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  1. Agarwal S, McDonald A, Campbell V, Chen D, Davis J, et al. “Pharmacokinetics and Pharmacodynamics of KT ‐474, a Novel Selective Interleukin‐1 Receptor–Associated Kinase 4 ( IRAK4 ) Degrader, in Healthy Adults,” Clinical and Translational Science. 2025-02-12; 18(3):e70181 10.1111/cts.70181
  2. Cho N, Guldberg S, Nabet B, Yu J, Kim E, et al. “T Cells Instruct Immune Checkpoint Inhibitor Therapy Resistance in Tumors Responsive to IL1 and TNFα Inflammation,” Cancer Immunology Research. 2025-01-06; 10.1158/2326-6066.CIR-24-0416
  3. Wallace K, Gerstenberg T, Ennis C, Perez-Bermejo J, Partridge J, et al. “A differentiated β-globin gene replacement strategy uses heterologous introns to restore physiological expression,” Molecular Therapy. 2/2025; 10.1016/j.ymthe.2025.02.036
  4. Livingston J, Blay J, Trent J, Valverde C, Agulnik M, et al. “A Phase 1 Study of FHD-609, a Heterobifunctional Degrader of Bromodomain-Containing Protein 9, in Patients With Advanced Synovial Sarcoma or SMARCB1-Deficient Tumors,” Clinical Cancer Research. 2024-12-11; 10.1158/1078-0432.CCR-24-2583
  5. Toh J, Reitsma A, Tajima T, Younes S, Ezeiruaku C, et al. “Multi-modal analysis reveals tumor and immune features distinguishing EBV-positive and EBV-negative post-transplant lymphoproliferative disorders,” Cell Reports Medicine. 2024-12-09; 10.1016/j.xcrm.2024.101851
  6. Babdor J, Patel R, Davidson B, Noecker C, Rahim M, et al. “Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states,” Immunology. 2024-12-03; 10.1101/2024.11.27.625750 [preprint]
  7. Bedia J, Huang Y, Gonzalez A, Gonzalez V, Funingana I, et al. “Coordinated protein modules define DNA damage responses to carboplatin at single cell resolution in human ovarian carcinoma models,” bioRxiv. 2024-11-26; 10.1101/2024.11.21.624591 [preprint]
  8. Sigal N, Simpson A, Miljkovic M, Magee K, Chronister W, et al. “58 It’s on-site: eliminating site-to-site variability with whole blood collection kits using 40+ marker TokuProfile mass cytometry assay,” Journal for ImmunoTherapy of Cancer. 2024/11/01; 10.1136/jitc-2024-SITC2024.0058
  9. Magee K, Sigal N, Medina C, Jarrell J, Leavitt L, et al. “57 It’s about time: rapid on-site fixation of whole blood samples prior to high-dimensional flow cytometric analysis,” Journal for ImmunoTherapy of Cancer. 2024/11/01; 10.1136/jitc-2024-SITC2024.0057
  10. Rachubinski A, Wallace E, Gurnee E, Estrada B, Worek K, et al. “JAK inhibition decreases the autoimmune burden in Down syndrome,” medRxiv. 2024-10-16; 10.1101/2024.06.13.24308783 [preprint]
  11. Tsimberidou A, Alayli F, Okrah K, Drakaki A, Khalil D, et al. “Immunologic signatures of response and resistance to nivolumab with ipilimumab in advanced metastatic cancer,” Journal of Experimental Medicine. 2024-10-07; 221(10):e20240152 10.1084/jem.20240152
  12. Garcia Castillo J, DeBarge R, Mende A, Tenvooren I, Marquez D, et al. “A mass cytometry method pairing T cell receptor and differentiation state analysis,” Nature Immunology. 2024-09; 25(9):1754-1763 10.1038/s41590-024-01937-3
  13. Drainas A, Hsu W, Dallas A, Poltorack C, Kim J, et al. “GCN2 is a determinant of the response to WEE1 kinase inhibition in small-cell lung cancer,” Cell Reports. 2024-08-27; 43(8):114606 10.1016/j.celrep.2024.114606
  14. Donovan M, Rachubinski A, Smith K, Araya P, Waugh K, et al. “Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndrome,” Cell Reports. 2024-08-27; 43(8):114599 10.1016/j.celrep.2024.114599
  15. McDonald A, Karnik R, Campbell V, Davis J, Chavoshi S, et al. “Interleukin 1 Receptor–Associated Kinase 4 is Overexpressed in Hidradenitis Suppurativa Skin and Correlates with Inflammatory Biomarkers,” Journal of Investigative Dermatology. 2024-07-29; 10.1016/j.jid.2024.04.035
