ProtoArray services and its associated products have been discontinued, information here is for reference.

ProtoArray microarrays are high-density, functional protein microarrays that enable rapid elucidation of protein interactions on a proteome scale. For your convenience, we have compiled references that describe applications of this powerful technology.

Pathogen Detection
  • Tribolet L et al. (2015) Probing of human proteome microarray with a recombinant pathogen protein reveals a novel mechanism by which hookworms suppress B-cell receptor signaling. J Infect Dis. 211: 416. 
  • Pugh C et al. (2014) Human Antibody Responses to the Polyclonal Dryvax Vaccine for Smallpox Prevention Can Be Distinguished from Responses to the Monoclonal Replacement Vaccine ACAM2000. Clin Vaccine Immunol. 21: 877.
  • Fernandez S et al. (2011) Antibody Recognition of the Dengue Virus Proteome and Implications for Development of Vaccines. Clin. Vaccine Immunol. 18: 523.
  • Keasey SL et al. (2009) Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis. Mol Cell Proteomics. 8: 924.
Immune Response Biomarker Profiling
  • Haseda F et al. (2016) Antibody to CMRF35-Like Molecule 2, CD300e A Novel Biomarker Detected in Patients with Fulminant Type 1 Diabetes. PLoS One. 11: e0160576. 
  • Meyer S et al. (2016) AIRE-Deficient Patients Harbor Unique High-Affinity Disease-Ameliorating Autoantibodies. Cell 166: 582. 
  • Sridharan V et al. (2016) Definitive chemoradiation alters the immunologic landscape and immune checkpoints in head and neck cancer. Br J Cancer 115: 252. 
  • Li Y et al. (2016) p27 is a Candidate Prognostic Biomarker and Metastatic Promoter in Osteosarcoma. Cancer Res. 76: 4002. 
  • DeMarshall CA et al. (2016) Detection of Alzheimer’s disease at mild cognitive impairment and disease progression using autoantibodies as blood-based biomarkers. Alzheimer’s & Dementia 3: 51. 
  • Chang DC et al. (2015) Use of a High-Density Protein Microarray to Identify Autoantibodies in Subjects with Type 2 Diabetes Mellitus and an HLA Background Associated with Reduced Insulin Secretion. PLoS One. 10:e0143551. 
  • DeMarshall CA et al. (2015) Potential utility of autoantibodies as blood-based biomarkers for early detection and diagnosis of Parkinson's disease. Immunol Lett. 168: 80. 
  • Furukawa H et al. (2015) Autoantibody Profiles in Collagen Disease Patients with Interstitial Lung Disease (ILD): Antibodies to Major Histocompatibility Complex Class I-Related Chain A (MICA) as Markers of ILD. Biomark Insights 10: 63. 
  • GuhaThakurta D et al. (2015) Humoral Immune Response against Nontargeted Tumor Antigens after Treatment with Sipuleucel-T and its Association with Improved Clinical Outcome. Clin Cancer Res. 21: 3619. 
  • Landegren N et al. (2015) Transglutaminase 4 as a prostate autoantigen in male subfertility. Sci Transl Med 7:292. 
  • Goto K et al. (2015) Identification of Cerebral Infarction-Specific Antibody Markers from Autoantibodies Detected in Patients with Systemic Lupus Erythematosus. J Mol Biomark Diagn. 6:219 
  • Antoine JC et al. (2015) Antifibroblast growth factor receptor 3 antibodies identify a subgroup of patients with sensory neuropathy. J Neurol Neurosurg Psychiatry. 86: 1347. 
  • Jackson AM et al (2015) Endothelial cell antibodies associated with novel targets and increased rejection. J Am Soc Nephrol. 26: 1161. 
  • Woo SH et al. (2015) Mapping Novel Immunogenic Epitopes in IgA Nephropathy. Clin J Am Soc Nephrol. 10: 372. 
  • Piesche M et al. (2015) Angiogenic cytokines are antibody targets during graft-versus-leukemia reactions. Clin Cancer Res. 21: 1010. 
  • Kinloch AJ et al. (2014) Vimentin is a dominant target of in situ humoral immunity in human lupus tubulointerstitial nephritis. Arthritis Rheumatol. 66: 3359. 
  • Kim SH et al. (2014) Autoimmunity as a Candidate for the Etiopathogenesis of Meniere's Disease: Detection of Autoimmune Reactions and Diagnostic Biomarker Candidate. PLoS One. 9: e111039. 
