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Publications

Here, you can links to each of my publications and datasets where applicable.

  1. Nishio K, Pasquet L, Camara K, DiSapio J, Hsu KS, Kato S, Bloom A, Richardson SK, Welsh JA, Jiang T, Jones JC, Cardell S, Watarai H, Terabe M, Olkhanud PB, Howell AR, Berzofsky JA. Lysosomal processing of sulfatide analogs alters target NKT cell specificity and immune responses in cancer. J Clin Invest. 2023 Dec 21;134(4):e165281. doi: 10.1172/JCI165281. [pdf, website]

  2. Welsh JA, Goberdhan DC, O'Driscoll L, Théry C, Witwer KW. MISEV2023: An updated guide to EV research and applications. J Extracell Vesicles. 2024 Feb;13(2):e12416. doi: 10.1002/jev2.12416. [pdf, website]

  3. Welsh JA, Goberdhan DCI, O'Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, Falcon-Perez JM, Fu QL, Hill AF, Lenassi M, Lim SK, Mahoney MG, Mohanty S, Möller A, Nieuwland R, Ochiya T, Sahoo S, Torrecilhas AC, Zheng L, Zijlstra A, Abuelreich S, Bagabas R, Bergese P, Bridges EM, Brucale M, Burger D, Carney RP, Cocucci E, Crescitelli R, Hanser E, Harris AL, Haughey NJ, Hendrix A, Ivanov AR, Jovanovic-Talisman T, Kruh-Garcia NA, Ku'ulei-Lyn Faustino V, Kyburz D, Lässer C, Lennon KM, Lötvall J, Maddox AL, Martens-Uzunova ES, Mizenko RR, Newman LA, Ridolfi A, Rohde E, Rojalin T, Rowland A, Saftics A, Sandau US, Saugstad JA, Shekari F, Swift S, Ter-Ovanesyan D, Tosar JP, Useckaite Z, Valle F, Varga Z, van der Pol E, van Herwijnen MJC, Wauben MHM, Wehman AM, Williams S, Zendrini A, Zimmerman AJ; MISEV Consortium; Théry C, Witwer KW. Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles. 2024 Feb;13(2):e12404. doi: 10.1002/jev2.12404. [pdf, website]

  4. Cook S, Tang VA, Lannigan J, Jones JC, Welsh JA. Quantitative flow cytometry enables end-to-end optimization of cross-platform extracellular vesicle studies. Cell Rep Methods. 2023 Dec 18;3(12):100664. doi: 10.1016/j.crmeth.2023.100664. [pdf, website]

  5. de Oliveira Junior GP, Welsh JA, Pinckney B, Palu CC, Lu S, Zimmerman A, Barbosa RH, Sahu P, Noshin M, Gummuluru S, Tigges J, Jones JC, Ivanov AR, Ghiran IC. Human red blood cells release microvesicles with distinct sizes and protein composition that alter neutrophil phagocytosis. J Extracell Biol. 2023 Nov;2(11):e107. doi: 10.1002/jex2.107. Epub 2023 Oct 25. [pdf, website]

  6. Pleet ML, Cook S, Tang VA, Stack E, Ford VJ, Lannigan J, Do N, Wenger E, Fraikin JL, Jacobson S, Jones JC, Welsh JA. Extracellular Vesicle Refractive Index Derivation Utilizing Orthogonal Characterization. Nano Lett. 2023 Oct 25;23(20):9195-9202. doi: 10.1021/acs.nanolett.3c00562. Epub 2023 Oct 3. [pdf, website]

  7. Pleet ML, Welsh JA, Stack EH, Cook S, Johnson DA, Killingsworth B, Traynor T, Clauze A, Hughes R, Monaco MC, Ngouth N, Ohayon J, Enose-Akahata Y, Nath A, Cortese I, Reich DS, Jones JC, Jacobson S. Viral Immune signatures from cerebrospinal fluid extracellular vesicles and particles in HAM and other chronic neurological diseases. Front Immunol. 2023 Aug 9;14:1235791. doi: 10.3389/fimmu.2023.1235791. [pdf, website]

  8. Arce JE, Welsh JA, Cook S, Tigges J, Ghiran I, Jones JC, Jackson A, Roth M, Milosavljevic A. The NanoFlow Repository. Bioinformatics. 2023 Jun 1;39(6):btad368. doi: 10.1093/bioinformatics/btad368. [pdf, website]