  16. Murphy K, Farrell J, Bendig J, Mitra A, Luff C, et al. “Optimized ultrasound neuromodulation for non-invasive control of behavior and physiology,” Neuron. 2024-07-24; 10.1016/j.neuron.2024.07.002
  17. Kim Y, Calderon A, Favaro P, Glass D, Tsai A, et al. “Terminal deoxynucleotidyl transferase and CD84 identify human multi-potent lymphoid progenitors,” Nature Communications. 2024-07-13; 15(1):5910 10.1038/s41467-024-49883-w
  18. Kusch N, Storm J, Macioszek A, Kisselmann E, Knabbe C, et al. “A Critical Role of Culture Medium Selection in Maximizing the Purity and Expansion of Natural Killer Cells,” Cells. 2024-07-05; 13(13):1148 10.3390/cells13131148
  19. Glitza I, Seo Y, Spencer C, Wortman J, Burton E, et al. “Randomized Placebo-Controlled, Biomarker-Stratified Phase Ib Microbiome Modulation in Melanoma: Impact of Antibiotic Preconditioning on Microbiome and Immunity,” Cancer Discovery. 2024-07-01; 14(7):1161-1175 10.1158/2159-8290.CD-24-0066
  20. Donovan M, Eduthan N, Smith K, Britton E, Lyford H, et al. “Variegated overexpression of chromosome 21 genes reveals molecular and immune subtypes of Down syndrome,” Nature Communications. 2024-06-28; 15(1):5473 10.1038/s41467-024-49781-1
  21. Siveke J, Yang J, Peng J, Fang R, Godfrey L, et al. “Combined targeted and epigenetic-based therapy enhances antitumor immunity by stabilizing GATA6-dependent MHCI expression in pancreatic ductal adenocarcinoma,” In Review. 2024-06-17; 10.21203/rs.3.rs-4555029/v1 [preprint]
  22. Shasha C, Glass D, Moelhman E, Islas L, Tian Y, et al. “Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy,” bioRxiv. 2024-06-04; 10.1101/2024.06.03.597178 [preprint]
  23. Verdonk F, Cambriel A, Hedou J, Ganio E, Bellan G, et al. “An immune signature of postoperative cognitive decline in elderly patients,” DOI.org (Crossref). 2024-03-05; [preprint]
  24. Baxter R, Cabrera-Martinez B, Ghosh T, Rester C, Moreno M, et al. “SARS-CoV-2 Vaccine-Elicited Immunity after B Cell Depletion in Multiple Sclerosis,” ImmunoHorizons. 2024-03-01; 8(3):254-268 10.4049/immunohorizons.2300108
  25. Revach O, Cicerchia A, Shorer O, Petrova B, Anderson S, et al. “Disrupting CD38-driven T cell dysfunction restores sensitivity to cancer immunotherapy,” DOI.org (Crossref). 2024-02-14; [preprint]
  26. Steinhubl S, Sekaric J, Gendy M, Guo H, Ward M, et al. “Wearable Sensor and Digital Twin Technology for the Development of a Personalized Digital Biomarker of Vaccine-Induced Inflammation,” DOI.org (Crossref). 2024-01-29; [preprint]
  27. Kovacsovics-Bankowski M, Sweere J, Healy C, Sigal N, Cheng L, et al. “Lower frequencies of circulating suppressive regulatory T cells and higher frequencies of CD4+ naïve T cells at baseline are associated with severe immune-related adverse events in immune checkpoint inhibitor-treated melanoma,” Journal for Immunotherapy of Cancer. 2024-1-17; 12(1):e008056 10.1136/jitc-2023-008056
  28. Castillo J, DeBarge R, Mende A, Tenvooren I, Marquez D, et al. “A mass cytometry approach to track the evolution of T cell responses during infection and immunotherapy by paired T cell receptor repertoire and T cell differentiation state analysis,” bioRxiv. 2024-1-12; 10.1101/2024.01.11.575237
  29. Hédou J, Marić I, Bellan G, Einhaus J, Gaudillière D, et al. “Discovery of sparse, reliable omic biomarkers with Stabl,” Nature Biotechnology. 2024-01-02; 10.1038/s41587-023-02033-x
  30. Porpiglia E, Blau H. “Chapter 3 - Novel single-cell technologies advance our mechanistic understanding of muscle stem cell function in skeletal muscle regeneration” in “Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies.” Academic Press; 2024-01-01.
