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For: Hu Z, Bhattacharya S, Butte AJ. Application of Machine Learning for Cytometry Data. Front Immunol 2022;12:787574. [PMID: 35046945 PMCID: PMC8761933 DOI: 10.3389/fimmu.2021.787574] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/14/2021] [Indexed: 01/23/2023]  Open
Number Cited by Other Article(s)
1
Bengs BD, Nde J, Dutta S, Li Y, Sardiu ME. Integrative approaches for predicting protein network perturbations through machine learning and structural characterization. J Proteomics 2025;316:105439. [PMID: 40228603 DOI: 10.1016/j.jprot.2025.105439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 03/14/2025] [Accepted: 04/08/2025] [Indexed: 04/16/2025]
2
Irvine A, Moustafa MM, Patel S, Patel A, Hardardottir L, Delvecchio F, Foreman T, Oak J, Bornheimer SJ, Cimbro R. Automation of flow cytometry data analysis with elastic image registration. Sci Rep 2025;15:16949. [PMID: 40374736 DOI: 10.1038/s41598-025-99118-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/17/2025] [Indexed: 05/18/2025]  Open
3
Sadighi Akha AA, Csomós K, Ujházi B, Walter JE, Kumánovics A. Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders. Immunol Allergy Clin North Am 2025;45:205-221. [PMID: 40287169 DOI: 10.1016/j.iac.2025.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2025]
4
Tursi AR, Lages CS, Quayle K, Koenig ZT, Loni R, Eswar S, Cobeña-Reyes J, Thornton S, Tilburgs T, Andorf S. CytoPheno: Automated descriptive cell type naming in flow and mass cytometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.11.639902. [PMID: 40161808 PMCID: PMC11952469 DOI: 10.1101/2025.03.11.639902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
5
Śliwa-Dominiak J, Czechowska K, Blanco A, Sielatycka K, Radaczyńska M, Skonieczna-Żydecka K, Marlicz W, Łoniewski I. Flow Cytometry in Microbiology: A Review of the Current State in Microbiome Research, Probiotics, and Industrial Manufacturing. Cytometry A 2025;107:145-164. [PMID: 40028773 DOI: 10.1002/cyto.a.24920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 12/22/2024] [Accepted: 01/25/2025] [Indexed: 03/05/2025]
6
Chen YM, Hsiao TH, Lin CH, Fann YC. Unlocking precision medicine: clinical applications of integrating health records, genetics, and immunology through artificial intelligence. J Biomed Sci 2025;32:16. [PMID: 39915780 PMCID: PMC11804102 DOI: 10.1186/s12929-024-01110-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 12/02/2024] [Indexed: 02/09/2025]  Open
7
Bongrand P. Should Artificial Intelligence Play a Durable Role in Biomedical Research and Practice? Int J Mol Sci 2024;25:13371. [PMID: 39769135 PMCID: PMC11676049 DOI: 10.3390/ijms252413371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 11/26/2024] [Accepted: 12/09/2024] [Indexed: 01/11/2025]  Open
8
Villegas-Valverde CA, Bencomo-Hernandez AA, Castillo-Aleman YM, Ventura-Carmenate Y, Casado-Hernandez I, Rivero-Jimenez RA. Application of mass cytometry to characterize hematopoietic stem cells in apheresis products of patients with hematological malignancies. Hematol Transfus Cell Ther 2024;46 Suppl 6:S59-S70. [PMID: 38177056 PMCID: PMC11726105 DOI: 10.1016/j.htct.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/25/2023] [Accepted: 10/20/2023] [Indexed: 01/06/2024]  Open
9
Wlosik J, Granjeaud S, Gorvel L, Olive D, Chretien AS. A beginner's guide to supervised analysis for mass cytometry data in cancer biology. Cytometry A 2024;105:853-869. [PMID: 39486897 DOI: 10.1002/cyto.a.24901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 09/16/2024] [Accepted: 10/01/2024] [Indexed: 11/04/2024]
10
Irvine A, Tahir S, Tripathi V, Oreizy F, Sen M, Giuliano A, Lin A, Chen A, Lai CH, Omana-Zapata I, Zeng Y, Jain P, Bornheimer SJ. Automated analysis of flow cytometry data with minimal training files: Research evaluation of an elastic image registration algorithm for TBNK, stem cell enumeration, and lymphoid screening tube assays. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2024. [PMID: 39417216 DOI: 10.1002/cyto.b.22210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 09/15/2024] [Accepted: 09/25/2024] [Indexed: 10/19/2024]
11
