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Gene expression analysis of the cerebellar cortex in essential tremor.

Martuscello RT, Kerridge CA, Chatterjee D, Hartstone WG, Kuo SH, Sims PA, Louis ED, Faust PL.

Neurosci Lett. 2019 Nov 7:134540. doi: 10.1016/j.neulet.2019.134540. [Epub ahead of print]


Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease.

Szabo PA, Levitin HM, Miron M, Snyder ME, Senda T, Yuan J, Cheng YL, Bush EC, Dogra P, Thapa P, Farber DL, Sims PA.

Nat Commun. 2019 Oct 17;10(1):4706. doi: 10.1038/s41467-019-12464-3.


Spatial metagenomic characterization of microbial biogeography in the gut.

Sheth RU, Li M, Jiang W, Sims PA, Leong KW, Wang HH.

Nat Biotechnol. 2019 Aug;37(8):877-883. doi: 10.1038/s41587-019-0183-2. Epub 2019 Jul 22.


Contextualizing the pathology in the essential tremor cerebellar cortex: a patholog-omics approach.

Louis ED, Kerridge CA, Chatterjee D, Martuscello RT, Diaz DT, Koeppen AH, Kuo SH, Vonsattel JG, Sims PA, Faust PL.

Acta Neuropathol. 2019 Nov;138(5):859-876. doi: 10.1007/s00401-019-02043-7. Epub 2019 Jul 17.


Dissecting lung development and fibrosis at single-cell resolution.

Farber DL, Sims PA.

Genome Med. 2019 May 24;11(1):33. doi: 10.1186/s13073-019-0645-7. Review.


Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry.

Hobson BD, Sims PA.

eNeuro. 2019 Jun 12;6(3). pii: ENEURO.0009-19.2019. doi: 10.1523/ENEURO.0009-19.2019. Print 2019 May/Jun.


Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice.

Das Sharma S, Metz JB, Li H, Hobson BD, Hornstein N, Sulzer D, Tang G, Sims PA.

Cell Rep. 2019 Mar 19;26(12):3313-3322.e5. doi: 10.1016/j.celrep.2019.02.086.


Generation and persistence of human tissue-resident memory T cells in lung transplantation.

Snyder ME, Finlayson MO, Connors TJ, Dogra P, Senda T, Bush E, Carpenter D, Marboe C, Benvenuto L, Shah L, Robbins H, Hook JL, Sykes M, D'Ovidio F, Bacchetta M, Sonett JR, Lederer DJ, Arcasoy S, Sims PA, Farber DL.

Sci Immunol. 2019 Mar 8;4(33). pii: eaav5581. doi: 10.1126/sciimmunol.aav5581.


De novo gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization.

Levitin HM, Yuan J, Cheng YL, Ruiz FJ, Bush EC, Bruce JN, Canoll P, Iavarone A, Lasorella A, Blei DM, Sims PA.

Mol Syst Biol. 2019 Feb 22;15(2):e8557. doi: 10.15252/msb.20188557.


Single-Cell Analysis of Regional Differences in Adult V-SVZ Neural Stem Cell Lineages.

Mizrak D, Levitin HM, Delgado AC, Crotet V, Yuan J, Chaker Z, Silva-Vargas V, Sims PA, Doetsch F.

Cell Rep. 2019 Jan 8;26(2):394-406.e5. doi: 10.1016/j.celrep.2018.12.044.


SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing.

Yuan J, Sheng J, Sims PA.

Genome Biol. 2018 Dec 24;19(1):227. doi: 10.1186/s13059-018-1607-x.


Cardiac recovery via extended cell-free delivery of extracellular vesicles secreted by cardiomyocytes derived from induced pluripotent stem cells.

Liu B, Lee BW, Nakanishi K, Villasante A, Williamson R, Metz J, Kim J, Kanai M, Bi L, Brown K, Di Paolo G, Homma S, Sims PA, Topkara VK, Vunjak-Novakovic G.

Nat Biomed Eng. 2018 May;2(5):293-303. doi: 10.1038/s41551-018-0229-7. Epub 2018 Apr 23.


Single-cell transcriptome analysis of lineage diversity in high-grade glioma.

Yuan J, Levitin HM, Frattini V, Bush EC, Boyett DM, Samanamud J, Ceccarelli M, Dovas A, Zanazzi G, Canoll P, Bruce JN, Lasorella A, Iavarone A, Sims PA.

Genome Med. 2018 Jul 24;10(1):57. doi: 10.1186/s13073-018-0567-9.


Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma.

Pan Y, Duron C, Bush EC, Ma Y, Sims PA, Gutmann DH, Radunskaya A, Hardin J.

PLoS One. 2018 May 22;13(5):e0190001. doi: 10.1371/journal.pone.0190001. eCollection 2018.


Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.

Ding H, Douglass EF Jr, Sonabend AM, Mela A, Bose S, Gonzalez C, Canoll PD, Sims PA, Alvarez MJ, Califano A.

