Jonathan Irish, PhD

Publications

• Canderan G, Muehling LM, Kadl A, Ladd S, Bonham C, Cross CE, Lima SM, Yin X, Sturek JM, Wilson JM, Keshavarz B, Enfield KB, Ramani C, Bryant N, Murphy DD, Cheon IS, Solga M, Pramoonjago P, McNamara CA, Sun J, Utz PJ, Dolatshahi S, Irish JM, Woodfolk JA. Distinct type 1 immune networks underlie the severity of restrictive lung disease after COVID-19. Nat Immunol. 2025 Apr;26(4):595-606. PubMed PMID: 40140496
• Schares HAM, Hayes MJ, Balsamo JA, Thirman HL, Bachmann BO, Irish JM. Multiplexed cytometry for single cell chemical biology. Methods Cell Biol. 2025;195:143-172. PubMed PMID: 40180452
• Thirman HL, Grider-Hayes MJ, Geben LC, Ihrie RA, Brown LE, Porco JA Jr, Irish JM. Connecting chemical structure to single cell signaling profiles. Commun Biol. 2025 Jul 31;8(1):1137. PubMed PMID: 40745386
• Froese JT, Balsamo JA, Reisman BJ, Barone SM, Irish JM, Bachmann BO. Multiplexed activity metabolomics for isolation of filipin macrolides from a hypogean actinomycete. J Antibiot (Tokyo). 2024 Dec 6. [Epub ahead of print] PubMed PMID: 39643649
• Syrimi E, Khan N, Murray P, Willcox C, Haigh T, Willcox B, Masand N, Bowen C, Dimakou DB, Zuo J, Barone SM, Irish JM, Kearns P, Taylor GS. Defects in NK cell immunity of pediatric cancer patients revealed by deep immune profiling. iScience. 2024 Sep 20;27(9):110837. PubMed PMID: 39310750
• Voss K, Bartkowiak T, Sewell AE, Chi C, Landis MD, Schaefer S, Pua HH, Connelly JA, Irish JM, Rathmell JC, Kaviany S. Peripheral T Cell Development and Immunophenotyping of Twins with Heterozygous FOXN1 Mutations. Immunohorizons. 2024 Jul 1;8(7):492-499. PubMed PMID: 39008056
• Tentori CA, Zhao LP, Tinterri B, Strange KE, Zoldan K, Dimopoulos K, Feng X, Riva E, Lim B, Simoni Y, Murthy V, Hayes MJ, Poloni A, Padron E, Cardoso BA, Cross M, Winter S, Santaolalla A, Patel BA, Groarke EM, Wiseman DH, Jones K, Jamieson L, Manogaran C, Daver N, Gallur L, Ingram W, Ferrell PB, Sockel K, Dulphy N, Chapuis N, Kubasch AS, Olsnes AM, Kulasekararaj A, De Lavellade H, Kern W, Van Hemelrijck M, Bonnet D, Westers TM, Freeman S, Oelschlaegel U, Valcarcel D, Raddi MG, Grønbæk K, Fontenay M, Loghavi S, Santini V, Almeida AM, Irish JM, Sallman DA, Young NS, van de Loosdrecht AA, Adès L, Della Porta MG, Cargo C, Platzbecker U, Kordasti S. Immune-monitoring of myelodysplastic neoplasms: Recommendations from the i4MDS consortium. Hemasphere. 2024 May;8(5):e64. PubMed PMID: 38756352
• Cross CE, Mayeda C, Medina S, Hayes MJ, Kaviany S, Connelly JA, Rathmell JC, Weaver KD, Thompson RC, Chambless LB, Ihrie RA, Irish JM. Velociraptor: Cross-Platform Quantitative Search Using Hallmark Cell Features. bioRxiv. 2024 May 4. PubMed PMID: 38746337
• Medina S, Brockman AA, Cross CE, Hayes MJ, Mobley BC, Mistry AM, Chotai S, Weaver KD, Thompson RC, Chambless LB, Ihrie RA, Irish JM. IL-8 Instructs Macrophage Identity in Lateral Ventricle Contacting Glioblastoma. bioRxiv. 2024 Mar 30. PubMed PMID: 38585888
• von Lersner AK, Fernandes F, Ozawa PMM, Jackson M, Masureel M, Ho H, Lima SM, Vagner T, Sung BH, Wehbe M, Franze K, Pua H, Wilson JT, Irish JM, Weaver AM, Di Vizio D, Zijlstra A. Multiparametric Single-Vesicle Flow Cytometry Resolves Extracellular Vesicle Heterogeneity and Reveals Selective Regulation of Biogenesis and Cargo Distribution. ACS Nano. 2024 Apr 16;18(15):10464-10484. PubMed PMID: 38578701
