Publications

Publications

* Equal Contribution

^#Co-corresponding Author

Pre-prints

Haage, V., Tuddenham, J.F., Commandante-Lou, N., Bautista, A., Monzel, A., Chiu, R., Fujita, M., Garcia, F.G., Bhattarai, P., Batel, R., Buonfiglioli, A., Idiarte, J., Herman, M., Rinderspacher, A., Mela, A., Zhao, W., Argenziano, M.G., Furnari, J.L., Banu, M., Landry, D.W., Bruce, J.N., Canoll, P., Zhang, Y., Nuriel, T., Kizil, C., Sproul, A.A., de Witte, L.D., Sims, P.A., Menon, V., Picard, M., De Jager, P.L. A pharmacological toolkit for human microglia identifies Topoisomerase I inhibitors as immunomodulators for Alzheimer's disease. bioRxiv (2024).

Goldberg, A.R., Dovas, A., Torres, D., Das Sharma, S., Mela, A., Merricks, E.M., Olabarria, M., Shokoohm, L.A., Zhao, H.T., Kotidis, C., Calvaresi, P., Viswanathan, A., Banu, M.A., Razavilar, A., Sudhakar, T.D., Saxena, A., Chokran, C., Humala, N., Mahajan, A., Xu, W., Metz, J.B., Chen, C., Bushong, E.A., Boassa, D., Ellisman, M.H., Hillman, E.M.C., McKhann II, G.M., Gill, B.J.A., Rosenfeld, S.S., Schevon, C.A., Bruce, J.N., Sims, P.A., Peterka, D.S., Canoll, P. Glioma-induced alterations in excitatory neurons are reversed by mTOR inhibition. bioRxiv (2024).

Jakubiak, K., Paryani, F., Kannan, A., Lee, J., Madden, N., Li, J., Chen, D., Mahajan, A., Xia, S., Flowers, X., Menon, V., Sulzer, D., Goldman, J., Sims, P.A., Al-Dalahmah, O. The spatial landscape of glial pathology and T cell response in Parkinsons's disease substantia nigra. bioRxiv (2024).

Wells, S.B., Rainbow, D.B., Mark, M., Szabo, P.A., Ergan, C., Maceiras, A.R., Caron, D.P., Rahmani, E., Benuck, E., Valiollah Pour Amiri, V., Chen, D., Wagner, A., Howlett, S.K., Jarvis, L.B., Ellis, K.L., Kubota, M., Matsumoto, R., Mahbubani, K., Saeb-Parsy, K., Dominguez-Conde, C., Richardson, L., Xu, C., Li, S., Mamanova, L., Bolt, L., Wilk, A., Teichmann, S.A.#, Farber, D.L.#, Sims, P.A.#, Jones, J.L.#, Yosef, N.# Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age. bioRxiv (2024).

Levitin, H.M., Zhao, W., Bruce, J.N., Canoll, P., Sims, P.A. Consensus scHPF identifies cell type-specific drug responses in glioma by integrating large-scale scRNA-seq. bioRxiv (2023).

Caron, D.P., Specht, W.L., Chen, D., Wells, S.B., Szabo, P.A., Jensen, I.J., Farber, D.L., Sims, P.A. Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues. bioRxiv (2023).

Banu M.A., Dovas, A., Argenziano M.G., Zhao, W., Grajal, H.C., Higgins, D.M.O., Sperring, C., Pereira, B., Ye, L.F., Mahajan, A., Humala, N., Furnari, J.L., Upadhyayula, P.S., Zandkarimi, F., Nguyen, T.T.T., Wu, P.B., Hai, L., Karan, C., Razavilar, A., Siegelin, M.D., Kitajewski, J., Bruce, J.N., Stockwell, B.R., Sims, P.A.#, Canoll, P.D.# A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma. bioRxiv (2023).

Olsen, T.R., Talla, P., Furnari, J., Bruce, J.N., Canoll, P., Zha, S., Sims, P.A. Scalable co-sequencing of RNA and DNA from individual nuclei. bioRxiv (2023).

Tuddenham, J.F., Taga, M., Haage, V., Roostaei, T., White, C., Lee, A., Fujita, M., Khairallah, A., Green, G., Hyman, B., Frosch, M., Hopp, S., Beach, T.G., Corboy, J., Habib, N., Klein, H.-U., Soni, R.K., Teich, A.F., Hickman, R.A., Alcalay, R.N., Schneider, N., Schneider, J., Sims, P.A., Bennett, D.A., Olah, M., Menon, V., De Jager, P.L. A cross-disease human microglial framework identifies disease-enriched subsets and tool compounds for microglial polarization. bioRxiv (2022).

Ballestar, E., Farber, D.L., Glover, S., Horwitz, B., Meyer, K., Nikolic, M., Ordovas-Montanes, J., Sims, P.A., Shalek, A.K., Vandamme, N., Vandekerckhove, L., Vento-Tormo, R., Villani, A.C., Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia, Single cell profiling of COVID-19 patients: an international data resource from multiple tissues. medRxiv (2020).

Ding, H., Burgenske, D.M., Zhao, W., Subramaniam, P.S., Bakken, K.K., He, L., Alvarez, M.J., Laise, P., Paull, E.O., Spinazzi, E.F., Dovas, A., Marie, T., Upadhyayula, P., Dela Cruz, F., Diolaiti, D., Kung, A., Bruce, J.N., Canoll, P.#, Sims, P.A.#, Sarkaria, J.N.#, Califano, A.# Single-cell based elucidation of molecularly distinct glioblastoma states and drug sensitivity. bioRxiv* (2019).