  • Delville M et al. (2014) A circulating antibody panel for pretransplant prediction of FSGS recurrence after kidney transplantation. Sci Transl Med 6: 256ra136 
  • Taguchi A et al. (2014) A Search for Novel Cancer/Testis Antigens in Lung Cancer Identifies VCX/Y Genes, Expanding the Repertoire of Potential Immunotherapeutic Targets. Cancer Res. 74: 4694. 
  • Kim YG et al. (2014) Role of Protein Phosphatase Magnesium-Dependent 1A and Anti-Protein Phosphatase Magnesium-Dependent 1A Autoantibodies in Ankylosing Spondylitis. Arthritis Rheumatol. 66: 2793. 
  • Hodi FS et al. (2014) Bevacizumab plus Ipilimumab in Patients with Metastatic Melanoma. Cancer Immunol Res. 2: 632. 
  • Koo BK et al. (2014) Identification of Novel Autoantibodies in Type 1 Diabetic Patients Using a High-Density Protein Microarray. Diabetes 63: 3022. 
  • Mias GI et al. (2014) Specific plasma autoantibody reactivity in myelodysplastic syndromes. Sci Rep. 3: 3311. 
  • Motts JA et al. (2014) Novel biomarkers of mercury-induced autoimmune dysfunction: A cross-sectional study in Amazonian Brazil. Eviron Res. 132C: 12-18. 
  • Bonsignori M et al. (2014) An autoreactive antibody from an SLE/HIV-1 individual broadly neutralizes HIV-1. J Clin Invest. 124: 1835-1843. 
  • Dema B et al. (2014) Autoreactive IgE Is Prevalent in Systemic Lupus Erythematosus and Is Associated with Increased Disease Activity and Nephritis. PLoS One. 9: e90424. 
  • May C et al. (2014) Highly Immunoreactive IgG Antibodies Directed against a Set of Twenty Human Proteins in the Sera of Patients with Amyotrophic Lateral Sclerosis Identified by Protein Array. PLoS One. 9: e89596. 
  • Hommel B et al. (2014) Chronic Malaria Revealed by a New Fluorescence Pattern on the Antinuclear Autoantibodies Test. PLoS One. 9: e88548. 
  • Beatty GL et al. (2014) Mesothelin-specific chimeric antigen receptor mRNA-engineered T cells induce anti-tumor activity in solid malignancies. Cancer Immunol Res. 2: 112. 
  • Mias GI et al. (2013) Specific Plasma Autoantibody Reactivity in Myelodysplastic Syndromes. Sci Rep 3: 3311. 
  • Querol L et al. (2013) Protein array-based profiling of CSF identifies RBPJ as an autoantigen in multiple sclerosis. Neurology. 81: 956-963. 
  • Nagele EP et al. (2013) Natural IgG autoantibodies are abundant and ubiquitous in human sera, and their number is influenced by age, gender, and disease. PLoS One. 8: e60726. 
  • Sidgel T et al. (2013) Immune response profiling identifies autoantibodies specific to Moyamoya patients. Orphanet J Rare Dis. 8: 45. 
  • Néron S and Roy A (2012) Overview of IgG-Reactivity in Therapeutic immunoglobulins Revealed by Protein Array Analysis. Biochem Anal Biochem S8: 001. 
  • Ghevaria N et al. (2012) Quality control for a large-scale study using protein arrays and protein beads to measure immune response in serum and plasma. Proteomics 12: 2802-2807.
  • Sidgel et al. (2012) Non-HLA Antibodies to Immunogenic Epitopes Predict the Evolution of Chronic Renal Allograft Injury. J Am Soc Nephrol. 23: 750-763.
  • Chen R et al. (2012) Personalized Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes. Cell 148: 1293-1307.
  • Liu M et al. (2012) Immune responses to self-antigens in asthma patients: clinical and immunopathological implications. Hum Immunol. 73: 511-516.
  • Postow MA et al. (2012) Immunologic correlates of the abscopal effect in a patient with melanoma. NEJM. 366: 925-931.
  • Han M et al. (2012) Diagnosis of Parkinson’s disease based on disease-specific autoantibody profiles in human sera. PLoS One. 7: e32383.
  • Mangé A et al. (2012) Serum autoantibody signature of ductal carcinoma in situ progression to invasive breast cancer. Clin Cancer Res. 18: 1992-2000.
