Read our publications

  1. SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity

    Oh DS, Kim E, Lu G, Normand R, Shook LL, Lyall A, Jasset O, Demidkin S, Gilbert E, Kim J, Akinwunmi B, Tantivit J, Tirard A, Arnold BY, Slowikowski K, Goldberg MB, Filbin MR, Hacohen N, Nguyen LH, Chan AT, Yu XG, Li JZ, Yonker L, Fasano A, Perlis RH, Pasternak O, Gray KJ, Choi GB, Drew DA, Sen P, Villani AC, Edlow AG, Huh JR

    medRxiv. 2024 Feb 07

    PMID: 38370801 PMCID: PMC10871456

  2. Immune Responses in Checkpoint Myocarditis Across Heart, Blood, and Tumor

    Blum SM, Zlotoff DA, Smith NP, Kernin IJ, Ramesh S, Zubiri L, Caplin J, Samanta N, Martin SC, Tirard A, Sen P, Song Y, Barth J, Slowikowski K, Nasrallah M, Tantivit J, Manakongtreecheep K, Arnold BY, McGuire J, Pinto CJ, McLoughlin D, Jackson M, Chan P, Lawless A, Sharova T, Nieman LT, Gainor JF, Juric D, Mino-Kenudsen M, Sullivan RJ, Boland GM, Stone JR, Thomas MF, Neilan TG, Reynolds KL, Villani AC

    bioRxiv. 2023 Nov 29

    PMID: 37790460 PMCID: PMC10542127

  3. Gene-based association study of rare variants in children of diverse ancestries implicates TNFRSF21 in the development of allergic asthma

    Clay S, Alladina J, Smith NP, Visness CM, Wood RA, O'Connor GT, Cohen RT, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Rivera-Spoljaric K, Robison RG, Gergen PJ, Busse WW, Villani AC, Cho JL, Medoff BD, Gern JE, Jackson DJ, Ober C, Dapas M

    J Allergy Clin Immunol. 2024 Mar

    PMID: 37944567

  4. The evolving landscape of immune-related adverse events that follow immune checkpoint immunotherapy in cancer patients

    Villani AC

    Immunol Rev. 2023 09

    PMID: 37632320

  5. A human model of asthma exacerbation reveals transcriptional programs and cell circuits specific to allergic asthma

    Alladina J, Smith NP, Kooistra T, Slowikowski K, Kernin IJ, Deguine J, Keen HL, Manakongtreecheep K, Tantivit J, Rahimi RA, Sheng SL, Nguyen ND, Haring AM, Giacona FL, Hariri LP, Xavier RJ, Luster AD, Villani AC, Cho JL, Medoff BD

    Sci Immunol. 2023 05 12

    PMID: 37146132 PMCID: PMC10440046

    View the data

  6. Protocol for bulk RNA sequencing of enriched human neutrophils from whole blood and estimation of sample purity

    Gonye ALK, LaSalle TJ, Freeman SS, Reyes M, Hacohen N, Villani AC, Sade-Feldman M

    STAR Protoc. 2023 03 17

    PMID: 36853705 PMCID: PMC9946790

  7. Soluble and cell-based markers of immune checkpoint inhibitor-associated nephritis

    Sise ME, Wang Q, Seethapathy H, Moreno D, Harden D, Smith RN, Rosales IA, Colvin RB, Chute S, Cornell LD, Herrmann SM, Fadden R, Sullivan RJ, Yang NJ, Barmettler S, Wells S, Gupta S, Villani AC, Reynolds KL, Farmer J

    J Immunother Cancer. 2023 01

    PMID: 36657813 PMCID: PMC9853261

  8. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

    Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS

    bioRxiv. 2022 Oct 28

    PMID: 36324805 PMCID: PMC9628199

  9. Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients

    LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Revach OY, Mehta A, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M