Nat Commun. 2018 Apr 16;9(1):1471. doi: 10.1038/s41467-018-03843-3.


Single-Cell Transcriptomic Analysis of Tumor Heterogeneity.

Levitin HM, Yuan J, Sims PA.

Trends Cancer. 2018 Apr;4(4):264-268. doi: 10.1016/j.trecan.2018.02.003. Epub 2018 Mar 9. Review.


Comparative dynamics of microglial and glioma cell motility at the infiltrative margin of brain tumours.

Juliano J, Gil O, Hawkins-Daarud A, Noticewala S, Rockne RC, Gallaher J, Massey SC, Sims PA, Anderson ARA, Swanson KR, Canoll P.

J R Soc Interface. 2018 Feb;15(139). pii: 20170582. doi: 10.1098/rsif.2017.0582.


Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics.

Kiryluk K, Bomback AS, Cheng YL, Xu K, Camara PG, Rabadan R, Sims PA, Barasch J.

Semin Nephrol. 2018 Jan;38(1):40-51. doi: 10.1016/j.semnephrol.2017.09.006. Review.


SPOTs fill a major gap in RNA quantification.

Yuan J, Sims PA.

Nat Methods. 2017 Nov 30;14(12):1137-1138. doi: 10.1038/nmeth.4515. No abstract available.


Whole tumor RNA-sequencing and deconvolution reveal a clinically-prognostic PTEN/PI3K-regulated glioma transcriptional signature.

Pan Y, Bush EC, Toonen JA, Ma Y, Solga AC, Sims PA, Gutmann DH.

Oncotarget. 2017 Apr 18;8(32):52474-52487. doi: 10.18632/oncotarget.17193. eCollection 2017 Aug 8.


PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.

Bush EC, Ray F, Alvarez MJ, Realubit R, Li H, Karan C, Califano A, Sims PA.

Nat Commun. 2017 Jul 24;8(1):105. doi: 10.1038/s41467-017-00136-z.


Climbing fiber-Purkinje cell synaptic pathology in tremor and cerebellar degenerative diseases.

Kuo SH, Lin CY, Wang J, Sims PA, Pan MK, Liou JY, Lee D, Tate WJ, Kelly GC, Louis ED, Faust PL.

Acta Neuropathol. 2017 Jan;133(1):121-138. doi: 10.1007/s00401-016-1626-1. Epub 2016 Oct 4.


An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq.

Yuan J, Sims PA.

Sci Rep. 2016 Sep 27;6:33883. doi: 10.1038/srep33883.


Controlled Frequency Breathing Reduces Inspiratory Muscle Fatigue.

Burtch AR, Ogle BT, Sims PA, Harms CA, Symons TB, Folz RJ, Zavorsky GS.

J Strength Cond Res. 2017 May;31(5):1273-1281. doi: 10.1519/JSC.0000000000001589.


Ligation-free ribosome profiling of cell type-specific translation in the brain.

Hornstein N, Torres D, Das Sharma S, Tang G, Canoll P, Sims PA.

Genome Biol. 2016 Jul 5;17(1):149. doi: 10.1186/s13059-016-1005-1.


Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses.

Pulko V, Davies JS, Martinez C, Lanteri MC, Busch MP, Diamond MS, Knox K, Bush EC, Sims PA, Sinari S, Billheimer D, Haddad EK, Murray KO, Wertheimer AM, Nikolich-┼Żugich J.

Nat Immunol. 2016 Aug;17(8):966-75. doi: 10.1038/ni.3483. Epub 2016 Jun 6.


Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire.

Sims JS, Grinshpun B, Feng Y, Ung TH, Neira JA, Samanamud JL, Canoll P, Shen Y, Sims PA, Bruce JN.

Proc Natl Acad Sci U S A. 2016 Jun 21;113(25):E3529-37. doi: 10.1073/pnas.1601012113. Epub 2016 Jun 3.


Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma.

Lescarbeau RS, Lei L, Bakken KK, Sims PA, Sarkaria JN, Canoll P, White FM.

Mol Cancer Ther. 2016 Jun;15(6):1332-43. doi: 10.1158/1535-7163.MCT-15-0692. Epub 2016 May 17.


Loss of Activin Receptor Type 1B Accelerates Development of Intraductal Papillary Mucinous Neoplasms in Mice With Activated KRAS.

Qiu W, Tang SM, Lee S, Turk AT, Sireci AN, Qiu A, Rose C, Xie C, Kitajewski J, Wen HJ, Crawford HC, Sims PA, Hruban RH, Remotti HE, Su GH.

Gastroenterology. 2016 Jan;150(1):218-228.e12. doi: 10.1053/j.gastro.2015.09.013. Epub 2015 Sep 25.


The mitotic kinesin KIF11 is a driver of invasion, proliferation, and self-renewal in glioblastoma.

Venere M, Horbinski C, Crish JF, Jin X, Vasanji A, Major J, Burrows AC, Chang C, Prokop J, Wu Q, Sims PA, Canoll P, Summers MK, Rosenfeld SS, Rich JN.