2024

Cheng, Y.L., Banu, M.A., Zhao, W., Rosenfeld, S.S., Canoll, P., Sims, P.A. Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. Cell Reports, 43, 114139 (2024).

Mi, X., Bekerman, W., Rustgi, A.K., Sims, P.A., Canoll, P.D., Hu, J. RZiMM-scRNA: A regularized zero-inflated mixture model framework for single-cell RNA-seq data. Annals of Applied Statistics, 18, 1 (2024).

2023

Liu, Z., Mela, A., Argenziano, M.G., Banu, M.A., Furnari, J., Kotidis, C., Sperring, C., Humala, N., Mahajan, A., Bruce, J.N., Canoll, P., Sims, P.A. Single-cell analysis of 5-aminolevuliniic acid intraoperative labeling specificity for glioblastoma. Journal of Neurosurgery, 140, 968 (2023).

Letter to the Editor: Decoding GBM: a singular insight into the precision of 5-ALA through single-cell analysis with our reply.

Letter to the Editor: ALA in the treatment of glioblastoma with our reply.

Matsumoto, R., Gray, J., Rybkina, K., Oppenheimer, H., Levy, L., Friedman, L.M., Khamaisi, M., Meng, W., Rosenfeld, A.M., Guyer, R.S., Bradley, M.C., Chen, D., Atkinson, M.A., Brusko, T.M., Brusko, M., Connors, T.J., Luning Prak, E.T., Hershberg, U., Sims, P.A., Hertz, T., Farber, D.L. Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity. Nature Immunology, 24, 1370 (2023).

Connors, T.J., Matsumoto, R., Verma, S., Szabo, P.A., Guyer, R., Gray, J., Wang, Z., Thapa, P., Dogra, P., Poon, M.M.L., Rybkina, K., Bradley, M.C., Idzikowski, E., McNichols, J., Kubota, M., Pethe K., Shen, Y., Atkinson, M.A., Brusko, M., Brusko, T.M., Yates, A.J., Sims, P.A., Farber, D.L. Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood. Immunity, 56, 1894 (2023).

Sugiura, K., Masuike, Y., Suzuki, K., Shin, A.E., Sakai, N., Matsubara, H., Ohtsuka, M., Sims, P.A., Lengner, C.J., Rustgi, A.K. LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3. JCI Insight, e167310 (2023).

Al-Dalahmah, O.#, Argenziano, M., Kannan, A., Mahajan, A., Furnari, J., Paryani, F., Boyett, D., Save, A., Humala, N., Khan, F., Li, J., Lu, H., Sun, Y., Tuddenham, J.F., Goldberg, A.R., Dovas, A., Banu, M.A., Sudhakar, T., Bush, E., Lassman, A.B., McKhann, G.M., Gill, B.J.A., Youngerman, B., Sisti, M.B., Bruce, J.N., Sims, P.A., Menon, V.#, Canoll, P.# Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states. Nature Communications, 14, 2586 (2023).

Hobson, B.D., Stanley, A.T., De Los Santos, M.B., Culbertson, B., Mosharov, E.V., Sims, P.A.#, Sulzer, D.# Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain, Behavior, and Immunity, 111, 277 (2023).

Featured as the Cover Article in Brain, Behavior, and Immunity.

Mundi, PS, Dela Cruz, FS, Grunn, A, Diolaiti, D, Mauguen, A, Rainey, AR, Guillan, K, Siddiquee, A, You, D, Realubit, R, Karan, C, Ortiz, MV, Douglass, EF, Accordino, M, Mistretta, S, Brogan, F, Bruce, JN, Caescu, CI, Carvajal, RD, Crew, KD, Decastro, G, Heaney, M, Henick, BS, Hershman, DL, Hou, JY, Iwamoto, FM, Jurcic, JG, Kiran, RP, Kluger, MD, Kreisl, T, Lamanna, N, Lassman, AB, Lim, EA, Manji, GA, McKhann, GM, McKiernan, JM, Neugut, AI, Olive, KP, Rosenblat, T, Schwartz, GK, Shu, CA, Sisti, MB, Tergas, A, Vattakalam, RM, Welch, M, Wenske, S, Wright, JD, Canoll, P, Hibshoosh, H, Kalinsky, K, Aburi, M, Sims, PA, Alvarez, MJ, Kung, AL, Califano, A. A transcriptome-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies. Cancer Discovery, CD-22-1020 (2023).

Poon, M.M.L., Caron, D.P., Wang, Z., Wells, S.B., Chen, D., Meng, W., Szabo, P.A., Lam, N., Kubota, M., Matsumoto, R., Rahman, A., Prak, E.T.L., Shen, Y., Sims, P.A., Farber, D.L. Tissue adaptation and clonal segregation of human memory T cells in barrier sites. Nature Immunology, 24, 309 (2023).