    Cell Rep Med. 2022 10 18

    PMID: 36208629 PMCID: PMC9510054

  10. Plasmacytoid dendritic cells: Welcome back to the DC fold

    Reynolds G, Tirard A, Villani AC

    Immunity. 2022 03 08

    PMID: 35263562

  11. Alveolar, Endothelial, and Organ Injury Marker Dynamics in Severe COVID-19

    Leisman DE, Mehta A, Thompson BT, Charland NC, Gonye ALK, Gushterova I, Kays KR, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Filbin MR, Goldberg MB

    Am J Respir Crit Care Med. 2022 03 01

    PMID: 34878969 PMCID: PMC8906476

  12. Association between serum lactate dehydrogenase and cutaneous immune-related adverse events among patients on immune checkpoint inhibitors for advanced melanoma

    Asdourian MS, Otto TS, Jacoby TV, Shah N, Thompson LL, Blum SM, Reynolds KL, Semenov YR, Lawrence DP, Sullivan RJ, Boland GM, Villani AC, Chen ST

    J Am Acad Dermatol. 2022 11

    PMID: 35192899 PMCID: PMC10796160

  13. Single-cell immunophenotyping of the fetal immune response to maternal SARS-CoV-2 infection in late gestation

    Matute JD, Finander B, Pepin D, Ai X, Smith NP, Li JZ, Edlow AG, Villani AC, Lerou PH, Kalish BT

    Pediatr Res. 2022 04

    PMID: 34750520 PMCID: PMC8573077

  14. Early cross-coronavirus reactive signatures of humoral immunity against COVID-19

    Kaplonek P, Wang C, Bartsch Y, Fischinger S, Gorman MJ, Bowman K, Kang J, Dayal D, Martin P, Nowak RP, Villani AC, Hsieh CL, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Sade-Feldman M, Feldman J, Julg B, Nilles EJ, Musk ER, Menon AS, Fischer ES, McLellan JS, Schmidt A, Goldberg MB, Filbin MR, Hacohen N, Lauffenburger DA, Alter G

    Sci Immunol. 2021 Oct 15

    PMID: 34652962 PMCID: PMC8943686

  15. Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients

    LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M

    bioRxiv. 2021 Oct 05

    PMID: 34642692 PMCID: PMC8509090

  16. Harnessing the Potential of Multiomics Studies for Precision Medicine in Infectious Disease

    Ward RA, Aghaeepour N, Bhattacharyya RP, Clish CB, Gaudillière B, Hacohen N, Mansour MK, Mudd PA, Pasupneti S, Presti RM, Rhee EP, Sen P, Spec A, Tam JM, Villani AC, Woolley AE, Hsu JL, Vyas JM

    Open Forum Infect Dis. 2021 Nov

    PMID: 34805429 PMCID: PMC8598922

  17. Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures

    Byrne EH, Farcasanu M, Bloom SM, Xulu N, Xu J, Hykes BL, Mafunda NA, Hayward MR, Dong M, Dong KL, Gumbi T, Ceasar FX, Ismail N, Ndung'u T, Gosmann C, Ghebremichael MS, Handley SA, Mitchell CM, Villani AC, Kwon DS

    Front Cell Infect Microbiol. 2021

    PMID: 34604114 PMCID: PMC8482842

  18. Altered interactions between circulating and tissue-resident CD8 T cells with the colonic mucosa define colitis associated with immune checkpoint inhibitors

    Thomas MF, Slowikowski K, Manakongtreecheep K, Sen P, Tantivit J, Nasrallah M, Smith NP, Ramesh S, Zubiri L, Tirard A, Arnold BY, Nieman LT, Chen JH, Eisenhaure T, Pelka K, Xu KH, Jorgji V, Pinto CJ, Sharova T, Glasser R, Chan EP, Sullivan RJ, Khalili H, Juric D, Boland GM, Dougan M, Hacohen N, Reynolds KL, Li B, Villani AC

    bioRxiv. 2021-09-20

    View the data

  19. Development of preclinical and clinical models for immune-related adverse events following checkpoint immunotherapy: a perspective from SITC and AACR