  • Wood JD et al. (2012) Anti-Enteric Neuronal Antibodies and the Irritable Bowel Syndrome. J Neurogastroenterol Motil. 18: 78-85.
  • Biernacki MA et al. (2012) Novel myeloma-associated antigens revealed in the context of syngeneic
  • hematopoietic stem cell transplantation. Blood. 119: 3142-3150.
  • Sigdel TK et al. (2011) Profiling of Autoantibodies in IgA Nephropathy, an Integrative Antibiomics Approach. Clin J Am Soc Nephrol. 6: 2775-2784.
  • Jansen FH et al. (2011) Profiling of antibody production against xenograft-released proteins by protein microarrays discovers prostate cancer markers. J. Proteome Res. 11: 728-735.
  • Winer DA et al. (2011) B cells promote insulin resistance through modulation of T cells and production of pathogenic IgG antibodies. Nat. Med 17: 610-618.
  • Hu S et al. (2011) Identification of autoantibody biomarkers for primary Sjögren’s syndrome using protein microarrays. Proteomics. 11: 1499-1507.
  • Nagele E et al. (2011) Diagnosis of Alzheimer's disease based on disease-specific autoantibody profiles in human sera. PLoS One. 6: e23112.
  • Dinavahi R et al. (2011) Antibodies reactive to non-HLA antigens in transplant glomerulopathy. J Am Soc Nephrol. 22: 1168-1178.
  • Vermeulen N et al. (2011) Identification of a novel autoantigen in inflammatory bowel disease by a protein microarray. Inflamm Bowel Dis. 17: 1291-1300.
  • Butte AJ et al. (2011) Protein Microarrays Discover Angiotensinogen and PRKRIP1 as Novel Targets for Autoantibodies in Chronic Renal Disease. Mol Cell Proteomics. 10: M110.000497.
  • Gnjatic S et al. (2010) Seromic profiling of ovarian and pancreatic cancer. Proc. Natl. Acad. Sci. USA, 107: 5088–5093.
  • Le Roux S et al. (2010) Biomarkers for the Diagnosis of the Stable Kidney Transplant and Chronic Transplant Injury Using the ProtoArray® Technology. Transplant Proc. 42: 3475-3481
  • Nguyen MC et al. (2010) Antibody responses to galectin-8, TARP and TRAP1 in prostate cancer patients treated with a GM-CSF-secreting cellular immunotherapy. Cancer Immunol Immunother. 59:1313-1323.
  • Porcheray F et al. (2010) Chronic Humoral Rejection of Human Kidney Allografts Associates With Broad Autoantibody Responses. Transplantation. 89: 1239-1246.
  • Jarius S et al. (2010) A new Purkinje cell antibody (anti-Ca) associated with subacute cerebellar ataxia: immunological characterization. J Neuroinflammation. 7: 21.
  • Orenes-Piñero E et al. (2010) Serum and Tissue Profiling in Bladder Cancer Combining Protein and Tissue Arrays. J Proteome Res. 9: 164-173.
  • Marina O et al. (2010) Serologic Markers of Effective Tumor Immunity against Chronic Lymphocytic Leukemia Include Nonmutated B-Cell Antigens. Cancer Res. 70: 1344-1355.
  • Li L et al. (2010) Compartmental Localization and Clinical Relevance of MICA Antibodies After Renal Transplantation. Transplantation. 89: 312-319.
  • Wadia PP et al. (2010) Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. Blood. 115: 2077-2087.
  • Biernacki MA et al. (2010) Efficacious immune therapy in chronic myelogenous leukemia (CML) recognizes antigens that are expressed on CML progenitor cells. Cancer Res. 70: 906–915.
  • Schweitzer B et al. (2010) Immune response biomarker profiling application on ProtoArray protein microarrays. Methods Mol Biol. 641:243-52.
  • Babel I et al. (2009) Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays. Mol Cell Proteomics. 8: 2382–2395.
  • Sutherland SM et al. (2009) Protein microarrays identify antibodies to protein kinase Cζ that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Kidney Int. 76: 1277–1283.
  • Li L et al. (2009) Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and “antibodyome” measures. Proc Natl Acad Sci USA. 106: 4148–4153.
  • Auger I et al. (2009) New autoantigens in rheumatoid arthritis: screening 8268 protein arrays with RA patients’ sera. Ann Rheum Dis. 68: 591–594.
  • Gunawardana CG et al. (2009) Identifying novel autoantibody signatures in ovarian cancer using high-density protein microarrays. Clin Biochem. 42: 426–429.