  31. Stelzer I, Feyaerts D, Ganio E, Amar J, Hédou J, et al. “Chapter 5 - From bench to bedside: Practical considerations for translational studies using single-cell mass cytometry” in “Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies.” Academic Press; 2024-01-01.
  32. Fuh K, Huang Y, Lomonosova E, Fantl W. “Chapter 6 - Developing predictive biomarkers for endometrial cancer immunotherapy with mass cytometry (CyTOF)” in “Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies.” Academic Press; 2024-01-01.
  33. Lui V, Hoenig M, Cabrera-Martinez B, Baxter R, Garcia-Perez J, et al. “A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation,” Journal of Experimental Medicine. 2024-01-01; 221(1):e20230927 10.1084/jem.20230927
  34. Wai K, Okholm T, Ha P, Marquez D, Tenvooren I, et al. “The tumor microenvironment of benign and malignant salivary gland tumors,” Head & Neck. 07/2024; 46(7):1625-1636 10.1002/hed.27716
  35. Glass D, Mayer-Blackwell K, Ramchurren N, Parks K, Duran G, et al. “Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma,” Cell Reports Medicine. 4/2024; 10.1016/j.xcrm.2024.101527
  36. Hickey J, Agmon E, Horowitz N, Tan T, Lamore M, et al. “Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy,” Cell Systems. 04/2024; 15(4):322-338.e5 10.1016/j.cels.2024.03.004
  37. Purde M, Cupovic J, Palmowski Y, Makky A, Schmidt S, et al. “A replicating LCMV-based vaccine for the treatment of solid tumors,” Molecular Therapy. 02/2024; 32(2):426-439 10.1016/j.ymthe.2023.11.026
  38. Maecker H. “Assessing global immune competence using CyTOF” in “Revealing Unchartered Biology with Single Intact Cells.” Elsevier; 2024.
  39. Andersen S, Kjær T, Ghimire K, Porpiglia E. “Identification and Analysis of Myogenic Progenitors In Vivo During Acute Skeletal Muscle Injury by High-Dimensional Single-Cell Mass Cytometry,” Journal of Visualized Experiments (JoVE). 2023-12-01; 10.3791/65944
  40. Lee A, Floyd K, Wu S, Fang Z, Tan T, et al. “BCG vaccination stimulates integrated organ immunity by feedback of the adaptive immune response to imprint prolonged innate antiviral resistance,” Nature Immunology. 2023-11-30; 10.1038/s41590-023-01700-0
  41. Capelle C, Ciré S, Hedin F, Hansen M, Pavelka L, et al. “Early-to-mid stage idiopathic Parkinson’s disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females,” Nature Communications. 2023-11-20; 14(1):7461 10.1038/s41467-023-43053-0
  42. Ackerman L, Acloque G, Bacchelli S, Schwartz H, Feinstein B, et al. “IRAK4 degrader in hidradenitis suppurativa and atopic dermatitis: a phase 1 trial,” Nature Medicine. 2023-11-13; 10.1038/s41591-023-02635-7
  43. Adamik J, Munson P, Maurer D, Hartmann F, Bendall S, et al. “Immuno-metabolic dendritic cell vaccine signatures associate with overall survival in vaccinated melanoma patients,” Nature Communications. 2023-11-08; 14(1):7211 10.1038/s41467-023-42881-4
  44. Sukhtankar D, Fung J, Kim M, Cayton T, Chiou V, et al. “GPC-100, a novel CXCR4 antagonist, improves in vivo hematopoietic cell mobilization when combined with propranolol,” PLOS ONE. Oct 25, 2023; 18(10):e0287863 10.1371/journal.pone.0287863
  45. Favaro P, Glass D, Borges L, Baskar R, Reynolds W, et al. “Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors,” bioRxiv. 2023-8-30; 10.1101/2023.08.30.555623