  9. Welsh JA, Arkesteijn GJA, Bremer M, Cimorelli M, Dignat-George F, Giebel B, Görgens A, Hendrix A, Kuiper M, Lacroix R, Lannigan J, van Leeuwen TG, Lozano-Andrés E, Rao S, Robert S, de Rond L, Tang VA, Tertel T, Yan X, Wauben MHM, Nolan JP, Jones JC, Nieuwland R, van der Pol E., A compendium of single extracellular vesicle flow cytometry, J Extracell Vesicles. 2021 Dec;10(14):e12182. doi: 10.1002/jev2.12182., 2023, DOI: 10.1002/jev2.12299 [pdf, website]

  10. Mateescu B, Jones JC, Alexander RP, Alsop E, An JY, Asghari M, Boomgarden A, Bouchareychas L, Cayota A, Chang HC, Charest A, Chiu DT, Coffey RJ, Das S, De Hoff P, deMello A, D'Souza-Schorey C, Elashoff D, Eliato KR, Franklin JL, Galas DJ, Gerstein MB, Ghiran IH, Go DB, Gould S, Grogan TR, Higginbotham JN, Hladik F, Huang TJ, Huo X, Hutchins E, Jeppesen DK, Jovanovic-Talisman T, Kim BYS, Kim S, Kim KM, Kim Y, Kitchen RR, Knouse V, LaPlante EL, Lebrilla CB, Lee LJ, Lennon KM, Li G, Li F, Li T, Liu T, Liu Z, Maddox AL, McCarthy K, Meechoovet B, Maniya N, Meng Y, Milosavljevic A, Min BH, Morey A, Ng M, Nolan J, De Oliveira Junior GP, Paulaitis ME, Phu TA, Raffai RL, Reátegui E, Roth ME, Routenberg DA, Rozowsky J, Rufo J, Senapati S, Shachar S, Sharma H, Sood AK, Stavrakis S, Stürchler A, Tewari M, Tosar JP, Tucker-Schwartz AK, Turchinovich A, Valkov N, Van Keuren-Jensen K, Vickers KC, Vojtech L, Vreeland WN, Wang C, Wang K, Wang Z, Welsh JA, Witwer KW, Wong DTW, Xia J, Xie YH, Yang K, Zaborowski MP, Zhang C, Zhang Q, Zivkovic AM, Laurent LC., Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research, iScience, 2022, DOI: 10.1016/j.isci.2022.104653 [pdf, website]

  11. Welsh JA, Killingsworth B, Kepley J, Traynor T, Cook S, Savage J, Marte J, Lee MJ, Maeng HM, Pleet ML, Magana S, Gorgens A, Maire CL, Lamszus K, Ricklefs FL, Merino MJ, Linehan WM, Greten T, Cooks T, Harris CC, Apolo A, Abdel-Mageed A, Ivanov AR, Trepel JB, Roth M, Tkach M, Milosavljevic A, Théry C, LeBlanc A, Berzofsky JA, Ruppin E, Aldape K, Camphausen K, Gulley JL, Ghiran I, Jacobson S, Jones JC., MPA(PASS) software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays, Cell Rep Methods, 2022, DOI: 10.1016/j.crmeth.2021.100136 [pdf, website]

  12. Nolan JP, Chiu DT, Welsh JA, Rigor and reproducibility: status and challenges for single vesicle analysis, Extracellular Vesicles and Circulating Nucleic Acids, 2022, DOI: 10.20517/evcna.2022.28 [pdf, website]

  13. Moles R, Sarkis S, Galli V, Omsland M, Artesi M, Bissa M, McKinnon K, Brown S, Hahaut V, Washington-Parks R, Welsh J, Venzon DJ, Gutowska A, Doster MN, Breed MW, Killoran KE, Kramer J, Jones J, Moniuszko M, Van den Broeke A, Pise-Masison CA, Franchini G., NK cells and monocytes modulate primary HTLV-1 infection, PLoS Pathog, 2022, DOI: 10.1371/journal.ppat.1010416 [pdf, website]

  14. Witwer KW, Goberdhan DC, O'Driscoll L, Théry C, Welsh JA, Blenkiron C, Buzás EI, Di Vizio D, Erdbrügger U, Falcón-Pérez JM, Fu QL, Hill AF, Lenassi M, Lötvall J, Nieuwland R, Ochiya T, Rome S, Sahoo S, Zheng L., Updating MISEV: Evolving the minimal requirements for studies of extracellular vesicles, J Extracell Vesicles, 2021, DOI: 10.1002/jev2.12182 [pdf, website]

