Peter Sims, Ph.D. - Publications

Affiliations: 
Columbia University, New York, NY 

44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Szabo PA, Levitin HM, Miron M, Snyder ME, Senda T, Yuan J, Cheng YL, Bush EC, Dogra P, Thapa P, Farber DL, Sims PA. Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Nature Communications. 10: 4706. PMID 31624246 DOI: 10.1038/s41467-019-12464-3  0.36
2019 Ma W, Lee J, Backenroth D, Zhou YJ, 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. PMID 31253076 DOI: 10.1186/s12860-019-0199-y  0.36
2019 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, ... ... Sims P, et al. Author Correction: Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Nature Medicine. PMID 30996326 DOI: 10.1038/s41591-019-0449-8  0.36
2019 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, ... ... Sims PA, et al. Generation and persistence of human tissue-resident memory T cells in lung transplantation. Science Immunology. 4. PMID 30850393 DOI: 10.1126/sciimmunol.aav5581  0.36
2019 Levitin HM, Yuan J, Cheng YL, Ruiz FJ, Bush EC, Bruce JN, Canoll P, Iavarone A, Lasorella A, Blei DM, Sims PA. gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization. Molecular Systems Biology. 15: e8557. PMID 30796088 DOI: 10.15252/msb.20188557  0.36
2019 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, ... ... Sims P, et al. Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Nature Medicine. PMID 30742119 DOI: 10.1038/s41591-019-0349-y  0.36
2019 Mizrak D, Levitin HM, Delgado AC, Crotet V, Yuan J, Chaker Z, Silva-Vargas V, Sims PA, Doetsch F. Single-Cell Analysis of Regional Differences in Adult V-SVZ Neural Stem Cell Lineages. Cell Reports. 26: 394-406.e5. PMID 30625322 DOI: 10.1016/j.celrep.2018.12.044  0.36
2018 Yuan J, Sheng J, Sims PA. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing. Genome Biology. 19: 227. PMID 30583733 DOI: 10.1186/s13059-018-1607-x  0.36
2018 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. Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Genome Medicine. 10: 57. PMID 30041684 DOI: 10.1186/s13073-018-0567-9  0.36
2018 Levitin HM, Yuan J, Sims PA. Single-Cell Transcriptomic Analysis of Tumor Heterogeneity. Trends in Cancer. 4: 264-268. PMID 29606308 DOI: 10.1016/j.trecan.2018.02.003  0.36
2017 Yuan J, Sims PA. SPOTs fill a major gap in RNA quantification. Nature Methods. 14: 1137-1138. PMID 29190269 DOI: 10.1038/nmeth.4515  0.36
2016 Yuan J, Sims PA. An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. Scientific Reports. 6: 33883. PMID 27670648 DOI: 10.1038/srep33883  0.36
2016 Hornstein N, Torres D, Das Sharma S, Tang G, Canoll P, Sims PA. Ligation-free ribosome profiling of cell type-specific translation in the brain. Genome Biology. 17: 149. PMID 27380875 DOI: 10.1186/s13059-016-1005-1  1
2016 Sims JS, Grinshpun B, Feng Y, Ung TH, Neira JA, Samanamud JL, Canoll P, Shen Y, Sims PA, Bruce JN. Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. Proceedings of the National Academy of Sciences of the United States of America. PMID 27261081 DOI: 10.1073/pnas.1601012113  1
2015 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. The mitotic kinesin KIF11 is a driver of invasion, proliferation, and self-renewal in glioblastoma. Science Translational Medicine. 7: 304ra143. PMID 26355032 DOI: 10.1126/scitranslmed.aac6762  1
2015 Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA. Scalable microfluidics for single cell RNA printing and sequencing. Genome Biology. 16: 120. PMID 26047807 DOI: 10.1186/s13059-015-0684-3  1
