RM Klevens, CCW Young, SW Olesen, A Osinski, D Church, J Muten, L Chou, T Segal, K Cranston. Evaluation of wastewater surveillance for SARS-CoV-2 in Massachusetts correctional facilities, 2020–2022. Frontiers in Water (2023). doi: 10.3389/frwa.2023.1083316

SW Olesen, CCW Young, C Duvallet. White paper: The effect of septic systems on wastewater-based epidemiology. Zenodo (2022). doi: 10.5281/zenodo.7130725

Bousbaine D, Fisch LI, London M, Bhagchandani P, Rezende de Castro TB, Mimee M, Olesen S, Reis BS, VanInsberghe D, Bortolatto J, Poyet M, Cheloha RW, Sidney J, Ling J, Gupta A, Lu TK, Sette A, Alm EJ, Moon JJ, Victora GD, Mucida D, Ploegh HL, Bilate AM. conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes. Science (2022). doi: 10.1126/science.abg5645

SW Olesen. Uses of mathematical modeling to estimate the impact of mass drug administration of antibiotics on antimicrobial resistance within and between communities. Infectious Diseases of Poverty (2022). doi: 10.1186/s40249-022-00997-7

SW Olesen and E Trabert. Infectious disease modeling: recommendations for public health decision makers. Disaster Medicine and Public Health Preparedness (2022). doi: 10.1017/dmp.2022.99

C Duvallet, F Wu, KA McElroy, M Imakaev, N Endo, A Xiao, J Zhang, R Floyd-O’Sullivan, MM Powell, S Mendola, ST Wilson, F Cruz, T Melman, CL Sathyanarayana, SW Olesen, TB Erickson, N Ghaeli, P Chai, EJ Alm, M Matus. Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States. ACS EST Water (2022). doi: 10.1021/acsestwater.1c00434

SW Olesen, N Endo, C Duvallet. Interpreting Covid-19 wastewater monitoring data from buildings to support disease mitigation. Proceedings: Public Health and Water Conference & Wastewater Disease Surveillance Summit. Cincinnati, OH. (March 21-24, 2022). doi: 10.2175/193864718825158289 pdf: pdf

SW Olesen, S Kanjilal, SM Kissler, DS Sun, YH Grad. Racial/ethnic disparities in antibiotic use and healthcare utilization, 2016/2018. medRxiv (2021). doi: 10.1101/2021.12.09.21266965

N Sharara, N Endo, C Duvallet, N Ghaeli, M Matus, J Heussner, SW Olesen, EJ Alm, PR Chai, TB Erickson. Wastewater network infrastructure in public health: Applications and learnings from the COVID-19 pandemic. PLOS Global Public Health (2021). doi: 10.1371/journal.pgph.0000061 pubmed: 34927170

SW Olesen. Interpreting building-level Covid-19 wastewater monitoring data. figshare (2021). doi: 10.6084/m9.figshare.16587068 pdf: pdf

SW Olesen, M Imakaev, C Duvallet. Making waves: Defining the lead time of wastewater-based epidemiology for COVID-19. Water Research (2021). doi: 10.1016/j.watres.2021.117433 pubmed: 34304074 pmc: PMC8282235

DS Sun, SM Kissler, S Kanjilal, SW Olesen, M Lipsitch, YH Grad. Large variation in the association between seasonal antibiotic use and resistance across multiple bacterial species and antibiotic classes. medRxiv (2021). doi: 10.1101/2020.12.21.20248670

SM Kissler, JR Fauver, C Mack, SW Olesen, C Tai, KY Shiue, CC Kalinich, S Jednak, IM Ott, CBF Vogels, J Wohlgemuth, J Weisberger, J DiFiori, DJ Anderson, J Mancell, DD Ho, ND Grubaugh, YG Grad. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLOS Biology (2021). doi: 10.1371/journal.pbio.3001333 pubmed: 34252080

J Chen, A Zaman, B Ramakrishna, SW Olesen. Stool banking for fecal microbiota transplantation: methods and operations at a large stool bank. Front Cell Infect Microbiol (2021). doi: 10.3389/fcimb.2021.622949

M Santiago, SW Olesen. 16S rRNA sequencing of samples from universal stool bank donors. BMC Research Notes (2021). doi: 10.1186/s13104-021-05520-z

A Zaman, T Qazi, P Pai, P Peters, S Nicolaysen, SW Olesen. Carriage rates of multidrug-resistant organisms among prospective stool donors. The Lancet Infectious Diseases (2021). doi: 10.1016/S1473-3099(21)00091-8

SW Olesen. Fecal microbiota transplantation “donor effects” are not clinically relevant for Clostridioides difficile infection. Gastroenterology (2020). doi: 10.1053/j.gastro.2020.12.057 pubmed: 33387515

D Bousbaine, P Bhagchandani, M London, M Mimee, SW Olesen, M Poyet, RW Cheloha, J Sidney, J Ling, A Gupta, TK Lu, A Sette, EJ Alm, D Mucida, AM Bilate, HL Ploegh. Antigen-specific induction of CD4+CD8αα+ intraepithelial T lymphocytes by Bacteroidetes species. bioRxiv (submitted elsewhere). doi: 10.1101/2020.08.05.236513