• Bewersdorf JP, Shallis RM, Sharon E, Park S, Ramaswamy R, Roe CE, Irish JM, Caldwell A, Wei W, Yacoub A, Madanat YF, Zeidner JF, Altman JK, Odenike O, Yerrabothala S, Kovacsovics T, Podoltsev NA, Halene S, Little RF, Piekarz R, Gore SD, Kim TK, Zeidan AM. A multicenter phase Ib trial of the histone deacetylase inhibitor entinostat in combination with pembrolizumab in patients with myelodysplastic syndromes/neoplasms or acute myeloid leukemia refractory to hypomethylating agents. Ann Hematol. 2024 Jan;103(1):105-116. PubMed PMID: 38036712
• Senosain MF, Zou Y, Patel K, Zhao S, Coullomb A, Rowe DJ, Lehman JM, Irish JM, Maldonado F, Kammer MN, Pancaldi V, Lopez CF. Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness. Cancer Res Commun. 2023 Jul;3(7):1350-1365. PubMed PMID: 37501683
• Norlander AE, Abney M, Cephus JY, Roe CE, Irish JM, Shelburne NJ, Newcomb DC, Hemnes AR, Peebles RS Jr. Prostaglandin I(2) Therapy Promotes Regulatory T Cell Generation in Patients with Pulmonary Arterial Hypertension. Am J Respir Crit Care Med. 2023 Sep 15;208(6):737-739. PubMed PMID: 37413696
• Bartkowiak T, Lima SM, Hayes MJ, Mistry AM, Brockman AA, Sinnaeve J, Leelatian N, Roe CE, Mobley BC, Chotai S, Weaver KD, Thompson RC, Chambless LB, Ihrie RA, Irish JM. An immunosuppressed microenvironment distinguishes lateral ventricle-contacting glioblastomas. JCI Insight. 2023 Jun 22;8(12). PubMed PMID: 37192001
• Alexander MR, Dale BL, Smart CD, Elijovich F, Wogsland CE, Lima SM, Irish JM, Madhur MS. Immune Profiling Reveals Decreases in Circulating Regulatory and Exhausted T Cells in Human Hypertension. JACC Basic Transl Sci. 2023 Mar;8(3):319-336. PubMed PMID: 37034287
• Geben LC, Brockman AA, Chalkley MBL, Sweet SR, Gallagher JE, Scheuing AL, Simerly RB, Ess KC, Irish JM, Ihrie RA. Dephosphorylation of 4EBP1/2 Induces Prenatal Neural Stem Cell Quiescence. bioRxiv. 2023 Feb 15. PubMed PMID: 36824760
• Brockman AA, Khurana R, Bartkowiak T, Thomas PL, Sivagnanam S, Betts CB, Coussens LM, Lovly CM, Irish JM, Ihrie RA. Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT. Cytometry B Clin Cytom. 2023 Sep;104(5):344-355. PubMed PMID: 36748312
• Medina S, Ihrie RA, Irish JM. Learning cell identity in immunology, neuroscience, and cancer. Semin Immunopathol. 2023 Jan;45(1):3-16. PubMed PMID: 36534139
• Balsamo JA, Penton KE, Zhao Z, Hayes MJ, Lima SM, Irish JM, Bachmann BO. An immunogenic cell injury module for the single-cell multiplexed activity metabolomics platform to identify promising anti-cancer natural products. J Biol Chem. 2022 Sep;298(9):102300. PubMed PMID: 35931117
• Huse K, Bai B, Hilden VI, Bollum LK, Våtsveen TK, Munthe LA, Smeland EB, Irish JM, Wälchli S, Myklebust JH. Mechanism of CD79A and CD79B Support for IgM+ B Cell Fitness through B Cell Receptor Surface Expression. J Immunol. 2022 Nov 15;209(10):2042-2053. PubMed PMID: 36426942
• Meghraoui-Kheddar A, Chousterman BG, Guillou N, Barone SM, Granjeaud S, Vallet H, Corneau A, Guessous K, de Roquetaillade C, Boissonnas A, Irish JM, Combadière C. Two New Neutrophil Subsets Define a Discriminating Sepsis Signature. Am J Respir Crit Care Med. 2022 Jan 1;205(1):46-59. PubMed PMID: 34731593
• Kramer KJ, Wilfong EM, Voss K, Barone SM, Shiakolas AR, Raju N, Roe CE, Suryadevara N, Walker LM, Wall SC, Paulo A, Schaefer S, Dahunsi D, Westlake CS, Crowe JE Jr, Carnahan RH, Rathmell JC, Bonami RH, Georgiev IS, Irish JM. Single-cell profiling of the antigen-specific response to BNT162b2 SARS-CoV-2 RNA vaccine. Nat Commun. 2022 Jun 16;13(1):3466. PubMed PMID: 35710908
