Publications |

For a full list of publications, click here.

Alveolar macrophages are early targets of mumps virus.

Patel AR, Garg A, Rosberger HT, Kowdle S, Reis RA, Frere JJ, Januska MN, Dawodu G, Valencia E, Yang MC, Stevens CS, Rao VN, Haas GD, Chen YW, Lee B, Lim JK.

Proc Natl Acad Sci U S A. 2024 Dec 24;121(52):e2410954121.

Immunological landscape of human lymphoid explants during measles virus infection.

Acklin JA, Patel AR, Kurland AP, Horiuchi S, Moss AS, DeGrace EJ, Ikegame S, Carmichael J, Kowdle S, Thibault PA, Imai N, Ueno H, Tweel B, Johnson JR, Rosenberg BR, Lee B, Lim JK.

JCI Insight. 2024 Jul 25;9(17).

Respiratory SARS-CoV-2 Infection Causes Skeletal Muscle Atrophy and Long-Lasting Energy Metabolism Suppression.

Homma ST, Wang X, Frere JJ, Gower AC, Zhou J, Lim JK, tenOever BR, Zhou L.

Biomedicines. 2024 Jun 28;12(7).

A Pocket Guide to CCR5-Neurotropic Flavivirus Edition.

Garg A, Lim JK.

Viruses. 2023 Dec 23;16(1).

C5a-licensed phagocytes drive sterilizing immunity during systemic fungal infection.

Desai JV, Kumar D, Freiwald T, Chauss D, Johnson MD, Abers MS, Steinbrink JM, Perfect JR, Alexander B, Matzaraki V, Snarr BD, Zarakas MA, Oikonomou V, Silva LM, Shivarathri R, Beltran E, Demontel LN, Wang L, Lim JK, Launder D, Conti HR, Swamydas M, McClain MT, Moutsopoulos NM, Kazemian M, Netea MG, Kumar V, Köhl J, Kemper C, Afzali B, Lionakis MS.

Cell. 2023 Jun 22;186(13):2802-2822.e22.

Metagenomics-enabled reverse-genetics assembly and characterization of myotis bat morbillivirus.

Ikegame S, Carmichael JC, Wells H, Furler O’Brien RL, Acklin JA, Chiu HP, Oguntuyo KY, Cox RM, Patel AR, Kowdle S, Stevens CS, Eckley M, Zhan S, Lim JK, Veit EC, Evans MJ, Hashiguchi T, Durigon E, Schountz T, Epstein JH, Plemper RK, Daszak P, Anthony SJ, Lee B.

Nat Microbiol. 2023 Jun;8(6):1108-1122.

Alpha-1-antitrypsin and its variant-dependent role in COVID-19 pathogenesis.

Stevens CS, Oguntuyo KY, Kowdle S, Brambilla L, Haas G, Gowlikar A, Siddiquey MN, Schilke RM, Woolard MD, Zhang H, Acklin JA, Ikegame S, Huang CT, Lim JK, Cross RW, Geisbert TW, Ivanov SS, Kamil JP, Lee B.

bioRxiv. 2023 May 8;.

Human Dectin-1 deficiency impairs macrophage-mediated defense against phaeohyphomycosis.

Drummond RA, Desai JV, Hsu AP, Oikonomou V, Vinh DC, Acklin JA, Abers MS, Walkiewicz MA, Anzick SL, Swamydas M, Vautier S, Natarajan M, Oler AJ, Yamanaka D, Mayer-Barber KD, Iwakura Y, Bianchi D, Driscoll B, Hauck K, Kline A, Viall NS, Zerbe CS, Ferré EM, Schmitt MM, DiMaggio T, Pittaluga S, Butman JA, Zelazny AM, Shea YR, Arias CA, Ashbaugh C, Mahmood M, Temesgen Z, Theofiles AG, Nigo M, Moudgal V, Bloch KC, Kelly SG, Whitworth MS, Rao G, Whitener CJ, Mafi N, Gea-Banacloche J, Kenyon LC, Miller WR, Boggian K, Gilbert A, Sincock M, Freeman AF, Bennett JE, Hasbun R, Mikelis CM, Kwon-Chung KJ, Belkaid Y, Brown GD, Lim JK, Kuhns DB, Holland SM, Lionakis MS.

J Clin Invest. 2022 Nov 15;132(22).

The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication.