SW Olesen. Power calculations for detecting differences in efficacy of fecal microbiota donors. Contemporary Clinical Trials Communications (2020). doi: 10.1016/j.conctc.2020.100674 pubmed: 33241161 pmc: PMC7672275

SW Olesen, A Zaman, M Osman, B Ramakrishna. Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation. Open Forum Infect Dis (2020). doi: 10.1093/ofid/ofaa499 pubmed: 33235890 pmc: PMC7665722

SW Olesen, M Lipsitch, YH Grad. The role of “spillover” in antibiotic resistance. PNAS (2020). doi: 10.1073/pnas.2013694117 pubmed: 33139558 pmc: PMC7682407

L Mamoon, SW Olesen. Fecal microbiota transplants annually and their positive clinical impact. Clin Transl Gastroenterol (2020). doi: 10.14309/ctg.0000000000000247 pubmed: 33259159 pmc: PMC7594930

C Zellmer, MRA Sater, MH Huntley, M Osman, SW Olesen, B Ramakrishna. Shiga toxin-producing E. coli transmission via fecal microbiota transplant. Clin Infect Dis (2020). doi: 10.1093/cid/ciaa1486 pubmed: 33159210

SW Olesen, Y Gerardin. Re-evaluating the evidence for fecal microbiota transplantation “super-donors” in inflammatory bowel disease. Journal of Crohn’s and Colitis (2020). doi: 10.1093/ecco-jcc/jjaa170 pubmed: 32808030 pdf: pdf

AM Tsou, SW Olesen (co-first), EJ Alm, SB Snapper. 16S rRNA sequencing analysis: the devil is in the details. Gut Microbes (2020). doi: 10.1080/19490976.2020.1747336 pubmed: 32329652 pmc: PMC7524321

SW Olesen, P Panchal, J Chen, S Budree, M Osman. Global disparities and underserved populations in fecal microbiota transplantation research. Lancet Gastro Hepatol (2020). doi: 10.1016/S2468-1253(19)30452-2 pubmed: 32061326 pdf: pdf

S Ryu, BJ Cowling, P Wu, SW Olesen, C Fraser, DS Sun, M Lipsitch, YH Grad. Case-based surveillance of antimicrobial resistance with full susceptibility profiles. JAC Antimicrob Resist (2019). doi: 10.1093/jacamr/dlz070 pubmed: 32280945 pmc: PMC7134534

BJ Sutherland, SW Olesen, H Kusumaatmaja, JWR Morgan, DJ Wales. Morphological analysis of chiral rod clusters from a coarse-grained single-site chiral potential. Soft Matter (2019). doi: 10.1039/C9SM01343A pubmed: 31589219

E Goldstein, SW Olesen, Z Karaca, CA Steiner, C Viboud, M Lipsitch. Levels of outpatient prescribing for four major antibiotic classes and rates of septicemia hospitalization in adults in different US states – a statistical analysis. BMC Public Health 19: 1139 (2019). doi: 10.1186/s12889-019-7431-8 pubmed: 31426780 pmc: PMC6701127

SW Olesen, D MacFadden, YH Grad. Cumulative probability of receiving an antibiotic prescription over time. NEJM 380(19): 1872–1873 (2019). doi: 10.1056/NEJMc1816699 pubmed: 31067381

RM Klevens, E Caten, SW Olesen, A DeMaria, S Troppy, YH Grad. Outpatient Antibiotic Prescribing in Massachusetts, 2011–2015. Open Forum Infectious Diseases 6(5): ofz169 (2019). doi: 10.1093/ofid/ofz169 pubmed: 31065563 pmc: PMC6499896

JI Miller, S Techtmann, J Fortney, N Mahmoudi, D Joyner, J Liu, SW Olesen, E Alm, A Fernandez, P Gardinali, N GaraJayeva, FS Askerov, TC Hazen. Oil hydrocarbon degradation by Caspian Sea microbial communities. Front Microbiol (2019). doi: 10.3389/fmicb.2019.00995 pubmed: 31143165 pmc: PMC6521576

SW Olesen, M Lipsitch, YH Grad. Response to comment on “The distribution of antibiotic use and its association with antibiotic resistance”. eLife 8:e47124 (2019). doi: 10.7554/eLife.47124 pubmed: 31050649 pmc: PMC6499536

DR MacFadden, M Lipsitch, SW Olesen, Y Grad. Multidrug-resistant Neisseria gonorrhoeae: implications for future treatment strategies. The Lancet Infectious Diseases (2018). doi: 10.1016/S1473-3099(18)30274-3 pubmed: 29856349

SW Olesen, ML Barnett, DR MacFadden, JS Brownstein, S Hernandez-Diaz, M Lipsitch, YH Grad. The distribution of antibiotic use and its association with antibiotic resistance. eLife 7:e39435 (2018). doi: 10.7554/eLife.39435 pubmed: 30560781 pmc: PMC6307856