  • Gnjatic S et al. (2009) Seromic analysis of antibody responses in non-small cell lung cancer patients and healthy donors using conformational protein arrays. J Immunol Methods. 341: 50–58.
  • Roche S et al. (2008) Autoantibody profiling on high-density protein microarrays for biomarker discovery in the cerebrospinal fluid. J Immunol Methods. 338: 75-78.
  • Hudson ME et al. (2007) Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci USA. 104: 17494-17499.
  • Lubomirski M et al. (2007) A consolidated approach to analyzing data from high-throughput protein microarrays with an application to immune response profiling in humans. J Comput Biol. 14: 350-359.
  • Lalive PH et al. (2006) Identification of new serum autoantibodies in neuromyelitis optica using protein microarrays. Neurology. 67: 176-177.
  • Mattoon D et al. (2005) Biomarker discovery using protein microarray technology platforms: Antibody-antigen complex profiling. Expert Rev Proteomics. 2: 879-889.
Protein-Protein Interactions
  • Keasey SL et al. (2016) Cell-free determination of binary complexes that comprise extended protein-protein interaction networks of Yersinia pestis. Mol Cell Proteomics. 15: 3220. 
  • Herling TW et al. (2016) A Microfluidic Platform for Real-Time Detection and Quantification of Protein-Ligand Interactions. Biophys J. 110: 1957. 
  • Dunning CJ et al. (2016) Direct High Affinity Interaction between Ab42 and GSK3a Stimulates Hyperphosphorylation of Tau. A New Molecular Link in Alzheimer's Disease? ACS Chem Neurosci. 7: 161. 
  • Ho JC et al. (2016) Targeting of nucleotide-binding proteins by HAMLET-a conserved tumor cell death mechanism. Oncogene. 35: 897. 
  • Müller J et al (2015) TRIM21, a negative modulator of LFG in breast carcinoma MDA-MB-231 cells in vitro. Int J Oncol. 47: 1634. 
  • Lu WJ et al (2015) NDRG1 promotes growth of hepatocellular carcinoma cells by directly interacting with GSK-3b and Nur77 to prevent b-catenin degradation. Oncotarget 6: 29847. 
  • Chua HH et al. (2015) RBMY, a novel inhibitor of GSK3b, increases tumor stemness and predicts poor prognosis of hepatocellular carcinoma. Hepatology 62: 1480. 
  • Burgardt NI et al. (2015) Parvulin 17-catalyzed Tubulin Polymerization Is Regulated by Calmodulin in a Calcium-dependent Manner. J Biol Chem 290: 16708. 
  • Beilina A et al (2014) Unbiased screen for interactors of leucine-rich repeat kinase 2 supports a common pathway for sporadic and familial Parkinson disease. PNAS 111(7): 2626-2631. 
  • Reyniers L et al. (2014) Differential protein-protein interactions of LRRK1 and LRRK2 indicate roles in distinct cellular signaling pathways. J Neurochem.131: 239-50.
  • Abd El Kader T et al. (2014) Direct interaction between CCN family protein 2 and fibroblast growth factor 1. J Cell Commun Signal. 8: 157-163. 
  • Lalioti VS et al. (2014) Sorcin Links Calcium Signaling to Vesicle Trafficking, Regulates Polo-Like Kinase 1 and Is Necessary for Mitosis. PLOS One 9: e85438. 
  • Miyajima M et al. (2013) Leucine-Rich α2-Glycoprotein Is a Novel Biomarker of Neurodegenerative Disease in Human Cerebrospinal Fluid and Causes Neurodegeneration in Mouse Cerebral Cortex. PLoS One 8: e77453. 
  • Tsuru M et al. (2013) Proline/arginine-rich end leucine-rich repeat protein converts stem cells to ligament tissue and Zn(II) influences its nuclear expression. Stem Cells Dev. 22: 2057 
  • Chen TC et al. (2013) Protein Phosphorylation Profiling Using an In Situ Proximity Ligation Assay: Phosphorylation of AURKA-Elicited EGFR-Thr654 and EGFR-Ser1046 in Lung Cancer Cells. PLoS One 8: e55657. 
  • Ngo HT et al. (2013) Modulation of mitogen-activated protein kinase-activated protein kinase 3 by hepatitis C virus core protein. J Virol. 87: 5718-5731. 