  46. Guldberg S, Okholm T, McCarthy E, Spitzer M. “Computational Methods for Single-Cell Proteomics,” Annual Review of Biomedical Data Science. 2023-08-10; 6(1):annurev-biodatasci-020422-050255 10.1146/annurev-biodatasci-020422-050255
  47. Chiot A, Roemer S, Ryner L, Bogachuk A, Emberley K, et al. “Elevated α5 integrin expression on myeloid cells in motor areas in amyotrophic lateral sclerosis is a therapeutic target,” Proceedings of the National Academy of Sciences. 2023-08-08; 120(32):e2306731120 10.1073/pnas.2306731120
  48. Stensland Z, Magera C, Broncucia H, Gomez B, Rios-Guzman N, et al. “Identification of an anergic BND cell–derived activated B cell population (BND2) in young-onset type 1 diabetes patients,” Journal of Experimental Medicine. 2023-08-07; 220(8):e20221604 10.1084/jem.20221604
  49. Lee A, Floyd K, Wu S, Fang Z, Tan T, et al. “Integrated Organ Immunity: Antigen-specific CD4-T cell-derived IFN-γ induced by BCG imprints prolonged lung innate resistance against respiratory viruses,” bioRxiv. 2023-08-02; 10.1101/2023.07.31.551354 [preprint]
  50. Galbraith M, Rachubinski A, Smith K, Araya P, Waugh K, et al. “Multidimensional definition of the interferonopathy of Down syndrome and its response to JAK inhibition,” Science Advances. 2023-06-28; 9(26):eadg6218 10.1126/sciadv.adg6218
  51. Robinson M, Glass D, Duran V, Agudelo Rojas O, Sanz A, et al. “Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics,” Science Advances. 2023-03-24; 9(12):eade7702 10.1126/sciadv.ade7702
  52. Rahim M, Okholm T, Jones K, McCarthy E, Liu C, et al. “Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes,” Cell. 2023/03/16; 186(6):1127-1143.e18 10.1016/j.cell.2023.02.021
  53. Mayer A, Holman D, Sood A, Tandon U, Bhate S, et al. “A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy,” Science Advances. 2023-01-20; 9(3):eadd1166 10.1126/sciadv.add1166
  54. Zhu B, Chen S, Bai Y, Chen H, Liao G, et al. “Robust single-cell matching and multimodal analysis using shared and distinct features,” Nature Methods. 2023-01-09; 10.1038/s41592-022-01709-7
  55. Borko T, Baxter R, Cabrera-Martinez B, Thiruppathi E, Sabalza M, et al. “SARS-CoV-2 mRNA vaccination induces an antigen-specific T cell response correlating with plasma interferon-gamma in B cell depleted patients,” Journal of Neuroimmunology. 10/2023; 383:578192 10.1016/j.jneuroim.2023.578192
  56. Rao M, Amouzgar M, Harden J, Lapasaran M, Trickey A, et al. “High-dimensional profiling of pediatric immune responses to solid organ transplantation,” Cell Reports Medicine. 08/2023; 4(8):101147 10.1016/j.xcrm.2023.101147
  57. Holtan S, Hoeschen A, Cao Q, Ustun C, Betts B, et al. “Phase II, Open-Label Clinical Trial of Urinary-Derived Human Chorionic Gonadotropin/Epidermal Growth Factor for Life-Threatening Acute Graft-Versus-Host Disease,” Transplantation and Cellular Therapy. 6/2023; 10.1016/j.jtct.2023.05.021
  58. Ho E, Qiu R, Miller E, Bilotta M, FitzGerald D, et al. “Antibody drug conjugates, targeting cancer-expressed EGFR, exhibit potent and specific antitumor activity,” Biomedicine & Pharmacotherapy. 01/2023; 157:114047 10.1016/j.biopha.2022.114047
  59. Fallahzadeh R, Bidoki N, Stelzer I, Becker M, Marić I, et al. “In‐Silico Generation of High‐Dimensional Immune Response Data in Patients using a Deep Neural Network,” Cytometry Part A. 2022-12-12; 10.1002/cyto.a.24709
  60. Schürch C. “Charakterisierung des Tumormikromilieus mittels Hochmultiplexmikroskopieverfahren,” Die Pathologie. 2022-12-01; 43(1):21-24 10.1007/s00292-022-01129-6