2022

Spinazzi, EF, Argenziano, MG, Upadhyayula, PS, Banu, MA, Neira, JA, Higgins, DMO, Wu, PB, Pereira, B, Mahajan, A, Humala, N, Al-Dalahmah, O, Zhao, W, Save, AV, Gill, BJA, Boyett, DM, Marie, T, Furnari, JL, Sudhakar, TD, Stopka, SA, Regan, MS, Catania, V, Good, L, Zacharoulis, S, Behl, M, Petridis, P, Jambawalikar, S, Mintz, A, Lignelli, A, Agar, NYR, Sims, PA, Welch, MR, Lassman, AB, Iwamoto, FM, D'Amico, RS, Grinband, J, Canoll, P, Bruce, JN. Chronic convection-enhanced delivery of topotecan for patients with recurrent glioblastoma: a first-in-patient, single-centre, single-arm, phase 1b trial. Lancet Oncology, 23, 1409 (2022).

Kenchappa, R.S., Dovas, A., Argenziano, M.G., Meyer, C.T., Stopfer, L.E., Banu, M.A., Pereira, B., Griffith, J., Mohammad, A., Talele, S., Haddock, A., Zarco, N., Elmquist, W., White, F., Quaranta, V., Sims, P., Canoll, P., Rosenfeld, S.S. Activation of STAT3 through combined SRC and EGFR signaling drives resistnace to a mitotic kinesin inhibitor in glioblastoma. Cell Reports, 39, 110991 (2022).

Dominguez Conde, C., Xu, C., Jarvis, L., Rainbow, D., Wells, S., Gomes, T., Howlett, S., Suchanek, O., Polanski, K., King, H., Mamanova, L., Huang, N., Szabo, P., Richardson, L., Bolt, L., Fasouli, E.S., Mahbubani, K., Prete, M., Tuck, E., Richoz, N., Tuong, Z.K., Campos, L., Mousa, H., Needham, E., Pritchard, S., Li, T., Elmentaite, R., Park, J.E., Rahmani, E., Chen, D., Menon, D., Bayraktar, O., James, L., Meyer, K., Yosef, N., Clatworthy, M., Sims, P.A., Farber, D., Saeb-Parsy, K.#, Jones, J.#, Teichmann, S.# Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science*, 376, 713 (2022).

Chait, M., Yilmaz, M.M., Shakil, S., Ku, A.W., Dogra, P., Connors, T.J., Szabo, P.A., Gray, J.I., Wells, S.B., Kubota, M., Matsumoto, R., Poon, M.M.I., Snyder, M.E., Baldwin, M.R., Sims, P.A., Saqi, A., Farber, D.L., Weisberg, S.P. Immune and epithelial determinants of age-related risk and alveolar injury in fatal COVID-19. JCI Insight, e157608 (2022).

Metz, J.B., Hornstein, N.J., Das Sharma, S., Worley, J., Gonzalez, C., Sims, P.A. High-throughput translational profiling with riboPLATE-seq. Scientific Reports, 12, 5718 (2022).

Snyder, M.E., Moghbeli, K., Bondonese, A., Craig, A., Popescu, I., Fan, L., Tabib, T., Lafyatis, R., Chen, K., Bittar, H.E.T., Lendermon, E., Pilewski, J., Johnson, B., Kilaru, S., Zhang, Y., Sanchez, P.G., Alder, J.K., Sims, P.A., McDyer, J.F. Modulation of tissue resident memory T cells by glucocorticoids after acute cellular rejection in lung transplantation. Journal of Experimental Medicine, 219, e20212059 (2022).

Perspective: Allo-reactive tissue-resident T cells causing damage: An inside job

Masuda, K., Kornberg, A., Miller, J., Lin, S., Suek, N., Botella, T., Secener, K.A., Bacarella, A.M., Cheng, L., Ingham, M., Rosario, V., Al-Masrou, A.M., Lee-Kong, S.A., Kiran, R.P., Stoeckius, M., Smibert, P., Del Portillo, A., Oberstein, P.E., Sims, P.A., Yan, K.S., Han, A. Multiplexed single-cell analysis reveals prognostic and non-prognostic T cell types in human colorectal cancer. JCI Insight, in press (2022).

Hobson, B.D., Choi, S.J., Mosharov, E.V., Soni, R.K., Sulzer, D.#, Sims, P.A.# Subcellular proteomics of dopamine neurons in the mouse brain. eLife, 11, e70921, (2022).

Swaminathan, B., Youn, S.-W., Naiche, L.A., Du, J., Villa, S.R., Metz, J.B., Feng, H., Zhang, C., Kopan, R., Sims, P.A., Kitajewski, J.K. Endothelial Notch signaling directly regulates the small GTPase RND1 to facilitate Notch suppression of endothelial migration. Scientific Reports, 12, 1655, (2022).

Agrafioti, P., Morin-Baxter, J., Tanagala, K.K.K., Dubey, S., Sims, P., Lalaa, E., Momen-Heravi, F. Decoding the role of macrophages in periodontitis and type 2 diabetes using single-cell RNA-sequencing. FASEB Journal, 36, e22136 (2022).

Hobson, B.D., Kong, L., Angelo, M.F., Lieberman, O.J., Mosharov, E.V., Herzog, E.#, Sulzer, D.#, Sims, P.A.# Subcellular and regional localization of mRNA translation in midbrain dopamine neurons. Cell Reports, 38, 110208 (2022).

2021

Bayin, N.S., Mizrak, D., Stephen, D.N., Lao, Z., Sims, P.A., Joyner, A.L. Injury-induced ASCL1 expression orchestrates a transitory cell state required for repair of the neonatal cerebellum. Science Advances, 7, 10.1126/sciadv.abj598 (2021).

