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Publications

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Publications

 

The following are a selection of recent publications that relate to protein microarrays in general or one of our services specifically. Click on the link to be sent to the respective PubMed (http://www.ncbi.nlm.nih.gov/pubmed) page.

 

Snapshot Proteomics™

 

Woodard CL, Goodwin CR, Wan J, Xia S, Newman R, Hu J, Zhang J, Hayward SD, Qian J, Laterra J, Zhu H. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One 8:e72671 (2013) PubMed 24023761

 

Merbl Y, Refour P, Patel H, Springer M, Kirschner MW. Profiling of ubiquitin-like modifications reveals features of mitotic control. Cell 152:1160-1172 (2013) PubMed 23452859

 

Loch CM and Strickler JE. A microarray of ubiquitylated proteins for profiling deubiquitylase activity reveals the critical roles of both chain and substrate. Biochim Biophys Acta 1823:2069-78 (2012) PubMed 22626734

 

REVIEW Merbl Y and Kirschner MW. Protein microarrays for genome-wide posttranslational modification analysis. WIREs Syst Biol Med 3:347-56 (2010) PubMed 20865779

 

Del Rincon SV, Rogers J, Widschwendter M, Sun D, Sieburg HB, Spruck C. Development and validation of a method for profiling post-translational modification activities using protein microarrays. PLoS One 5(6):e11332 (2010) PubMed 20596523

 

Merbl Y and Kirschner MW. Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. PNAS 106:2543-2548 (2009) PubMed 19181856

 

 

Basic Science/UMAP™

 

Xu Z, Li X, Zhou S, Xie W, Wang J, Cheng L, Wang S, Guo S, Xu Z, Cao X, Zhang M, Yu B, Narimatsu H, Tao SC, Zhang Y. Systematic identification of the protein substrates of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T1/T2/T3 using a human proteome microarray. Proteomics.10.1002/pmic.201600485 (2017) PubMed 28394504

 

Huang BY, Chen PC, Chen BH, Wang CC, Liu HF, Chen YZ, Chen CS, Yang YS. High-Throughput Screening of Sulfated Proteins by Using a Genome-Wide Proteome Microarray and Protein Tyrosine Sulfation System. Anal Chem. 89(6):3278-3284. doi: 10.1021/acs.analchem.6b02853. (2017) PubMed 28211678

 

Jung JG, Stoeck A, Guan B, Wu RC, Zhu H, Blackshaw S, Shih IeM, Wang TL. Notch3 interactome analysis identified WWP2 as a negative regulator of Notch3 signaling in ovarian cancer. PLoS Genet 10(10):e1004751 (2015) PubMed 25356737

 

Tribolet L, Cantacessi C, Pickering DA, Navarro S, Doolan DL, Trieu A, Fei H, Chao Y, Hofmann A, Gasser RB, Giacomin PR, Loukas A. Probing of a human proteome microarray with a recombinant pathogen protein reveals a novel mechanism by which hookworms suppress B-cell receptor signaling. J Infect Dis 211(3):416-25 (2015) PubMed 25139017

 

Olia AS, Barker K, McCullough CE, Tang HY, Speicher DW, Qiu J, LaBaer J, Marmorstein R. Nonenzymatic Protein Acetylation Detected by NAPPA Protein Arrays. ACS Chem Biol. 18;10(9):2034-47. (2015) PubMed 26083674

 

Yu X, LaBaer J. High-throughput identification of proteins with AMPylation using self-assembled human protein (NAPPA) microarrays. Nat Protoc. 10(5):756-67. (2015) PubMed 25881200

 

Yu X, Decker KB, Barker K, Neunuebel MR, Saul J, Graves M, Westcott N, Hang H, LaBaer J, Qiu J, Machner MP. Host-pathogen interaction profiling using self-assembling human protein arrays. J Proteome Res. 14(4):1920-36. (2015) PubMed 25739981

 

Dwyer SF, Gao L, Gelman IH. Identification of novel focal adhesion kinase substrates: role for FAK in NFκB signaling. Int J Biol Sci 11(4):404-10 (2015) PubMed 25798060

 