Eslami M, Moseley RC, Eramian H, Bryce D, Haase SB. AutoGater: a weakly supervised neural network model to gate cells in flow cytometric analyses. Sci Rep 2024;14:23581. [PMID: 39384769 PMCID: PMC11479614 DOI: 10.1038/s41598-024-66936-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/05/2024] [Indexed: 10/11/2024]  Open
12
Zhang W, Sen A, Pena JK, Reitsma A, Alexander OC, Tajima T, Martinez OM, Krams SM. Application of Mass Cytometry Platforms to Solid Organ Transplantation. Transplantation 2024;108:2034-2044. [PMID: 38467594 PMCID: PMC11390974 DOI: 10.1097/tp.0000000000004925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
13
Wasilewski T, Kamysz W, Gębicki J. AI-Assisted Detection of Biomarkers by Sensors and Biosensors for Early Diagnosis and Monitoring. BIOSENSORS 2024;14:356. [PMID: 39056632 PMCID: PMC11274923 DOI: 10.3390/bios14070356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
14
Ng DP, Simonson PD, Tarnok A, Lucas F, Kern W, Rolf N, Bogdanoski G, Green C, Brinkman RR, Czechowska K. Recommendations for using artificial intelligence in clinical flow cytometry. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2024;106:228-238. [PMID: 38407537 DOI: 10.1002/cyto.b.22166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
15
Bogdanoski G, Lucas F, Kern W, Czechowska K. Translating the regulatory landscape of medical devices to create fit-for-purpose artificial intelligence (AI) cytometry solutions. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2024;106:294-307. [PMID: 38396223 DOI: 10.1002/cyto.b.22167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024]
16
Dutta S, Mudaranthakam DP, Li Y, Sardiu ME. PerSEveML: a web-based tool to identify persistent biomarker structure for rare events using an integrative machine learning approach. Mol Omics 2024;20:348-358. [PMID: 38690925 DOI: 10.1039/d4mo00008k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
17
Cheng FM, Lo SC, Lin CC, Lo WJ, Chien SY, Sun TH, Hsu KC. Deep learning assists in acute leukemia detection and cell classification via flow cytometry using the acute leukemia orientation tube. Sci Rep 2024;14:8350. [PMID: 38594383 PMCID: PMC11004172 DOI: 10.1038/s41598-024-58580-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/01/2024] [Indexed: 04/11/2024]  Open
18
Nollmann C, Moskorz W, Wimmenauer C, Jäger PS, Cadeddu RP, Timm J, Heinzel T, Haas R. Characterization of CD34+ Cells from Patients with Acute Myeloid Leukemia (AML) and Myelodysplastic Syndromes (MDS) Using a t-Distributed Stochastic Neighbor Embedding (t-SNE) Protocol. Cancers (Basel) 2024;16:1320. [PMID: 38610998 PMCID: PMC11010974 DOI: 10.3390/cancers16071320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]  Open
19
Lewis JE, Cooper LAD, Jaye DL, Pozdnyakova O. Automated Deep Learning-Based Diagnosis and Molecular Characterization of Acute Myeloid Leukemia Using Flow Cytometry. Mod Pathol 2024;37:100373. [PMID: 37925056 DOI: 10.1016/j.modpat.2023.100373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023]
20
Shetab Boushehri S, Essig K, Chlis NK, Herter S, Bacac M, Theis FJ, Glasmacher E, Marr C, Schmich F. Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies. Nat Commun 2023;14:7888. [PMID: 38036503 PMCID: PMC10689847 DOI: 10.1038/s41467-023-43429-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/09/2023] [Indexed: 12/02/2023]  Open
21
Na S, Choo Y, Yoon TH, Paek E. CyGate Provides a Robust Solution for Automatic Gating of Single Cell Cytometry Data. Anal Chem 2023;95:16918-16926. [PMID: 37946317 PMCID: PMC10666088 DOI: 10.1021/acs.analchem.3c03006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
22
Montante S, Chen Y, Brinkman RR. flowSim: Near duplicate detection for flow cytometry data. Cytometry A 2023;103:889-901. [PMID: 37530476 PMCID: PMC10834853 DOI: 10.1002/cyto.a.24776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/22/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023]
23
Dutta S, Box AC, Li Y, Sardiu ME. Identifying dynamical persistent biomarker structures for rare events using modern integrative machine learning approach. Proteomics 2023;23:e2200290. [PMID: 36852539 PMCID: PMC11503472 DOI: 10.1002/pmic.202200290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/30/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
