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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title Author Journal Name PubMedID Journal Abbreviation Publication Date
CDR-H3 diversity is not required for antigen recognition by synthetic antibodies. Persson H, Ye W, Wernimont A, Adams JJ, Koide A, Koide S, Lam R, Sidhu SS Journal of molecular biology 23219464 J Mol Biol 2013 Feb 22
Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S PloS one 26437229 PLoS One 2015
A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J Molecular & cellular proteomics : MCP 26290498 Mol Cell Proteomics 2015 Oct
A roadmap to generate renewable protein binders to the human proteome. Colwill K, Renewable Protein Binder Working Group, Gräslund S Nature methods 21572409 Nat Methods 2011 May 15
Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Paduch M, Koide A, Uysal S, Rizk SS, Koide S, Kossiakoff AA Methods (San Diego, Calif.) 23280336 Methods 2013 Mar 15
Applications for an engineered Protein-G variant with a pH controllable affinity to antibody fragments. Bailey LJ, Sheehy KM, Hoey RJ, Schaefer ZP, Ura M, Kossiakoff AA Journal of immunological methods 25450256 J Immunol Methods 2014 Dec 15
Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Sun J, Paduch M, Kim SA, Kramer RM, Barrios AF, Lu V, Luke J, Usatyuk S, Kossiakoff AA, Tan S Proceedings of the National Academy of Sciences of the United States of America 30224453 Proc Natl Acad Sci U S A 2018 Oct 2
Generating Conformation and Complex-Specific Synthetic Antibodies. Paduch M, Kossiakoff AA Methods in molecular biology (Clifton, N.J.) 28255876 Methods Mol Biol 2017
Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis. Pan Y, Sackmann EK, Wypisniak K, Hornsby M, Datwani SS, Herr AE Scientific reports 28008969 Sci Rep 2016 Dec 23
An improved single-chain Fab platform for efficient display and recombinant expression. Koerber JT, Hornsby MJ, Wells JA Journal of molecular biology 25481745 J Mol Biol 2015 Jan 30
A New Versatile Immobilization Tag Based on the Ultra High Affinity and Reversibility of the Calmodulin-Calmodulin Binding Peptide Interaction. Mukherjee S, Ura M, Hoey RJ, Kossiakoff AA Journal of molecular biology 26159704 J Mol Biol 2015 Aug 14
A polar ring endows improved specificity to an antibody fragment. Schaefer ZP, Bailey LJ, Kossiakoff AA Protein science : a publication of the Protein Society 27334407 Protein Sci 2016 Jul
The NIH Protein Capture Reagents Program (PCRP): a standardized protein affinity reagent toolbox. Blackshaw S, Venkataraman A, Irizarry J, Yang K, Anderson S, Campbell E, Gatlin CL, Freeman NL, Basavappa R, Stewart R, Loss MA, Pino I, Zhu H, Bader JS Nature methods 27684578 Nat Methods 2016 Sep 29
Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions. Oyinlade O, Wei S, Kammers K, Liu S, Wang S, Ma D, Huang ZY, Qian J, Zhu H, Wan J, Xia S Epigenetics 30058478 Epigenetics 2018
Overview of protein microarrays. Sutandy FX, Qian J, Chen CS, Zhu H Current protocols in protein science 23546620 Curr Protoc Protein Sci 2013 Apr
Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration. Wan J, Su Y, Song Q, Tung B, Oyinlade O, Liu S, Ying M, Ming GL, Song H, Qian J, Zhu H, Xia S eLife 28553926 Elife 2017 May 29
New centromere autoantigens identified in systemic sclerosis using centromere protein microarrays. Song G, Hu C, Zhu H, Wang L, Zhang F, Li Y, Wu L The Journal of rheumatology 23418382 J Rheumatol 2013 Apr
Toward a systems-level view of dynamic phosphorylation networks. Newman RH, Zhang J, Zhu H Frontiers in genetics 25177341 Front Genet 2014
DNA methylation presents distinct binding sites for human transcription factors. Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho HS, Woodard C, Xia S, Liu S, Lyu H, Ming GL, Wade H, Song H, Qian J, Zhu H eLife 24015356 Elife 2013 Sep 3
Interactome mapping: using protein microarray technology to reconstruct diverse protein networks. Uzoma I, Zhu H Genomics, proteomics & bioinformatics 23395178 Genomics Proteomics Bioinformatics 2013 Feb
