Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
Keywords
Last Name
Institution

Jonathan Irish

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-PEDS
ORCID ORCID Icon0000-0001-9428-8866 Additional info

    Collapse Biography 
    Collapse education and training
    Stanford University, Palo Alto, CAPhD04/2004Cancer Biology
    University of Michigan, Ann Arbor, MIBS, Chem.05/1998Chemistry
    University of Michigan, Ann Arbor, MIBS05/1998Biology, Honors
    University of Michigan, Ann Arbor, MIBS05/1998Biochemistry

    Collapse Overview 
    Collapse overview
    The Irish lab studies how signaling governs cell identity in healthy human tissue and in diseases, including brain tumors, blood cancers, and immune disorders. Dr. Irish is an expert in the identification and functional characterization of human cells. Research in the Irish lab emphasizes integrated creation and use of bench and computational techniques. The Irish lab leads the CytoLab data science team at CU Anschutz and is based in Pediatrics-Neurology. Dr. Irish previously trained at Stanford for PhD and postdoc (2004-2011) and directed a research group and shared resource at Vanderbilt University (2012-2024).

    Irish Lab Website:
    https://www.irishlab.org/

    Jonathan Irish on Google Scholar:
    https://scholar.google.com/citations?user=-IJndUMAAAAJ

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Wallace PK, Jellison ER, Thornton S, Kluepfel K, Back J, Beadnell TC, Bebes A, Behrends J, Belkina AC, Black M, Bogdanoski G, Bollati-Fogolín M, Bonte S, Van der Borght K, Brinkman RR, Brundage K, Bushnell T, Chiu DT, Chow N, Ciccolella CO, Cochran M, Czechowska K, Dagla K, Daniel B, de la Cruz G, Van Duyse J, Font LF, Fornas Ò, Garcia-Garcia S, Gardner R, Van Gassen S, Gimenes D, Grenfell R, Grider-Hayes MJ, Grose R, Hall C, Hally KE, Hameetman M, Hogg K, Houston J, Irish JM, Isterdael GV, Jaimes M, Janetzki S, Kim C, Koladiya A, Lamote J, Lannigan J, Leconte J, Litwin V, Longhini A, Loof N, Lozano-Andrés E, Lundsten K, Mage P, Mair F, Martins CG, McCausland M, McGuire HM, Meskas J, Murphy W, Nolan J, Oliveira B, Ordoñez-Rueda D, Orlowski-Oliver E, Petersen CC, Poulton NJ, Putri G, Quadrini KJ, Ramasz B, Ruhrmund D, Singh VV, Small SJ, Smith NJ, Spidlen J, Stegen C, Tak T, Thompson S, Thomson M, Vocelle D, Walker RV, Walsh RE, Wang L, Wang YF, Weglarz M, Winker M, Wood JCS, Woolard S, Yeh NY, Yuecel R, Rajwa B. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2025 Conference Workshops. Cytometry A. 2025 Dec 30. PMID: 41472424.
      View in: PubMed
    2. Thirman HL, Grider-Hayes MJ, Geben LC, Ihrie RA, Brown LE, Porco JA, Irish JM. Connecting chemical structure to single cell signaling profiles. Commun Biol. 2025 Jul 31; 8(1):1137. PMID: 40745386.
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    3. 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. PMID: 40140496.
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    4. 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). 2025 Jan; 78(2):78-89. PMID: 39643649.
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    5. 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. PMID: 39310750.
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    6. 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 07 01; 8(7):492-499. PMID: 39008056.
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    7. 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. PMID: 38756352.
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    8. Thirman HL, Hayes MJ, Brown LE, Porco JA, Irish JM. Single Cell Profiling Distinguishes Leukemia-Selective Chemotypes. bioRxiv. 2024 May 03. PMID: 38826485.
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    9. 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 04 16; 18(15):10464-10484. PMID: 38578701.
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    10. 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. PMID: 38585888.
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    11. 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. PMID: 38036712.
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    12. Norlander AE, Abney M, Cephus JY, Roe CE, Irish JM, Shelburne NJ, Newcomb DC, Hemnes AR, Peebles RS. Reply to Yasuma et al. Am J Respir Crit Care Med. 2023 12 01; 208(11):1249-1250. PMID: 37774400.
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    13. Norlander AE, Abney M, Cephus JY, Roe CE, Irish JM, Shelburne NJ, Newcomb DC, Hemnes AR, Peebles RS. Prostaglandin I2 Therapy Promotes Regulatory T Cell Generation in Patients with Pulmonary Arterial Hypertension. Am J Respir Crit Care Med. 2023 09 15; 208(6):737-739. PMID: 37413696.
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    14. 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 07; 3(7):1350-1365. PMID: 37501683.
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    15. 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. PMID: 40180452.
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    16. 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 06 22; 8(12). PMID: 37192001.
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    17. 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. PMID: 36824760.
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    18. 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 09; 104(5):344-355. PMID: 36748312.
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    19. 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. PMID: 37034287.
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    20. Medina S, Ihrie RA, Irish JM. Learning cell identity in immunology, neuroscience, and cancer. Semin Immunopathol. 2023 01; 45(1):3-16. PMID: 36534139.
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    21. 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 11 15; 209(10):2042-2053. PMID: 36426942.
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    22. 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 09; 298(9):102300. PMID: 35931117.
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    23. 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 07 15; 6(7):447-464. PMID: 35840326.
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    24. Ferrari M, Mattavelli D, Tomasoni M, Raffetti E, Bossi P, Schreiber A, Orlandi E, Taboni S, Rampinelli V, Gualtieri T, Turri-Zanoni M, Battaglia P, Arosio AD, Bignami M, Tartaro T, Molteni M, Bertazzoni G, Fiaux-Camous D, Jourdaine C, Verillaud B, Eu D, Nair D, Moiyadi A, Shetty P, Ghosh-Laskar S, Budrukkar A, Magrini SM, Guillerm S, Faivre S, Piazza C, Gilbert RW, Irish JC, de Almeida JR, Pai P, Herman P, Castelnuovo P, Nicolai P. The MUSES*: a prognostic study on 1360 patients with sinonasal cancer undergoing endoscopic surgery-based treatment: *MUlti-institutional collaborative Study on Endoscopically treated Sinonasal cancers. Eur J Cancer. 2022 08; 171:161-182. PMID: 35724468.