Poon, M.M.L., Byington, E., Meng, W., Kubota, M., Matsumoto, R., Grifoni, A., Weiskopf, D., Dogra, P., Lam, N., Szabo, P.A., Ural, B.B., Wells, S.B., Rosenfeld, A.M., Brusko, M.A., Brusko, T.M., Connors, T.J., Sette, A., Sims, P.A., Prak, E.T.L, Shen, Y., Farber, D.L. Heterogeneity of human anti-viral immunity shaped by virus, tissue, age, and sex. Cell Reports, 37, 110071 (2021).

Arrieta, V.A., Chen, A.X., Kane, J.R., Kang, S.J., Kassab, C., Dmello, C., Zhao, J., Burdett, K.B., Upadhyayula, P.S., Lee-Chang, C., Shilati, J., Jaishankar, D., Chen, L., Gould, A., Zhang, D., Yuan, J., Zhao, W., Ling, X., Burks, J.K., Laffleur, B., Amidei, C., Bruce, J.N., Lukas, R.V, Yamaguchi, J.T., Cieremans, D., Rothschild, G., Basu, U., McCord, M., Brat, D.J., Zhang, H., Cooper, L.A.D, Zhang, B., Sims, P., Cloughesy, T.F., Prins, R., Canoll, P., Stupp, R., Heimberger, A.B, Horbinski, C., Iwamoto, F.M.#, Rabadan, R.#, Sonabend, A.M.# ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma. Nature Cancer, 10.1038/s43018-021-00260-2, (2021).

Kenchappa, R.S., Liu, Y., Argenziano, M.G., Banu, M.A., Mladek, A.C., West, R., Luu, A., Quinones-Hinojosa, A., Hambardzumyan, D., Justilien, V., Leitges, M., Sarkaria, J.N., Sims, P.A., Canoll, P., Murray, N.R.#, Fields, A.P.#, Rosenfeld, S.S.# Protein kinase C_Ι and SRC signaling define reciprocally related subgroups of glioblastoma with distinct therapeutic vulnerabilities. Cell Reports, 37, 110054 (2021).

Capdevila, C., Trifas, M., Miller, J., Anderson, T., Sims, P.A., Yan, K.S. Cellular origins and lineage relationships of the intestinal epithelium. American Journal of Physiology: Gastrointestinal and Liver Physiology, 321, G413 (2021).

Chen, A.X., Gartrell, R.D., Zhao, J., Upadhyayula, P.S., Zhao, W., Yuan, J., Minns, H.E., Dovas, A., Bruce, J.N., Lasorella, A., Iavarone, A., Canoll, P., Sims, P.A., Rabadan, R. Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker. Genome Medicine, 13, 88 (2021).

Zhao, W., Dovas, A., Spinazzi, E.F., Levitin, H.M., Banu, M.A., Upadhyayula, P., Sudhakar, T., Marie, T., Otten, M.L., Sisti, M., Bruce, J.N., Canoll, P.#, Sims, P.A.# Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq. Genome Medicine*, 13, 82 (2021).

Affo, S., Nair, A., Brundu, F., Ravichandra, A., Bhattacharjee, S., Matsuda, M., Chin, L., Filliol, A., Wen, W., Song, X., Decker, A., Worley, J., Caviglia, J.M., Yu, L., Yin, D., Saito, Y., Savage, T., Wells, R.G., Mack, M., Zender, L., Arpaia, N., Remotti, H.E., Rabadan, R., Sims, P., Leblond, A.-L., Weber, A., Riener, M.-O., Stockwell, B.R., Gaublomme, J., Llovet, J.M., Michalopoulos, G.K., Seki, E., Sia, D., Chen, X., Califano, A., Schwabe, R.F. Promotion of cholangiocarinoma growth by diverse cancer-associated fibroblast subpopulations. Cancer Cell, 39, 866 (2021).

Bhattacharjee, S., Hamberger, F., Ravichandra, A., Miller, M., Nair, A., Affo, S., Filliol, A., Chin, L., Savage, T.M., Yin, D., Wirsik, N.M., Mehal, A., Arpaia, N., Seki, E., Mack, M., Zhu, D., Sims, P.A., Stanger, B.Z., Olive, K.P., Schmidt, T., Wells, R.G., Mederacke, I. Schwabe, R.F. Tumor restriction by type I collagen opposes tumor-promoting effects of cancer-associated fibroblasts. Journal of Clinical Investigation, 146987 (2021).

Yun, T.J., Igarashi, S., Zhao, H., Perez, O.A., Pereira, M.R., Zorn, E., Shen, Y., Goodrun, F., Rahman, A., Sims, P.A., Farber, D.L., Reizis, B. Human plasmacytoid dendritic cells mount a distinct antiviral response to virus-infected cells. Science Immunology, 6, eabc7302 (2021).

Szabo, P.A., Dogra, P., Gray, J.I., Wells, S.B., Connors, T.J., Weisberg, S.P., Krupska, I., Matsumoto, R., Poon, M.M.L., Idzikowski, E., Morris, S.E., Chloe, P., Yates, A.J., Ku, A., Chait, M., Davis-Porada, J.M, Guo, X.V., Zhou, J., Steinle, M., MacKay, S., Saqi, A., Baldwin, M.R., Sims, P.A., Farber, D.L. Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19. Immunity, 54, 1 (2021).