2015 Worthley DL, Churchill M, Compton JT, Tailor Y, Rao M, Si Y, Levin D, Schwartz MG, Uygur A, Hayakawa Y, Gross S, Renz BW, Setlik W, Martinez AN, Chen X, ... ... Sims P, et al. Gremlin 1 identifies a skeletal stem cell with bone, cartilage, and reticular stromal potential. Cell. 160: 269-84. PMID 25594183 DOI: 10.1016/j.cell.2014.11.042  1
2014 Gonzalez C, Sims JS, Hornstein N, Mela A, Garcia F, Lei L, Gass DA, Amendolara B, Bruce JN, Canoll P, Sims PA. Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 34: 10924-36. PMID 25122893 DOI: 10.1523/JNEUROSCI.0084-14.2014  1
2014 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, ... ... Sims PA, et al. MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma. Proceedings of the National Academy of Sciences of the United States of America. 111: 12550-5. PMID 25114226 DOI: 10.1073/pnas.1405839111  1
2014 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, et al. The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression. Cancer Research. 74: 1440-51. PMID 24390738 DOI: 10.1158/0008-5472.CAN-13-2150  1
2013 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. Murine cell line model of proneural glioma for evaluation of anti-tumor therapies. Journal of Neuro-Oncology. 112: 375-82. PMID 23504257 DOI: 10.1007/s11060-013-1082-x  1
2013 Grinshpun B, Sims J, Canoll P, Bruce JN, Sims P, Shen Y. Analyzing T cell repertoire diversity by high-throughput sequencing 2013 Ieee Global Conference On Signal and Information Processing, Globalsip 2013 - Proceedings. 53-56. DOI: 10.1109/GlobalSIP.2013.6736810  1
2012 Hoehl MM, Lu PJ, Sims PA, Slocum AH. Rapid and robust detection methods for poison and microbial contamination. Journal of Agricultural and Food Chemistry. 60: 6349-58. PMID 22630610 DOI: 10.1021/jf300817h  1
2012 Men Y, Fu Y, Chen Z, Sims PA, Greenleaf WJ, Huang Y. Digital polymerase chain reaction in an array of femtoliter polydimethylsiloxane microreactors. Analytical Chemistry. 84: 4262-6. PMID 22482776 DOI: 10.1021/ac300761n  1
2012 Shiroguchi K, Jia TZ, Sims PA, Xie XS. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proceedings of the National Academy of Sciences of the United States of America. 109: 1347-52. PMID 22232676 DOI: 10.1073/pnas.1118018109  1
2012 Lu PJ, Hoehl MM, Macarthur JB, Sims PA, Hongshen M, Slocum AH. Robust and economical multi-sample, multi-wavelength UV/vis absorption and fluorescence detector for biological and chemical contamination Aip Advances. 2. DOI: 10.1063/1.4738962  1
2011 Sims PA, Greenleaf WJ, Duan H, Xie XS. Fluorogenic DNA sequencing in PDMS microreactors. Nature Methods. 8: 575-80. PMID 21666670 DOI: 10.1038/nmeth.1629  1
2009 Sims PA, Xie XS. Probing dynein and kinesin stepping with mechanical manipulation in a living cell. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 10: 1511-6. PMID 19504528 DOI: 10.1002/cphc.200900113  1
2009 Sims JS, Militello KT, Sims PA, Patel VP, Kasper JM, Wirth DF. Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle. Eukaryotic Cell. 8: 327-38. PMID 19151330 DOI: 10.1128/EC.00340-08  1
2008 Nan X, Sims PA, Xie XS. Organelle tracking in a living cell with microsecond time resolution and nanometer spatial precision. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 9: 707-12. PMID 18383236 DOI: 10.1002/cphc.200700839  1
2007 Lu PJ, Sims PA, Oki H, Macarthur JB, Weitz DA. Target-locking acquisition with real-time confocal (TARC) microscopy. Optics Express. 15: 8702-12. PMID 19547205 DOI: 10.1364/OE.15.008702  1