• Kaviany S, Bartkowiak T, Dulek DE, Khan YW, Hayes MJ, Schaefer SG, Ye X, Dahunsi DO, Connelly JA, Irish JM, Rathmell JC. Systems Immunology Analyses of STAT1 Gain-of-Function Immune Phenotypes Reveal Heterogeneous Response to IL-6 and Broad Immunometabolic Roles for STAT1. Immunohorizons. 2022 Jul 15;6(7):447-464. PubMed PMID: 35840326
• Wilfong EM, Bartkowiak T, Vowell KN, Westlake CS, Irish JM, Kendall PL, Crofford LJ, Bonami RH. High-Dimensional Analysis Reveals Distinct Endotypes in Patients With Idiopathic Inflammatory Myopathies. Front Immunol. 2022;13:756018. PubMed PMID: 35371068
• Senosain MF, Zou Y, Novitskaya T, Vasiukov G, Balar AB, Rowe DJ, Doxie DB, Lehman JM, Eisenberg R, Maldonado F, Zijlstra A, Novitskiy SV, Irish JM, Massion PP. HLA-DR cancer cells expression correlates with T cell infiltration and is enriched in lung adenocarcinoma with indolent behavior. Sci Rep. 2021 Jul 13;11(1):14424. PubMed PMID: 34257356
• Chattopadhyay PK, Filby A, Jellison ER, Ferrari G, Green C, Cherian S, Irish J, Litwin V. A Cytometrist's Guide to Coordinating and Performing Effective COVID-19 Research. Cytometry A. 2021 Jan;99(1):11-18. PubMed PMID: 32881296
• Barone SM, Paul AG, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. Elife. 2021 Aug 5;10. PubMed PMID: 34350827
• Le Gallou S, Lhomme F, Irish JM, Mingam A, Pangault C, Monvoisin C, Ferrant J, Azzaoui I, Rossille D, Bouabdallah K, Damaj G, Cartron G, Godmer P, Le Gouill S, Casasnovas RO, Molina TJ, Houot R, Lamy T, Tarte K, Fest T, Roussel M. Nonclassical Monocytes Are Prone to Migrate Into Tumor in Diffuse Large B-Cell Lymphoma. Front Immunol. 2021;12:755623. PubMed PMID: 34975843
• Ramsey HE, Stengel K, Pino JC, Johnston G, Childress M, Gorska AE, Arrate PM, Fuller L, Villaume M, Fischer MA, Ferrell PB Jr, Roe CE, Zou J, Lubbock ALR, Stubbs M, Zinkel S, Irish JM, Lopez CF, Hiebert S, Savona MR. Selective Inhibition of JAK1 Primes STAT5-Driven Human Leukemia Cells for ATRA-Induced Differentiation. Target Oncol. 2021 Sep;16(5):663-674. PubMed PMID: 34324169
• Reisman BJ, Barone SM, Bachmann BO, Irish JM. DebarcodeR increases fluorescent cell barcoding capacity and accuracy. Cytometry A. 2021 Sep;99(9):946-953. PubMed PMID: 33960644
• Healey DCC, Cephus JY, Barone SM, Chowdhury NU, Dahunsi DO, Madden MZ, Ye X, Yu X, Olszewski K, Young K, Gerriets VA, Siska PJ, Dworski R, Hemler J, Locasale JW, Poyurovsky MV, Peebles RS Jr, Irish JM, Newcomb DC, Rathmell JC. Targeting In Vivo Metabolic Vulnerabilities of Th2 and Th17 Cells Reduces Airway Inflammation. J Immunol. 2021 Mar 15;206(6):1127-1139. PubMed PMID: 33558372
• Yeh AC, Varelias A, Reddy A, Barone SM, Olver SD, Chilson K, Onstad LE, Ensbey KS, Henden AS, Samson L, Jaeger CA, Bi T, Dahlman KB, Kim TK, Zhang P, Degli-Esposti MA, Newell EW, Jagasia MH, Irish JM, Lee SJ, Hill GR. CMV exposure drives long-term CD57+ CD4 memory T-cell inflation following allogeneic stem cell transplant. Blood. 2021 Dec 30;138(26):2874-2885. PubMed PMID: 34115118
• Levine LS, Hiam-Galvez KJ, Marquez DM, Tenvooren I, Madden MZ, Contreras DC, Dahunsi DO, Irish JM, Oluwole OO, Rathmell JC, Spitzer MH. Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8(+) T cells during the primary immune response. Immunity. 2021 Apr 13;54(4):829-844.e5. PubMed PMID: 33705706
