University of Pennsylvania
Derek Jones
297 John Morgan Building
3620 Hamilton Walk
Philadelphia, PA 19104
https://www.med.upenn.edu/cytomics/
RRID: RRID:SCR_022376
Cell Sorting
Consultation
Experimental Design
FACS Cell Sorting
Flow Cytometric Analysis
Flow Cytometry
Flow Cytometry Data Analysis
High Dimensional Flow Cytometry Analysis
Sample Preparation
Single-Cell Analysis
Spectral Flow Cytometry
Training
1.) Eldaboush A, Ricco C, Musante L, Dhiman R, Liu ML, Werth VP (2026 Jan). Characterizing Keratinocyte-Derived Extracellular Vesicles in UVB-Irradiated Murine Skin. JID innovations : skin science from molecules to population health, 6(1), 100406. . PMCID: 12581760.
2.) Chislock EM, Pan TC, Pant D, Chen Y, Woodfield G, Graves J, Lawrence-Paul MR, Belka GK, Wang J, Bayne L, Blanchard T, Smith M, Ji X, Shih NN, Soucier-Ernst D, Goodman N, Nivar I, Goodspeed B, DeLuca S, Ndicu J, Clark C, Langer M, William Stavropoulos S, DeMuth W, Morschauser A, Murphy W, Nayak A, Feldman M, Clark A, Yu L, Judge K, Bornheimer S, Pletcher CH Jr, Moore JS, DeMichele A, Chodosh LA (2025 Nov 24). DTC-Flow: a flow cytometry-based detection platform for characterizing bone marrow disseminated tumor cells in breast cancer NPJ Breast Cancer, 11(), 139. . PMCID: 12686464.
3.) Melamed JR, Muscat-Rivera J, Kegel M, Chaboub LS, Perez-Tremble R, Bhalla NS, Ni H, Sun H, Weissman D (2025 Oct 17). Anionic lipids modulate mRNA-lipid nanoparticle immunogenicity and confer protection in a mouse model of multiple sclerosis. bioRxiv : the preprint server for biology, (), . . PMCID: 12632872.
4.) Londregan J, Rozich I, Gaudette BT, Tursi NJ, Weiner DB, Maillard I, Allman D (2025 Oct 12). Notch2 signaling instructs viral and bacterial TLR responsiveness in B cells bioRxiv, (), 2025.10.10.681480. . PMCID: 12632369.
5.) Pawar AS, Somers P, Alex A, Grana J, Feist VK, George SS, Jalnapurkar SS, Antony C, Verner R, White-Brown SK, Khera M, Mendoza-Figueroa MS, Liu KF, Morrissette JJD, Gurbuxani S, Paralkar VR (2025 Oct 1). Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness. Genes & development, 39(19), 1219-1240. . PMCID: 12340699.
6.) Sams EI, Feist VK, Gray EM, George SS, Antony C, Henrich JA, Wald J, Dunagin MC, Wang Z, Erlitzki N, Raj A, Signer RAJ, Paralkar VR (2025 Aug 1). Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis. bioRxiv : the preprint server for biology, (), . . PMCID: 12324415.
7.) Wang Z, Kulkarni S, Nong J, Zamora M, Ebrahimimojarad A, Hood E, Shuvaeva T, Zaleski M, Gullipalli D, Wolfe E, Espy C, Arguiri E, Wu J, Wang Y, Marcos-Contreras OA, Song W, Muzykantov VR, Fu J, Radhakrishnan R, Myerson JW, Brenner JS (2025 Jul 24). A percolation phase transition controls complement protein coating of surfaces. Cell, 188(15), 4058-4073.e25. . PMCID: 12243617.
8.) Skuli SJ, Bakayoko A, Kruidenier M, Manning B, Pammer P, Salimov A, Riley O, Brake-Sillá G, Dopkin D, Bowman M, Martinez-Gutierrez LN, Anderson CC, Reisz JA, Buono R, Paul M, Saland E, Liccardo F, DeVine A, Wong S, Xu JP, Nee E, Hausler R, Boettcher S, Sebti SM, Lai C, Maxwell KN, Sarry JE, Fruman DA, D’Alessandro A, Mesaros C, Keith B, Simon MC, Sung PJ, Wertheim G, Skuli N, Bowman RL, Matthews A, Carroll M (2025 Jul 9). Chemoresistance of TP53 mutant acute myeloid leukemia requires the mevalonate byproduct, geranylgeranyl pyrophosphate, for induction of an adaptive stress response Leukemia, 39(9), 2087-2098. . PMCID: 12380605.
