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Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells.

Zhang P, Gaffrey MJ, Zhu Y, Chrisler WB, Fillmore TL, Yi L, Nicora CD, Zhang T, Wu H, Jacobs J, Tang K, Kagan J, Srivastava S, Rodland KD, Qian WJ, Smith RD, Liu T, Wiley HS, Shi T.

Anal Chem. 2019 Jan 15;91(2):1441-1451. doi: 10.1021/acs.analchem.8b04258. Epub 2018 Dec 28.


Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

Shi T, Gaffrey MJ, Fillmore TL, Nicora CD, Yi L, Zhang P, Shukla AK, Wiley HS, Rodland KD, Liu T, Smith RD, Qian WJ.

Commun Biol. 2018 Aug 6;1:103. doi: 10.1038/s42003-018-0107-6. eCollection 2018.


A systems perspective of heterocellular signaling.

Wells A, Wiley HS.

Essays Biochem. 2018 Oct 26;62(4):607-617. doi: 10.1042/EBC20180015. Print 2018 Oct 26. Review.


Blazing Signature Filter: a library for fast pairwise similarity comparisons.

Lee JY, Fujimoto GM, Wilson R, Wiley HS, Payne SH.

BMC Bioinformatics. 2018 Jun 11;19(1):221. doi: 10.1186/s12859-018-2210-6.


Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway.

Yi L, Shi T, Gritsenko MA, X'avia Chan CY, Fillmore TL, Hess BM, Swensen AC, Liu T, Smith RD, Wiley HS, Qian WJ.

Anal Chem. 2018 Apr 17;90(8):5256-5263. doi: 10.1021/acs.analchem.8b00071. Epub 2018 Apr 3.


How low can you go?

Wiley HS.

Elife. 2018 Jan 4;7. pii: e33604. doi: 10.7554/eLife.33604.


Decoding Signal Processing at the Single-Cell Level.

Wiley HS.

Cell Syst. 2017 Dec 27;5(6):542-543. doi: 10.1016/j.cels.2017.12.003.


Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.

Lindemann SR, Mobberley JM, Cole JK, Markillie LM, Taylor RC, Huang E, Chrisler WB, Wiley HS, Lipton MS, Nelson WC, Fredrickson JK, Romine MF.

Front Microbiol. 2017 Jun 13;8:1020. doi: 10.3389/fmicb.2017.01020. eCollection 2017.


Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS.

Sci Signal. 2016 Jul 12;9(436):rs6. doi: 10.1126/scisignal.aaf0891.


Science Signaling Podcast for 12 July 2016: Adaptor proteins limit signaling.

Wiley HS, VanHook AM.

Sci Signal. 2016 Jul 12;9(436):c16. doi: 10.1126/scisignal.aah4492.


Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment.

Shi T, Gao Y, Gaffrey MJ, Nicora CD, Fillmore TL, Chrisler WB, Gritsenko MA, Wu C, He J, Bloodsworth KJ, Zhao R, Camp DG 2nd, Liu T, Rodland KD, Smith RD, Wiley HS, Qian WJ.

Anal Chem. 2015 Jan 20;87(2):1103-10. doi: 10.1021/ac503797x. Epub 2014 Dec 31.


Open questions: the disrupted circuitry of the cancer cell.

Wiley HS.

BMC Biol. 2014 Oct 18;12:88. doi: 10.1186/s12915-014-0088-y. No abstract available.


Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.

Beliaev AS, Romine MF, Serres M, Bernstein HC, Linggi BE, Markillie LM, Isern NG, Chrisler WB, Kucek LA, Hill EA, Pinchuk GE, Bryant DA, Wiley HS, Fredrickson JK, Konopka A.

ISME J. 2014 Nov;8(11):2243-55. doi: 10.1038/ismej.2014.69. Epub 2014 Apr 29.


Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.

Taylor RC, Webb Robertson BJ, Markillie LM, Serres MH, Linggi BE, Aldrich JT, Hill EA, Romine MF, Lipton MS, Wiley HS.

Integr Biol (Camb). 2013 Nov;5(11):1393-406. doi: 10.1039/c3ib40120k. Epub 2013 Sep 30.


Autocrine HBEGF expression promotes breast cancer intravasation, metastasis and macrophage-independent invasion in vivo.

Zhou ZN, Sharma VP, Beaty BT, Roh-Johnson M, Peterson EA, Van Rooijen N, Kenny PA, Wiley HS, Condeelis JS, Segall JE.

Oncogene. 2014 Jul 17;33(29):3784-93. doi: 10.1038/onc.2013.363. Epub 2013 Sep 9.


Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics.

Hess BM, Xue J, Markillie LM, Taylor RC, Wiley HS, Ahring BK, Linggi B.

PLoS One. 2013 Jun 19;8(6):e66104. doi: 10.1371/journal.pone.0066104. Print 2013.


Integrated experimental and model-based analysis reveals the spatial aspects of EGFR activation dynamics.

