. Sci. USA. 2007; 104:7588-7593. Article (pdf), Supplementary material
  
• P. Trapman, M.C.J. Bootsma. A useful relationship between epidemiology and queueing theory: the distribution of the number of infectives at the moment of the first detection. Math. Biosci. 2009; 219: 15-22 arXiv preprint or MBS site
• M.W. Wassenberg, M.C. Bootsma, A. Troelstra, J.A. Kluytmans, M.J. Bonten. Transmissibility of livestock-associated methicillin-resistant Staphylococcus aureus (ST398) in Dutch hospitals. Clin Microbiol Infect. 2010. Clin Microbiol Infect. site
• M.C.J. Bootsma, M.W.M. Wassenberg, P. Trapman, M.J.M. Bonten. The nosocomial transmission rate of Animal-associated ST398 Methicillin-resistant Staphylococcus aureus.J. R. Soc. Interface. 2011:8 578-84.
• R. van Mansfeld, I. Jongerden, M. Bootsma, A. Buiting, M. Bonten, R. Willems. The population genetics of Pseudomonas aerigunosa isolates from different patient populations exhibit high-level host-specificity. Accepted for PLoS One, 2010
• Anne Marie G A de Smet, Jan A J W Kluytmans, Hetty E M Blok, Ellen M Mascini, Robin F J Benus, Alexandra T Bernards, Ed J Kuijper, Maurine A Leverstein-van Hall, Arjan R Jansz, Bartelt M de Jongh, Gerard J van Asselt, Ine H M E Frenay, Steven F T Thijsen, Simon N M Conijn, Jan A Kaan, Jan P Arends, Patrick D J Sturm, Martin C J Bootsma, Marc J M Bonten. Selective digestive tract decontamination and selective oropharyngeal decontamination and antibiotic resistance in patients in intensive-care units: an open-label, clustered group-randomised, crossover study. The Lancet Infectious Diseases. Early Online Publication, 21 March 2011 doi:10.1016/S1473-3099(11)70035-4
• Gijs Hubben, Martin Bootsma, Michiel Luteijn, Diarmuid Glynn, David Bishai, Marc Bonten, Maarten Postma. Modelling the costs and effects of selective and universal hospital admission screening for methicillin-resistant Staphylococcus aureus. PLoS ONE 6(3): e14783. doi:10.1371/journal.pone.0014783
• T.G. Guryeva, M.C.J. Bootsma, M.J.M. Bonten. The successfull veteran affairs initiative to prevent methicillin-resistant Staphylococcus aureus revisited. CID. Accepted.

Chapter in Book

• "Nosocomial transmission: Meticillin-resistant Staphylococcus aureus (MRSA)." Marc Bonten and Martin Bootsma. In "Modern Infectious Disease Epidemiology: Concepts, Methods, Mathematical Models, and Public Health (Statistics for Biology and Health)" (2010). Editors: Alexander Krämer, Mirjam Kretzschmar and Klaus Krickeberg.