Nilsson-Payant BE, Uhl S, Grimont A, Doane AS, Cohen P, Patel RS, Higgins CA, Acklin JA, Bram Y, Chandar V, Blanco-Melo D, Panis M, Lim JK, Elemento O, Schwartz RE, Rosenberg BR, Chandwani R, tenOever BR

J Virol. 2021 Nov 9;95(23):e0125721.

Cardiomyocytes recruit monocytes upon SARS-CoV-2 infection by secreting CCL2.

Yang L, Nilsson-Payant BE, Han Y, Jaffré F, Zhu J, Wang P, Zhang T, Redmond D, Houghton S, Møller R, Hoagland D, Carrau L, Horiuchi S, Goff M, Lim JK, Bram Y, Richardson C, Chandar V, Borczuk A, Huang Y, Xiang J, Ho DD, Schwartz RE, tenOever BR, Evans T, Chen S

Stem Cell Reports. 2021 Oct 12;16(10):2565.

Zoonotic potential of a novel bat morbillivirus.

Lee B, Ikegame S, Carmichael J, Wells H, Furler R, Acklin J, Chiu HP, Oguntuyo K, Cox R, Patel A, Kowdle S, Stevens C, Eckley M, Zhan S, Lim J, Hashiguchi T, Durigon EL, Schountz T, Epstein J, Plemper R, Daszak P, Anthony S.

Res Sq. 2021 Sep 29;

Response to Comments on “Aberrant type 1 immunity drives susceptibility to mucosal fungal infections”.

Break TJ, Oikonomou V, Dutzan N, Desai JV, Swidergall M, Freiwald T, Chauss D, Harrison OJ, Alejo J, Williams DW, Pittaluga S, Lee CR, Bouladoux N, Swamydas M, Hoffman KW, Greenwell-Wild T, Bruno VM, Rosen LB, Lwin W, Renteria A, Pontejo SM, Shannon JP, Myles IA, Olbrich P, Ferré EMN, Schmitt M, Martin D, Barber DL, Solis NV, Notarangelo LD, Serreze DV, Matsumoto M, Hickman HD, Murphy PM, Anderson MS, Lim JK, Holland SM, Filler SG, Afzali B, Belkaid Y, Moutsopoulos NM, Lionakis MS.

Science. 2021 Sep 17;373(6561):eabi8835.

SARS-CoV-2 infection induces beta cell transdifferentiation.

Tang X, Uhl S, Zhang T, Xue D, Li B, Vandana JJ, Acklin JA, Bonnycastle LL, Narisu N, Erdos MR, Bram Y, Chandar V, Chong ACN, Lacko LA, Min Z, Lim JK, Borczuk AC, Xiang J, Naji A, Collins FS, Evans T, Liu C, tenOever BR, Schwartz RE, Chen S.

Cell Metab. 2021 Aug 3;33(8):1577-1591.e7.

An Immuno-Cardiac Model for Macrophage-Mediated Inflammation in COVID-19 Hearts.

Yang L, Han Y, Jaffré F, Nilsson-Payant BE, Bram Y, Wang P, Zhu J, Zhang T, Redmond D, Houghton S, Uhl S, Borczuk A, Huang Y, Richardson C, Chandar V, Acklin JA, Lim JK, Chen Z, Xiang J, Ho DD, tenOever BR, Schwartz RE, Evans T, Chen S.

Circ Res. 2021 Jun 25;129(1):33-46.

Evaluating the Safety of West Nile Virus Immunity During Congenital Zika Virus Infection in Mice.

Acklin JA, Cattle JD, Moss AS, Brown JA, Foster GA, Krysztof D, Stramer SL, Lim JK.Front

Immunol. 2021;12:686411.

Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity.

Hoagland DA, Møller R, Uhl SA, Oishi K, Frere J, Golynker I, Horiuchi S, Panis M, Blanco-Melo D, Sachs D, Arkun K, Lim JK, tenOever BR.

Immunity. 2021 Mar 9;54(3):557-570.e5.

Quantifying Absolute Neutralization Titers against SARS-CoV-2 by a Standardized Virus Neutralization Assay Allows for Cross-Cohort Comparisons of COVID-19 Sera.