Cox E, Uzoma I, Guzzo C, Jeong JS, Matunis M, Blackshaw S, Zhu H. Identification of SUMO E3 ligase-specific substrates using the HuProt human proteome microarray. Methods Mol Biol 1295:455-63 (2015) PubMed 25820740

 

Zhang HN, Yang L, Ling JY, Czajkowsky DM, Wang JF, Zhang XW, Zhou YM, Ge F, Yang MK, Xiong Q, Guo SJ, Le HY, Wu SF, Yan W, Liu B, Zhu H, Chen Z, Tao SC. Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic. Proc Natl Acad Sci USA 112(49):15084-9 (2015) PubMed 26598702

 

Ainscough JS, Gerberick GF, Kimber I, Dearman RJ Interleukin-1B processing is dependent on a calcium-mediated interaction with calmodulin. J Biol Chem 290(52):31151-61 (2015) PubMed 26559977

 

Charlaftis N, Suddason T, Wu X, Anwar S, Karin M, Gallagher E. The MEKK1 PHD ubiquitinates TAB1 to activate MAPKs in response to cytokines. EMBO J. 3;33(21):2581-96. doi: 10.15252/embj.201488351. (2014) PubMed 25260751

 

Lee YI, Giovinazzo D, Kang HC, Lee Y, Jeong JS, Doulias PT, Xie Z, Hu J, Ghasemi M, Ischiropoulos H, Qian J, Zhu H, Blackshaw S, Dawson VL, Dawson TM Protein microarray characterization of the S-nitrosoproteome. Mol Cell Proteomics 13(1):63-72 (2014) PubMed 24105792

 

Fan Q, Huang L, Zhu X, Zhang K, Ye H, Luo Y, Sun X, Zhou P, Lu Y. Identification of proteins that interact with alpha A-crystallin using a human proteome microarray. Mol Vis 20:117-124 (2014) PubMed 24453475

 

Deng RP, He X, Guo SJ, Liu WF, Tao Y, Tao SC. Global identification of O-GlcNAc Transferase (OGT) interactors by a human proteome microarray and the construction of an OGT interactome. Proteomics 10.1002/pmic.201300144 (2014) PubMed 24536041

 

Zhang QF, Gu J, Gong P, Wang XD, Tu S, Bi LJ, Yu ZN, Zhang ZP, Cui ZQ, Wei HP, Tao SC, Zhang XE, Deng JY. Reversibly acetylated lysine residues play important roles in the enzymatic activity of Escherichia coli N-hydroxyarylamine O-acetyltransferase. FEBS J 280:1966-79 (2013) PubMed 23452042

 

Li N, Stein RS, He W, Komives E, Wang W. Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. Mol Cell Proteomics 12:2750-60 (2013) PubMed 23842000

 

Newman RH, Hu J, Rho H, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras A, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks. Molecular Systems Biology 9:655 (2013) PubMed 23549483

 

Lu KY, Tao SC, Yang TC, Ho YH, Lee CH, Lin CC, Juan HF, Huang HC, Yang CY, Chen MS, Lin YY, Lu JY, Zhu H, Chen CS. Profiling lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. Mol Cell Proteomics 11:1177-90 (2012) PubMed 22843995

 

Loch CM, Eddins MJ, Strickler JE. Protein microarrays for the identification of Praja1 E3 ubiquitin ligase substrates. Cell Biochem Biophys 60:127-35 (2011) PubMed 21461837

 

Balut CM, Loch CM, Devor DC. Role of ubiquitylation and USP8-dependent deubiquitylation in the endocytosis and lysosomal targeting of plasma membrane KCa3.1. FASEB J. 25:3938-48 (2011) PubMed 21828287

 

Mok J, Im H, Snyder M. Global identification of protein kinase substrates by protein microarray analysis. Nat Protoc 4:1820-7 (2009) PubMed 20010933

 

Bua DJ, Kuo AJ, Cheung P, Liu CL, Migliori V, Espejo A, Casadio F, Bassi C, Amati B, Bedford MT, Guccione E, Gozani O. Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks. PLoS One 4(8):e6789 (2009) PubMed 19956676

 

Foster MW, Forrester MT, Stamler JS. A protein microarray-based analysis of S-nitrosylation. Proc Natl Acad Sci USA 106:18948-53 (2009) PubMed 19864628