24
Dutta S, Mudaranthakam DP, Li Y, Sardiu ME. PerSEveML: A Web-Based Tool to Identify Persistent Biomarker Structure for Rare Events Using Integrative Machine Learning Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564000. [PMID: 38196661 PMCID: PMC10775315 DOI: 10.1101/2023.10.25.564000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
25
Robles EE, Jin Y, Smyth P, Scheuermann RH, Bui JD, Wang HY, Oak J, Qian Y. A cell-level discriminative neural network model for diagnosis of blood cancers. Bioinformatics 2023;39:btad585. [PMID: 37756695 PMCID: PMC10563151 DOI: 10.1093/bioinformatics/btad585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]  Open
26
Lewis JE, Cooper LA, Jaye DL, Pozdnyakova O. Automated Deep Learning-Based Diagnosis and Molecular Characterization of Acute Myeloid Leukemia using Flow Cytometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558289. [PMID: 37808719 PMCID: PMC10557578 DOI: 10.1101/2023.09.18.558289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
27
Saihi H, Bessant C, Alazawi W. Automated and reproducible cell identification in mass cytometry using neural networks. Brief Bioinform 2023;24:bbad392. [PMID: 37930029 PMCID: PMC10630086 DOI: 10.1093/bib/bbad392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 11/07/2023]  Open
28
Sadighi Akha AA, Csomós K, Ujházi B, Walter JE, Kumánovics A. Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders. Clin Lab Med 2023;43:467-483. [PMID: 37481324 DOI: 10.1016/j.cll.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
29
Räuber S, Nelke C, Schroeter CB, Barman S, Pawlitzki M, Ingwersen J, Akgün K, Günther R, Garza AP, Marggraf M, Dunay IR, Schreiber S, Vielhaber S, Ziemssen T, Melzer N, Ruck T, Meuth SG, Herty M. Classifying flow cytometry data using Bayesian analysis helps to distinguish ALS patients from healthy controls. Front Immunol 2023;14:1198860. [PMID: 37600819 PMCID: PMC10434536 DOI: 10.3389/fimmu.2023.1198860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023]  Open
30
Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023;12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]  Open
31
Keyes TJ, Koladiya A, Lo YC, Nolan GP, Davis KL. tidytof: a user-friendly framework for scalable and reproducible high-dimensional cytometry data analysis. BIOINFORMATICS ADVANCES 2023;3:vbad071. [PMID: 37351311 PMCID: PMC10281957 DOI: 10.1093/bioadv/vbad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/03/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
32
Yang L, Dutta P, Davuluri RV, Wang J. Rapid, High-Throughput Single-Cell Multiplex In Situ Tagging (MIST) Analysis of Immunological Disease with Machine Learning. Anal Chem 2023;95:7779-7787. [PMID: 37141575 PMCID: PMC10365012 DOI: 10.1021/acs.analchem.3c01157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
33
Hourani T, Perez-Gonzalez A, Khoshmanesh K, Luwor R, Achuthan AA, Baratchi S, O'Brien-Simpson NM, Al-Hourani A. Label-free macrophage phenotype classification using machine learning methods. Sci Rep 2023;13:5202. [PMID: 36997576 PMCID: PMC10061362 DOI: 10.1038/s41598-023-32158-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/23/2023] [Indexed: 04/01/2023]  Open
34
Robles EE, Jin Y, Smyth P, Scheuermann RH, Bui JD, Wang HY, Oak J, Qian Y. A cell-level discriminative neural network model for diagnosis of blood cancers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.07.23285606. [PMID: 36798344 PMCID: PMC9934808 DOI: 10.1101/2023.02.07.23285606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
35
Obstfeld AE. Hematology and Machine Learning. J Appl Lab Med 2023;8:129-144. [PMID: 36610431 DOI: 10.1093/jalm/jfac108] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/09/2023]
36
Barbetta A, Rocque B, Sarode D, Bartlett JA, Emamaullee J. Revisiting transplant immunology through the lens of single-cell technologies. Semin Immunopathol 2023;45:91-109. [PMID: 35980400 PMCID: PMC9386203 DOI: 10.1007/s00281-022-00958-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
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