  61. Jayakumar P, Thomas S, Brown S, Kümmerli R. “Collective decision-making in Pseudomonas aeruginosa involves transient segregation of quorum-sensing activities across cells,” Current Biology. 2022-11-22; 10.1016/j.cub.2022.10.052
  62. Kim Y, Calderon A, Favaro P, Glass D, Tsai A, et al. “Expression of terminal deoxynucleotidyl transferase (TdT) identifies lymphoid-primed progenitors in human bone marrow,” bioRxiv. 2022-10-31; 10.1101/2022.10.30.514380 [preprint]
  63. Rovira-Clavé X, Drainas A, Jiang S, Bai Y, Baron M, et al. “Spatial epitope barcoding reveals clonal tumor patch behaviors,” Cancer Cell. 2022-10-13; 10.1016/j.ccell.2022.09.014
  64. Adamik J, Munson P, Hartmann F, Combes A, Pierre P, et al. “Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells,” Nature Communications. 2022-09-02; 13(1):5184 10.1038/s41467-022-32849-1
  65. Feyaerts D, Hédou J, Gillard J, Chen H, Tsai E, et al. “Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19,” Cell Reports Medicine. 2022-07-19; 10.1016/j.xcrm.2022.100680
  66. Delgado-Gonzalez A, Huang Y, Porpiglia E, Donoso K, Gonzalez V, et al. “Measuring trogocytosis between ovarian tumor and natural killer cells,” STAR Protocols. June 17, 2022; 3(2):101425 10.1016/j.xpro.2022.101425
  67. Burnett C, Hauge Okholm T, Tenvooren I, Marquez D, Tamaki S, et al. “Mass cytometry reveals a conserved immune trajectory of recovery in hospitalized COVID-19 patients,” Immunity. June 7, 2022; 10.1016/j.immuni.2022.06.004
  68. Padrón L, Maurer D, O’Hara M, O’Reilly E, Wolff R, et al. “Sotigalimab and/or nivolumab with chemotherapy in first-line metastatic pancreatic cancer: clinical and immunologic analyses from the randomized phase 2 PRINCE trial,” Nature Medicine. 2022-06-03; 10.1038/s41591-022-01829-9
  69. Simons L, Moayedi M, Coghill R, Stinson J, Angst M, et al. “Signature for Pain Recovery IN Teens (SPRINT): protocol for a multisite prospective signature study in chronic musculoskeletal pain,” BMJ Open. 2022/06/01; 12(6):e061548 10.1136/bmjopen-2022-061548
  70. Baskar R, Chen A, Favaro P, Reynolds W, Mueller F, et al. “Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment,” Cell Reports Methods. 2022-03-28; 2(3):100188 10.1016/j.crmeth.2022.100188
  71. Burnett C, Okholm T, Tenvooren I, Marquez D, Tamaki S, et al. “A conserved immune trajectory of recovery in hospitalized COVID-19 patients,” bioRxiv. 2022-3-16; 10.1101/2022.03.15.484467
  72. Galbraith M, Kinning K, Sullivan K, Araya P, Smith K, et al. “Specialized interferon action in COVID-19,” Proceedings of the National Academy of Sciences. 2022-03-15; 119(11):e2116730119 10.1073/pnas.2116730119
  73. Ivison G, Vendrame E, Martínez-Colón G, Ranganath T, Vergara R, et al. “Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients,” Frontiers in Cellular and Infection Microbiology. 2022-2-10; 12:757846 10.3389/fcimb.2022.757846
  74. Lee M, Bedia J, Bhate S, Barlow G, Phillips D, et al. “CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images,” BMC Bioinformatics. January 18, 2022; 23(1):46 10.1186/s12859-022-04570-9
  75. Shekarian T, Zinner C, Bartoszek E, Duchemin W, Wachnowicz A, et al. “Immunotherapy of glioblastoma explants induces interferon-γ responses and spatial immune cell rearrangements in tumor center, but not periphery,” Science Advances. 07/2022; 8(26):eabn9440 10.1126/sciadv.abn9440