9.) Murthy A, Rodríguez LR, Barboza WR, Tomer Y, Bui S, Carson P, Dimopoulos T, Iyer S, Chavez K, Cooper CH, Katzen JB, Beers MF (2025 Jul 5). REGULATORY T CELLS PROTECT AGAINST ABERRANT REMODELING IN A MOUSE MODEL OF PULMONARY FIBROSIS bioRxiv, (), 2025.07.02.662777. . PMCID: 12236608.
10.) Dooling LJ, Anlaş AA, Tobin MP, Ontko NM, Marchena T, Wang M, Andrechak JC, Discher DE (2025 Jul 1). Clustered macrophages cooperate to eliminate tumors via coordinated intrudopodia Proceedings of the National Academy of Sciences of the United States of America, 122(27), e2425452122. . PMCID: 12260397.
11.) Rodríguez LR, Alysandratos KD, Katzen J, Murthy A, Roque Barboza W, Tomer Y, Bui S, Acín-Pérez R, Petcherski A, Minakin K, Carson P, Iyer S, Chavez K, Cooper CH, Babu A, Weiner AI, Vaughan AE, Arany Z, Shirihai OS, Kotton DN, Beers MF (2025 Jul 1). Impaired AMPK control of alveolar epithelial cell metabolism promotes pulmonary fibrosis JCI Insight, 10(15), e182578. . PMCID: 12333953.
12.) Knox JJ, Lee I, Blumberg EA, Rosenfeld AM, Meng W, Liu F, Kearns C, O’Doherty U, Shaked A, Olthoff KM, Luning Prak ET (2025 Jun 3). B-Cell Subset Representation Predicts SARS-CoV-2 Vaccine Response in Solid Organ Transplant Recipients The Journal of Infectious Diseases, 232(3), e466-e475. . PMCID: 12455301.
13.) Mears KS, Denny JE, Maslanka JR, Mdluli NV, Hulit EN, Matsuda R, Furth EE, Buffie CG, Abt MC (2025 Apr 22). Therapeutic activation of IL-22-producing innate lymphoid cells enhances host defenses to Clostridioides difficile infection. Cell reports, 44(4), 115438. . PMCID: 12115236.
14.) Ahmadi M, Zhao Z, Dmochowski IJ (2025 Apr 8). RIBOsensor for FRET-based, real-time ribose measurements in live cells Chemical Science, (), . . PMCID: 11977553.
15.) Niethamer TK, Planer JD, Morley MP, Babu A, Zhao G, Basil MC, Cantu E, Frank DB, Diamond JM, Nottingham AN, Li S, Sharma A, Hallquist H, Levin LI, Zhou S, Vaughan AE, Morrisey EE (2025 Feb 6). Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states. Cell stem cell, 32(2), 302-321.e6. . PMCID: 11805657.
16.) Swingle KL, Hamilton AG, Safford HC, Geisler HC, Thatte AS, Palanki R, Murray AM, Han EL, Mukalel AJ, Han X, Joseph RA, Ghalsasi AA, Alameh MG, Weissman D, Mitchell MJ (2024 Dec 11). Placenta-tropic VEGF mRNA lipid nanoparticles ameliorate murine pre-eclampsia Nature, 637(8045), 412-421. . PMCID: 12205896.
17.) YADAV A, GIONET G, KARAJ A, KOSSENKOV AV, KANNAN T, PUTT ME, SHIELDS AJ, ASHARE RL, COLLMAN RG (2024 Sep 13). Association of smoking with neurocognition, inflammatory and myeloid cell activation profiles in people with HIV on ART AIDS (London, England), 38(15), 2010-2020. . PMCID: 11666410.
18.) Lee CS, Chen S, Berry CT, Kelly AR, Herman PJ, Oh S, O’Connor RS, Payne AS, Ellebrecht CT (2024 Aug 28). Fate induction in CD8 CAR T cells through asymmetric cell division Nature, 633(8030), 670-677. . PMCID: 11410665.
19.) Kadam PS, Yang Z, Lu Y, Zhu H, Atiyas Y, Shah N, Fisher S, Nordgren E, Kim J, Issadore D, Eberwine J (2024 Jul 29). Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons BMC Biology, 22(), 162. . PMCID: 11287894.