• Roe CE, Hayes MJ, Barone SM, Irish JM. Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data. Curr Protoc Cytom. 2020 Mar;93(1):e71. PubMed PMID: 32250555
• Roussel M, Lhomme F, Roe CE, Bartkowiak T, Gravelle P, Laurent C, Fest T, Irish JM. Mass cytometry defines distinct immune profile in germinal center B-cell lymphomas. Cancer Immunol Immunother. 2020 Mar;69(3):407-420. PubMed PMID: 31919622
• Lim SP, Costantini B, Mian SA, Perez Abellan P, Gandhi S, Martinez Llordella M, Lozano JJ, Antunes Dos Reis R, Povoleri GAM, Mourikis TP, Abarrategi A, Ariza-McNaughton L, Heck S, Irish JM, Lombardi G, Marsh JCW, Bonnet D, Kordasti S, Mufti GJ. Treg sensitivity to FasL and relative IL-2 deprivation drive idiopathic aplastic anemia immune dysfunction. Blood. 2020 Aug 13;136(7):885-897. PubMed PMID: 32294156
• Leelatian N, Sinnaeve J, Mistry AM, Barone SM, Brockman AA, Diggins KE, Greenplate AR, Weaver KD, Thompson RC, Chambless LB, Mobley BC, Ihrie RA, Irish JM. Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells. Elife. 2020 Jun 23;9. PubMed PMID: 32573435
• Beckermann KE, Hongo R, Ye X, Young K, Carbonell K, Healey DCC, Siska PJ, Barone S, Roe CE, Smith CC, Vincent BG, Mason FM, Irish JM, Rathmell WK, Rathmell JC. CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation. JCI Insight. 2020 Aug 20;5(16). PubMed PMID: 32814710
• Ferrer-Font L, Mayer JU, Old S, Hermans IF, Irish J, Price KM. High-Dimensional Data Analysis Algorithms Yield Comparable Results for Mass Cytometry and Spectral Flow Cytometry Data. Cytometry A. 2020 Aug;97(8):824-831. PubMed PMID: 32293794
• Ferrant J, Lhomme F, Le Gallou S, Irish JM, Roussel M. Circulating Myeloid Regulatory Cells: Promising Biomarkers in B-Cell Lymphomas. Front Immunol. 2020;11:623993. PubMed PMID: 33603754
• Czechowska K, Lannigan J, Aghaeepour N, Back JB, Begum J, Behbehani G, Bispo C, Bitoun D, Fernández AB, Boova ST, Brinkman RR, Ciccolella CO, Cotleur B, Davies D, Dela Cruz GV, Del Rio-Guerra R, Des Lauriers-Cox AM, Douagi I, Dumrese C, Bonilla Escobar DL, Estevam J, Ewald C, Fossum A, Gaudillière B, Green C, Groves C, Hall C, Haque Y, Hedrick MN, Hogg K, Hsieh EWY, Irish J, Lederer J, Leipold M, Lewis-Tuffin LJ, Litwin V, Lopez P, Nasdala I, Nedbal J, Ohlsson-Wilhelm BM, Price KM, Rahman AH, Rayanki R, Rieger AM, Robinson JP, Shapiro H, Sun YS, Tang VA, Tesfa L, Telford WG, Walker R, Welsh JA, Wheeler P, Tárnok A. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops. Cytometry A. 2019 Dec;95(12):1236-1274. PubMed PMID: 31833655
• Roussel M, Bartkowiak T, Irish JM. Picturing Polarized Myeloid Phagocytes and Regulatory Cells by Mass Cytometry. Methods Mol Biol. 2019;1989:217-226. PubMed PMID: 31077108
• Greenplate AR, McClanahan DD, Oberholtzer BK, Doxie DB, Roe CE, Diggins KE, Leelatian N, Rasmussen ML, Kelley MC, Gama V, Siska PJ, Rathmell JC, Ferrell PB, Johnson DB, Irish JM. Computational Immune Monitoring Reveals Abnormal Double-Negative T Cells Present across Human Tumor Types. Cancer Immunol Res. 2019 Jan;7(1):86-99. PubMed PMID: 30413431
• Gandelman JS, Byrne MT, Mistry AM, Polikowsky HG, Diggins KE, Chen H, Lee SJ, Arora M, Cutler C, Flowers M, Pidala J, Irish JM, Jagasia MH. Machine learning reveals chronic graft-versus-host disease phenotypes and stratifies survival after stem cell transplant for hematologic malignancies. Haematologica. 2019 Jan;104(1):189-196. PubMed PMID: 30237265