    Bayless NL, Bluestone JA, Bucktrout S, Butterfield LH, Jaffee EM, Koch CA, Roep BO, Sharpe AH, Murphy WJ, Villani AC, Walunas TL

    J Immunother Cancer. 2021 09

    PMID: 34479924 PMCID: PMC8420733

  20. Effect of a multidisciplinary Severe Immunotherapy Complications Service on outcomes for patients receiving immune checkpoint inhibitor therapy for cancer

    Zubiri L, Molina GE, Mooradian MJ, Cohen J, Durbin SM, Petrillo L, Boland GM, Juric D, Dougan M, Thomas MF, Faje AT, Rengarajan M, Guidon AC, Chen ST, Okin D, Medoff BD, Nasrallah M, Kohler MJ, Schoenfeld SR, Karp-Leaf RS, Sise ME, Neilan TG, Zlotoff DA, Farmer JR, Bardia A, Sullivan RJ, Blum SM, Semenov YR, Villani AC, Reynolds KL

    J Immunother Cancer. 2021 09

    PMID: 34544895 PMCID: PMC8454442

  21. SARS-CoV-2 viremia is associated with distinct proteomic pathways and predicts COVID-19 outcomes

    Li Y, Schneider AM, Mehta A, Sade-Feldman M, Kays KR, Gentili M, Charland NC, Gonye AL, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Parry BA, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Regan J, Flynn JP, Villani AC, Hacohen N, Goldberg MB, Filbin MR, Li JZ

    J Clin Invest. 2021 07 01

    PMID: 34196300 PMCID: PMC8245177

  22. Immune-related adverse events associated with immune checkpoint inhibitors: a call to action for collecting and sharing clinical trial and real-world data

    Reynolds KL, Arora S, Elayavilli RK, Louv WC, Schaller TH, Khandelwal A, Rothenberg M, Khozin S, Guidon AC, Dougan M, Zubiri L, Petrillo L, Sise ME, Villani AC, Johnson DB, Rahma O, Sharon E

    J Immunother Cancer. 2021 07

    PMID: 34215691 PMCID: PMC8256840

  23. Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro

    Reyes M, Filbin MR, Bhattacharyya RP, Sonny A, Mehta A, Billman K, Kays KR, Pinilla-Vera M, Benson ME, Cosimi LA, Hung DT, Levy BD, Villani AC, Sade-Feldman M, Baron RM, Goldberg MB, Blainey PC, Hacohen N

    Sci Transl Med. 2021 06 16

    PMID: 34103408 PMCID: PMC8432955

  24. The positive effect of immune checkpoint inhibitor-induced thyroiditis on overall survival accounting for immortal time bias: a retrospective cohort study of 6596 patients

    Street S, Chute D, Strohbehn I, Zhao S, Rengarajan M, Faje A, Seethapathy H, Lee M, Seethapathy R, Drobni Z, Rahma O, Neilan TG, Sullivan RJ, Villani AC, Zubiri L, Mooradian MJ, Reynolds KL, Sise ME

    Ann Oncol. 2021 08

    PMID: 34020034 PMCID: PMC8814352

  25. The Known Unknowns of the Immune Response to Coccidioides

    Ward RA, Thompson GR, Villani AC, Li B, Mansour MK, Wuethrich M, Tam JM, Klein BS, Vyas JM

    J Fungi (Basel). 2021 May 11

    PMID: 34065016 PMCID: PMC8151481

  26. Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions

    Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB

    Cell Rep Med. 2021 05 18

    PMID: 33969320 PMCID: PMC8091031

  27. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

    Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A

    Nature. 2021 07

    PMID: 33915569 PMCID: PMC8919505

  28. Temporal Trends and Outcomes Among Patients Admitted for Immune-Related Adverse Events: A Single-Center Retrospective Cohort Study from 2011 to 2018

