Publications

• Detection of live attenuated measles virus in the respiratory tract following subcutaneous MMR Vaccination.Watkins TA, Brockhurst JK, Germain G, Griffin DE, Foxman EF. J Infect Dis. 2024 Nov 6; 2024 Nov 6. PMID: 39504437.
• High burden of viruses and bacterial pathobionts drives heightened nasal innate immunity in children.Watkins TA, Green AB, Amat JAR, Cheemarla NR, Hänsel K, Lozano R, Dudgeon SN, Germain G, Landry ML, Schulz WL, Foxman EF. J Exp Med. 2024 Sep 2; 2024 Jul 1. PMID: 38949638.
• Considerations for viral co-infection studies in human populations.Chin T, Foxman EF, Watkins TA, Lipsitch M. mBio. 2024 Jul 17; 2024 Jun 7. PMID: 38847531.
• Viral Interference During Influenza A-SARS-CoV-2 Coinfection of the Human Airway Epithelium and Reversal by Oseltamivir.Cheemarla NR, Watkins TA, Mihaylova VT, Foxman EF. J Infect Dis. 2024 May 15. PMID: 37722683.
• Double-take: SARS-CoV-2 has evolved to evade human innate immunity, twice.Foxman EF. Trends Immunol. 2024 Jan; 2023 Dec 24. PMID: 38143224.
• Causal identification of single-cell experimental perturbation effects with CINEMA-OT.Dong M, Wang B, Wei J, de O Fonseca AH, Perry CJ, Frey A, Ouerghi F, Foxman EF, Ishizuka JJ, Dhodapkar RM, van Dijk D. Nat Methods. 2023 Nov; 2023 Nov 2. PMID: 37919419.
• PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection.Xu D, Jiang W, Wu L, Gaudet RG, Park ES, Su M, Cheppali SK, Cheemarla NR, Kumar P, Uchil PD, Grover JR, Foxman EF, Brown CM, Stansfeld PJ, Bewersdorf J, Mothes W, Karatekin E, Wilen CB, MacMicking JD. Nature. 2023 Jul; 2023 Jul 12. PMID: 37438530.
• Respiratory viruses: New frontiers-a Keystone Symposia report.Cable J, Sun J, Cheon IS, Vaughan AE, Castro IA, Stein SR, López CB, Gostic KM, Openshaw PJM, Ellebedy AH, Wack A, Hutchinson E, Thomas MM, Langlois RA, Lingwood D, Baker SF, Folkins M, Foxman EF, Ward AB, Schwemmle M, Russell AB, Chiu C, Ganti K, Subbarao K, Sheahan TP, Penaloza-MacMaster P, Eddens T. Ann N Y Acad Sci. 2023 Apr; 2023 Feb 1. PMID: 36722473.
• Counterintuitive effect of antiviral therapy on influenza A-SARS-CoV-2 coinfection due to viral interference.Cheemarla NR, Mihaylova VT, Watkins TA, Foxman EF. bioRxiv. 2023 Feb 8; 2023 Feb 8. PMID: 36798412.
• Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study.Cheemarla NR, Hanron A, Fauver JR, Bishai J, Watkins TA, Brito AF, Zhao D, Alpert T, Vogels CBF, Ko AI, Schulz WL, Landry ML, Grubaugh ND, van Dijk D, Foxman EF. Lancet Microbe. 2023 Jan. PMID: 36586415.
• Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics.Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. J Exp Med. 2021 Aug 2; 2021 Jun 15. PMID: 34128960.
• Complement Plays a Critical Role in Inflammation-Induced Immunoprophylaxis Failure in Mice.Escamilla-Rivera V, Santhanakrishnan M, Liu J, Gibb DR, Forsmo JE, Foxman EF, Eisenbarth SC, Luckey CJ, Zimring JC, Hudson KE, Stowell SR, Hendrickson JE. Front Immunol. 2021; 2021 Jun 25. PMID: 34249009.
• Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. PLoS Biol. 2021 Mar; 2021 Mar 17. PMID: 33730024.
• Magnitude and timing of the antiviral response determine SARS-CoV-2 replication early in infection.Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. medRxiv. 2021 Jan 27; 2021 Jan 27. PMID: 33532783.
• Viral interference cannot be concluded from datasets containing only symptomatic patients - Authors' reply.Wu A, Mihaylova VT, Landry ML, Foxman EF. Lancet Microbe. 2021 Jan. PMID: 35544223.
• An in vivo atlas of host-pathogen transcriptomes during Streptococcus pneumoniae colonization and disease.D'Mello A, Riegler AN, Martínez E, Beno SM, Ricketts TD, Foxman EF, Orihuela CJ, Tettelin H. Proc Natl Acad Sci U S A. 2020 Dec 29; 2020 Dec 14. PMID: 33318198.