Damaghi, M., West, J., Robertson-Tessi, M., Xu, L., Ferrall-Fairbanks, M.C., Stewart, P.A., Persi, E.A., Fridley, L.F., Altrock, P.M., Gatenby, R., Sims, P.A., Anderson, A.R., Gillies, R.J. The harsh microenvironment in early breast cancer selects for a Warburg phenotype. Proc. Natl. Acad. Sci. USA, 118, e2011342118 (2021).

Garofano, L., Migliozzi, S., Oh, Y.T., D'Angelo, F., Najac, R.D., Ko, A., Frangaj, B., Caruso, F.P., Yu, K., Yuan, J., Zhao, W., Di Stefano, A.L., Bielle, F., Jiang, T., Sims, P., Suva, M.L., Tang, F., Su, X., Ceccarelli, M., Sanson, M., Lasorella, A., Iavarone, A. Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities. Nature Cancer, 2, 141 (2021).

2020

Liu, Z., Yuan, J., Lasorella, A., Iavarone, A., Bruce, J.N., Canoll, P., Sims, P.A. Integrating single-cell RNA-seq and imaging with SCOPE-seq2. Scientific Reports, 19482 (2020).

Arriaga, J.M., Panja, S., Alshalalfa, M., Zhao, J., Zou, M., Giacobbe, A., Madubata, C.J., Kim, J.Y., Rodriguez, A., Coleman, I., Virk, R.K., Hibshoosh, H., Ertunc, O., Ozbek, B., Fountain, J., Karnes, R.J., Luo, J., Antonarakis, E.S., Nelson, P.S., Feng, F.Y., Rubin, M.A., De Marzo, A.M., Rabadan, R., Sims, P.A., Mitrofanova, A.#, Abate-Shen, C.# A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nature Cancer, 1, 1082 (2020).

Caruso, F., Garofano, L., D'Angelo, F., Yu, K., Tang, F., Yuan, J., Zhang, J., Cerulo, L., Pagnotta, S.M. Bedognetti, D., Sims, P.A., Suva, M., Su, X.D., Lasorella, A., Iavarone, A., Ceccarelli, M. A map of tumor-host interactions in glioma at single-cell resolution. GigaScience, giaa109 (2020).

Pan, H., Xue, C., Auerbach, B.J., Fan, J., Bashore, A.C., Cui, J., Yang, D.Y., Trignano, S.B., Liu, W., Shi, J., Ihuegbu, C.O., Bush, E.C., Worley, J., Vlahos, L., Laise, P., Solomon, R.A., Connolly, E.S., Califano, A., Sims, P.A., Zhang, H., Li, M., Reilly, M.P. Single-cell genomics reveals a novel cell state during smooth muscle cell phenotypic switching and potential therapuetic targets for atherosclerosis in mouse and human. Circulation, in press (2020).

Hobson, B.D., Kong, L., Hartwick, E.W., Gonzalez, R.L. Jr., Sims, P.A. Elongation Inhibitors do not Prevent the Release of Puromycylated Nascent Polypeptide Chains from Ribosomes. eLife, 9, e60048 (2020).

Capdevila, C., Calderon, R.I., Bush, E.C., Sheldon-Collins, K., Sims, P.A., Yan, K.S. Single-cell transcriptional profiling of the intestinal epithelium. Methods in Molecular Biology, 2171, 129 (2020).

Mizrak, D., Bayin, N.S., Yuan, J., Liu, Z., Siciu, R., Niphakis, M.J., Ngo, N., Lum, K.M., Cravatt, B.F., Joyner, A.L., Sims, P.A. Single-cell profiling and SCOPE-seq reveal the lineage dynamics of adult V-SVZ neurogenesis and NOTUM as a key regulator. Cell Reports, 31, 107805 (2020).

Martuscello, R.T., Kerridge, C.A., Chatterjee, D., Hartstone, W.G., Kuo, S.H., Sims, P.A., Louis, E.D., Faust, P.L. Gene expression analysis of the cerebellar cortex in essential tremor. Neuroscience Letters, 721, 134540 (2020).

2019

Szabo, P.A., Levitin, H.M., Miron, M., Snyder, M.E., Senda, T., Yuan, J., Cheng, Y.L., Bush, E.C., Dogra, P., Thapa, P., Farber, D.L.#, Sims, P.A.# Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Nature Communications, 10, 4706 (2019).

Featured in the Top 50 Life and Biological Sciences Articles Collection

Sheth, R.U., Li, M., Jiang, W., Sims, P.A., Leong, K.W., Wang, H.H. Spatial metagenomic characterization of microbial biogeography in the gut. Nature Biotechnology, 37, 877 (2019).

Louis, E.D., Kerridge, C.A., Chatterjee, D., Martuscello, R.T., Diaz, D.T., Koeppen, A.H., Kuo, S.H., Vonsattel, J.P.G., Sims, P.A., Faust, P.L. Contextualizing the pathology in the essential tremor cerebellar cortex: a patholog-omics approach. Acta Neuropathologica, in press (2019).

Ma, W., Lee, J., Backenroth, D., Zhou, Y.J., Bush, E., Sims, P., Liu, K., Shen, Y. Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose. BMC Molecular and Cell Biology, 20, 20 (2019).

Farber, D.L.#, Sims, P.A.# Dissecting lung development and fibrosis at single-cell resolution. Genome Medicine, 11, 33 (2019).