    Molina GE, Zubiri L, Cohen JV, Durbin SM, Petrillo L, Allen IM, Murciano-Goroff YR, Dougan M, Thomas MF, Faje AT, Rengarajan M, Guidon AC, Chen ST, Okin D, Medoff BD, Nasrallah M, Kohler MJ, Schoenfeld SR, Karp Leaf RS, Sise ME, Neilan TG, Zlotoff DA, Farmer JR, Mooradian MJ, Bardia A, Mai M, Sullivan RJ, Semenov YR, Villani AC, Reynolds KL

    Oncologist. 2021 06

    PMID: 33655682 PMCID: PMC8176966

  29. SARS-CoV-2 Viremia is Associated with Distinct Proteomic Pathways and Predicts COVID-19 Outcomes

    Li Y, Schneider AM, Mehta A, Sade-Feldman M, Kays KR, Gentili M, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Parry BA, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Regan J, Flynn JP, Villani AC, Hacohen N, Goldberg MB, Filbin MR, Li JZ

    medRxiv. 2021 Feb 26

    PMID: 33655257 PMCID: PMC7924277

  30. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

    Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe A, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Bloom-Ackerman Z, Barkas N, Ganna A, Gomez J, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jane-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A

    bioRxiv. 2021 Feb 25

    PMID: 33655247 PMCID: PMC7924267

  31. Developmental cell programs are co-opted in inflammatory skin disease

    Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N, Olabi B, Dubois A, Dixon D, Green K, Maunder D, Engelbert J, Efremova M, Polanski K, Jardine L, Jones C, Ness T, Horsfall D, McGrath J, Carey C, Popescu DM, Webb S, Wang XN, Sayer B, Park JE, Negri VA, Belokhvostova D, Lynch MD, McDonald D, Filby A, Hagai T, Meyer KB, Husain A, Coxhead J, Vento-Tormo R, Behjati S, Lisgo S, Villani AC, Bacardit J, Jones PH, O'Toole EA, Ogg GS, Rajan N, Reynolds NJ, Teichmann SA, Watt FM, Haniffa M

    Science. 2021 01 22

    PMID: 33479125 PMCID: PMC7611557

  32. Altered ratio of dendritic cell subsets in skin-draining lymph nodes promotes Th2-driven contact hypersensitivity

    Miller HL, Andhey PS, Swiecki MK, Rosa BA, Zaitsev K, Villani AC, Mitreva M, Artyomov MN, Gilfillan S, Cella M, Colonna M

    Proc Natl Acad Sci U S A. 2021 01 19

    PMID: 33431694 PMCID: PMC7826349

  33. Widespread haploid-biased gene expression enables sperm-level natural selection

    Bhutani K, Stansifer K, Ticau S, Bojic L, Villani AC, Slisz J, Cremers CM, Roy C, Donovan J, Fiske B, Friedman RC

    Science. 2021 Mar 05

    PMID: 33446482

  34. Decreased Absolute Lymphocyte Count and Increased Neutrophil/Lymphocyte Ratio With Immune Checkpoint Inhibitor-Associated Myocarditis

    Drobni ZD, Zafar A, Zubiri L, Zlotoff DA, Alvi RM, Lee C, Hartmann S, Gilman HK, Villani AC, Nohria A, Groarke JD, Sullivan RJ, Reynolds KL, Zhang L, Neilan TG

    J Am Heart Assoc. 2020 12

    PMID: 33190570 PMCID: PMC7763791

  35. Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients

    Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB

    bioRxiv. 2020 Nov 03

    PMID: 33173871 PMCID: PMC7654866

  36. Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity

    Shrock E, Fujimura E, Kula T, Timms RT, Lee IH, Leng Y, Robinson ML, Sie BM, Li MZ, Chen Y, Logue J, Zuiani A, McCulloch D, Lelis FJN, Henson S, Monaco DR, Travers M, Habibi S, Clarke WA, Caturegli P, Laeyendecker O, Piechocka-Trocha A, Li JZ, Khatri A, Chu HY, Villani AC, Kays K, Goldberg MB, Hacohen N, Filbin MR, Yu XG, Walker BD, Wesemann DR, Larman HB, Lederer JA, Elledge SJ