C Tedijanto, SW Olesen, YH Grad, M Lipsitch. Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora. PNAS (2018). doi: 10.1073/pnas.1810840115 pubmed: 30559213 pmc: PMC6304942

SW Olesen, YH Grad. Racial/ethnic disparities in antimicrobial drug use, United States, 2014-2015. Emerging Infectious Diseases 24(11): 2126-2128 (2018). doi: 10.3201/eid2411.180762 pubmed: 30334733 pmc: PMC6199984

K Arora-Williams, SW Olesen, BP Scandella, K Delwiche, SJ Spencer, EM Myers, S Abraham, A Sooklal, SP Preheim. Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake. Microbiome (2018). doi: 10.1186/s40168-018-0556-7 pubmed: 30227897 pmc: PMC6145348

SW Olesen, EA Torrone, JR Papp, RD Kirkcaldy, M Lipsitch, YH Grad. Azithromycin susceptibility in Neisseria gonorrhoeae and seasonal macrolide use. Journal of Infectious Diseases (2018). doi: 10.1093/infdis/jiy551 pubmed: 30239814 pmc: PMC6350947

SW Olesen, ML Barnett, DR MacFadden, M Lipsitch, YH Grad. Trends in outpatient antibiotic prescribing practice among US older adults, 2011–2015: observational study. BMJ (2018). doi: 10.1136/bmj.k3155 pubmed: 30054353 pmc: PMC6062849

N Wilck, MG Matus, SM Kearney, SW Olesen, K Forslund, H Bartolomaeus, S Haase, A Mahler, A Balogh, L Marko, O Vvedenskaya, FH Kleiner, D Tsvetkov, L Klug, PI Costea, S Sunagawa, L Maier, N Rakova, V Schatz, P Neubert, C Fratzer, A Krannich, M Gollasch, DA Grohme, BF Corte-Real, RG Gerlach, M Basic, A Typas, C Wu, JM Titze, J Jantsch, M Boschmann, R Dechend, M Kleinewietfeld, S Kempa, P Bork, RA Linker, EJ Alm, DN Muller. Salt-responsive gut commensal modules TH17 axis and disease. Nature (2017). doi: 10.1038/nature24628 pubmed: 29143823 pmc: PMC6070150

SW Olesen, ML Leier, EJ Alm, SA Kahn. Searching for superstool: maximizing the therapeutic potential of FMT. Nature Reviews Gastroenterology & Hepatology 15, 387–388 (2018). doi: 10.1038/s41575-018-0019-4 pubmed: 29703976 pdf: pdf

SW Olesen, C Duvallet, EJ Alm. dbOTU3: A new implementation of distribution-based OTU calling. PLOS ONE 12(5): e0176335 (2017). doi: 10.1371/journal.pone.0176335 pubmed: 28472072 pmc: PMC5417438

SW Olesen*, T Gurry* (co-first), EJ Alm. Designing fecal microbiota transplant trials that account for stool donor heterogeneity. Statistical Methods in Medical Research 27(10), 2906–2917 (2017). doi: 10.1177/0962280216688502 pubmed: 28178876

SW Olesen, EJ Alm. Dysbiosis is not an answer. Nature Microbiology 1: 16228 (2016). doi: 10.1038/nmicrobiol.2016.228 pubmed: 27886190 pdf: pdf

SP Preheim*, SW Olesen* (co-first), A Materna, C Varadharajan, M Blackburn, J Friedman, J Rodriguez, H Hemond, EJ Alm. Surveys, simulations, and single-cell assays relate function and phylogeny in a lake ecosystem. Nature Microbiology 1: 16130 (2016). doi: 10.1038/nmicrobiol.2016.130 pubmed: 27562262

Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodriguez J, Hazen TC, Alm EJ. A novel analysis method for paired-sample microbial ecology experiments. PLOS ONE 11: e0154804 (2016). doi: 10.1371/journal.pone.0154804 pubmed: 27152415 pmc: PMC4859510

Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA, Jr, Preheim SP, Sanders MS, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 6, e00326-15 (2015). doi: 10.1128/mBio.00326-15 pubmed: 25968645 pmc: PMC4436078

SW Olesen, SN Fejer, D Chakrabarti, and DJ Wales. A left-handed building block self-assembles into right-and left-handed helices. RSC Advances, 3, 12905-12908 (2013). doi: 10.1039/C3RA41813H

D Bingemann, MR Allen, SW Olesen. Single molecules reveal the dynamics of heterogeneities in a polymer at the glass transition. Journal of Chemical Physics, 134, 024513 (2011). doi: 10.1063/1.3516516 pubmed: 21241126

Other work

SW Olesen. Quantitative modeling for microbial ecology and clinical trials. PhD thesis, MIT (2016). DSpace; source code

SW Olesen. Processing 16S data: an informal primer about 16S rRNA amplicon data (Mar 2021). file; source code

SW Olesen, EJ Alm. “Leveraging microbes when responding to an oil spill.” HSE NOW (Dec 2016).