  76. McCarthy E, Odorizzi P, Lutz E, Smullin C, Tenvooren I, et al. “A cytotoxic-skewed immune set point predicts low neutralizing antibody levels after Zika virus infection,” Cell Reports. 05/2022; 39(7):110815 10.1016/j.celrep.2022.110815
  77. Jiang S, Chan C, Rovira-Clavé X, Chen H, Bai Y, et al. “Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments,” Immunity. 4/2022; 10.1016/j.immuni.2022.03.020
  78. Glass M, Glass D, Oliveria J, Mbiribindi B, Esquivel C, et al. “Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets,” Cell Reports. 04/2022; 39(3):110728 10.1016/j.celrep.2022.110728
  79. Stensland Z, Coleman B, Rihanek M, Baxter R, Gottlieb P, et al. “Peripheral immunophenotyping of AITD subjects reveals alterations in immune cells in pediatric vs adult-onset AITD,” iScience. 01/2022; 25(1):103626 10.1016/j.isci.2021.103626
  80. Calderon A, Kim Y, Favaro P, Baskar R, Valainis J, et al. “Multi-Omic Single Cell Identification of Lin- CD34- Natural Killer Cell Progenitors in Human Hematopoiesis,” SSRN Electronic Journal. 2022; 10.2139/ssrn.4234724
  81. Gonzalez V, Huang Y, Fantl W. “Mass Cytometry for the Characterization of Individual Cell Types in Ovarian Solid Tumors” in “Ovarian Cancer: Methods and Protocols.” Springer US; 2022.
  82. Fragiadakis G, Bjornson-Hooper Z, Madhireddy D, Sachs K, Chen H, et al. “Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types,” Frontiers in Immunology. 2022;
  83. Bjornson-Hooper Z, Fragiadakis G, Spitzer M, Chen H, Madhireddy D, et al. “A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates,” Frontiers in Immunology. 2022;
  84. McIlwain D, Chen H, Rahil Z, Bidoki N, Jiang S, et al. “Human influenza virus challenge identifies cellular correlates of protection for oral vaccination,” Cell Host & Microbe. 2021-12-08; 29(12):1828-1837.e5 10.1016/j.chom.2021.10.009
  85. Mettu N, Ulahannan S, Bendell J, Garrido-Laguna I, Strickler J, et al. “A Phase 1a/b Open-Label, Dose-Escalation Study of Etigilimab Alone or in Combination with Nivolumab in Patients with Locally Advanced or Metastatic Solid Tumors,” Clinical Cancer Research. 2021-11-29; 10.1158/1078-0432.CCR-21-2780
  86. Phillips D, Matusiak M, Gutierrez B, Bhate S, Barlow G, et al. “Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma,” Nature Communications. 2021-11-18; 12(1):6726 10.1038/s41467-021-26974-6
  87. Dong S, Hiam-Galvez K, Mowery C, Herold K, Gitelman S, et al. “The effect of low-dose IL-2 and Treg adoptive cell therapy in patients with type 1 diabetes,” JCI insight. 2021-09-22; 6(18):e147474 10.1172/jci.insight.147474
  88. Ando K, Hédou J, Feyaerts D, Han X, Ganio E, et al. “A Peripheral Immune Signature of Labor Induction,” Frontiers in Immunology. 2021-09-09; 10.3389/fimmu.2021.725989
  89. Wang V, Blaser B, Patel R, Behbehani G, Rao A, et al. “Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis,” Blood Cancer Discovery. 2021-09-01; 2(5):434-449 10.1158/2643-3230.BCD-21-0055
  90. Gonzalez V, Huang Y, Delgado-Gonzalez A, Chen S, Donoso K, et al. “High-grade serous ovarian tumor cells modulate NK cell function to create an immune-tolerant microenvironment,” Cell Reports. 2021-08-31; 36(9):109632 10.1016/j.celrep.2021.109632
  91. McGuire H, Mei H, Saeys Y. “Use of Mass Cytometry to Study Human Diseases involving the Immune System.” Frontiers Media SA; 2021-08-30.