  15. Maire CL, Fuh MM, Kaulich K, Fita KD, Stevic I, Heiland DH, Welsh JA, Jones JC, Görgens A, Ricklefs T, Dührsen L, Sauvigny T, Joosse SA, Reifenberger G, Pantel K, Glatzel M, Miklosi AG, Felce JH, Caselli M, Pereno V, Reimer R, Schlüter H, Westphal M, Schüller U, Lamszus K, Ricklefs FL., Genome-wide methylation profiling of glioblastoma cell-derived extracellular vesicle DNA allows tumor classification, Neuro Oncol, 2021, DOI: 10.1093/neuonc/noab012 [pdf, website]

  16. Welsh JA, Killingsworth B, Kepley J, Traynor T, McKinnon K, Savage J, Appel D, Aldape K, Camphausen K, Berzofsky JA, Ivanov AR, Ghiran IH, Jones JC., A simple, high-throughput method of protein and label removal from extracellular vesicle samples, Nanoscale, 2021, DOI: 10.1039/d0nr07830a [pdf, website]

  17. Killingsworth B, Welsh JA, Jones JC., EV Translational Horizons as Viewed Across the Complex Landscape of Liquid Biopsies, Front Cell Dev Biol, 2021, DOI: 10.3389/fcell.2021.556837 [pdf, website]

  18. van der Pol E, Welsh JA, Nieuwland R., Minimum information to report about a flow cytometry experiment on extracellular vesicles: Communication from the ISTH SSC subcommittee on vascular biology, J Thromb Haemost, 2021, DOI: 10.1111/jth.15540 [pdf, website]

  19. Welsh JA, Jenkins LM, Kepley J, Lyons GC, Moore DM, Traynor T, Berzofsky JA, Jones JC., High Sensitivity Protein Gel Electrophoresis Label Compatible with Mass-Spectrometry, Biosensors (Basel), 2020, DOI: 10.3390/bios10110160 [pdf, website]

  20. Welsh JA, Van Der Pol E, Arkesteijn GJA, Bremer M, Brisson A, Coumans F, Dignat-George F, Duggan E, Ghiran I, Giebel B, Görgens A, Hendrix A, Lacroix R, Lannigan J, Libregts SFWM, Lozano-Andrés E, Morales-Kastresana A, Robert S, De Rond L, Tertel T, Tigges J, De Wever O, Yan X, Nieuwland R, Wauben MHM, Nolan JP, Jones JC., MIFlowCyt-EV: a framework for standardized reporting of extracellular vesicle flow cytometry experiments, J Extracell Vesicles, 2020, DOI: 10.1080/20013078.2020.1713526 [pdf, website]

  21. Morales-Kastresana A, Welsh JA, Jones JC., Detection and Sorting of Extracellular Vesicles and Viruses Using nanoFACS, Curr Protoc Cytom, 2020, DOI: 10.1002/cpcy.81 [pdf, website]

  22. Welsh JA, van der Pol E, Bettin BA, Carter DRF, Hendrix A, Lenassi M, Langlois MA, Llorente A, van de Nes AS, Nieuwland R, Tang V, Wang L, Witwer KW, Jones JC., Towards defining reference materials for measuring extracellular vesicle refractive index, epitope abundance, size and concentration, J Extracell Vesicles, 2020, DOI: 10.1080/20013078.2020.1816641 [pdf, website]

  23. Welsh JA, Jones JC., Small Particle Fluorescence and Light Scatter Calibration Using FCM(PASS) Software, Curr Protoc Cytom, 2020, DOI: 10.1002/cpcy.79 [pdf, website]

  24. Butement JT, Holloway PM, Welsh JA, Holloway JA, Englyst NA, Horak P, West J, Wilkinson JS., Monolithically-integrated cytometer for measuring particle diameter in the extracellular vesicle size range using multi-angle scattering, Lab Chip, 2020, DOI: 10.1039/c9lc01182j [pdf, website]

  25. Burnie J, Tang VA, Welsh JA, Persaud AT, Thaya L, Jones JC, Guzzo C., Flow Virometry Quantification of Host Proteins on the Surface of HIV-1 Pseudovirus Particles, Viruses, 2020, DOI: 10.3390/v12111296 [pdf, website]