Sci Transl Med. 2015 Sep 9;7(304):304ra143. doi: 10.1126/scitranslmed.aac6762.


Scalable microfluidics for single-cell RNA printing and sequencing.

Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA.

Genome Biol. 2015 Jun 6;16:120. doi: 10.1186/s13059-015-0684-3.


Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors.

Gonzalez C, Sims JS, Hornstein N, Mela A, Garcia F, Lei L, Gass DA, Amendolara B, Bruce JN, Canoll P, Sims PA.

J Neurosci. 2014 Aug 13;34(33):10924-36. doi: 10.1523/JNEUROSCI.0084-14.2014.


MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma.

Gill BJ, Pisapia DJ, Malone HR, Goldstein H, Lei L, Sonabend A, Yun J, Samanamud J, Sims JS, Banu M, Dovas A, Teich AF, Sheth SA, McKhann GM, Sisti MB, Bruce JN, Sims PA, Canoll P.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12550-5. doi: 10.1073/pnas.1405839111. Epub 2014 Aug 11.


The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression.

Sonabend AM, Bansal M, Guarnieri P, Lei L, Amendolara B, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P.

Cancer Res. 2014 Mar 1;74(5):1440-1451. doi: 10.1158/0008-5472.CAN-13-2150. Epub 2014 Jan 3.


Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD.

Thomas LM, Harper AR, Miner WA, Ajufo HO, Branscum KM, Kao L, Sims PA.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jul;69(Pt 7):730-2. doi: 10.1107/S1744309113015170. Epub 2013 Jun 27.


Murine cell line model of proneural glioma for evaluation of anti-tumor therapies.

Sonabend AM, Yun J, Lei L, Leung R, Soderquist C, Crisman C, Gill BJ, Carminucci A, Sisti J, Castelli M, Sims PA, Bruce JN, Canoll P.

J Neurooncol. 2013 May;112(3):375-82. doi: 10.1007/s11060-013-1082-x. Epub 2013 Mar 16.


Rapid and robust detection methods for poison and microbial contamination.

Hoehl MM, Lu PJ, Sims PA, Slocum AH.

J Agric Food Chem. 2012 Jun 27;60(25):6349-58. doi: 10.1021/jf300817h. Epub 2012 Jun 15.


Digital polymerase chain reaction in an array of femtoliter polydimethylsiloxane microreactors.

Men Y, Fu Y, Chen Z, Sims PA, Greenleaf WJ, Huang Y.

Anal Chem. 2012 May 15;84(10):4262-6. doi: 10.1021/ac300761n. Epub 2012 Apr 12.


Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.

Shiroguchi K, Jia TZ, Sims PA, Xie XS.

Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1347-52. doi: 10.1073/pnas.1118018109. Epub 2012 Jan 9.


Fluorogenic DNA sequencing in PDMS microreactors.

Sims PA, Greenleaf WJ, Duan H, Xie XS.

Nat Methods. 2011 Jun 12;8(7):575-80. doi: 10.1038/nmeth.1629.


Probing dynein and kinesin stepping with mechanical manipulation in a living cell.

Sims PA, Xie XS.

Chemphyschem. 2009 Jul 13;10(9-10):1511-6. doi: 10.1002/cphc.200900113.


Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle.

Sims JS, Militello KT, Sims PA, Patel VP, Kasper JM, Wirth DF.

Eukaryot Cell. 2009 Mar;8(3):327-38. doi: 10.1128/EC.00340-08. Epub 2009 Jan 16.


Organelle tracking in a living cell with microsecond time resolution and nanometer spatial precision.

Nan X, Sims PA, Xie XS.

Chemphyschem. 2008 Apr 4;9(5):707-12. doi: 10.1002/cphc.200700839.


Target-locking acquisition with real-time confocal (TARC) microscopy.

Lu PJ, Sims PA, Oki H, Macarthur JB, Weitz DA.

Opt Express. 2007 Jul 9;15(14):8702-12.


Observation of individual microtubule motor steps in living cells with endocytosed quantum dots.

Nan X, Sims PA, Chen P, Xie XS.

J Phys Chem B. 2005 Dec 29;109(51):24220-4.


Structure and catalytic properties of an engineered heterodimer of enolase composed of one active and one inactive subunit.

Sims PA, Menefee AL, Larsen TM, Mansoorabadi SO, Reed GH.

J Mol Biol. 2006 Jan 20;355(3):422-31. Epub 2005 Nov 8.


Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems.

Sims PA, Wong CF, Vuga D, McCammon JA, Sefton BM.

J Comput Chem. 2005 May;26(7):668-81.


The inositol 1,4,5-trisphosphate receptor regulates epidermal cell migration in Caenorhabditis elegans.

Thomas-Virnig CL, Sims PA, Simske JS, Hardin J.

Curr Biol. 2004 Oct 26;14(20):1882-7.


Charge optimization of the interface between protein kinases and their ligands.

Sims PA, Wong CF, McCammon JA.

J Comput Chem. 2004 Aug;25(11):1416-29.


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