 

Persaud A, Alberts P, Amsen EM, Xiong X, Wasmuth J, Saadon Z, Fladd C, Parkinson J, Rotin D. Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays. Molecular Systems Biology 5:333 (2009) PubMed 19953087

 

Lin YY, Lu JY, Zhang J, Walter W, Dang W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, Berger SL, Zhu H. Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136:1073-84 (2009) PubMed 19303850

 

Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D. Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Sys Biol 3:116 (2007) PubMed 17551511

 

Boyle SN, Michaud GA, Schweitzer B, Predki PF, Koleske AJ. A critical role for cortactin phosphorylation by Abl-family kinases in PDGF-induced dorsal-wave formation. Curr Biol 17:445-51 (2007) PubMed 17306540

 

Oh YH, Hong MY, Jin Z, Lee T, Han MK, Park S, Kim SH. Chip-based analysis of SUMO conjugation to a target protein. Biosens Bioelectron 22:1260-7 (2007) PubMed 16820290

 

Jones RB, Gordus A., Krall JA, MacBeath G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439:168-174 (2006) PubMed 16273093

 

 

Preclinical Drug Characterization/SMART™

 

REVIEW Tu S, Jiang HW, Liu CX, Zhou SM, Tao SC. Protein microarrays for studies of drug mechanisms and biomarker discovery in the era of systems biology. Curr Pharm Des 20:49-55 (2014) PubMed 23530501

 

Gur S, Sikka SC, Abdel-Mageed AB, Abd Elmageed ZY, Rezk B, Pankey E, Kadowitz PJ, Hellstrom WJ. Imatinib mesylate (Gleevec) induces human corpus cavernosum relaxation by inhibiting receptor tyrosine kinases (RTKs): identification of new RTK targets. Urology 82:745.e11-6 (2013) PubMed 23856589

 

REVIEW Uzoma I, Zhu H. Interactome mapping: using protein microarray technology to reconstruct diverse protein networks. Genomics Proteomics Bioinformatics 11:18-28 (2013) PubMed 23395178

 

Loch CM, Cuccherini CL, Leach CA, Strickler JE. Deubiquitylase, deSUMOylase, and deISGylase activity microarrays for assay of substrate preference and functional modifiers. Mol Cell Proteomics 10:M110.002402 (2011) PubMed 20956615

 

REVIEW Michaud GA, Salcius M, Zhou F, Papov VV, Merkel J, Murtha M, Predki P, Schweitzer B. Applications of protein arrays for small molecule drug discovery and characterization. Biotechnol Genet Eng Rev 22:197-211 (2006) PubMed 18476332

 

Michaud GA, Samuels ML, Schweitzer B. Functional protein arrays to facilitate drug discovery and development. IDrugs 9:266-72 (2006) PubMed 16596480

 

 

Biomarker Discovery/ProActiN™

 

Lessa-Aquino C, Lindow JC, Randall A, Wunder E, Pablo J, Nakajima R, Jasinskas A, Cruz JS, Damião AO, Nery N, Ribeiro GS, Costa F, Hagan JE, Reis MG, Ko AI, Medeiros MA, Felgner PL. Distinct antibody responses of patients with mild and severe leptospirosis determined by whole proteome microarray analysis. PLoS Negl Trop Dis. 31;11(1):e0005349. doi: 10.1371/journal.pntd.0005349. (2017) PubMed 28141801

 

Hu CJ, Pan JB, Song G, Wen XT, Wu ZY, Chen S, Mo WX, Zhang FC, Qian J, Zhu H, Li YZ. Identification of Novel Biomarkers for Behcet Disease Diagnosis Using Human Proteome Microarray Approach. Mol Cell Proteomics. (2):147-156. doi: 10.1074/mcp.M116.061002. (2017) PubMed 27777341

 

DeMarshall CA, Nagele EP, Sarkar A, Acharya NK, Godsey G, Goldwaser EL, Kosciuk M, Thayasivam U, Han M, Belinka B, Nagele RG. Detection of Alzheimer’s disease at mild cognitive impairment and disease progression using autoantibodies as blood-based biomarkers. Alzheimers Dement (Amst). 3:51-62. (2016) PubMed 27239548