• Interference between rhinovirus and influenza A virus: a clinical data analysis and experimental infection study.Wu A, Mihaylova VT, Landry ML, Foxman EF. Lancet Microbe. 2020 Oct; 2020 Sep 5. PMID: 33103132.
• Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets.Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Catherine Muenker M, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Tokuyama M, Venkataraman A, Weizman OE, Wong P, Yang Y, Cheemarla NR, White EB, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz CS, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND. Nat Microbiol. 2020 Oct; 2020 Jul 10. PMID: 32651556.
• Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium.Ravindra NG, Alfajaro MM, Gasque V, Habet V, Wei J, Filler RB, Huston NC, Wan H, Szigeti-Buck K, Wang B, Wang G, Montgomery RR, Eisenbarth SC, Williams A, Pyle AM, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, van Dijk D, Wilen CB. bioRxiv. 2020 Jul 13; 2020 Jul 13. PMID: 32511382.
• Host response-based screening to identify undiagnosed cases of COVID-19 and expand testing capacity.Cheemarla NR, Brito AF, Fauver JR, Alpert T, Vogels CBF, Omer SB, Ko A, Grubaugh ND, Landry ML, Foxman EF. medRxiv. 2020 Jun 5; 2020 Jun 5. PMID: 32577694.
• Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States.Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Cell. 2020 May 28; 2020 May 7. PMID: 32386545.
• Poly(I:C) causes failure of immunoprophylaxis to red blood cells expressing the KEL glycoprotein in mice.Escamilla-Rivera V, Liu J, Gibb DR, Santhanakrishnan M, Liu D, Forsmo JE, Eisenbarth SC, Foxman EF, Stowell SR, Luckey CJ, Zimring JC, Hudson KE, Hendrickson JE. Blood. 2020 May 28. PMID: 32266378.
• Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology.Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott I, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. medRxiv. 2020 Mar 26; 2020 Mar 26. PMID: 32511630.
• Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus.Mihaylova VT, Kong Y, Fedorova O, Sharma L, Dela Cruz CS, Pyle AM, Iwasaki A, Foxman EF. Cell Rep. 2018 Sep 11. PMID: 30208323.
• Antiviral Response in the Nasopharynx Identifies Patients With Respiratory Virus Infection.Landry ML, Foxman EF. J Infect Dis. 2018 Mar 5. PMID: 29281100.
• Early local immune defences in the respiratory tract.Iwasaki A, Foxman EF, Molony RD. Nat Rev Immunol. 2017 Jan; 2016 Nov 28. PMID: 27890913.
• Two interferon-independent double-stranded RNA-induced host defense strategies suppress the common cold virus at warm temperature.Foxman EF, Storer JA, Vanaja K, Levchenko A, Iwasaki A. Proc Natl Acad Sci U S A. 2016 Jul 26; 2016 Jul 11. PMID: 27402752.
• Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells.Foxman EF, Storer JA, Fitzgerald ME, Wasik BR, Hou L, Zhao H, Turner PE, Pyle AM, Iwasaki A. Proc Natl Acad Sci U S A. 2015 Jan 20; 2015 Jan 5. PMID: 25561542.
• Genome-virome interactions: examining the role of common viral infections in complex disease.Foxman EF, Iwasaki A. Nat Rev Microbiol. 2011 Apr. PMID: 21407242.
• Use of the fetal fibronectin test in decisions to admit to hospital for preterm labor.Foxman EF, Jarolim P. Clin Chem. 2004 Mar. PMID: 14981040.
• Inflammatory mediators in uveitis: differential induction of cytokines and chemokines in Th1- versus Th2-mediated ocular inflammation.Foxman EF, Zhang M, Hurst SD, Muchamuel T, Shen D, Wawrousek EF, Chan CC, Gery I. J Immunol. 2002 Mar 1. PMID: 11859142.
• Chemotaxis assays for eukaryotic cells.Zigmond SH, Foxman EF, Segall JE. Curr Protoc Cell Biol. 2001 May. PMID: 18228315.
• Integrating conflicting chemotactic signals. The role of memory in leukocyte navigation.Foxman EF, Kunkel EJ, Butcher EC. J Cell Biol. 1999 Nov 1. PMID: 10545501.
• Multistep navigation and the combinatorial control of leukocyte chemotaxis.Foxman EF, Campbell JJ, Butcher EC. J Cell Biol. 1997 Dec 1. PMID: 9382879.
• Chemoattractant receptor cross talk as a regulatory mechanism in leukocyte adhesion and migration.Campbell JJ, Foxman EF, Butcher EC. Eur J Immunol. 1997 Oct. PMID: 9368612.