20.) Geisler HC, Ghalsasi AA, Safford HC, Swingle KL, Thatte AS, Mukalel AJ, Gong N, Hamilton AG, Han EL, Nachod BE, Padilla MS, Mitchell MJ (2024 Jul). EGFR-targeted ionizable lipid nanoparticles enhance in vivo mRNA delivery to the placenta. Journal of controlled release : official journal of the Controlled Release Society, 371(), 455-469. . PMCID: 11259947.
21.) Kadam PS, Yang Z, Lu Y, Zhu H, Atiyas Y, Shah N, Fisher S, Nordgren E, Kim J, Issadore D, Eberwine J (2024 Jun 19). Single-Mitochondrion Sequencing Uncovers Distinct Mutational Patterns and Heteroplasmy Landscape in Mouse Astrocytes and Neurons bioRxiv, (), 2024.06.13.598906. . PMCID: 11195285.
22.) Atsavapranee E, Haley RM, Billingsley MM, Chan A, Ruan B, Figueroa-Espada CG, Gong N, Mukalel AJ, Bryan PN, Mitchell MJ (2024 Jun). Ionizable lipid nanoparticles for RAS protease delivery to inhibit cancer cell proliferation. Journal of controlled release : official journal of the Controlled Release Society, 370(), 614-625. . PMCID: 11210981.
23.) Denny JE, Alam MZ, Mdluli NV, Maslanka JR, Lieberman LA, Abt MC (2024 May 1). Monoclonal antibody-mediated neutralization of Clostridioides difficile toxin does not diminish induction of the protective innate immune response to infection Anaerobe, 88(), 102859. . PMCID: 11347114.
24.) Wong KG, Cheng YC, Wu VH, Kiseleva AA, Li J, Poleshko A, Smith CL, Epstein JA (2024 Mar 13). Growth factor–induced activation of MSK2 leads to phosphorylation of H3K9me2S10 and corresponding changes in gene expression Science Advances, 10(11), eadm9518. . PMCID: 10936876.
25.) Goldman N, Chandra A, Johnson I, Sullivan MA, Patil AR, Vanderbeck A, Jay A, Zhou Y, Ferrari EK, Mayne L, Aguilan J, Xue HH, Faryabi RB, Wherry EJ, Sidoli S, Maillard I, Vahedi G (2023 Aug 17). Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity Nature immunology, 24(10), 1698-1710. . PMCID: 10919931.
26.) Omo-Lamai S, Zamora ME, Patel MN, Wu J, Nong J, Wang Z, Peshkova A, Chase LS, Essien EO, Muzykantov V, Marcos-Contreras O, Myerson JW, Brenner JS (2023 Jul 25). Physicochemical Targeting of Lipid Nanoparticles to the Lungs Induces Clotting: Mechanisms and Solutions bioRxiv, (), 2023.07.21.550080. . PMCID: 10401951.
27.) Antony C, Somers P, Gray EM, Pimkin M, Paralkar VR (2023 Jul 22). FISH-Flow to quantify nascent and mature ribosomal RNA in mouse and human cells STAR Protocols, 4(3), 102463. . PMCID: 10374870.
28.) Egan KP, Awasthi S, Tebaldi G, Hook LM, Naughton AM, Fowler BT, Beattie M, Alameh MG, Weissman D, Cohen GH, Friedman HM (2023 Jun 30). A Trivalent HSV-2 gC2, gD2, gE2 Nucleoside-Modified mRNA-LNP Vaccine Provides Outstanding Protection in Mice against Genital and Non-Genital HSV-1 Infection, Comparable to the Same Antigens Derived from HSV-1 Viruses, 15(7), 1483. . PMCID: 10384700.
Penn Cytomics is the sole flow cytometry shared resource laboratory (SRL) at the University of Pennsylvania. Our facility has 35+ instruments, which include analyzers and cell sorters, several of which have spectral and imaging capabilities. We also have a dual-fluorescence cell counter/viability instrument and a tissue dissociator for cell preparation. We provide both on-site and off-site support to our instrument users, including analyzer and cell sorter training. We also have a research and development team that collaborates/consults with principal investigators in developing high-dimensional panels, as well as staining, acquisition, and analysis. The core has ~10 nearby satellite locations to accommodate instrument user needs.