  26. Welsh JA, Jones JC, Tang VA., Fluorescence and Light Scatter Calibration Allow Comparisons of Small Particle Data in Standard Units across Different Flow Cytometry Platforms and Detector Settings, Cytometry A, 2020, DOI: 10.1002/cyto.a.24029 [pdf, website]

  27. Welsh JA, Tang VA, van der Pol E, Görgens A., MIFlowCyt-EV: The Next Chapter in the Reporting and Reliability of Single Extracellular Vesicle Flow Cytometry Experiments, Cytometry A, 2020, DOI: 10.1002/cyto.a.24268 [pdf, website]

  28. de Rond L, Coumans FAW, Welsh JA, Nieuwland R, van Leeuwen TG, van der Pol E., Quantification of Light Scattering Detection Efficiency and Background in Flow Cytometry, Cytometry A, 2020, DOI: 10.1002/cyto.a.24243 [pdf, website]

  29. Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A., exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids, Cell, 2019, DOI: 10.1016/j.cell.2019.02.018 [pdf, website]

  30. Görgens A, Bremer M, Ferrer-Tur R, Murke F, Tertel T, Horn PA, Thalmann S, Welsh JA, Probst C, Guerin C, Boulanger CM, Jones JC, Hanenberg H, Erdbrügger U, Lannigan J, Ricklefs FL, El-Andaloussi S, Giebel B., Optimisation of imaging flow cytometry for the analysis of single extracellular vesicles by using fluorescence-tagged vesicles as biological reference material, J Extracell Vesicles, 2019, DOI: 10.1080/20013078.2019.1587567 [pdf, website]

  31. Clayton A, Boilard E, Buzas EI, Cheng L, Falcón-Perez JM, Gardiner C, Gustafson D, Gualerzi A, Hendrix A, Hoffman A, Jones J, Lässer C, Lawson C, Lenassi M, Nazarenko I, O'Driscoll L, Pink R, Siljander PR, Soekmadji C, Wauben M, Welsh JA, Witwer K, Zheng L, Nieuwland R., Considerations towards a roadmap for collection, handling and storage of blood extracellular vesicles, J Extracell Vesicles, 2019, DOI: 10.1080/20013078.2019.1647027 [pdf, website]

  32. 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, DOI: 10.1002/cyto.a.23941 [pdf, website]

  33. Morales-Kastresana A, Musich TA, Welsh JA, Telford W, Demberg T, Wood JCS, Bigos M, Ross CD, Kachynski A, Dean A, Felton EJ, Van Dyke J, Tigges J, Toxavidis V, Parks DR, Overton WR, Kesarwala AH, Freeman GJ, Rosner A, Perfetto SP, Pasquet L, Terabe M, McKinnon K, Kapoor V, Trepel JB, Puri A, Kobayashi H, Yung B, Chen X, Guion P, Choyke P, Knox SJ, Ghiran I, Robert-Guroff M, Berzofsky JA, Jones JC., High-fidelity detection and sorting of nanoscale vesicles in viral disease and cancer, J Extracell Vesicles, 2019, DOI: 10.1080/20013078.2019.1597603 [pdf, website]

  34. Tang VA, Fritzsche AK, Renner TM, Burger D, van der Pol E, Lannigan JA, Brittain GC, Welsh JA, Jones JC, Langlois M,, Engineered Retroviruses as Fluorescent Biological ReferenceParticles for Small Particle Flow Cytometry, BioRxiv, 2019, DOI: 10.1101/614461 [pdf, website]

  35. Welsh JA, Horak P, Wilkinson JS, Ford VJ, Jones JC, Smith D, Holloway JA, Englyst NA., FCM(PASS) Software Aids Extracellular Vesicle Light Scatter Standardization, Cytometry A, 2019, DOI: 10.1002/cyto.a.23782 [pdf, website]