  92. Sullivan K, Galbraith M, Kinning K, Bartsch K, Levinsky N, et al. “The COVIDome Explorer researcher portal,” Cell Reports. August 17, 2021; 36(7):109527 10.1016/j.celrep.2021.109527
  93. Hickey J, Tan Y, Nolan G, Goltsev Y. “Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data,” Frontiers in Immunology. 2021-08-13; 10.3389/fimmu.2021.727626
  94. Ptacin J, Caffaro C, Ma L, San Jose Gall K, Aerni H, et al. “An engineered IL-2 reprogrammed for anti-tumor therapy using a semi-synthetic organism,” Nature Communications. 2021-08-09; 12(1):4785 10.1038/s41467-021-24987-9
  95. Black S, Phillips D, Hickey J, Kennedy-Darling J, Venkataraaman V, et al. “CODEX multiplexed tissue imaging with DNA-conjugated antibodies,” Nature Protocols. 2021-08; 16(8):3802-3835 10.1038/s41596-021-00556-8
  96. Bai Y, Zhu B, Rovira-Clave X, Chen H, Markovic M, et al. “Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images,” Frontiers in Immunology. 2021-07-05; 10.3389/fimmu.2021.652631
  97. Stensland Z, Smith M. “Enrichment and Detection of Antigen-Binding B Cells for Mass Cytometry,” Magnetochemistry (Basel, Switzerland). 2021-07; 7(7):92 10.3390/magnetochemistry7070092
  98. McCarthy E, Odorizzi P, Lutz E, Smullin C, Tenvooren I, et al. “Distinct cellular immune signatures in acute Zika virus infection are associated with high or low persisting neutralizing antibody titers,” bioRxiv. 2021-05-28; 10.1101/2021.05.27.446054 [preprint]
  99. Stelzer I, Ghaemi M, Han X, Ando K, Hédou J, et al. “Integrated trajectories of the maternal metabolome, proteome, and immunome predict labor onset,” Science Translational Medicine. 2021-05-05; 13(592):eabd9898 10.1126/scitranslmed.abd9898
  100. Levine L, Hiam-Galvez K, Marquez D, Tenvooren I, Madden M, et al. “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 10.1016/j.immuni.2021.02.018
  101. Galbraith M, Kinning K, Sullivan K, Baxter R, Araya P, et al. “Seroconversion stages COVID19 into distinct pathophysiological states,” eLife. March 16, 2021; 10:e65508 10.7554/eLife.65508
  102. Leonard M, Silvester J, Leffler D, Fasano A, Kelly C, et al. “Evaluating Responses to Gluten Challenge: A Randomized, Double-Blind, 2-Dose Gluten Challenge Trial,” Gastroenterology. 2021-02; 160(3):720-733.e8 10.1053/j.gastro.2020.10.040
  103. Okamato Y, Ghosh T, Okamoto T, Schuyler R, Seifert J, et al. “Subjects at-risk for future development of rheumatoid arthritis demonstrate a PAD4-and TLR-dependent enhanced histone H3 citrullination and proinflammatory cytokine production in CD14hi monocytes,” Journal of Autoimmunity. 2021-02; 117:102581 10.1016/j.jaut.2020.102581
  104. Hartmann F, Mrdjen D, McCaffrey E, Glass D, Greenwald N, et al. “Single-cell metabolic profiling of human cytotoxic T cells,” Nature Biotechnology. 2021-02; 39(2):186-197 10.1038/s41587-020-0651-8
  105. Estevam J, Krutzik P, Vander Tuig J, McAuliffe W, Smithson G. “Development and validation of a high-parameter mass cytometry workflow to decipher immunomodulatory changes in celiac disease,” Cytometry. Part B, Clinical Cytometry. 2021-01; 100(1):92-102 10.1002/cyto.b.21986
  106. Furman S, Stern A, Uttam S, Taylor D, Pullara F, et al. “In situ functional cell phenotyping reveals microdomain networks in colorectal cancer recurrence,” Cell Reports Methods. 09/2021; 1(5):100072 10.1016/j.crmeth.2021.100072
  107. Wastyk H, Fragiadakis G, Perelman D, Dahan D, Merrill B, et al. “Gut-microbiota-targeted diets modulate human immune status,” Cell. 08/2021; 184(16):4137-4153.e14 10.1016/j.cell.2021.06.019
  108. Bashiri R, Khalili M, Weiner S, et al. “Rehabilitation of Oral Cancer Patients using Dental Implants and Maxillofacial Prosthetics” in “Early Detection and Treatment of Head & Neck Cancers: Practical Applications and Techniques for Detection, Diagnosis, and Treatment.” Springer International Publishing; 2021.