  • Binder M et al. (2013) CLL B-cell receptors can recognize themselves: alternative epitopes and structural clues for autostimulatory mechanisms in CLL. Blood 121: 239-241. 
  • Pitek AS et al. (2012) Transferrin Coated Nanoparticles: Study of the Bionano Interface in Human Plasma. PLoS One 7: e40685.
  • Meehan M et al. (2012) Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase oncogene. Mol Cancer. 11: 6.
  • Storm P et al. (2011) Conserved features of cancer cells define their sensitivity to HAMLET-induced death; c-Myc and glycolysis. Oncogene. 30: 4765–4779.
  • De Denato M et al. (2011) Class III β-tubulin and the cytoskeletal gateway for drug resistance in ovarian cancer. J Cell Physiol. 227: 1034-1041.
  • Babij C et al. (2011) STK33 kinase activity is nonessential in KRAS-dependent cancer cells. Cancer Res. 71: 5818-5826.
  • Lee HK et al. (2011) Odontogenic ameloblasts-associated protein (ODAM), via phosphorylation by bone morphogenetic protein receptor type IB (BMPR–IB), is implicated in ameloblast differentiation. J Cell Biochem. 113: 1754-1765.
  • Virok DP et al. (2011) Protein Array Based Interactome Analysis of Amyloid-β Indicates an Inhibition of Protein Translation. J. Proteome Res. 10: 1538–1547.
  • Wu YY et al. (2011) SCUBE3 is an endogenous TGF-b receptor ligand and regulates the epithelial-mesenchymal transition in lung cancer. Oncogene 30: 3682–3693.
  • Analysis Of LNX1 Interacting Proteins. PLoS One 6: e26248.
  • Echtenkamp FJ et al. (2011) Global Functional Map of the p23 Molecular Chaperone Reveals an Extensive Cellular Network. Molecular Cell 43: 229–241. 10. Bauer M et al. (2011) Protein networks involved in vesicle fusion, transport, and storage revealed by array-based proteomics. Methods Mol Biol. 781: 47-58.
  • Olah J et al. (2011) Interactions of Pathological Hallmark Proteins: Tubulin Polymerization Promoting protein/p25, β-Amyloid, and α-Synuclein. J Biol Chem. 286: 34088-34100.
  • Li D et al (2011) Binding of Lactoferrin to IGBP1 Triggers Apoptosis in a Lung Adenocarcinoma Cell Line. Anticancer Res. 31: 529-534.
  • Al-Mulla F et al (2011) Raf Kinase Inhibitor Protein RKIP Enhances Signaling by Glycogen Synthase Kinase-3 β. Cancer Res. 71: 1334-1343.
  • Morikawa H et al. (2010) The bacterial effector Cif interferes with SCF ubiquitin ligase function by inhibiting deneddylation of Cullin1. Biochem Biophys Res Commun. 401: 268-274.
  • Paidas MJ et al. (2010) A genomic and proteomic investigation of the impact of preimplantation factor on human decidual cells. Am J Obstet Gynecol. 202:459.e1-8.
  • Sumiyoshi K et al. (2010) Protein microarray analysis identifies cyclic nucleotide phosphodiesterase as an interactor of Nogo-A. Neuropathology. 30: 7–14.
  • Fenner BJ et al. (2010) Expanding the Substantial Interactome of NEMO Using Protein Microarrays. PLoS One. 5: e8799.
  • Tong Y et al. (2008) Pituitary tumor transforming gene 1 regulates Aurora kinase A activity. Oncogene. 27: 6385–6395.
  • Schnack C et al. (2008) Protein array analysis of oligomerization-induced changes in alpha-synuclein protein-protein interactions points to an interference with Cdc42 effector proteins. Neuroscience. 154: 1450–1457.
  • Li Z. et al. (2008). Cdc34p ubiquitin-conjugating enzyme is a component of the tombusvirus replicase complex and ubiquitinates p33 replication protein. J Virol. 82: 6911-6926.
  • Satoh J et al. (2008). Protein microarray analysis identifies human cellular prion protein interactors. Neuropathol Appl Neurobiol. 35: 16–35.
  • Poltermann S et al. (2007) Gpm1p is a Factor H-, FHL-1-, and plasminogen-binding surface protein of Candida albicans. J Biol Chem. 282: 37537-37544.
  • Salamat-Miller N et al. (2007) A network-based analysis of polyanion-binding proteins utilizing human protein arrays. J Biol Chem. 282: 10153-10163.