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    25. 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, 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 06 16; 13(1):3466. PMID: 35710908.
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    26. 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. PMID: 35371068.
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    27. 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 01 01; 205(1):46-59. PMID: 34731593.
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    28. 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 12 30; 138(26):2874-2885. PMID: 34115118.
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    29. 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. PMID: 34975843.
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    30. 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 08 05; 10. PMID: 34350827.
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    31. Ramsey HE, Stengel K, Pino JC, Johnston G, Childress M, Gorska AE, Arrate PM, Fuller L, Villaume M, Fischer MA, Ferrell PB, 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 09; 16(5):663-674. PMID: 34324169.
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    32. 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. PMID: 34257356.
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    33. Reisman BJ, Barone SM, Bachmann BO, Irish JM. DebarcodeR increases fluorescent cell barcoding capacity and accuracy. Cytometry A. 2021 09; 99(9):946-953. PMID: 33960644.
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    34. 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 04 13; 54(4):829-844.e5. PMID: 33705706.
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    35. 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, Irish JM, Newcomb DC, Rathmell JC. Targeting In Vivo Metabolic Vulnerabilities of Th2 and Th17 Cells Reduces Airway Inflammation. J Immunol. 2021 03 15; 206(6):1127-1139. PMID: 33558372.
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    36. 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. PMID: 33603754.
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    37. Barone SM, Paul AGA, 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. bioRxiv. 2020 Nov 04. PMID: 32766581.
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    38. 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 01; 99(1):11-18. PMID: 32881296.
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    39. 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 08 20; 5(16). PMID: 32814710.
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    40. 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 08 13; 136(7):885-897. PMID: 32294156.
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    41. 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 06 23; 9. PMID: 32573435.
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    42. 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 08; 97(8):824-831. PMID: 32293794.
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    43. 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 03; 93(1):e71. PMID: 32250555.
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    44. 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. PMID: 31919622.
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    45. 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 12; 95(12):1236-1274. PMID: 31833655.
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    46. 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 04; 2(2). PMID: 30910807.
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    47. 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 04; 95(4):442-449. PMID: 30838773.
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    48. 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 04; 286(8):1523-1539. PMID: 30549207.
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    49. Roussel M, Bartkowiak T, Irish JM. Picturing Polarized Myeloid Phagocytes and Regulatory Cells by Mass Cytometry. Methods Mol Biol. 2019; 1989:217-226. PMID: 31077108.
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    50. 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 01; 7(1):86-99. PMID: 30413431.
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    51. 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 01; 104(1):189-196. PMID: 30237265.
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    52. 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 11; 31(6):708-719. PMID: 29778085.
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    53. 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. PMID: 30079384.
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    54. Diggins KE, Gandelman JS, Roe CE, Irish JM. Generating Quantitative Cell Identity Labels with Marker Enrichment Modeling (MEM). Curr Protoc Cytom. 2018 01 18; 83:10.21.1-10.21.28. PMID: 29345329.
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    55. Earl DC, Ferrell PB, 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 01 02; 9(1):39. PMID: 29295987.
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    56. 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 02 15; 24(4):870-881. PMID: 29217528.
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    57. 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. PMID: 28689360.
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    58. 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). PMID: 28614802.
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    59. Roussel M, Ferrell PB, 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. PMID: 28400539.
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    60. Bernstein JM, Irish JC, Brown DH, Goldstein D, Chung P, Razak ARA, Catton C, Gilbert RW, Gullane PJ, O'Sullivan B. Survival outcomes for cutaneous angiosarcoma of the scalp versus face. Head Neck. 2017 06; 39(6):1205-1211. PMID: 28398688.
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    61. 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 04 03; 118:25C.1.1-25C.1.23. PMID: 28369679.
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    62. 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. PMID: 28135256.
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    63. 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. PMID: 27933753.
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    64. 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 02 09; 129(6):759-770. PMID: 28011673.
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    65. 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 01; 77(5):1063-1074. PMID: 27932399.
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    66. 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. PMID: 27729552.
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    67. 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 01; 92(1):68-78. PMID: 27598832.
