J Chen, A Zaman, B Ramakrishna, SW Olesen. Stool banking for fecal microbiota transplantation: methods and operations at a large stool bank. medRxiv (submitted elsewhere). doi: 10.1101/2020.09.03.20187583

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. medRxiv (under review). doi: 10.1101/2020.04.16.20068361

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

SW Olesen, M Lipsitch, YH Grad. The role of “spillover” in antibiotic resistance. PNAS (2020). doi: 10.1101/536714

L Mamoon, SW Olesen. The public health impact of fecal microbiota transplantation. Clin Transl Gastroenterol (2020). doi: 10.1101/2020.04.07.20056952

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

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 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

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 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

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, and 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. Leanpub (2016).

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