Oguntuyo KY, Stevens CS, Hung CT, Ikegame S, Acklin JA, Kowdle SS, Carmichael JC, Chiu HP, Azarm KD, Haas GD, Amanat F, Klingler J, Baine I, Arinsburg S, Bandres JC, Siddiquey MNA, Schilke RM, Woolard MD, Zhang H, Duty AJ, Kraus TA, Moran TM, Tortorella D, Lim JK, Gamarnik AV, Hioe CE, Zolla-Pazner S, Ivanov SS, Kamil JP, Krammer F, Lee B.

mBio. 2021 Feb 16;12(1).

GPER1 is required to protect fetal health from maternal inflammation.
Harding AT, Goff MA, Froggatt HM, Lim JK, Heaton NS.
Science. 2021 Jan 15;371(6526):271-276.

Aberrant type 1 immunity drives susceptibility to mucosal fungal infections.
Break TJ, Oikonomou V, Dutzan N, Desai JV, Swidergall M, Freiwald T, Chauss D, Harrison OJ, Alejo J, Williams DW, Pittaluga S, Lee CR, Bouladoux N, Swamydas M, Hoffman KW, Greenwell-Wild T, Bruno VM, Rosen LB, Lwin W, Renteria A, Pontejo SM, Shannon JP, Myles IA, Olbrich P, Ferré EMN, Schmitt M, Martin D, Barber DL, Solis NV, Notarangelo LD, Serreze DV, Matsumoto M, Hickman HD, Murphy PM, Anderson MS, Lim JK, Holland SM, Filler SG, Afzali B, Belkaid Y, Moutsopoulos NM, Lionakis MS.
Science. 2021 Jan 15;371(6526)

SARS-CoV-2 Infected Cardiomyocytes Recruit Monocytes by Secreting CCL2.
Chen S, Yang L, Nilsson-Payant B, Han Y, Jaffré F, Zhu J, Wang P, Zhang T, Redmond D, Houghton S, Møller R, Hoagland D, Horiuchi S, Acklin J, Lim J, Bram Y, Richardson C, Chandar V, Borczuk A, Huang Y, Xiang J, Ho D, Schwartz R, tenOever B, Evans T.
Res Sq. 2020 Nov 17;

Protective Activity of Programmed Cell Death Protein 1 Blockade and Synergy With Caspofungin in a Murine Invasive Pulmonary Aspergillosis Model.
Wurster S, Robinson P, Albert ND, Tarrand JJ, Goff M, Swamydas M, Lim JK, Lionakis MS, Kontoyiannis DP.
J Infect Dis. 2020 Aug 17;222(6):989-994.

The Global Phosphorylation Landscape of SARS-CoV-2 Infection.
Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O’Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ.
Cell. 2020 Aug 6;182(3):685-712.e19.

Zika virus tropism during early infection of the testicular interstitium and its role in viral pathogenesis in the testes.

Tsetsarkin KA, Acklin JA, Liu G, Kenney H, Teterina NL, Pletnev AG, Lim JK.

PLoS Pathog. 2020 Jul;16(7):e1008601.

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.

Blanco-Melo D, Nilsson-Payant BE, Liu WC, Uhl S, Hoagland D, Møller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT, Schwartz RE, Lim JK, Albrecht RA, tenOever BR.

Cell. 2020 May 28;181(5):1036-1045.e9.

Passenger Mutations Confound Phenotypes of SARM1-Deficient Mice.

Uccellini MB, Bardina SV, Sánchez-Aparicio MT, White KM, Hou YJ, Lim JK, García-Sastre A.

Cell Rep. 2020 Apr 7;31(1):107498.

Zika virus envelope nanoparticle antibodies protect mice without risk of disease enhancement.

Shukla R, Shanmugam RK, Ramasamy V, Arora U, Batra G, Acklin JA, Krammer F, Lim JK, Swaminathan S, Khanna N.

EBioMedicine. 2020 Apr;54:102738.

Human Monoclonal Antibodies Potently Neutralize Zika Virus and Select for Escape Mutations on the Lateral Ridge of the Envelope Protein.

Bailey MJ, Broecker F, Freyn AW, Choi A, Brown JA, Fedorova N, Simon V, Lim JK, Evans MJ, García-Sastre A, Palese P, Tan GS.

J Virol.2019 Jul 15;93(14).

Lymphocyte-driven regional immunopathology in pneumonitis caused by impaired central immune tolerance.