Hobson, B.D.#, Sims, P.A.# Critical analysis of particle detection artifacts in synaptosome flow cytometry. eNeuro, 10.1523/ENEURO.0009-19.2019 (2019).

Zhang, J., Caruso, F.P., Sa, J.K., Justesen, S., Nam, D.H., Sims, P., Ceccarelli, M., Lasorella, A., Iavarone, A. The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival. Communications Biology, 2, 135 (2019).

Das Sharma, S., Metz, J.B., Li, H., Hobson, B.D., Hornstein, N., Sulzer, D., Tang, G., Sims, P.A. Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knock-Out Mice. Cell Reports, 26, 3313 (2019).

Snyder M.E., Finlayson, M.O., Connors, T.J., Dogra, P., Senda, T., Bush, E., Carpenter, D., Marboe, C., Benvenuto, L., Shah, L., Robbins, H., Hook, J.L., Sykes, M., D’Ovidio, F., Bacchetta, M., Sonett, J.R., Lederer, D.J., Arcasoy, S., Sims, P.A., Farber, D.L. Generation and persistence of human tissue-resident memory T cells in lung transplantation. Science Immunology, 4, eaav5581 (2019).

Levitin, H.M., Yuan, J., Cheng, Y.L., Ruiz, F.J.R., Bush, E.C., Bruce, J.N., Canoll, P., Iavarone, A., Lasorella, A., Blei, D.M.#, Sims, P.A.# De novo Gene Signature Identification from Single-Cell RNA-Seq with Hierarchical Poisson Factorization. Molecular Systems Biology, 15, e8557 (2019).

Zhao, J., Chen, A.X., Gartrell, R.B., Silverman, A.M., Aparicio, L., Chu, T., Borbar, D., Shan, D., Samanamud, J., Mahajan, A., Filip, I., Orenbuch, R., Goetz, M., Yamaguchi, J.T., Cloney, M., Horbinski, C., Lukas, R.V., Raizer, J., Rae, A.I., Yuan, J., Canoll, P., Bruce, J.N., Saenger, Y.M., Sims, P., Iwamoto, F.M.^#, Sonabend, A.M.^#, Rabadan, R.^# Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Nature Medicine, 25, 462 (2019).

Mizrak, D., Levitin, H.M., Delgado, A.C., Crotet, V., Yuan, J., Chaker, Z., Silva-Vargas, V., Sims, P.A.^#, Doetsch, F.^# Single cell analysis of regional differences in adult V-SVZ neural stem cell lineages. Cell Reports, 26, 394 (2019).

2018

Yuan, J., Sheng, J., Sims, P.A. SCOPE-seq: A Scalable Technology for Linking Live Cell Imaging and Single-Cell RNA-seq. Genome Biology, 19, 227 (2018).

Yuan, J., Levitin, H.M., Frattini, V., Bush, E.C., Boyett, D.M., Samanamud, J., Ceccarelli, M., Dovas, A., Zanazzi, G., Canoll, P., Bruce, J.N., Lasorella, A., Iavarone, A., Sims, P.A. Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Genome Medicine, 10, 57 (2018).

Pan, Y., Duron, G., Bush, E.C., Ma, Y., Sims, P.A., Gutmann, D.H., Radunskaya, A., Hardin, J. Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma. PLoS One, 22, e0190001 (2018).

Liu, B., Lee, B.W., Nakanishi, K., Villasante, A., Williamson, R., Metz, J., Kim, J., Kanai, M., Bi, L., Brown, K., Di Paolo, G., Homma, S., Sims, P.A., Topkara, V.K., Vunjak-Novakovic, G. Cardiac recovery via extended cell-free delivery of extracellular vesicles secreted by cardiomycocytes derived from iPS cells. Nature Biomedical Engineering, 2, 293 (2018).

Levitin, H.M., Yuan, J., Sims, P.A. Single-cell transcriptomic analysis of tumor heterogeneity. Trends in Cancer, 4, 4, 264 (2018).

Juliano, J., Gil, O., Hawkins-Daarud, A., Noticewala, S., Rockne, R.C., Gallaher, J., Massey, S.C., Sims, P.A., Anderson, A.R.A., Swanson, K.R., Canoll, P. Comparative dynamics of microglial and glioma cell motility at the infiltrative margin of brain tumors. J. R. Soc. Interface, 15, 139 (2018).

Ding, H., Douglass Jr., E.F., Sonabend, A.M., Mela, A., Bose, S., Gonzalez, C., Canoll, P., Sims, P.A., Alvarez, M.J., Califano, A. Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. Nature Communications, 9, 1471 (2018).

Kiryluk, K., Bomback, A.S., Cheng, Y.L., Xu, K., Camara, P.G., Rabadan, R., Sims, P.A., Barasch, J. Precision medicine for acute kidney injury (AKI): Redefining AKI by agnostic kidney tissue interrogation and genetics. Seminars in Nephrology, 1, 40 (2018).

2017

Yuan, J., Sims. P.A. SPOTS fill a major gap in RNA quantification. Nature Methods, 14, 1137-1138 (2017).

Bush, E.C., Ray, F., Alvarez, M., Realubit, R., Li, H., Karan, C., Califano, A.^#, Sims, P.A.^#PLATE-Seq for Genome-Wide Regulatory Network Analysis of High-Throughput Screens. Nature Communications, 8, 105 (2017).

