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Items: 47

1.

Cell-based reference samples designed with specific differences in microRNA biomarkers.

Pine PS, Lund SP, Stass SA, Kukuruga D, Jiang F, Sorbara L, Srivastava S, Salit M.

BMC Biotechnol. 2018 Mar 20;18(1):17. doi: 10.1186/s12896-018-0423-4.

2.

Summarizing performance for genome scale measurement of miRNA: reference samples and metrics.

Pine PS, Lund SP, Parsons JR, Vang LK, Mahabal AA, Cinquini L, Kelly SC, Kincaid H, Crichton DJ, Spira A, Liu G, Gower AC, Pass HI, Goparaju C, Dubinett SM, Krysan K, Stass SA, Kukuruga D, Van Keuren-Jensen K, Courtright-Lim A, Thompson KL, Rosenzweig BA, Sorbara L, Srivastava S, Salit ML.

BMC Genomics. 2018 Mar 6;19(1):180. doi: 10.1186/s12864-018-4496-1.

3.

Two approaches for estimating the lower limit of quantitation (LLOQ) of microRNA levels assayed as exploratory biomarkers by RT-qPCR.

Wolfinger RD, Beedanagari S, Boitier E, Chen T, Couttet P, Ellinger-Ziegelbauer H, Guillemain G, Mariet C, Mouritzen P, O'Lone R, Pine PS, Sharapova T, Yan J, Yuen PS, Thompson KL.

BMC Biotechnol. 2018 Feb 2;18(1):6. doi: 10.1186/s12896-018-0415-4.

4.

Absolute Measurement of Cardiac Injury-Induced microRNAs in Biofluids across Multiple Test Sites.

Thompson KL, Boitier E, Chen T, Couttet P, Ellinger-Ziegelbauer H, Goetschy M, Guillemain G, Kanki M, Kelsall J, Mariet C, de La Moureyre-Spire C, Mouritzen P, Nassirpour R, O'Lone R, Pine PS, Rosenzweig BA, Sharapova T, Smith A, Uchiyama H, Yan J, Yuen PS, Wolfinger R.

Toxicol Sci. 2016 Nov;154(1):115-125. Epub 2016 Sep 7.

PMID:
27605421
5.

External RNA Controls Consortium Beta Version Update.

Lee H, Pine PS, McDaniel J, Salit M, Oliver B.

J Genomics. 2016 Jul 26;4:19-22. doi: 10.7150/jgen.16082. eCollection 2016.

6.

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.

Pine PS, Munro SA, Parsons JR, McDaniel J, Lucas AB, Lozach J, Myers TG, Su Q, Jacobs-Helber SM, Salit M.

BMC Biotechnol. 2016 Jun 24;16(1):54. doi: 10.1186/s12896-016-0281-x.

7.

An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1.

Devonshire AS, Sanders R, Whale AS, Nixon GJ, Cowen S, Ellison SL, Parkes H, Pine PS, Salit M, McDaniel J, Munro S, Lund S, Matsukura S, Sekiguchi Y, Kawaharasaki M, Granjeiro JM, Falagan-Lotsch P, Saraiva AM, Couto P, Yang I, Kwon H, Park SR, Demšar T, Žel J, Blejec A, Milavec M, Dong L, Zhang L, Sui Z, Wang J, Viroonudomphol D, Prawettongsopon C, Partis L, Baoutina A, Emslie K, Takatsu A, Akyurek S, Akgoz M, Vonsky M, Konopelko LA, Cundapi EM, Urquiza MP, Huggett JF, Foy CA.

Biomol Detect Quantif. 2016 Jun 6;8:15-28. doi: 10.1016/j.bdq.2016.05.003. eCollection 2016 Jun.

8.

Using mixtures of biological samples as process controls for RNA-sequencing experiments.

Parsons J, Munro S, Pine PS, McDaniel J, Mehaffey M, Salit M.

BMC Genomics. 2015 Sep 17;16:708. doi: 10.1186/s12864-015-1912-7.

9.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M.

Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125.

PMID:
25254650
10.

Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films.

Baker BA, Pine PS, Chatterjee K, Kumar G, Lin NJ, McDaniel JH, Salit ML, Simon CG Jr.

Biomaterials. 2014 Aug;35(25):6716-26. doi: 10.1016/j.biomaterials.2014.04.075. Epub 2014 May 17.

PMID:
24840613
11.

The determination of stem cell fate by 3D scaffold structures through the control of cell shape.

Kumar G, Tison CK, Chatterjee K, Pine PS, McDaniel JH, Salit ML, Young MF, Simon CG Jr.

Biomaterials. 2011 Dec;32(35):9188-96. doi: 10.1016/j.biomaterials.2011.08.054. Epub 2011 Sep 3.

12.
13.

Overview of laser microbeam applications as related to antibody targeting.