• Rushing GV, Brockman AA, Bollig MK, Leelatian N, Mobley BC, Irish JM, Ess KC, Fu C, Ihrie RA. Location-dependent maintenance of intrinsic susceptibility to mTORC1-driven tumorigenesis. Life Sci Alliance. 2019 Apr;2(2). PubMed PMID: 30910807
• Huse K, Wogsland CE, Polikowsky HG, Diggins KE, Smeland EB, Myklebust JH, Irish JM. Human Germinal Center B Cells Differ from Naïve and Memory B Cells in CD40 Expression and CD40L-Induced Signaling Response. Cytometry A. 2019 Apr;95(4):442-449. PubMed PMID: 30838773
• Mistry AM, Greenplate AR, Ihrie RA, Irish JM. Beyond the message: advantages of snapshot proteomics with single-cell mass cytometry in solid tumors. FEBS J. 2019 Apr;286(8):1523-1539. PubMed PMID: 30549207
• Doxie DB, Greenplate AR, Gandelman JS, Diggins KE, Roe CE, Dahlman KB, Sosman JA, Kelley MC, Irish JM. BRAF and MEK inhibitor therapy eliminates Nestin-expressing melanoma cells in human tumors. Pigment Cell Melanoma Res. 2018 Nov;31(6):708-719. PubMed PMID: 29778085
• Josefsson SE, Huse K, Kolstad A, Beiske K, Pende D, Steen CB, Inderberg EM, Lingjærde OC, Østenstad B, Smeland EB, Levy R, Irish JM, Myklebust JH. T Cells Expressing Checkpoint Receptor TIGIT Are Enriched in Follicular Lymphoma Tumors and Characterized by Reversible Suppression of T-cell Receptor Signaling. Clin Cancer Res. 2018 Feb 15;24(4):870-881. PubMed PMID: 29217528
• Greenplate A, Wang K, Tripathi RM, Palma N, Ali SM, Stephens PJ, Miller VA, Shyr Y, Guo Y, Reddy NM, Kozhaya L, Unutmaz D, Chen X, Irish JM, Davé UP. Genomic Profiling of T-Cell Neoplasms Reveals Frequent JAK1 and JAK3 Mutations With Clonal Evasion From Targeted Therapies. JCO Precis Oncol. 2018;2018. PubMed PMID: 30079384
• Diggins KE, Gandelman JS, Roe CE, Irish JM. Generating Quantitative Cell Identity Labels with Marker Enrichment Modeling (MEM). Curr Protoc Cytom. 2018 Jan 18;83:10.21.1-10.21.28. PubMed PMID: 29345329
• Earl DC, Ferrell PB Jr, Leelatian N, Froese JT, Reisman BJ, Irish JM, Bachmann BO. Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics. Nat Commun. 2018 Jan 2;9(1):39. PubMed PMID: 29295987
• Siska PJ, Beckermann KE, Mason FM, Andrejeva G, Greenplate AR, Sendor AB, Chiang YJ, Corona AL, Gemta LF, Vincent BG, Wang RC, Kim B, Hong J, Chen CL, Bullock TN, Irish JM, Rathmell WK, Rathmell JC. Mitochondrial dysregulation and glycolytic insufficiency functionally impair CD8 T cells infiltrating human renal cell carcinoma. JCI Insight. 2017 Jun 15;2(12). PubMed PMID: 28614802
• Leelatian N, Doxie DB, Greenplate AR, Mobley BC, Lehman JM, Sinnaeve J, Kauffman RM, Werkhaven JA, Mistry AM, Weaver KD, Thompson RC, Massion PP, Hooks MA, Kelley MC, Chambless LB, Ihrie RA, Irish JM. Single Cell Analysis of Human Tissues and Solid Tumors with Mass Cytometry. Cytometry B Clin Cytom. 2017 Jul 18. [Epub ahead of print] PubMed PMID: 28719730
• Leelatian N, Doxie DB, Greenplate AR, Sinnaeve J, Ihrie RA, Irish JM. Preparing Viable Single Cells from Human Tissue and Tumors for Cytomic Analysis. Curr Protoc Mol Biol. 2017 Apr 3;118:25C.1.1-25C.1.23. PubMed PMID: 28369679
• Udyavar AR, Wooten DJ, Hoeksema M, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V. Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity. Cancer Res. 2017 Mar 1;77(5):1063-1074. PubMed PMID: 27932399