    Science. 2020 11 27

    PMID: 32994364 PMCID: PMC7857405

  37. Induction of a regulatory myeloid program in bacterial sepsis and severe COVID-19

    Reyes M, Filbin MR, Bhattacharyya RP, Sonny A, Mehta A, Billman K, Kays KR, Pinilla-Vera M, Benson ME, Cosimi LA, Hung DT, Levy BD, Villani AC, Sade-Feldman M, Baron RM, Goldberg MB, Blainey PC, Hacohen N

    bioRxiv. 2020 Sep 02

    PMID: 32908980 PMCID: PMC7480031

  38. Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

    Li B, Gould J, Yang Y, Sarkizova S, Tabaka M, Ashenberg O, Rosen Y, Slyper M, Kowalczyk MS, Villani AC, Tickle T, Hacohen N, Rozenblatt-Rosen O, Regev A

    Nat Methods. 2020 08

    PMID: 32719530 PMCID: PMC7437817

  39. Incidence and Clinical Features of Immune-Related Acute Kidney Injury in Patients Receiving Programmed Cell Death Ligand-1 Inhibitors

    Seethapathy H, Zhao S, Strohbehn IA, Lee M, Chute DF, Bates H, Molina GE, Zubiri L, Gupta S, Motwani S, Leaf DE, Sullivan RJ, Rahma O, Blumenthal KG, Villani AC, Reynolds KL, Sise ME

    Kidney Int Rep. 2020 Oct

    PMID: 33102962 PMCID: PMC7569697

  40. The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection

    Abbas A, Vu Manh TP, Valente M, Collinet N, Attaf N, Dong C, Naciri K, Chelbi R, Brelurut G, Cervera-Marzal I, Rauwel B, Davignon JL, Bessou G, Thomas-Chollier M, Thieffry D, Villani AC, Milpied P, Dalod M, Tomasello E

    Nat Immunol. 2020 09

    PMID: 32690951

  41. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

    Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, Li S, Hacohen N, Rozenblatt-Rosen O, Shalek AK, Villani AC, Regev A, Levin JZ

    Nat Biotechnol. 2020 06

    PMID: 32341560 PMCID: PMC7289686

  42. Transcriptomic Analysis and High-dimensional Phenotypic Mapping of Mononuclear Phagocytes in Mesenteric Lymph Nodes Reveal Differences Between Ulcerative Colitis and Crohn's Disease

    Chapuy L, Bsat M, Rubio M, Harvey F, Motta V, Schwenter F, Wassef R, Richard C, Deslandres C, Nguyen BN, Soucy G, Hacohen N, Fritz J, Villani AC, Mehta H, Sarfati M

    J Crohns Colitis. 2020 Mar 13

    PMID: 31541232

  43. SLAMF6 deficiency augments tumor killing and skews toward an effector phenotype revealing it as a novel T cell checkpoint

    Hajaj E, Eisenberg G, Klein S, Frankenburg S, Merims S, Ben David I, Eisenhaure T, Henrickson SE, Villani AC, Hacohen N, Abudi N, Abramovich R, Cohen JE, Peretz T, Veillette A, Lotem M

    Elife. 2020 03 03

    PMID: 32122464 PMCID: PMC7075692

  44. IL-12 and Mucosal CD14+ Monocyte-Like Cells Induce IL-8 in Colonic Memory CD4+ T Cells of Patients With Ulcerative Colitis but not Crohn's Disease

    Chapuy L, Bsat M, Rubio M, Sarkizova S, Therrien A, Bouin M, Orlicka K, Weber A, Soucy G, Villani AC, Sarfati M

    J Crohns Colitis. 2020 Jan 01

    PMID: 31206576

  45. The Incidence, Causes, and Risk Factors of Acute Kidney Injury in Patients Receiving Immune Checkpoint Inhibitors

    Seethapathy H, Zhao S, Chute DF, Zubiri L, Oppong Y, Strohbehn I, Cortazar FB, Leaf DE, Mooradian MJ, Villani AC, Sullivan RJ, Reynolds K, Sise ME