Abstracts

• S. Nijssen, M. Bootsma, M. Bonten, and A. Hoepelman. Dynamics of colonization with third generation cephalosporin-resistant enterobacteriaceae in icu patients. 2002. abstract no: 2179 ICAAC.
• M. Bootsma, M. Kooistra-Smid, H. Verburgh, O. Diekmann, and M. Bonten. A mathematical model for the transmission of s. aureus (sa) in a burn wound center. 2002. abstract no: K106, 42nd ICAAC.
• M. Bootsma, M. Bonten, I. Pelupessy, A. Hoepelman, and O. Diekmann. Nosocomial infection (ni) and length of stay (los) in intensive care: A simple observation on cause and effect. 2002. abstract no: K-656, 42nd ICAAC.
• M.C.J. Bootsma, O. Diekmann, and M.J.M. Bonten. How to control interhospital spread (ihs) of multi-drug resistant pathogens (mdrp): Preditions from a mathematical model. 2003. abstract no: K1102.
• K. Schurink, M. Bootsma, and M. Bonten. Early- and late-onset ventilatorassociated pneumonia (vap): Relevance of definition. 2003. abstract no: K-452 43rd ICAAC.
• M.C.J. Bootsma, O. Diekmann, and M.J.M. Bonten. A mathematical model (mm) for the effects of selective digestive decontamination (sdd) on antibiotic resistance. 2003. abstract no: K698, 43rd ICAAC.
• S. Nijssen, J. Top, R. Willems, M. Bootsma, A. Fluit, and M. Bonten. Prospective validation of a mathematical model to determine relative importance of different acquisition routes in intensive care units. 2003. abstract no: K-124, 43rd ICAAC.
• M.C.J. Bootsma, O. Diekmann, and M.J.M. Bonten. Estimating transmission parameters for infectious diseases in small hospital units. In Design and Analysis of Infectious Disease Studies, Mathematisches Forschungsinstitut Oberwolfach. Report No. 49/2004.
• A. van der Zee, M. Bootsma, R. Radersma, J. Nelson, and A. Buiting. A comparision of mathematic modeling and molecular genotyping for assesment of transmission routes of escherichia coli among icu patients. 2005. abstract no: 16B, IMMEM7.
• M.C.J. Bootsma, O. Diekmann, and M.J.M. Bonten. Efficacy of search and destroy (s&d) in high endemic mrsa settings (hes): Results from a simulation model (sm). 2005. abstract no: K548/419, 45th ICAAC.
• M.C.J. Bootsma, O. Diekmann, and M.J.M. Bonten. Quantitative effects of individual measures of search and destroy (s&d) of mrsa. 2005. abstract no: K549/420, 45thICAAC.
• M.C.J. Bootsma, O. Diekmann, and M.J.M. Bonten. Pros and cons of rapid diagnostic testing (rdt) for controlling mrsa. 2005. abstract no: K550/421, 45th ICAAC.
• M.C.J. Bootsma, B. Hota, O. Diekmann, R.A. Weinstein, and M.J.M. Bonten. A mathematical model to determine the growth rate of ca-mrsa and options for control. 2006. abstract no: K-1680. 46th ICAAC
• M.C.J. Bootsma, O. Diekmann, and M.J.M. Bonten. The influence of High-Risk Units (HRUs) on the Spread of Antibiotic Resistant Bacteria (ARB). 2007. abstract no: K-2143 47th ICAAC
• M.C.J. Bootsma, P. Trapman, M.W.M. Wassenberg, M.J.M. Bonten. A birth-death model with detection to estimate nosocomial transmission rates of two methicillin-resistant Staphylococcus aureus strains. 2008. Epidemics conference, Asilomar CA, USA.
• M.C.J. Bootsma, A.H. Havelaar, M.J.M. Bonten, J.A. Wagenaar. Modeling the ban of fluoroquinolone use in the poultry industry on fluoroquinolone-resistance among Campylobacter species. 2008 Epidemics conference, Asilomar CA, USA.
• K.R. Philipsen,M.C.J. Bootsma, M.A. Leverstein-Van Hall, J.C. Stuart, M.L.E. Christiansen, H. Madsen, M.J.M. Bonten. Parameter estimation for a discrete stochastic model of ESBL colonization in a human population. Conference of the Eastern Mediterranean Region of the International Biometric Society, 2009, Istanbul, Turkey
• K.R. Philipsen, M.C.J. Bootsma, M.A. Leverstein-van Hall, J. Cohen Stuart, M.J.M. Bonten Dynamics of extended-spectrum beta-lactamases in ,Escherichia coli and Klebsiella pneumoniae: a mathematical model (2009) 19th ECCMID P 668
• T. Gurieva, M.C.J. Bootsma, M.J.M. Bonten. Quantitative analysis of different approaches to control methicillin-resistant Staphylococcus aureus in hospitals. Epidemics conference, Athens, Greece, 2009.
• T. Gurieva, M.C.J. Bootsma, M.J.M. Bonten. Cost-effectiveness of different admission screening strategies to control the spread of methicillin-resistant Staphylococcus aureus Epidemics conference, Athens, Greece, 2009.
• M.C.J. Bootsma, H. Barreto dos Santos, R. de Souza Kuchenbecker, M. Bernardes Wagner, M.J.M. Bonten. Detrimental effects of patient isolation in controlling methicillin-resistant Staphyloccoccus aureus transmission due to increased workload. Epidemics conference, Athens, Greece, 2009.