ORCID 0000-0001-5400-4945

SW Olesen, M Lipsitch, YH Grad. Outpatient antibiotic stewardship interventions: geographic scale and associations between antibiotic use and resistance. bioRxiv (2019). doi: 10.1101/536714

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

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:

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

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

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; bioRxiv

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

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

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

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; supplement

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

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

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

Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez 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

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

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

Things that are not peer-reviewed papers

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

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

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

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).

SW Olesen. “What you think usearch does might not be what it does.” MIT Center for Microbiome Informatics and Therapeutics Blog (Feb 2016).

EJ Alm and SW Olesen. “Genomic data and machine learning for spill response strategy.” Technical memo for BP Microbiology (2015).