    Clin J Am Soc Nephrol. 2019 12 06

    PMID: 31672794 PMCID: PMC6895474

  46. Decoding human fetal liver haematopoiesis

    Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M

    Nature. 2019 10

    PMID: 31597962 PMCID: PMC6861135

  47. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

    Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A

    Cell. 2019 07 25

    PMID: 31348891 PMCID: PMC6662628

  48. Cardiotoxicity of Immune Checkpoint Inhibitors

    Zhang L, Jones-O'Connor M, Awadalla M, Zlotoff DA, Thavendiranathan P, Groarke JD, Villani AC, Lyon AR, Neilan TG

    Curr Treat Options Cardiovasc Med. 2019 Jun 08

    PMID: 31175469

  49. Targeting the CBM complex causes Treg cells to prime tumours for immune checkpoint therapy

    Di Pilato M, Kim EY, Cadilha BL, Prüßmann JN, Nasrallah MN, Seruggia D, Usmani SM, Misale S, Zappulli V, Carrizosa E, Mani V, Ligorio M, Warner RD, Medoff BD, Marangoni F, Villani AC, Mempel TR

    Nature. 2019 06

    PMID: 31092922 PMCID: PMC6656391

  50. Two distinct colonic CD14+ subsets characterized by single-cell RNA profiling in Crohn's disease

    Chapuy L, Bsat M, Sarkizova S, Rubio M, Therrien A, Wassef E, Bouin M, Orlicka K, Weber A, Hacohen N, Villani AC, Sarfati M

    Mucosal Immunol. 2019 05

    PMID: 30670762

  51. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

    Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N

    Cell. 2019 Jan 10

    PMID: 30633907

  52. Targeting individual cells by barcode in pooled sequence libraries

    Ranu N, Villani AC, Hacohen N, Blainey PC

    Nucleic Acids Res. 2019 01 10

    PMID: 30256981 PMCID: PMC6326790

  53. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

    Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N

    Genome Res. 2018 12

    PMID: 30446528

  54. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

    Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N

    Cell. 2018 11 01

    PMID: 30388456 PMCID: PMC6641984

  55. Large-Scale Human Dendritic Cell Differentiation Revealing Notch-Dependent Lineage Bifurcation and Heterogeneity

    Balan S, Arnold-Schrauf C, Abbas A, Couespel N, Savoret J, Imperatore F, Villani AC, Vu Manh TP, Bhardwaj N, Dalod M

    Cell Rep. 2018 08 14

    PMID: 30110645 PMCID: PMC6113934

  56. Systems Immunology: Learning the Rules of the Immune System

    Villani AC, Sarkizova S, Hacohen N

    Annu Rev Immunol. 2018 04 26

    PMID: 29677477 PMCID: PMC6597491

  57. A transcriptomic atlas of aged human microglia

    Olah M, Patrick E, Villani AC, Xu J, White CC, Ryan KJ, Piehowski P, Kapasi A, Nejad P, Cimpean M, Connor S, Yung CJ, Frangieh M, McHenry A, Elyaman W, Petyuk V, Schneider JA, Bennett DA, De Jager PL, Bradshaw EM

    Nat Commun. 2018 02 07

    PMID: 29416036 PMCID: PMC5803269

  58. Landscape of X chromosome inactivation across human tissues

    Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG

    Nature. 2017 10 11

    PMID: 29022598

  59. Aryl Hydrocarbon Receptor Controls Monocyte Differentiation into Dendritic Cells versus Macrophages

    Goudot C, Coillard A, Villani AC, Gueguen P, Cros A, Sarkizova S, Tang-Huau TL, Bohec M, Baulande S, Hacohen N, Amigorena S, Segura E