Pine PS.

Methods Mol Biol. 2010;588:203-17. doi: 10.1007/978-1-59745-324-0_22. Review.

PMID:
20012833
14.

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples.

Pine PS, Boedigheimer M, Rosenzweig BA, Turpaz Y, He YD, Delenstarr G, Ganter B, Jarnagin K, Jones WD, Reid LH, Thompson KL.

Pharmacogenomics. 2008 Nov;9(11):1753-63. doi: 10.2217/14622416.9.11.1753.

15.

Comparison of the diagnostic performance of human whole genome microarrays using mixed-tissue RNA reference samples.

Thompson KL, Pine PS.

Toxicol Lett. 2009 Apr 10;186(1):58-61. doi: 10.1016/j.toxlet.2008.08.018. Epub 2008 Sep 7.

PMID:
18822358
16.

Assessment of repeated microarray experiments using mixed tissue RNA reference samples.

Mongan MA, Higgins M, Pine PS, Afshari C, Hamadeh H.

Biotechniques. 2008 Sep;45(3):283-92. doi: 10.2144/000112914. Erratum in: Biotechniques. 2008 Dec;45(6):607. Mongan, Ann [corrected to Mongan, M Ann]; Pine, Scott [corrected to Pine, P Scott].

17.
18.

Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions.

Han T, Melvin CD, Shi L, Branham WS, Moland CL, Pine PS, Thompson KL, Fuscoe JC.

BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S17.

19.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr.

Nat Biotechnol. 2006 Sep;24(9):1151-61.

20.

Using RNA sample titrations to assess microarray platform performance and normalization techniques.

Shippy R, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, Pine PS, Boysen C, Guo X, Chudin E, Sun YA, Willey JC, Thierry-Mieg J, Thierry-Mieg D, Setterquist RA, Wilson M, Lucas AB, Novoradovskaya N, Papallo A, Turpaz Y, Baker SC, Warrington JA, Shi L, Herman D.

Nat Biotechnol. 2006 Sep;24(9):1123-31.

21.

Workgroup report: Review of genomics data based on experience with mock submissions--view of the CDER Pharmacology Toxicology Nonclinical Pharmacogenomics Subcommittee.

Leighton JK, Brown P, Ellis A, Harlow P, Harrouk W, Pine PS, Robison T, Rosario L, Thompson K.

Environ Health Perspect. 2006 Apr;114(4):573-8. Review.

22.

Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.

Thompson KL, Rosenzweig BA, Pine PS, Retief J, Turpaz Y, Afshari CA, Hamadeh HK, Damore MA, Boedigheimer M, Blomme E, Ciurlionis R, Waring JF, Fuscoe JC, Paules R, Tucker CJ, Fare T, Coffey EM, He Y, Collins PJ, Jarnagin K, Fujimoto S, Ganter B, Kiser G, Kaysser-Kranich T, Sina J, Sistare FD.

Nucleic Acids Res. 2005 Dec 23;33(22):e187.

23.

Determination of plasma and brain levels of isotretinoin in mice following single oral dose by high-performance liquid chromatography.

Yang Y, Faustino PJ, Pine PS, Davis H, Grunberg N, Phillips J, Lyon RC, Yu LX, Ciavarella AB, Del Grosso AV, Hanig JP.

J Pharm Biomed Anal. 2005 Feb 7;37(1):157-63.

PMID:
15664756
24.

Developmental neurotoxicity of ketamine: morphometric confirmation, exposure parameters, and multiple fluorescent labeling of apoptotic neurons.

Scallet AC, Schmued LC, Slikker W Jr, Grunberg N, Faustino PJ, Davis H, Lester D, Pine PS, Sistare F, Hanig JP.

Toxicol Sci. 2004 Oct;81(2):364-70. Epub 2004 Jul 14.

PMID:
15254342
25.

Identification of platform-independent gene expression markers of cisplatin nephrotoxicity.

Thompson KL, Afshari CA, Amin RP, Bertram TA, Car B, Cunningham M, Kind C, Kramer JA, Lawton M, Mirsky M, Naciff JM, Oreffo V, Pine PS, Sistare FD.

Environ Health Perspect. 2004 Mar;112(4):488-94.

26.

Dye bias correction in dual-labeled cDNA microarray gene expression measurements.

Rosenzweig BA, Pine PS, Domon OE, Morris SM, Chen JJ, Sistare FD.

Environ Health Perspect. 2004 Mar;112(4):480-7.

27.

Virtual neuropathology: three-dimensional visualization of lesions due to toxic insult.

Lester DS, Pine PS, Delnomdedieu M, Johannessen JN, Johnson GA.

Toxicol Pathol. 2000 Jan-Feb;28(1):100-4.

PMID:
10668995
28.

