* Equal Contribution

#Co-corresponding Author


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. bioRxiv (2018).

Yuan, J., Levitin, H.M., Frattini, V., Bush, E.C., 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 and microenvironment in high-grade glioma. bioRxiv (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).



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).

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).

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).


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). 

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).


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).

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).



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).


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).