• Diggins KE, Greenplate AR, Leelatian N, Wogsland CE, Irish JM. Characterizing cell subsets using marker enrichment modeling. Nat Methods. 2017 Mar;14(3):275-278. PubMed PMID: 28135256
• Wogsland CE, Greenplate AR, Kolstad A, Myklebust JH, Irish JM, Huse K. Mass Cytometry of Follicular Lymphoma Tumors Reveals Intrinsic Heterogeneity in Proteins Including HLA-DR and a Deficit in Nonmalignant Plasmablast and Germinal Center B-Cell Populations. Cytometry B Clin Cytom. 2017 Jan;92(1):79-87. PubMed PMID: 27933753
• Leelatian N, Doxie DB, Greenplate AR, Mobley BC, Lehman JM, Sinnaeve J, Kauffmann RM, Werkhaven JA, Mistry AM, Weaver KD, Thompson RC, Massion PP, Hooks MA, Kelley MC, Chambless LB, Ihrie RA, Irish JM. Single cell analysis of human tissues and solid tumors with mass cytometry. Cytometry B Clin Cytom. 2017 Jan;92(1):68-78. PubMed PMID: 27598832
• Myklebust JH, Brody J, Kohrt HE, Kolstad A, Czerwinski DK, Wälchli S, Green MR, Trøen G, Liestøl K, Beiske K, Houot R, Delabie J, Alizadeh AA, Irish JM, Levy R. Distinct patterns of B-cell receptor signaling in non-Hodgkin lymphomas identified by single-cell profiling. Blood. 2017 Feb 9;129(6):759-770. PubMed PMID: 28011673
• Roussel M, Irish JM, Menard C, Lhomme F, Tarte K, Fest T. Regulatory myeloid cells: an underexplored continent in B-cell lymphomas. Cancer Immunol Immunother. 2017 Aug;66(8):1103-1111. PubMed PMID: 28689360
• Roussel M, Ferrell PB Jr, Greenplate AR, Lhomme F, Le Gallou S, Diggins KE, Johnson DB, Irish JM. Mass cytometry deep phenotyping of human mononuclear phagocytes and myeloid-derived suppressor cells from human blood and bone marrow. J Leukoc Biol. 2017 Aug;102(2):437-447. PubMed PMID: 28400539
• Kordasti S, Costantini B, Seidl T, Perez Abellan P, Martinez Llordella M, McLornan D, Diggins KE, Kulasekararaj A, Benfatto C, Feng X, Smith A, Mian SA, Melchiotti R, de Rinaldis E, Ellis R, Petrov N, Povoleri GA, Chung SS, Thomas NS, Farzaneh F, Irish JM, Heck S, Young NS, Marsh JC, Mufti GJ. Deep phenotyping of Tregs identifies an immune signature for idiopathic aplastic anemia and predicts response to treatment. Blood. 2016 Sep 1;128(9):1193-205. PubMed PMID: 27281795
• Nicholas KJ, Greenplate AR, Flaherty DK, Matlock BK, Juan JS, Smith RM, Irish JM, Kalams SA. Multiparameter analysis of stimulated human peripheral blood mononuclear cells: A comparison of mass and fluorescence cytometry. Cytometry A. 2016 Mar;89(3):271-80. PubMed PMID: 26599989
• Greenplate AR, Johnson DB, Roussel M, Savona MR, Sosman JA, Puzanov I, Ferrell PB, Irish JM. Myelodysplastic Syndrome Revealed by Systems Immunology in a Melanoma Patient Undergoing Anti-PD-1 Therapy. Cancer Immunol Res. 2016 Jun;4(6):474-480. PubMed PMID: 26966176
• Greenplate AR, Johnson DB, Ferrell PB Jr, Irish JM. Systems immune monitoring in cancer therapy. Eur J Cancer. 2016 Jul;61:77-84. PubMed PMID: 27155446
• Chong KM, Leelatian N, Deguire SM, Brockman AA, Earl D, Ihrie RA, Irish JM, Bachmann BO, Sulikowski GA. The use of fluorescently-tagged apoptolidins in cellular uptake and response studies. J Antibiot (Tokyo). 2016 Apr;69(4):327-30. PubMed PMID: 26956792
• Simmons AJ, Scurrah CR, McKinley ET, Herring CA, Irish JM, Washington MK, Coffey RJ, Lau KS. Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks. Sci Signal. 2016 Oct 11;9(449):rs11. PubMed PMID: 27729552