  • Satoh J et al. (2006) Rapid identification of 14-3-3-binding proteins by protein microarray analysis. J Neurosci Methods. 152: 278-288.
  • Salamat-Miller N et al. (2006) A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays. Mol Cell Proteomics. 5: 2263-2278.
  • Jin F. et al. (2006) A pooling-deconvolution strategy for biological network elucidation. Nat Methods. 3: 183-189.
  • Hesselberth J et al. (2006) Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biol. 7: R30.
Kinase Substrate Interactions
  • Guen VJ et al (2016) STAR syndrome-associated CDK10/Cyclin M regulates actin network architecture and ciliogenesis. Cell Cycle 15: 678. 
  • Schneider P et al. (2015) Identification of a novel actin-dependent signal transducing module allows for the targeted degradation of GLI1. Nat Commun. 6: 8023. 
  • Dwyer SF et al. (2015) Identification of novel focal adhesion kinase substrates: role for FAK in NFkB signaling. Int J Biol Sci. 11: 404. 
  • Pham TH et al. (2013) Escherichia coli Virulence Protein NleH1 Interaction with the v-Crk Sarcoma Virus CT10 Oncogene-like Protein (CRKL) Governs NleH1 Inhibition of the Ribosomal Protein S3 (RPS3)/Nuclear Factor κB (NF-κB) Pathway. J Biol Chem 288: 34567-34574. 
  • Duong MT et al. (2013) Hbo1 is a cyclin E/CDK2 substrate that enriches breast cancer stem-like cells. Cancer Res. 73: 5556. 
  • Radu M et al. (2013) ArhGAP15, a Rac-specific GTPase-activating protein, plays a dual role in inhibiting small GTPase signaling. J Biol Chem 288: 21117.
  • Kinuka I et al. (2012) cGMP-dependent protein kinase I promotes cell apoptosis through hyperactivation of death-associated protein kinase 2. Biochem and Biophys Res Commun. 422: 2.
  • Kottom TJ and Limper AH. (2011) Substrate analysis of the Pneumocystis carinii protein kinases PcCbk1 and PcSte20 using yeast proteome microarrays provides a novel method for Pneumocystis signalling biology. Yeast. 10: 707-719.
  • De la Mota-Peynado A et al. (2011) Identification of the atypical MAPK Erk3 as a novel substrate for p21-activated kinase (Pak) activity. J Biol Chem. 286: 13603-13611.
  • Schnack C et al. (2008). Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high-density protein microarrays. Proteomics. 8: 1980-1986.
  • Meng L et al. (2008) Protein kinase substrate identification on functional protein arrays. BMC Biotechnol. 8: 22.
  • Boyle SN et al. (2007) A critical role for cortactin phosphorylation by Abl-family kinases in PDGF-induced dorsalwave formation. Curr Biol. 17: 1.
  • Ptacek J et al. (2005) Global analysis of protein phosphorylation in yeast. Nature. 438: 679-684.
  • Mah A et al. (2005) Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening. BMC Biochem. 6: 22.
Antibody Specificity Profiling
  • Brändle SM et al. (2016) Distinct oligoclonal band antibodies in multiple sclerosis recognize ubiquitous self-proteins. Proc Natl Acad Sci. 113: 7864. 
  • Bradley T et al. (2016) Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site. Cell Rep. 14: 43.
  • Chaturvedi S et al. (2015) Development and validation of panoptic Meso scale discovery assay to quantify total systemic interleukin-6. Br J Clin Pharmacol. 80: 687. 
  • Montesinos-Rongen M et al. (2015) Primary Central Nervous System (CNS) Lymphoma B Cell Receptors Recognize CNS Proteins. J Immunol 195: 1312. 
  • Hong SH et al (2015) The antibody atliximab attenuates collagen-induced arthritis by neutralizing AIMP1, an inflammatory cytokine that enhances osteoclastogenesis. Biomaterials 44: 45. 
  • Yang G et al. (2013) Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies. J Exp Med 210: 241-256. Néron S et al. (2013) Large-Scale In Vitro Expansion of Polyclonal Human Switched-Memory B Lymphocytes PLoS One 7: e51946.
  • Stafford P et al. (2012) Physical Characterization of the “Immunosignaturing Effect”. Mol Cell Proteomics 11: M111.011593.
  • Diehnelt CW et al. (2010) Discovery of High-Affinity Protein Binding Ligands – Backwards. PLoS One. 5: e10728.