Overview of laser microbeam applications as related to antibody targeting.

Pine PS.

Methods Mol Biol. 1999;115:159-74. Review. No abstract available.

PMID:
10098178
29.

A semiautomated fluorescence-based cell-to-cell fusion assay for gp120-gp41 and CD4 expressing cells.

Pine PS, Weaver JL, Oravecz T, Pall M, Ussery M, Aszalos A.

Exp Cell Res. 1998 Apr 10;240(1):49-57.

PMID:
9570920
30.

Inhibition of HIV infection of H9 cells by chlorpromazine derivatives.

Hewlett I, Lee S, Molnar J, Foldeak S, Pine PS, Weaver JL, Aszalos A.

J Acquir Immune Defic Syndr Hum Retrovirol. 1997 May 1;15(1):16-20.

PMID:
9215649
31.

Effect of combination of suboptimal concentrations of P-glycoprotein blockers on the proliferation of MDR1 gene expressing cells.

Hwang M, Ahn CH, Pine PS, Yin JJ, Hrycyna CA, Licht T, Aszalos A.

Int J Cancer. 1996 Jan 26;65(3):389-97.

32.

Behavior of N-acylated daunorubicins in MDR1 gene transfected and parental cells.

Aszalos A, Pine PS, Pandey R, Gottesman MM.

Biochem Pharmacol. 1995 Sep 7;50(6):889-92.

PMID:
7575653
33.

Cross-linking of CD4 in a TCR/CD3-juxtaposed inhibitory state: a pFRET study.

Szabó G Jr, Weaver JL, Pine PS, Rao PE, Aszalos A.

Biophys J. 1995 Mar;68(3):1170-6.

34.

Cytochalasin D modulates CD4 crosslinking sensitive mitogenic signal in T lymphocytes.

Aszalos A, Pine PS, Weaver JL, Rao PE.

Cell Immunol. 1994 Aug;157(1):81-91.

PMID:
7913666
35.

The L-selectin (Leu8) molecule is associated with the TcR/CD3 receptor; fluorescence energy transfer measurements on live cells.

Szabo G Jr, Pine PS, Weaver JL, Rao PE, Aszalos A.

Immunol Cell Biol. 1994 Aug;72(4):319-25.

PMID:
7528722
36.

The interaction of immunosuppressive compounds in tandem stimulated peripheral human lymphocytes.

Weaver JL, Pine PS, Aszalos A.

Immunopharmacol Immunotoxicol. 1994 May;16(2):179-90.

PMID:
7521360
37.

Overview of laser microbeam applications as related to antibody targeting.

Pine PS.

Methods Mol Biol. 1994;34:349-65. Review. No abstract available.

PMID:
7711865
38.

Specific disengagement of cell-bound anti-LAM-1 (anti-L-selectin) antibodies by aurintricarboxylic acid.

Szabó G Jr, Weaver JL, Pine PS, Aszalos A.

Mol Immunol. 1993 Dec;30(18):1689-94.

PMID:
7505884
39.

The effect of ion channel blockers, immunosuppressive agents, and other drugs on the activity of the multi-drug transporter.

Weaver JL, Szabo G Jr, Pine PS, Gottesman MM, Goldenberg S, Aszalos A.

Int J Cancer. 1993 May 28;54(3):456-61.

PMID:
7685326
40.

CD4 changes conformation upon ligand binding.

Szabò G Jr, Pine PS, Weaver JL, Rao PE, Aszalos A.

J Immunol. 1992 Dec 1;149(11):3596-604.

PMID:
1431129
41.

Prevention of binding of rgp120 by anti-HIV active tannins.

Weaver JL, Pine PS, Dutschman G, Cheng YC, Lee KH, Aszalos A.

Biochem Pharmacol. 1992 Jun 9;43(11):2479-80.

PMID:
1610410
42.
43.

Laser scanning and confocal microscopy of daunorubicin, doxorubicin, and rhodamine 123 in multidrug-resistant cells.

Weaver JL, Pine PS, Aszalos A, Schoenlein PV, Currier SJ, Padmanabhan R, Gottesman MM.

Exp Cell Res. 1991 Oct;196(2):323-9.

PMID:
1680064
44.
45.

Aurin tricarboxylic acid, the anti-AIDS compound, prevents the binding of interferon-alpha to its receptor.

Gan YX, Weaver JL, Pine PS, Zoon KC, Aszalos A.

Biochem Biophys Res Commun. 1990 Nov 15;172(3):1298-303.

PMID:
2147104
46.

Polyionic compounds selectively alter availability of CD4 receptors for HIV coat protein rgp120.

Weaver JL, Gergely P, Pine PS, Patzer E, Aszalos A.

AIDS Res Hum Retroviruses. 1990 Sep;6(9):1125-30.

PMID:
1979910
47.

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