Shankaran H, Zhang Y, Chrisler WB, Ewald JA, Wiley HS, Resat H.

Mol Biosyst. 2012 Nov;8(11):2868-82. doi: 10.1039/c2mb25190f. Epub 2012 Sep 5.


Improving RNA-Seq Precision with MapAl.

Labaj PP, Linggi BE, Wiley HS, Kreil DP.

Front Genet. 2012 Apr 2;3:28. doi: 10.3389/fgene.2012.00028. eCollection 2012.


Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data.

Waters KM, Liu T, Quesenberry RD, Willse AR, Bandyopadhyay S, Kathmann LE, Weber TJ, Smith RD, Wiley HS, Thrall BD.

PLoS One. 2012;7(3):e34515. doi: 10.1371/journal.pone.0034515. Epub 2012 Mar 29.


Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

Łabaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP.

Bioinformatics. 2011 Jul 1;27(13):i383-91. doi: 10.1093/bioinformatics/btr247.


Integrating multiple types of data for signaling research: challenges and opportunities.

Wiley HS.

Sci Signal. 2011 Feb 15;4(160):pe9. doi: 10.1126/scisignal.2001826.


Oscillatory dynamics of the extracellular signal-regulated kinase pathway.

Shankaran H, Wiley HS.

Curr Opin Genet Dev. 2010 Dec;20(6):650-5. doi: 10.1016/j.gde.2010.08.002. Review.


The heparin-binding domain of HB-EGF mediates localization to sites of cell-cell contact and prevents HB-EGF proteolytic release.

Prince RN, Schreiter ER, Zou P, Wiley HS, Ting AY, Lee RT, Lauffenburger DA.

J Cell Sci. 2010 Jul 1;123(Pt 13):2308-18. doi: 10.1242/jcs.058321. Epub 2010 Jun 8.


Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context.

Joslin EJ, Shankaran H, Opresko LK, Bollinger N, Lauffenburger DA, Wiley HS.

Mol Biosyst. 2010 Jul;6(7):1293-306. doi: 10.1039/c003921g. Epub 2010 May 10.


An analysis pipeline for the inference of protein-protein interaction networks.

Taylor RC, Singhal M, Daly DS, Gilmore J, Cannon WR, Domico K, White AM, Auberry DL, Auberry KJ, Hooker BS, Hurst G, McDermott JE, McDonald WH, Pelletier DA, Schmoyer D, Wiley HS.

Int J Data Min Bioinform. 2009;3(4):409-30.


Basic fibroblast growth factor regulates persistent ERK oscillations in premalignant but not malignant JB6 cells.

Weber TJ, Shankaran H, Wiley HS, Opresko LK, Chrisler WB, Quesenberry RD.

J Invest Dermatol. 2010 May;130(5):1444-56. doi: 10.1038/jid.2009.383. Epub 2009 Dec 17.


Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor.

Shankaran H, Ippolito DL, Chrisler WB, Resat H, Bollinger N, Opresko LK, Wiley HS.

Mol Syst Biol. 2009;5:332. doi: 10.1038/msb.2009.90. Epub 2009 Dec 1.


HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cells.

Zhang Y, Opresko L, Shankaran H, Chrisler WB, Wiley HS, Resat H.

BMC Cell Biol. 2009 Oct 31;10:78. doi: 10.1186/1471-2121-10-78.


An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells.

Heibeck TH, Ding SJ, Opresko LK, Zhao R, Schepmoes AA, Yang F, Tolmachev AV, Monroe ME, Camp DG 2nd, Smith RD, Wiley HS, Qian WJ.

J Proteome Res. 2009 Aug;8(8):3852-61. doi: 10.1021/pr900044c.


Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models.

Rogers S, Girolami M, Kolch W, Waters KM, Liu T, Thrall B, Wiley HS.

Bioinformatics. 2008 Dec 15;24(24):2894-900. doi: 10.1093/bioinformatics/btn553. Epub 2008 Oct 30.


Multiple mechanisms are responsible for transactivation of the epidermal growth factor receptor in mammary epithelial cells.

Rodland KD, Bollinger N, Ippolito D, Opresko LK, Coffey RJ, Zangar R, Wiley HS.

J Biol Chem. 2008 Nov 14;283(46):31477-87. doi: 10.1074/jbc.M800456200. Epub 2008 Sep 9.


Smad signaling dynamics: insights from a parsimonious model.

Shankaran H, Wiley HS.

Sci Signal. 2008 Sep 9;1(36):pe41. doi: 10.1126/scisignal.136pe41.


A general system for studying protein-protein interactions in Gram-negative bacteria.

Pelletier DA, Hurst GB, Foote LJ, Lankford PK, McKeown CK, Lu TY, Schmoyer DD, Shah MB, Hervey WJ 4th, McDonald WH, Hooker BS, Cannon WR, Daly DS, Gilmore JM, Wiley HS, Auberry DL, Wang Y, Larimer FW, Kennel SJ, Doktycz MJ, Morrell-Falvey JL, Owens ET, Buchanan MV.