  • Predki PF et al. (2005) Protein microarrays: A new tool for profiling antibody cross-reactivity. Hum Antibodies. 14: 7.
  • Bangham R et al. (2005) Protein microarray-based screening of antibody specificity. Methods Mol Med. 114: 173.
  • Michaud GA et al. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol. 21: 1509.
Small Molecule Interactions
  • Hett EC et al. (2016) Selectivity determination of a small molecule chemical probe using protein microarray and affinity capture techniques. ACS Comb Sci. 18: 611. 
  • Tomita T et al. (2014) ZFC3H1, a zinc finger protein, modulates IL-8 transcription by binding with celastramycin A, a potential immune suppressor. PLoS One 9: e108957. 
  • Zhao J et al. (2014) Antitumor activity of FL118, a survivin, Mcl-1, XIAP, and cIAP2 selective inhibitor, is highly dependent on its primary structure and steric configuration. Mol Pharm. 11: 457.
  • To C et al. (2010) Synthetic Triterpenoids Target the ARP2/3 Complex and Inhibit Branched Actin Polymerization. JBC. 285: 27944.
  • Conrad A et al. (2010) Proteomic Analysis of Potential Keratan Sulfate, Chondroitin Sulfate A, and Hyaluronic Acid Molecular Interactions. Invest Ophthalmol Vis Sci. 51: 4500.
  • Singh J et al. (2008) DcpS as a therapeutic target for spinal muscular atrophy. ACS Chem Biol. 3: 711.
Post Translation Modification Profiling
  • Teixeira FR et al. (2016) Gsk3b and Tomm20 are substrates of the SCFFbxo7/PARK15 ubiquitin ligase associated with Parkinson's disease. Biochem J. 473: 3563. 
  • Reynoird N et al. (2016) Coordination of stress signals by the lysine methyltransferase SMYD2 promotes pancreatic cancer. Genes Dev. 30: 772. 
  • Pineda CT et al. (2015) Degradation of AMPK by a Cancer-Specific Ubiquitin Ligase. Cell 160: 715-728. 
  • Charlaftis N et al. (2014) The MEKK1 PHD ubiquitinates TAB1 to activate MAPKs in response to cytokines. EMBO J. 33: 2581. 
  • Acebron SP et al. (2014) Mitotic Wnt signaling promotes protein stabilization and regulates cell size. Mol Cell. 54: 663. 
  • Mazur PK et al. (2014) SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Nature. 510: 283. 
  • Paolino M et al. (2014) The E3 ligase Cbl-b and TAM receptors regulate cancer metastasis via natural killer cells. Nature. 507: 508. 
  • Teixeira FR et al. (2013) The F-box protein FBXO25 promotes the proteasome-dependent degradation of ELK-1. J Biol Chem. 288: 28152.
  • Levy D et al. (2011) A proteomic approach for the identification of novel lysine methyltransferase substrates. Epigenetics & Chromatin. 4: 19.
  • Loch CM et al. (2011) Protein Microarrays for the Identification of Praja1 E3 Ubiquitin Ligase Substrates Cell Biochem Biophys. 60: 127.
  • Troiani S et al. (2011) Identification of candidate substrates for Poly(ADP-ribose) polymerase-2 (PARP2) in the absence of DNA damage using high-density protein microarrays. FEBS J. 278: 3676.
  • Rincón et al. (2010) Development and Validation of a Method for Profiling Post-Translational Modification Activities Using Protein Microarrays. PLoS One. 5: e11332.
  • Merbl Y and Kirschner MW. (2009) Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. Proc Natl Acad Sci USA. 106: 2543.
  • Tao et al. (2009) Studies of the Expression of Human Poly(ADP-ribose) Polymerase-1 in Saccharomyces cerevisiae and Identification of PARP-1 Substrates by Yeast Proteome Microarray Screening. Biochemistry 48: 11745.
  • Lin Y et al. (2009) Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136: 1073.
  • Gupta R. et al. (2007) Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Systems Biol. 3: 1.
DNA/RNA-Protein Interactions
  • Kakiuchi-Kiyota S et al. (2016) Development of a Method for Profiling Protein Interactions with LNA-Modified Antisense Oligonucleotides Using Protein Microarrays. Nucleic Acid Ther. 26: 93. 
  • Durruthy-Durruthy J et al. (2016) The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming. Nat Genet. 48: 44. 
  • Siprashvili Z et al. (2016) The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nat Genet. 48: 53. 