Ferré EMN, Break TJ, Burbelo PD, Allgäuer M, Kleiner DE, Jin D, Xu Z, Folio LR, Mollura DJ, Swamydas M, Gu W, Hunsberger S, Lee CR, Bondici A, Hoffman KW, Lim JK, Dobbs K, Niemela JE, Fleisher TA, Hsu AP, Snow LN, Darnell DN, Ojaimi S, Cooper MA, Bozzola M, Kleiner GI, Martinez JC, Deterding RR, Kuhns DB, Heller T, Winer KK, Rajan A, Holland SM, Notarangelo LD, Fennelly KP, Olivier KN, Lionakis MS.

Sci Transl Med. 2019 Jun 5;11(495).

Dengue and Zika: The Complexities of Being Related.

Krammer F, Lim JK.

Trends Immunol. 2019 Jun;40(6):467-469.

Atovaquone Inhibits Arbovirus Replication through the Depletion of Intracellular Nucleotides.

Cifuentes Kottkamp A, De Jesus E, Grande R, Brown JA, Jacobs AR, Lim JK, Stapleford KA.

J Virol. 2019 Jun 1;93(11).

Dengue Virus Immunity Increases Zika Virus-Induced Damage during Pregnancy.

Brown JA, Singh G, Acklin JA, Lee S, Duehr JE, Chokola AN, Frere JJ, Hoffman KW, Foster GA, Krysztof D, Cadagan R, Jacobs AR, Stramer SL, Krammer F, García-Sastre A, Lim JK.

Immunity. 2019 Mar 19;50(3):751-762.e5.

Sex differences in cytokine production following West Nile virus infection: Implications for symptom manifestation.

Hoffman KW, Lee JJ, Foster GA, Krysztof D, Stramer SL, Lim JK.

Pathog Dis. 2019 Mar 1;77(2).

CCL7 Is a Negative Regulator of Cutaneous Inflammation Following Leishmania major Infection.

Ford J, Hughson A, Lim K, Bardina SV, Lu W, Charo IF, Lim JK, Fowell DJ.

Front Immunol. 2018;9:3063.

P2X Antagonists Inhibit HIV-1 Productive Infection and Inflammatory Cytokines Interleukin-10 (IL-10) and IL-1β in a Human Tonsil Explant Model.

Soare AY, Durham ND, Gopal R, Tweel B, Hoffman KW, Brown JA, O’Brien M, Bhardwaj N, Lim JK, Chen BK, Swartz TH.

J Virol. 2019 Jan 1;93(1).

Human antibodies targeting Zika virus NS1 provide protection against disease in a mouse model.

Bailey MJ, Duehr J, Dulin H, Broecker F, Brown JA, Arumemi FO, Bermúdez González MC, Leyva-Grado VH, Evans MJ, Simon V, Lim JK, Krammer F, Hai R, Palese P, Tan GS.

Nat Commun. 2018 Nov 1;9(1):4560.

Anti-α4β7 therapy targets lymphoid aggregates in the gastrointestinal tract of HIV-1-infected individuals.

Uzzan M, Tokuyama M, Rosenstein AK, Tomescu C, SahBandar IN, Ko HM, Leyre L, Chokola A, Kaplan-Lewis E, Rodriguez G, Seki A, Corley MJ, Aberg J, La Porte A, Park EY, Ueno H, Oikonomou I, Doron I, Iliev ID, Chen BK, Lui J, Schacker TW, Furtado GC, Lira SA, Colombel JF, Horowitz A, Lim JK, Chomont N, Rahman AH, Montaner LJ, Ndhlovu LC, Mehandru S.Sci Transl Med. 2018 Oct 3;10(461).

Aspergillosis, eosinophilic esophagitis, and allergic rhinitis in signal transducer and activator of transcription 3 haploinsufficiency.

Natarajan M, Hsu AP, Weinreich MA, Zhang Y, Niemela JE, Butman JA, Pittaluga S, Sugui J, Collar AL, Lim JK, Zangeneh T, Carr T, Oler AJ, Similuk M, Rosen LB, Desai JV, Freeman AF, Holland SM, Kwon-Chung KJ, Milner JD, Lionakis MS.

J Allergy Clin Immunol. 2018 Sep;142(3):993-997.e3.

The homozygous CX3CR1-M280 mutation impairs human monocyte survival.

Collar AL, Swamydas M, O’Hayre M, Sajib MS, Hoffman KW, Singh SP, Mourad A, Johnson MD, Ferre EM, Farber JM, Lim JK, Mikelis CM, Gutkind JS, Lionakis MS.