J Proteome Res. 2008 Aug;7(8):3319-28. doi: 10.1021/pr8001832. Epub 2008 Jul 1.


The mammary epithelial cell secretome and its regulation by signal transduction pathways.

Jacobs JM, Waters KM, Kathmann LE, Camp DG 2nd, Wiley HS, Smith RD, Thrall BD.

J Proteome Res. 2008 Feb;7(2):558-69. doi: 10.1021/pr0704377. Epub 2008 Jan 1.


EGF-receptor-mediated mammary epithelial cell migration is driven by sustained ERK signaling from autocrine stimulation.

Joslin EJ, Opresko LK, Wells A, Wiley HS, Lauffenburger DA.

J Cell Sci. 2007 Oct 15;120(Pt 20):3688-99. Epub 2007 Sep 25.


Statistically inferring protein-protein associations with affinity isolation LC-MS/MS assays.

Sharp JL, Anderson KK, Hurst GB, Daly DS, Pelletier DA, Cannon WR, Auberry DL, Schmoyer DD, McDonald WH, White AM, Hooker BS, Victry KD, Buchanan MV, Kery V, Wiley HS.

J Proteome Res. 2007 Sep;6(9):3788-95. Epub 2007 Aug 11.


Cell surface receptors for signal transduction and ligand transport: a design principles study.

Shankaran H, Resat H, Wiley HS.

PLoS Comput Biol. 2007 Jun;3(6):e101. Epub 2007 Apr 20. Review.


Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager.

Shah AR, Singhal M, Klicker KR, Stephan EG, Wiley HS, Waters KM.

Bioinformatics. 2007 Apr 1;23(7):906-9. Epub 2007 Feb 25.


High speed method for in situ multispectral image registration.

Perrine KA, Lamarche BL, Hopkins DF, Budge SE, Opresko LK, Wiley HS, Sowa MB.

Microsc Res Tech. 2007 Apr;70(4):382-9.


The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks.

Sakaki Y, Kholodenko BN, Hatakeyama M, Kitano H, Kolch W, De Meyts P, Yarden Y, Westerhoff HV, Wiley HS.

Syst Biol (Stevenage). 2005 Jun;152(2):53-4. No abstract available.


Modeling the effects of HER/ErbB1-3 coexpression on receptor dimerization and biological response.

Shankaran H, Wiley HS, Resat H.

Biophys J. 2006 Jun 1;90(11):3993-4009. Epub 2006 Mar 13.


Cholesterol dictates the freedom of EGF receptors and HER2 in the plane of the membrane.

Orr G, Hu D, Ozçelik S, Opresko LK, Wiley HS, Colson SD.

Biophys J. 2005 Aug;89(2):1362-73. Epub 2005 May 20.


The membrane-anchoring domain of epidermal growth factor receptor ligands dictates their ability to operate in juxtacrine mode.

Dong J, Opresko LK, Chrisler W, Orr G, Quesenberry RD, Lauffenburger DA, Wiley HS.

Mol Biol Cell. 2005 Jun;16(6):2984-98. Epub 2005 Apr 13.


Simple protein complex purification and identification method for high-throughput mapping of protein interaction networks.

Markillie LM, Lin CT, Adkins JN, Auberry DL, Hill EA, Hooker BS, Moore PA, Moore RJ, Shi L, Wiley HS, Kery V.

J Proteome Res. 2005 Mar-Apr;4(2):268-74.


A model of cytokine shedding induced by low doses of gamma radiation.

Miller JH, Zheng F, Jin S, Opresko LK, Wiley HS, Resat H.

Radiat Res. 2005 Mar;163(3):337-42.


Ligand accumulation in autocrine cell cultures.

Monine MI, Berezhkovskii AM, Joslin EJ, Wiley HS, Lauffenburger DA, Shvartsman SY.

Biophys J. 2005 Apr;88(4):2384-90. Epub 2005 Jan 14.


Parsing ERK activation reveals quantitatively equivalent contributions from epidermal growth factor receptor and HER2 in human mammary epithelial cells.

Hendriks BS, Orr G, Wells A, Wiley HS, Lauffenburger DA.

J Biol Chem. 2005 Feb 18;280(7):6157-69. Epub 2004 Nov 29.


Should software hold data hostage?

Wiley HS, Michaels GS.

Nat Biotechnol. 2004 Aug;22(8):1037-8. No abstract available.


Induced autocrine signaling through the epidermal growth factor receptor contributes to the response of mammary epithelial cells to tumor necrosis factor alpha.

Chen WN, Woodbury RL, Kathmann LE, Opresko LK, Zangar RC, Wiley HS, Thrall BD.

J Biol Chem. 2004 Apr 30;279(18):18488-96. Epub 2004 Feb 20.

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