2006 Li Y, Rogulski K, Zhou Q, Sims PJ, Prochownik EV. The negative c-Myc target onzin affects proliferation and apoptosis via its obligate interaction with phospholipid scramblase 1. Molecular and Cellular Biology. 26: 3401-13. PMID 16611984 DOI: 10.1128/MCB.26.9.3401-3413.2006  0.32
2005 Nan X, Sims PA, Chen P, Xie XS. Observation of individual microtubule motor steps in living cells with endocytosed quantum dots. The Journal of Physical Chemistry. B. 109: 24220-4. PMID 16375416 DOI: 10.1021/jp056360w  1
2005 Zhou Q, Ben-Efraim I, Bigcas JL, Junqueira D, Wiedmer T, Sims PJ. Phospholipid scramblase 1 binds to the promoter region of the inositol 1,4,5-triphosphate receptor type 1 gene to enhance its expression. The Journal of Biological Chemistry. 280: 35062-8. PMID 16091359 DOI: 10.1074/jbc.M504821200  0.32
2005 Sims PA, Wong CF, Vuga D, McCammon JA, Sefton BM. Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. Journal of Computational Chemistry. 26: 668-81. PMID 15754303 DOI: 10.1002/jcc.20207  0.72
2004 Wiedmer T, Zhao J, Li L, Zhou Q, Hevener A, Olefsky JM, Curtiss LK, Sims PJ. Adiposity, dyslipidemia, and insulin resistance in mice with targeted deletion of phospholipid scramblase 3 (PLSCR3). Proceedings of the National Academy of Sciences of the United States of America. 101: 13296-301. PMID 15328404 DOI: 10.1073/pnas.0405354101  0.32
2004 Dong B, Zhou Q, Zhao J, Zhou A, Harty RN, Bose S, Banerjee A, Slee R, Guenther J, Williams BR, Wiedmer T, Sims PJ, Silverman RH. Phospholipid scramblase 1 potentiates the antiviral activity of interferon. Journal of Virology. 78: 8983-93. PMID 15308695 DOI: 10.1128/JVI.78.17.8983-8993.2004  0.32
2004 Zhao KW, Li X, Zhao Q, Huang Y, Li D, Peng ZG, Shen WZ, Zhao J, Zhou Q, Chen Z, Sims PJ, Wiedmer T, Chen GQ. Protein kinase Cdelta mediates retinoic acid and phorbol myristate acetate-induced phospholipid scramblase 1 gene expression: its role in leukemic cell differentiation. Blood. 104: 3731-8. PMID 15308560 DOI: 10.1182/blood-2004-04-1630  0.32
2004 Sims PA, Wong CF, McCammon JA. Charge optimization of the interface between protein kinases and their ligands. Journal of Computational Chemistry. 25: 1416-29. PMID 15185335 DOI: 10.1002/jcc.20067  0.72
2004 Ben-Efraim I, Zhou Q, Wiedmer T, Gerace L, Sims PJ. Phospholipid scramblase 1 is imported into the nucleus by a receptor-mediated pathway and interacts with DNA. Biochemistry. 43: 3518-26. PMID 15035622 DOI: 10.1021/bi0356911  0.32
2003 Nanjundan M, Sun J, Zhao J, Zhou Q, Sims PJ, Wiedmer T. Plasma membrane phospholipid scramblase 1 promotes EGF-dependent activation of c-Src through the epidermal growth factor receptor. The Journal of Biological Chemistry. 278: 37413-8. PMID 12871937 DOI: 10.1074/jbc.M306182200  0.32
2003 Sims PA, Wong CF, McCammon JA. A computational model of binding thermodynamics: the design of cyclin-dependent kinase 2 inhibitors. Journal of Medicinal Chemistry. 46: 3314-25. PMID 12852762 DOI: 10.1021/jm0205043  0.72
2002 Zhou Q, Zhao J, Wiedmer T, Sims PJ. Normal hemostasis but defective hematopoietic response to growth factors in mice deficient in phospholipid scramblase 1. Blood. 99: 4030-8. PMID 12010804 DOI: 10.1182/blood-2001-12-0271  0.32
2002 Silverman RH, Halloum A, Zhou A, Dong B, Al-Zoghaibi F, Kushner D, Zhou Q, Zhao J, Wiedmer T, Sims PJ. Suppression of ovarian carcinoma cell growth in vivo by the interferon-inducible plasma membrane protein, phospholipid scramblase 1. Cancer Research. 62: 397-402. PMID 11809687  0.32
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