JCI Insight. 2018 Feb 8;3(3).

Tick-Borne Encephalitis Virus Vaccine-Induced Human Antibodies Mediate Negligible Enhancement of Zika Virus Infection InVitro and in a Mouse Model.

Duehr J, Lee S, Singh G, Foster GA, Krysztof D, Stramer SL, Bermúdez González MC, Menichetti E, Geretschläger R, Gabriel C, Simon V, Lim JK, Krammer F.

mSphere. 2018 Jan-Feb;3(1).

Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology.

Jones JE, Long KM, Whitmore AC, Sanders W, Thurlow LR, Brown JA, Morrison CR, Vincent H, Peck KM, Browning C, Moorman N, Lim JK, Heise MT.

mBio. 2017 Nov 14;8(6).

Alveolar macrophages are critical for broadly-reactive antibody-mediated protection against influenza A virus in mice.

He W, Chen CJ, Mullarkey CE, Hamilton JR, Wong CK, Leon PE, Uccellini MB, Chromikova V, Henry C, Hoffman KW, Lim JK, Wilson PC, Miller MS, Krammer F, Palese P, Tan GS.

Nat Commun. 2017 Oct 10;8(1):846.

Chemokine Receptor Ccr7 Restricts Fatal West Nile Virus Encephalitis.

Bardina SV, Brown JA, Michlmayr D, Hoffman KW, Sum J, Pletnev AG, Lira SA, Lim JK.

J Virol. 2017 May 15;91(10).

Enhancement of Zika virus pathogenesis by preexisting antiflavivirus immunity.

Bardina SV, Bunduc P, Tripathi S, Duehr J, Frere JJ, Brown JA, Nachbagauer R, Foster GA, Krysztof D, Tortorella D, Stramer SL, García-Sastre A, Krammer F, Lim JK.

Science. 2017 Apr 14;356(6334):175-180.

Contribution of the Purinergic Receptor P2X7 to Development of Lung Immunopathology during Influenza Virus Infection.

Leyva-Grado VH, Ermler ME, Schotsaert M, Gonzalez MG, Gillespie V, Lim JK, García-Sastre A.

mBio. 2017 Mar 28;8(2).

A novel Zika virus mouse model reveals strain specific differences in virus pathogenesis and host inflammatory immune responses.

Tripathi S, Balasubramaniam VR, Brown JA, Mena I, Grant A, Bardina SV, Maringer K, Schwarz MC, Maestre AM, Sourisseau M, Albrecht RA, Krammer F, Evans MJ, Fernandez-Sesma A, Lim JK, García-Sastre A.

PLoS Pathog. 2017 Mar;13(3):e1006258.

Extrapulmonary Aspergillus infection in patients with CARD9 deficiency.

Rieber N, Gazendam RP, Freeman AF, Hsu AP, Collar AL, Sugui JA, Drummond RA, Rongkavilit C, Hoffman K, Henderson C, Clark L, Mezger M, Swamydas M, Engeholm M, Schüle R, Neumayer B, Ebel F, Mikelis CM, Pittaluga S, Prasad VK, Singh A, Milner JD, Williams KW, Lim JK, Kwon-Chung KJ, Holland SM, Hartl D, Kuijpers TW, Lionakis MS.

JCI Insight. 2016 Oct 20;1(17):e89890.

Batf3-dependent CD103(+) dendritic cell accumulation is dispensable for mucosal and systemic antifungal host defense.

Break TJ, Hoffman KW, Swamydas M, Lee CC, Lim JK, Lionakis MS.

Virulence. 2016 Oct 2;7(7):826-35.

Differences in Early Cytokine Production Are Associated With Development of a Greater Number of Symptoms Following West Nile Virus Infection.

Hoffman KW, Sachs D, Bardina SV, Michlmayr D, Rodriguez CA, Sum J, Foster GA, Krysztof D, Stramer SL, Lim JK.

J Infect Dis.2016 Aug 15;214(4):634-43.

Dual Function of Ccr5 during Langat Virus Encephalitis: Reduction in Neutrophil-Mediated Central Nervous System Inflammation and Increase in T Cell-Mediated Viral Clearance.

Michlmayr D, Bardina SV, Rodriguez CA, Pletnev AG, Lim JK.

J Immunol. 2016 Jun 1;196(11):4622-31.