• Johnson DB, Estrada MV, Salgado R, Sanchez V, Doxie DB, Opalenik SR, Vilgelm AE, Feld E, Johnson AS, Greenplate AR, Sanders ME, Lovly CM, Frederick DT, Kelley MC, Richmond A, Irish JM, Shyr Y, Sullivan RJ, Puzanov I, Sosman JA, Balko JM. Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy. Nat Commun. 2016 Jan 29;7:10582. PubMed PMID: 26822383
• Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-a-induced apoptosis in vivo. Mol Syst Biol. 2016 Aug 29;12(8):881. PubMed PMID: 27574014
• Ferrell PB Jr, Diggins KE, Polikowsky HG, Mohan SR, Seegmiller AC, Irish JM. High-Dimensional Analysis of Acute Myeloid Leukemia Reveals Phenotypic Changes in Persistent Cells during Induction Therapy. PLoS One. 2016;11(4):e0153207. PubMed PMID: 27074138
• Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-a-induced apoptosis in vivo. Mol Syst Biol. 2015 Oct 30;11(10):835. PubMed PMID: 26519361
• Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW. NetworkPainter: dynamic intracellular pathway animation in Cytobank. BMC Bioinformatics. 2015 May 25;16:172. PubMed PMID: 26003204
• Diggins KE, Ferrell PB Jr, Irish JM. Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data. Methods. 2015 Jul 1;82:55-63. PubMed PMID: 25979346
• Shah AT, Diggins KE, Walsh AJ, Irish JM, Skala MC. In Vivo Autofluorescence Imaging of Tumor Heterogeneity in Response to Treatment. Neoplasia. 2015 Dec;17(12):862-870. PubMed PMID: 26696368
• Polikowsky HG, Wogsland CE, Diggins KE, Huse K, Irish JM. Cutting Edge: Redox Signaling Hypersensitivity Distinguishes Human Germinal Center B Cells. J Immunol. 2015 Aug 15;195(4):1364-1367. PubMed PMID: 26157177
• Leelatian N, Diggins KE, Irish JM. Characterizing Phenotypes and Signaling Networks of Single Human Cells by Mass Cytometry. Methods Mol Biol. 2015;1346:99-113. PubMed PMID: 26542718
• Green MR, Kihira S, Liu CL, Nair RV, Salari R, Gentles AJ, Irish J, Stehr H, Vicente-Dueñas C, Romero-Camarero I, Sanchez-Garcia I, Plevritis SK, Arber DA, Batzoglou S, Levy R, Alizadeh AA. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1116-25. PubMed PMID: 25713363
• Irish JM. Beyond the age of cellular discovery. Nat Immunol. 2014 Dec;15(12):1095-7. PubMed PMID: 25396342
• Irish JM, Doxie DB. High-dimensional single-cell cancer biology. Curr Top Microbiol Immunol. 2014;377:1-21. PubMed PMID: 24671264
• Pyne S, Lee SX, Wang K, Irish J, Tamayo P, Nazaire MD, Duong T, Ng SK, Hafler D, Levy R, Nolan GP, Mesirov J, McLachlan GJ. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. PLoS One. 2014;9(7):e100334. PubMed PMID: 24983991
• Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL, Kela I, Hopmans ES, Myklebust JH, Ji H, Plevritis SK, Levy R, Alizadeh AA. Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood. 2013 Feb 28;121(9):1604-11. PubMed PMID: 23297126
• Myklebust JH, Irish JM, Brody J, Czerwinski DK, Houot R, Kohrt HE, Timmerman J, Said J, Green MR, Delabie J, Kolstad A, Alizadeh AA, Levy R. High PD-1 expression and suppressed cytokine signaling distinguish T cells infiltrating follicular lymphoma tumors from peripheral T cells. Blood. 2013 Feb 21;121(8):1367-76. PubMed PMID: 23297127
• Blix ES, Irish JM, Husebekk A, Delabie J, Tierens AM, Myklebust JH, Kolstad A. Altered BCR and CD40 signalling are associated with clinical outcome in small lymphocytic lymphoma/chronic lymphocytic leukaemia and marginal zone lymphoma patients. Br J Haematol. 2012 Dec;159(5):604-8. PubMed PMID: 23043253
