Publications

* Equal Contribution

#Co-corresponding Author.

2014

Bose, S., Sims, P.A. Genome-Wide Analysis of Single Cells and the Role of Microfluidics. Wiley-Blackwell Biotechnology Series, in press (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, published online (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).

 

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)