  36. Théry C, Witwer KW, Aikawa E, Alcaraz MJ, Anderson JD, Andriantsitohaina R, Antoniou A, Arab T, Archer F, Atkin-Smith GK, Ayre DC, Bach JM, Bachurski D, Baharvand H, Balaj L, Baldacchino S, Bauer NN, Baxter AA, Bebawy M, Beckham C, Bedina Zavec A, Benmoussa A, Berardi AC, Bergese P, Bielska E, Blenkiron C, Bobis-Wozowicz S, Boilard E, Boireau W, Bongiovanni A, Borràs FE, Bosch S, Boulanger CM, Breakefield X, Breglio AM, Brennan MÁ, Brigstock DR, Brisson A, Broekman ML, Bromberg JF, Bryl-Górecka P, Buch S, Buck AH, Burger D, Busatto S, Buschmann D, Bussolati B, Buzás EI, Byrd JB, Camussi G, Carter DR, Caruso S, Chamley LW, Chang YT, Chen C, Chen S, Cheng L, Chin AR, Clayton A, Clerici SP, Cocks A, Cocucci E, Coffey RJ, Cordeiro-da-Silva A, Couch Y, Coumans FA, Coyle B, Crescitelli R, Criado MF, D'Souza-Schorey C, Das S, Datta Chaudhuri A, de Candia P, De Santana EF, De Wever O, Del Portillo HA, Demaret T, Deville S, Devitt A, Dhondt B, Di Vizio D, Dieterich LC, Dolo V, Dominguez Rubio AP, Dominici M, Dourado MR, Driedonks TA, Duarte FV, Duncan HM, Eichenberger RM, Ekström K, El Andaloussi S, Elie-Caille C, Erdbrügger U, Falcón-Pérez JM, Fatima F, Fish JE, Flores-Bellver M, Försönits A, Frelet-Barrand A, et al., Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines, J Extracell Vesicles, 2018, DOI: 10.1080/20013078.2018.1535750 [pdf, website]

  37. Welsh JA, Kepley J, Rosner A, Horak P, Berzofsky JA, Jones JC., Prospective Use of High-Refractive Index Materials for Single Molecule Detection in Flow Cytometry, Sensors (Basel), 2018, DOI: 10.3390/s18082461 [pdf, website]

  38. Wiklander OPB, Bostancioglu RB, Welsh JA, Zickler AM, Murke F, Corso G, Felldin U, Hagey DW, Evertsson B, Liang XM, Gustafsson MO, Mohammad DK, Wiek C, Hanenberg H, Bremer M, Gupta D, Björnstedt M, Giebel B, Nordin JZ, Jones JC, El Andaloussi S, Görgens A., Systematic Methodological Evaluation of a Multiplex Bead-Based Flow Cytometry Assay for Detection of Extracellular Vesicle Surface Signatures, Front Immunol, 2018, DOI: 10.3389/fimmu.2018.01326 [pdf, website]

  39. Welsh JA, Scorletti E, Clough GF, Englyst NA, Byrne CD., Leukocyte extracellular vesicle concentration is inversely associated with liver fibrosis severity in NAFLD, J Leukoc Biol, 2018, DOI: 10.1002/JLB.5A1217-501R [pdf, website]

  40. Clayton A, Buschmann D, Byrd JB, Carter DRF, Cheng L, Compton C, Daaboul G, Devitt A, Falcon-Perez JM, Gardiner C, Gustafson D, Harrison P, Helmbrecht C, Hendrix A, Hill A, Hoffman A, Jones JC, Kalluri R, Kang JY, Kirchner B, Lässer C, Lawson C, Lenassi M, Levin C, Llorente A, Martens-Uzunova ES, Möller A, Musante L, Ochiya T, Pink RC, Tahara H, Wauben MHM, Webber JP, Welsh JA, Witwer KW, Yin H, Nieuwland R., Summary of the ISEV workshop on extracellular vesicles as disease biomarkers, held in Birmingham, UK, during December 2017, J Extracell Vesicles, 2018, DOI: 10.1080/20013078.2018.1473707 [pdf, website]

  41. Welsh JA, Holloway JA, Wilkinson JS, Englyst NA., Extracellular Vesicle Flow Cytometry Analysis and Standardization, Front Cell Dev Biol, 2017, DOI: 10.3389/fcell.2017.00078 [pdf, website]

  42. Ramirez MI, Amorim MG, Gadelha C, Milic I, Welsh JA, Freitas VM, Nawaz M, Akbar N, Couch Y, Makin L, Cooke F, Vettore AL, Batista PX, Freezor R, Pezuk JA, Rosa-Fernandes L, Carreira ACO, Devitt A, Jacobs L, Silva IT, Coakley G, Nunes DN, Carter D, Palmisano G, Dias-Neto E., Technical challenges of working with extracellular vesicles, Nanoscale, 2017, DOI: 10.1039/c7nr08360b [pdf, website]

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