Featured on GenomeWeb - "PLATE-Seq Method Adds Expression, Regulatory Insights to Cell Screens"
Featured here - "PLATE-Seq to Advance Personalized Cancer Treatment"

Pan, Y., Bush, E.C., Toonen, J.A., Ma, Y., Solga, A.C., Sims, P.A.^#, Gutmann, D.H.^# Whole tumor RNA-sequencing and deconvolution reveal a clinically prognostic PTEN/PI3K-regulated glioma transcriptional signature. Oncotarget, doi: 10.18632/oncotarget.17193 (2017).

2016

Kuo, S.H., Lin, C.Y., Wang, J., Sims, P.A. Pan, M.K., Liou, J.Y., Lee, D., Tate, W.J., Kelly, G.C., Louis, E.D., Faust, P.L., Climbing fiber-Purkinje cell synaptic pathology in tremor and cerebellar degenerative diseases, Acta Neuropathol., doi:10.1007/s00401-016-1626-1, (2016).

Yuan, J., Sims, P.A., An automated microwell platform for large-scale single cell RNA-Seq, Scientific Reports, 6, 33883 (2016).

Featured here - "Automated, Single Cell RNA-Seq Enables Research on Tumor Ecology"

Hornstein, N.^, Torres, D.^, Das Sharma, S., Tang, G., Canoll, P.^#, Sims, P.A.^#, Ligation-free ribosome profiling of cell type-specific translation in the brain, Genome Biology, 17, 149, (2016).

Pulko, V., Davies, J.S., Martinez, C., Lanteri, M.C., Busch, M.P., Diamond, M.S., Knox, K., Bush,E.C., Sims, P.A., Sinari, S., Billheimer, D., Haddad, E.K., Murray, K.O., Wertheimer, A.M.,Nikolich-Zugich, J., Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses, Nature Immunology, 17, 966-975, (2016).

Sims, J.S., Grinshpun, B., Feng, Y., Ung, T.H., Neira, J.A., Samanamud, J.L., Canoll, P., Shen, Y.^#, Sims, P.A.^#, Bruce, J.N.^# Diversity and Divergence of the Glioma-Infiltrating T Cell Receptor Repertoire. Proc. Natl. Acad. Sci. USA, doi:10.1073/pnas.1601012113 (2016).

Featured in Translational Cancer Research - "New applications for deep sequencing of the T cell receptor repertoire in cancer patients"

Lescarbeau, R., Lei, L., Bakken, K.K., Sims, P.A., Sarkaria, J.N., Canoll, P., White, F.M. Quantitative phosphoproteomics reveals Wee1 kinase as a therapeutic target in a model of proneural glioblastoma. Molecular Cancer Therapeutics, 15, 1332 (2016).

Bose, S., Sims, P.A. Genome-Wide Analysis of Single Cells and the Role of Microfluidics. Wiley-Blackwell Biotechnology Series: Micro- and Nanosystems for Biotechnology (2016).

Qiu, W., Tang, S.M., Lee, S., Turk, A.T., Sireci, A.N., Qiu, A., Rose, C., Xie, C., Kitajewski, J., Wen, H., Crawford, H.C., Sims, P.A., Hruban, R.H., Remotti, H.E., Su, G. Loss of Activin Receptor Type 1B Accelerates Development of Intraductal Papillary Mucinous Neoplasms in Mice with Activated KRAS. Gastroenterology, 150, 218-228 (2016).

2015

Venere, M., Horbinski, C., Crish, J.F., Jin, X., Vasanji, A., Major, J., Burrows, A.C., Chang, C., Prokop, J., Wu, Q., Sims, P.A., Canoll, P., Summers, M.K., Rosenfeld, S.S., Rich, J.N. The mitotic kinesin KIF11 is a driver of invasion, proliferation, and self-renewal in glioblastoma. Science Translational Medicine, 7, 304ra143 (2015).

Bose, S., Wan, Z., Carr, A., Rizvi, A.H., Vieira, G., Pe'er, D., Sims, P.A. Scalable Microfluidics for Single Cell RNA Printing and Sequencing. Genome Biology, 16, 120 (2015).

Highlighted in Genome Biology - "Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics"
Featured on GenomeWeb - "Microwell Device for Single-Cell RNA Capture Shows Potential for High-Throughput Applications"
"Highly Accessed" Designation in Genome Biology.

Shelanski, M., Shin, W., Aubry, S., Sims, P., Alvarez, M.J., Califano, A. A Systems Approach to Drug Discovery in Alzheimer's Disease. Neurotherapeutics, 12, 126-131 (2015).

Worthley, D.L., Churchill, M., Compton, J.T., Tailor, Y., Rao, M., Si, Y., Levin, D., Schwartz, M.G., Uygur, A., Hayakawa, Y., Gross, S., Renz B.W., Setlik, W., Martinez, A.N., Chen, X., Nizami, S., Lee, H.G., Kang, H.P., Caldwell, J.M., Asfaha, S., Westphalen, C.B., Graham, T., Jin, G., Nagar, K., Wang, H., Kheirbek, M.A., Kolhe, A., Carpenter, J., Glaire, M., Nair, A., Renders, S., Manieri, N., Muthupalani, S., Fox, J.G., Reichert, M., Giraud, A.S., Schwabe, R.F., Pradere, J.P., Walton, K., Prakash, A., Gumucio, D., Rustgi, A.K., Stappenbeck, T.S., Friedman, R.A., Gershon, M.D., Sims, P., Grikscheit, T., Lee, F.Y., Karsenty, G., Mukherjee, S., Wang, T.C. Gremlin 1 Identifies a Skeletal Stem Cell with Bone, Cartilage, and Reticular Stromal Potential. Cell, 160, 269-284 (2015).