• Blix ES, Irish JM, Husebekk A, Delabie J, Forfang L, Tierens AM, Myklebust JH, Kolstad A. Phospho-specific flow cytometry identifies aberrant signaling in indolent B-cell lymphoma. BMC Cancer. 2012 Oct 16;12:478. PubMed PMID: 23072591
• Irish JM, Myklebust JH, Alizadeh AA, Houot R, Sharman JP, Czerwinski DK, Nolan GP, Levy R. B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12747-54. PubMed PMID: 20543139
• Kotecha N, Krutzik PO, Irish JM. Web-based analysis and publication of flow cytometry experiments. Curr Protoc Cytom. 2010 Jul;Chapter 10:Unit10.17. PubMed PMID: 20578106
• Houot R, Goldstein MJ, Kohrt HE, Myklebust JH, Alizadeh AA, Lin JT, Irish JM, Torchia JA, Kolstad A, Chen L, Levy R. Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by Treg depletion. Blood. 2009 Oct 15;114(16):3431-8. PubMed PMID: 19641184
• Hammer MM, Kotecha N, Irish JM, Nolan GP, Krutzik PO. WebFlow: a software package for high-throughput analysis of flow cytometry data. Assay Drug Dev Technol. 2009 Feb;7(1):44-55. PubMed PMID: 19187010
• Sachs K, Gentles AJ, Youland R, Itani S, Irish J, Nolan GP, Plevritis SK. Characterization of patient specific signaling via augmentation of Bayesian networks with disease and patient state nodes. Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:6624-7. PubMed PMID: 19963681
• Kotecha N, Flores NJ, Irish JM, Simonds EF, Sakai DS, Archambeault S, Diaz-Flores E, Coram M, Shannon KM, Nolan GP, Loh ML. Single-cell profiling identifies aberrant STAT5 activation in myeloid malignancies with specific clinical and biologic correlates. Cancer Cell. 2008 Oct 7;14(4):335-43. PubMed PMID: 18835035
• Van Meter ME, Díaz-Flores E, Archard JA, Passegué E, Irish JM, Kotecha N, Nolan GP, Shannon K, Braun BS. K-RasG12D expression induces hyperproliferation and aberrant signaling in primary hematopoietic stem/progenitor cells. Blood. 2007 May 1;109(9):3945-52. PubMed PMID: 17192389
• Irish JM, Anensen N, Hovland R, Skavland J, Børresen-Dale AL, Bruserud O, Nolan GP, Gjertsen BT. Flt3 Y591 duplication and Bcl-2 overexpression are detected in acute myeloid leukemia cells with high levels of phosphorylated wild-type p53. Blood. 2007 Mar 15;109(6):2589-96. PubMed PMID: 17105820
• Irish JM, Czerwinski DK, Nolan GP, Levy R. Altered B-cell receptor signaling kinetics distinguish human follicular lymphoma B cells from tumor-infiltrating nonmalignant B cells. Blood. 2006 Nov 1;108(9):3135-42. PubMed PMID: 16835385
• Irish JM, Kotecha N, Nolan GP. Mapping normal and cancer cell signalling networks: towards single-cell proteomics. Nat Rev Cancer. 2006 Feb;6(2):146-55. PubMed PMID: 16491074
• Irish JM, Czerwinski DK, Nolan GP, Levy R. Kinetics of B cell receptor signaling in human B cell subsets mapped by phosphospecific flow cytometry. J Immunol. 2006 Aug 1;177(3):1581-9. PubMed PMID: 16849466
• Irish JM, Hovland R, Krutzik PO, Perez OD, Bruserud Ø, Gjertsen BT, Nolan GP. Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell. 2004 Jul 23;118(2):217-28. PubMed PMID: 15260991
• Krutzik PO, Irish JM, Nolan GP, Perez OD. Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. Clin Immunol. 2004 Mar;110(3):206-21. PubMed PMID: 15047199
• Armstrong JS, Steinauer KK, Hornung B, Irish JM, Lecane P, Birrell GW, Peehl DM, Knox SJ. Role of glutathione depletion and reactive oxygen species generation in apoptotic signaling in a human B lymphoma cell line. Cell Death Differ. 2002 Mar;9(3):252-63. PubMed PMID: 11859408