  • Howarth M et al. (2014) Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis. J Clin Invest 124: 5275. 
  • Kretz M et al. (2013) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 493: 231. 
  • Siprashvili Z et al. (2012) Identification of proteins binding coding and non-coding human RNAs using protein microarrays. BMC Genomics 13: 633.
  • Scherrer T et al (2010) A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PLoS One. 5: e15499.
  • Hu S et al. (2009) Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling. Cell. 139: 610.
  • Hall D. et al. (2004) Regulation of gene expression by a metabolic enzyme. Science. 306: 482.
Reviews
  • Ayoglu B et al. (2016) Antigen arrays for profiling autoantibody repertoires. Bioanalysis 8: 1105. 
  • Yuan J et al. (2016) Immune Monitoring Technology Primer: protein microarray ('seromics'). J Immunother Cancer 4: 2. 
  • Yuan J et al. (2016) Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer 4: 3. 
  • Gallardo E et al (2014) Cortactin Autoantibodies in Myasthenia Gravis. Autoimmun Rev. 13: 1003. 
  • Vivelo CA and Leung AK. (2014) Proteomics approaches to identify mono(ADP-ribosyl)ated and poly(ADP-ribosyl)ated proteins. Proteomics. 15: 203. 
  • Sutandy FX et al (2014) High throughput platform to explore RNA-protein interactomes. Crit Rev Biotechnol. 15: 1. 
  • Carlson SM and Gozani O. (2014) Emerging Technologies to Map the Protein Methylome. J Mol Bio. S0022-2836(14)00223-X.
  • Luo M. (2012) Current Chemical Biology Approaches to Interrogate Protein Methyltransferases. ACS Chem Biol. 7: 443.
  • DesMetz C et al. (2011) Autoantibody signatures: progress and perspectives for early cancer detection.J Cell Mol Med. 15: 2013.
  • Yang L et al. (2011) Protein microarrays for systems biology. Acta Biochim Biophys. Sin 43: 161–171.
  • Martin K et al (2011) Exploring the Immunoproteome for Ovarian Cancer Biomarker Discovery Int. J. Mol. Sci. 12: 410.
  • Vaughan R and Sacks S. (2010) Genomics in human renal transplantation. Curr Opin Immunol. 22: 689.
  • Wu T et al. (2010) Biomarkers of rheumatoid arthritis: recent progress. Exp Op Med Diag. 4: 293.
  • Naesens M and Sarwal MM. (2010) Molecular Diagnostics in Transplantation. Nat Rev Nephrol. 6: 614.
  • Michaud GA et al. (2006) Functional protein arrays to facilitate drug discovery and development. IDrugs. 9: 266.
  • Michaud GA et al. (2006) Applications of protein arrays for small molecule drug discovery and characterization. Biotechnol Genet Eng Rev. 22: 197.
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  • Predki PF (2004) Functional protein microarrays: Ripe for discovery. Curr Opin Chem Biol. 8: 8.
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  • Michaud GA and Snyder M (2002) Proteomic approaches for the global analysis of proteins. Biotechniques. 33: 1308.
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Book Chapters
  • DeMarshall C et al. (2015) Utility of Autoantibodies as Biomarkers for Diagnosis and Staging of Neurodegenerative Diseases. In M. Hurley (ed.), International Review of Neurobiology, Omic Studies of Neurodegenerative Disease,vol. 122 (pp 1-51) .
  • DeLuca DS, Marina O, Ray S, Zhang GL, Wu CJ, and Brusic V (2011) Data Processing and Analysis for Protein Microarrays. In Catherine J. Wu (ed.), Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, vol. 723 (pp 337-347) Springer Science+Business Media.
  • Smith MG, Ptacek J, & Snyder M (2011) Kinase Substrate Interactions. In Catherine J. Wu (ed.), Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, vol. 723 (pp 201-212) Springer Science+Business Media.
  • Wadia PP, Sahaf B, & Miklos DB (2011) Recombinant Antigen Microarrays for Serum/Plasma Antibody Detection. In Catherine J. Wu (ed.), Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, vol. 723 (pp 81-104) Springer Science+Business Media.
  • Persaud A & Rotin D (2011) Use of Proteome Arrays to Globally Identify Substrates for E3 Ubiquitin Ligases. In Castrillo JI & Oliver SG (eds.), Yeast Systems Biology, Methods in Molecular Biology, vol 759 (pp 215-224) Springer Science+Business Media.

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