 

Yang L, Wang J, Li J, Zhang H, Guo S, Yan M, Zhu Z, Lan B, Ding Y, Xu M, Li W, Gu X, Qi C, Zhu H, Shao Z, Liu B, Tao SC. Identification of serum biomarkers for gastric cancer diagnosis using a human proteome microarray. Mol Cell Proteomics 15(2)614-23 (2016) PubMed 26598640

 

Anderson KS, Cramer DW, Sibani S, Wallstrom G, Wong J, Park J, Qiu J, Vitonis A, LaBaer J. Autoantibody signature for the serologic detection of ovarian cancer. J Proteome Res.14(1):578-86. (2015) PubMed 25365139

 

Hu C, Huang W, Chen H, Song G, Li P, Shan Q, Zhang X, Zhang F, Zhu H, Wu L, Li Y. Autoantibody profiling on human proteome microarray for biomarker discovery in cerebrospinal fluid and sera of neuropsychiatric lupus. PLoS One 10(5):e0126643 (2015) PubMed 25954975

 

REVIEW Tu S, Jiang HW, Liu CX, Zhou SM, Tao SC. Protein microarrays for studies of drug mechanisms and biomarker discovery in the era of systems biology. Curr Pharm Des 20:49-55 (2014) PubMed 23530501

 

Rho JH, Lampe PD. High-throughput screening for native autoantigen-autoantibody complexes using antibody microarrays. J Proteome Res. 12:2311-20 (2013) PubMed 23541305

 

REVIEW Yeste A, Quintana FJ. Antigen microarrays for the study of autoimmune diseases. Clin Chem 59:1036-44 (2013) PubMed 23487172

 

Ramirez AB, Lampe PD. Discovery and validation of ovarian cancer biomarkers utilizing high density antibody microarrays. Cancer Biomark 8:293-307 (2011) PubMed 22045360

 

Natesan M, Ulrich RG. Protein microarrays and biomarkers of infectious disease. Int J Mol Sci 11:5165-83 (2010) PubMed 21614200

 

Ramirez AB, Loch CM, Zhang Y, Liu Y, Wang X, Wayner EA, Sargent JE, Sibani S, Hainsworth E, Mendoza EA, Eugene R, Labaer J, Urban ND, McIntosh MW, Lampe PD. Use of a single-chain antibody library for ovarian cancer biomarker discovery. Mol Cell Proteomics 9:1449-60 (2010) PubMed 20467042

 

Chen CS, Sullivan S, Anderson T, Tan AC, Alex PJ, Brant SR, Cuffari C, Bayless TM, Talor MV, Burek CL, Wang H, Li R, Datta LW, Wu Y, Winslow RL, Zhu H, Li X. Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics 8:1765-76 (2009) PubMed 19357087

 

Scholler N, Gross JA, Garvik B, Wells L, Liu Y, Loch CM, Ramirez AB, McIntosh MW, Lampe PD, Urban N. Use of cancer-specific yeast-secreted in vivo biotinylated recombinant antibodies for serum biomarker discovery. J Transl Med. 6:41 (2008) PubMed 18652693

 

Loch CM, Ramirez AB, Liu Y, Sather CL, Delrow JJ, Scholler N, Garvik BM, Urban ND, McIntosh MW, Lampe PD. Use of high density antibody arrays to validate and discover cancer serum biomarkers. Mol Oncol 1:313-20 (2007) PubMed 19383305

 

Hudson ME, Pozdnyakova I, Haines K, Mor G, Snyder M. Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci USA 104:17494-9 (2007) PubMed 17954908

 

Antibody Specificity Profiling

 

Qi L, Zhou L, Lu M, Yuan K, Li Z, Wu G, Huang X, Shen Y, Zhao M, Fu W, Chu B, Wang G, Ren F, Ma D, Chen J. Development of a highly specific HER2 monoclonal antibody for immunohistochemistry using protein microarray chips. Biochem Biophys Res Commun.484(2):248-254. doi: 10.1016/j.bbrc.2017.01.086. (2017) PubMed 28111342

 

 

 

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