  109. Tsai A, Einhaus J, Hedou J, Tsai E, Gaudilliere D, et al. “The Role of Mass Cytometry in Early Detection, Diagnosis, and Treatment of Head and Neck Cancer” in “Early Detection and Treatment of Head & Neck Cancers: Practical Applications and Techniques for Detection, Diagnosis, and Treatment.” Springer International Publishing; 2021.
  110. Phillips D, Schürch C, Khodadoust M, Kim Y, Nolan G, et al. “Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging,” Frontiers in Immunology. 2021;
  111. Peterson L, Hedou J, Ganio E, Stelzer I, Feyaerts D, et al. “Single-Cell Analysis of the Neonatal Immune System Across the Gestational Age Continuum,” Frontiers in Immunology. 2021;
  112. Kotliar D, Lin A, Logue J, Hughes T, Khoury N, et al. “Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics,” Cell. 2020-11-25; 183(5):1383-1401.e19 10.1016/j.cell.2020.10.002
  113. Rahil Z, Leylek R, Schürch C, Chen H, Bjornson-Hooper Z, et al. “Landscape of coordinated immune responses to H1N1 challenge in humans,” The Journal of Clinical Investigation. 2020-11-02; 130(11):5800-5816 10.1172/JCI137265
  114. Culos A, Tsai A, Stanley N, Becker M, Ghaemi M, et al. “Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions,” Nature Machine Intelligence. 2020-10-12; 2(10):619-628 10.1038/s42256-020-00232-8
  115. Schürch C, Bhate S, Barlow G, Phillips D, Noti L, et al. “Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front,” Cell. 2020-09-03; 182(5):1341-1359.e19 10.1016/j.cell.2020.07.005
  116. Stanley N, Stelzer I, Tsai A, Fallahzadeh R, Ganio E, et al. “VoPo leverages cellular heterogeneity for predictive modeling of single-cell data,” Nature Communications. 2020-07-27; 11(1):3738 10.1038/s41467-020-17569-8
  117. Ganio E, Stanley N, Lindberg-Larsen V, Einhaus J, Tsai A, et al. “Preferential inhibition of adaptive immune system dynamics by glucocorticoids in patients after acute surgical trauma,” Nature Communications. 2020-07-27; 11(1):3737 10.1038/s41467-020-17565-y
  118. Glass D, Tsai A, Oliveria J, Hartmann F, Kimmey S, et al. “An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity,” Immunity. July 14, 2020; 53(1):217-232.e5 10.1016/j.immuni.2020.06.013
  119. McElroy A, Akondy R, Mcllwain D, Chen H, Bjornson-Hooper Z, et al. “Immunologic timeline of Ebola virus disease and recovery in humans,” JCI insight. 2020-05-21; 5(10):137260 10.1172/jci.insight.137260
  120. Hartmann F, Mrdjen D, McCaffrey E, Glass D, Greenwald N, et al. “Multiplexed Single-cell Metabolic Profiles Organize the Spectrum of Cytotoxic Human T Cells,” bioRxiv. 2020-01-17; 10.1101/2020.01.17.909796 [preprint]
  121. Han X, Ghaemi M, Ando K, Peterson L, Ganio E, et al. “Differential Dynamics of the Maternal Immune System in Healthy Pregnancy and Preeclampsia,” Frontiers in Immunology. 2019;