2014

Gill, B., Pisapia, D., Malone, H., Goldstein, H., Lei, L., Sonabend, A., Yun, J., Samanamud, J., Sims, J., Banu, M., Dovas, A., Teich, A.F., Sheth, S., McKhann, G., Sisti, M., Bruce, J.N.^#, Sims, P.A.^#, Canoll, P.^# MRI-Localized Biospies Reveal Subtype-Specific Differences in Molecular and Cellular Composition at the Margins of Glioblastoma. Proc. Natl. Acad. Sci. USA, 111, 12550-12555 (2014).

Highlighted and Reviewed in Neuro-Oncology - "Deconvolving Infiltration in Glioblastoma"

Gonzalez, C., Sims, J.S., Hornstein, N., Mela, A., Garcia, F., Lei, L., Gass, D.A., Amendolara, Bruce, J.N., Canoll, P.^#, Sims, P.A.^# Ribosome Profiling Reveals a Cell Type-Specific Translational Landscape in Brain Tumors. J. Neuroscience, 34, 10924-10936 (2014).

Sonabend, A.M., Bansal, M., Guarnieri, P., Lei, L., Amendolara, B., Soderquist, C., Leung, L., Yun, J., Kennedy, B., Sisti, J., Bruce, S., Bruce, R., Shakya, R., Ludwig, T., Rosenfeld, S., Sims, P.A., Bruce, J.N., Califano, A., Canoll, P. The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected during Tumor Progression. Cancer Research, 74, 1440 (2014).

2013

Sonabend, A.M., Yun, J., Lei, L., Leung, R., Soderquist, C., Crisman, C., Gill, B.J., Carminucci, A., Sisti, J., Castelli, M., Sims, P.A., Bruce, J.N., Canoll, P. Murine cell line model of proneural glioma for evaluation of anti-tumor therapies. J. Neuro-Oncology, 112, 375, (2013).

2012

Lu, P.J., Hoehl, M.M., Macarthur, J.B., Sims, P.A., Ma, H., Slocum, A.H. Robust and economical multi-sample, multi-wavelength UV/vis absorption and fluorescence detector for biological and chemical contamination. AIP Advances, 2, 032110 (2012).

Hoehl, M.M., Lu, P.J., Sims, P.A., Slocum, A.H. Rapid and Robust Detection Methods for Poison and Microbial Contamination. J. Agric. Food Chem., 60, 6349-6358 (2012).

Men, Y., Fu, Y., Chen, Z., Sims, P.A., Greenleaf, W.J., Huang, Y. Digital Polymerase Chain Reaction in an Array of Femtoliter Polydimethylsiloxane Microreactors. Analytical Chemistry, 84, 4262-4266 (2012).

Shiroguchi, K., Jia, T.Z., Sims, P.A., Xie. X.S. Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Single Molecule Barcodes. Proc. Natl. Acad. Sci. USA, 109, 1347-1352 (2012).

Prior to 2012

Sims, P.A., Greenleaf, W.J., Duan, H., Xie, X.S. Fluorogenic DNA sequencing in PDMS microreactors. Nature Methods, 8, 575-580 (2011).

Featured in Chemical & Engineering News, Nature Methods, NIH NHGRI Genome Advance of the Month, GenomeWeb / In Sequence, and Faculty of 1000.

Sims, P.A., Xie, X.S. Probing dynein and kinesin stepping with mechanical manipulation in a living cell. ChemPhysChem, 10, 1511-1516 (2009).

Sims, J.S., Militello, K.T., Sims, P.A., Patel, V.P., Kasper, J.M., Wirth, D.F. Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle. Eurkaryot. Cell, 8, 327-338 (2009).

Nan, X., Sims, P.A., Xie, X.S. Organelle tracking in a living cell with microsecond time resolution and nanometer spatial precision. ChemPhysChem, 9, 707-712 (2008).

Featured as the Cover Article in ChemPhysChem.

Lu, P.J., Sims, P.A., Oki, H., MacArthur, J., Weitz, D.A. Target-locking acquisition with real-time confocal (TARC) microscopy. Optics Express, 15, 8702-8712 (2007).

Nan, X., Sims, P.A., Chen, P., Xie, X.S. Observation of individual microtubule motor steps in living cells with endocytosed quantum dots. J. Phys. Chem. B, 109, 24220-24224 (2005).

Featured in Chemical & Engineering News.

Sims, P.A., Wong, C.F., Vuga, D., McCammon, J.A., Sefton, B.M. Relative contributions of desolvation, inter-, and intramolecular interactions to binding affinity in protein kinase systems. J. Comp. Chem., 26, 668-681 (2005).

Sims, P.A., Wong, C.F., McCammon, J.A. Charge optimization of the interface between protein kinases and their ligands. J. Comp. Chem., 25, 1416-1429 (2004).

Sims, P.A., Wong, C.F., McCammon, J.A. A computational model of binding thermodynamics: The design of cyclin-dependent kinase 2 inhibitors. J. Med. Chem., 46, 3314-3325 (2003).