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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 Jul 17. doi: 10.1007/s00401-019-02043-7. [Epub ahead of print]


Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose.

Ma W, Lee J, Backenroth D, Zhou YJ, Bush E, Sims P, Liu K, Shen Y.

BMC Mol Cell Biol. 2019 Jun 28;20(1):20. doi: 10.1186/s12860-019-0199-y.


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.


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.


The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival.

Zhang J, Caruso FP, Sa JK, Justesen S, Nam DH, Sims P, Ceccarelli M, Lasorella A, Iavarone A.

Commun Biol. 2019 Apr 23;2:135. doi: 10.1038/s42003-019-0369-7. eCollection 2019.


Author Correction: Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.

Zhao J, Chen AX, Gartrell RD, Silverman AM, Aparicio L, Chu T, Bordbar D, Shan D, Samanamud J, Mahajan A, Filip I, Orenbuch R, Goetz M, Yamaguchi JT, Cloney M, Horbinski C, Lukas RV, Raizer J, Rae AI, Yuan J, Canoll P, Bruce JN, Saenger YM, Sims P, Iwamoto FM, Sonabend AM, Rabadan R.

Nat Med. 2019 Jun;25(6):1022. doi: 10.1038/s41591-019-0449-8.


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.


Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.

Zhao J, Chen AX, Gartrell RD, Silverman AM, Aparicio L, Chu T, Bordbar D, Shan D, Samanamud J, Mahajan A, Filip I, Orenbuch R, Goetz M, Yamaguchi JT, Cloney M, Horbinski C, Lukas RV, Raizer J, Rae AI, Yuan J, Canoll P, Bruce JN, Saenger YM, Sims P, Iwamoto FM, Sonabend AM, Rabadan R.

Nat Med. 2019 Mar;25(3):462-469. doi: 10.1038/s41591-019-0349-y. Epub 2019 Feb 11. Erratum in: Nat Med. 2019 Apr 17;:.


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.


Effect of IAPP on the proteome of cultured Rin-5F cells.

Miraee-Nedjad S, Sims PFG, Schwartz JM, Doig AJ.

BMC Biochem. 2018 Nov 12;19(1):9. doi: 10.1186/s12858-018-0099-3.


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.


Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions.

Talavera D, Kershaw CJ, Costello JL, Castelli LM, Rowe W, Sims PFG, Ashe MP, Grant CM, Pavitt GD, Hubbard SJ.

Sci Rep. 2018 May 21;8(1):7949. doi: 10.1038/s41598-018-26170-5.


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.


Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses.

Costello JL, Kershaw CJ, Castelli LM, Talavera D, Rowe W, Sims PFG, Ashe MP, Grant CM, Hubbard SJ, Pavitt GD.

Genome Biol. 2017 Oct 27;18(1):201. doi: 10.1186/s13059-017-1338-4.


Synthesis and Structural and Optical Properties of Ga(As1-xPx)Ge3 and (GaP)yGe5-2y Semiconductors Using Interface-Engineered Group IV Platforms.

Wallace PM, Sims PE, Xu C, Poweleit CD, Kouvetakis J, Menéndez J.

ACS Appl Mater Interfaces. 2017 Oct 11;9(40):35105-35113. doi: 10.1021/acsami.7b09272. Epub 2017 Sep 26.


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.


Applicability and Utility of Parameters of Care to Patient Care.

Sims PG, Lieblich SE.

J Oral Maxillofac Surg. 2017 Aug;75(8S):e6. doi: 10.1016/j.joms.2017.04.033. No abstract available.


Application of Parameters of Care to Clinical Practice.

Sims PG, Lieblich SE.

J Oral Maxillofac Surg. 2017 Aug;75(8S):e5. doi: 10.1016/j.joms.2017.04.037. No abstract available.



Sims PG, Lieblich SE.

J Oral Maxillofac Surg. 2017 Aug;75(8S):e4. doi: 10.1016/j.joms.2017.04.036. No abstract available.


SERS substrates fabricated using ceramic filters for the detection of bacteria: Eliminating the citrate interference.

Mosier-Boss PA, Sorensen KC, George RD, Sims PC, O'braztsova A.

Spectrochim Acta A Mol Biomol Spectrosc. 2017 Jun 5;180:161-167. doi: 10.1016/j.saa.2017.03.021. Epub 2017 Mar 7.


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.


Ultralow Resistivity Ge:Sb heterostructures on Si Using Hydride Epitaxy of Deuterated Stibine and Trigermane.

Xu C, Senaratne CL, Sims P, Kouvetakis J, Menéndez J.

ACS Appl Mater Interfaces. 2016 Sep 14;8(36):23810-9. doi: 10.1021/acsami.6b06161. Epub 2016 Aug 29.


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.


Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths.

Gül OT, Pugliese KM, Choi Y, Sims PC, Pan D, Rajapakse AJ, Weiss GA, Collins PG.

Biosensors (Basel). 2016 Jun 24;6(3). pii: E29. doi: 10.3390/bios6030029.


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-Žugich 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.


NKTR-214, an Engineered Cytokine with Biased IL2 Receptor Binding, Increased Tumor Exposure, and Marked Efficacy in Mouse Tumor Models.

Charych DH, Hoch U, Langowski JL, Lee SR, Addepalli MK, Kirk PB, Sheng D, Liu X, Sims PW, VanderVeen LA, Ali CF, Chang TK, Konakova M, Pena RL, Kanhere RS, Kirksey YM, Ji C, Wang Y, Huang J, Sweeney TD, Kantak SS, Doberstein SK.

Clin Cancer Res. 2016 Feb 1;22(3):680-90. doi: 10.1158/1078-0432.CCR-15-1631.


Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring.

Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PF, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ.

Mol Cell Proteomics. 2016 Apr;15(4):1309-22. doi: 10.1074/mcp.M115.054288. Epub 2016 Jan 10.


Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p.

Kershaw CJ, Costello JL, Talavera D, Rowe W, Castelli LM, Sims PF, Grant CM, Ashe MP, Hubbard SJ, Pavitt GD.

Sci Rep. 2015 Oct 23;5:15518. doi: 10.1038/srep15518.


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.


Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits.

Pugliese KM, Gul OT, Choi Y, Olsen TJ, Sims PC, Collins PG, Weiss GA.

J Am Chem Soc. 2015 Aug 5;137(30):9587-94. doi: 10.1021/jacs.5b02074. Epub 2015 Jul 17.


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.


The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation.

Castelli LM, Talavera D, Kershaw CJ, Mohammad-Qureshi SS, Costello JL, Rowe W, Sims PF, Grant CM, Hubbard SJ, Ashe MP, Pavitt GD.

PLoS Genet. 2015 May 14;11(5):e1005233. doi: 10.1371/journal.pgen.1005233. eCollection 2015 May.


Observing lysozyme's closing and opening motions by high-resolution single-molecule enzymology.

Akhterov MV, Choi Y, Olsen TJ, Sims PC, Iftikhar M, Gul OT, Corso BL, Weiss GA, Collins PG.

ACS Chem Biol. 2015 Jun 19;10(6):1495-501. doi: 10.1021/cb500750v. Epub 2015 Mar 20.


Global mRNA selection mechanisms for translation initiation.

Costello J, Castelli LM, Rowe W, Kershaw CJ, Talavera D, Mohammad-Qureshi SS, Sims PF, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP.

Genome Biol. 2015 Jan 5;16:10. doi: 10.1186/s13059-014-0559-z.

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