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    68. 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 01; 128(9):1193-205. PMID: 27281795.
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    69. Greenplate AR, Johnson DB, Ferrell PB, Irish JM. Systems immune monitoring in cancer therapy. Eur J Cancer. 2016 Jul; 61:77-84. PMID: 27155446.
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    70. Ferrell PB, 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. PMID: 27074138.
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    71. 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. PMID: 26966176.
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    72. 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 04; 69(4):327-30. PMID: 26956792.
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    73. 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. PMID: 26822383.
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    74. 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. PMID: 26696368.
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    75. 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. PMID: 26599989.
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    76. 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. PMID: 26519361.
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    77. 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. PMID: 26157177.
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    78. 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. PMID: 26003204.
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    79. Diggins KE, Ferrell PB, Irish JM. Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data. Methods. 2015 Jul 01; 82:55-63. PMID: 25979346.
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    80. 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. PMID: 25713363.
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    81. 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. PMID: 26542718.
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    82. Irish JM. Beyond the age of cellular discovery. Nat Immunol. 2014 Dec; 15(12):1095-7. PMID: 25396342.
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    83. Turner-Ivey B, Guest ST, Irish JC, Kappler CS, Garrett-Mayer E, Wilson RC, Ethier SP. KAT6A, a chromatin modifier from the 8p11-p12 amplicon is a candidate oncogene in luminal breast cancer. Neoplasia. 2014 Aug; 16(8):644-55. PMID: 25220592.
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    84. 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. PMID: 24983991.
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    85. Irish JM, Doxie DB. High-dimensional single-cell cancer biology. Curr Top Microbiol Immunol. 2014; 377:1-21. PMID: 24671264.
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    86. 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. PMID: 23297126.
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    87. 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. PMID: 23297127.
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    88. Goldstein DP, Bachar GY, Lea J, Shrime MG, Patel RS, Gullane PJ, Brown DH, Gilbert RW, Kim J, Waldron J, Perez-Ordonez B, Davis AM, Cheng L, Xu W, Irish JC. Outcomes of squamous cell cancer of the oral tongue managed at the Princess Margaret Hospital. Head Neck. 2013 May; 35(5):632-41. PMID: 22544679.
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    89. Ross G, Yla-Kotola TM, Goldstein D, Zhong T, Gilbert R, Irish J, Gullane PJ, Hofer SO, Neligan PC. Second free flaps in head and neck reconstruction. J Plast Reconstr Aesthet Surg. 2012 Sep; 65(9):1165-8. PMID: 22487583.
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    90. Kotecha N, Krutzik PO, Irish JM. Web-based analysis and publication of flow cytometry experiments. Curr Protoc Cytom. 2010 Jul; Chapter 10:Unit10.17. PMID: 20578106.
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    91. 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. PMID: 20543139.
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    92. 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. PMID: 19641184.
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    93. Irish J, Sandhu N, Simpson C, Wood R, Gilbert R, Gullane P, Brown D, Goldstein D, Devins G, Barker E. Quality of life in patients with maxillectomy prostheses. Head Neck. 2009 Jun; 31(6):813-21. PMID: 19280665.
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    94. 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. PMID: 19187010.
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    95. 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. PMID: 19963681.
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    96. 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 07; 14(4):335-43. PMID: 18835035.
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    97. 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. PMID: 17105820.
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    98. 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 01; 177(3):1581-9. PMID: 16849466.
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    99. 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 01; 108(9):3135-42. PMID: 16835385.
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    100. Irish JM, Kotecha N, Nolan GP. Mapping normal and cancer cell signalling networks: towards single-cell proteomics. Nat Rev Cancer. 2006 02; 6(2):146-55. PMID: 16491074.
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    101. Mäkitie AA, Reis PP, Irish J, Zhang T, Chin SF, Chen X, Marriott C, Keller A, Perez-Ordonez B, Kamel-Reid S, Siu LL. Correlation of Epstein-Barr virus DNA in cell-free plasma, functional imaging and clinical course in locally advanced nasopharyngeal cancer: a pilot study. Head Neck. 2004 Sep; 26(9):815-22. PMID: 15350028.
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    102. 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. PMID: 15260991.
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    103. 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. PMID: 15047199.
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    104. Dimitroulakos J, Marhin WH, Tokunaga J, Irish J, Gullane P, Penn LZ, Kamel-Reid S. Microarray and biochemical analysis of lovastatin-induced apoptosis of squamous cell carcinomas. Neoplasia. 2002 Jul-Aug; 4(4):337-46. PMID: 12082550.
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    105. 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. PMID: 11859408.
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    106. Liavaag PG, Cheung RK, Kerrebijn JD, Freeman JL, Irish JC, Dosch HM. The physiologic reservoir of Epstein-Barr virus does not map to upper aerodigestive tissues. Laryngoscope. 1998 Jan; 108(1 Pt 1):42-6. PMID: 9432065.
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