    Immunity. 2017 09 19

    PMID: 28930664

  60. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

    Villani AC, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N

    Science. 2017 04 21

    PMID: 28428369 PMCID: PMC5775029

  61. Single-Cell RNA Sequencing of Human T Cells

    Villani AC, Shekhar K

    Methods Mol Biol. 2017

    PMID: 27787803

  62. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

    Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA

    Science. 2016 Apr 08

    PMID: 27124452 PMCID: PMC4944528

  63. Sex Differences in Plasmacytoid Dendritic Cell Levels of IRF5 Drive Higher IFN-a Production in Women

    Griesbeck M, Ziegler S, Laffont S, Smith N, Chauveau L, Tomezsko P, Sharei A, Kourjian G, Porichis F, Hart M, Palmer CD, Sirignano M, Beisel C, Hildebrandt H, Cénac C, Villani AC, Diefenbach TJ, Le Gall S, Schwartz O, Herbeuval JP, Autran B, Guéry JC, Chang JJ, Altfeld M

    J Immunol. 2015 Dec 01

    PMID: 26519527 PMCID: PMC4654231

  64. Common genetic variants modulate pathogen-sensing responses in human dendritic cells

    Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N

    Science. 2014 Mar 07

    PMID: 24604203

  65. Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach

    Lee MN, Roy M, Ong SE, Mertins P, Villani AC, Li W, Dotiwala F, Sen J, Doench JG, Orzalli MH, Kramnik I, Knipe DM, Lieberman J, Carr SA, Hacohen N

    Nat Immunol. 2013 Feb

    PMID: 23263557 PMCID: PMC3838897

  66. Genetic risk factors for post-infectious irritable bowel syndrome following a waterborne outbreak of gastroenteritis

    Villani AC, Lemire M, Thabane M, Belisle A, Geneau G, Garg AX, Clark WF, Moayyedi P, Collins SM, Franchimont D, Marshall JK

    Gastroenterology. 2010 Apr

    PMID: 20044998

  67. [Bacterial recognition of the intestinal microbial flora: an important risk factor for Crohn's disease]

    Villani AC, Franchimont D

    Med Sci (Paris). 2010 Jan

    PMID: 20132772

  68. Genetic variation in the familial Mediterranean fever gene (MEFV) and risk for Crohn's disease and ulcerative colitis

    Villani AC, Lemire M, Louis E, Silverberg MS, Collette C, Fortin G, Nimmo ER, Renaud Y, Brunet S, Libioulle C, Belaiche J, Bitton A, Gaudet D, Cohen A, Langelier D, Rioux JD, Arnott ID, Wild GE, Rutgeerts P, Satsangi J, Vermeire S, Hudson TJ, Franchimont D

    PLoS One. 2009 Sep 28

    PMID: 19784369 PMCID: PMC2745755

  69. The contribution of genetic studies in shifting the immunopathogenesis paradigm of Crohn's disease

    Villani AC, Franchimont D

    Expert Rev Clin Immunol. 2009 Jul

    PMID: 20477033

  70. L-carnitine, a diet component and organic cation transporter OCTN ligand, displays immunosuppressive properties and abrogates intestinal inflammation

    Fortin G, Yurchenko K, Collette C, Rubio M, Villani AC, Bitton A, Sarfati M, Franchimont D

    Clin Exp Immunol. 2009 Apr

    PMID: 19175620

  71. Common variants in the NLRP3 region contribute to Crohn's disease susceptibility

    Villani AC, Lemire M, Fortin G, Louis E, Silverberg MS, Collette C, Baba N, Libioulle C, Belaiche J, Bitton A, Gaudet D, Cohen A, Langelier D, Fortin PR, Wither JE, Sarfati M, Rutgeerts P, Rioux JD, Vermeire S, Hudson TJ, Franchimont D

    Nat Genet. 2009 Jan

    PMID: 19098911 PMCID: PMC2728932

  72. Tumor necrosis factor receptor gene polymorphisms in Crohn's disease: association with clinical phenotypes

    Waschke KA, Villani AC, Vermeire S, Dufresne L, Chen TC, Bitton A, Cohen A, Thomson AB, Wild GE

    Am J Gastroenterol. 2005 May

    PMID: 15842589