Construction of human activity-based phosphorylation networks. Newman RH, Hu J, Rho HS, 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 AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J Molecular systems biology 23549483 Mol Syst Biol 2013
VirD: a virion display array for profiling functional membrane proteins. Hu S, Feng Y, Henson B, Wang B, Huang X, Li M, Desai P, Zhu H Analytical chemistry 23941274 Anal Chem 2013 Sep 3
Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP. Mita P, Lhakhang T, Li D, Eichinger DJ, Fenyo D, Boeke JD Biological procedures online 27528826 Biol Proced Online 2016
Characterization of monoclonal antibody's binding kinetics using oblique-incidence reflectivity difference approach. Liu S, Zhang H, Dai J, Hu S, Pino I, Eichinger DJ, Lyu H, Zhu H mAbs 25530170 MAbs 2015
Antibody Specificity Profiling Using Protein Microarrays. Ramos-López P, Irizarry J, Pino I, Blackshaw S Methods in molecular biology (Clifton, N.J.) 29714021 Methods Mol Biol 2018
Targeting UDP-α-D-glucose 6-dehydrogenase inhibits glioblastoma growth and migration. Oyinlade O, Wei S, Lal B, Laterra J, Zhu H, Goodwin CR, Wang S, Ma D, Wan J, Xia S Oncogene 29479058 Oncogene 2018 May
Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu J, Hu S, Vera C, Bayron-Poueymiroy D, Rivera-Pacheco ZA, Ramos L, Torres-Castro C, Qian J, Bonaventura J, Boeke JD, Yap WY, Pino I, Eichinger DJ, Zhu H, Blackshaw S Molecular & cellular proteomics : MCP 22307071 Mol Cell Proteomics 2012 Jun
Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. Zhu H, Cox E, Qian J Proteomics. Clinical applications 23027439 Proteomics Clin Appl 2012 Dec
Integrin-mediated protein kinase A activation at the leading edge of migrating cells. Lim CJ, Kain KH, Tkachenko E, Goldfinger LE, Gutierrez E, Allen MD, Groisman A, Zhang J, Ginsberg MH Molecular biology of the cell 18784251 Mol Biol Cell 2008 Nov
PhosphoNetworks: a database for human phosphorylation networks. Hu J, Rho HS, Newman RH, Zhang J, Zhu H, Qian J Bioinformatics (Oxford, England) 24227675 Bioinformatics 2014 Jan 1
A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S Nature methods 29638227 Nat Methods 2018 May
Label-free, real-time detection of the dynamic processes of protein degradation using oblique-incidence reflectivity difference method. Liu S, Zhu JH, He LP, Dai J, Lu HB, Wu L, Jin KJ, Yang GZ, Zhu H Applied physics letters 24803682 Appl Phys Lett 2014 Apr 21
A human proteome microarray identifies that the heterogeneous nuclear ribonucleoprotein K (hnRNP K) recognizes the 5' terminal sequence of the hepatitis C virus RNA. Fan B, Lu KY, Reymond Sutandy FX, Chen YW, Konan K, Zhu H, Kao CC, Chen CS Molecular & cellular proteomics : MCP 24113282 Mol Cell Proteomics 2014 Jan
Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction. Hu J, Neiswinger J, Zhang J, Zhu H, Qian J PLoS computational biology 26393507 PLoS Comput Biol 2015
YcgC represents a new protein deacetylase family in prokaryotes. Tu S, Guo SJ, Chen CS, Liu CX, Jiang HW, Ge F, Deng JY, Zhou YM, Czajkowsky DM, Li Y, Qi BR, Ahn YH, Cole PA, Zhu H, Tao SC eLife 26716769 Elife 2015 Dec 30
Applications in high-content functional protein microarrays. Moore CD, Ajala OZ, Zhu H Current opinion in chemical biology 26599287 Curr Opin Chem Biol 2016 Feb
Large scale production of phage antibody libraries using a bioreactor. Ferrara F, Kim CY, Naranjo LA, Bradbury AR mAbs 25524379 MAbs 2015
Specific binder for Lightning-Link® biotinylated proteins from an antibody phage library. Ferrara F, Naranjo LA, D'Angelo S, Kiss C, Bradbury AR Journal of immunological methods 23850993 J Immunol Methods 2013 Sep 30
Deep sequencing in library selection projects: what insight does it bring? Glanville J, D'Angelo S, Khan TA, Reddy ST, Naranjo L, Ferrara F, Bradbury AR Current opinion in structural biology 26451649 Curr Opin Struct Biol 2015 Aug
From deep sequencing to actual clones. D'Angelo S, Kumar S, Naranjo L, Ferrara F, Kiss C, Bradbury AR Protein engineering, design & selection : PEDS 25183780 Protein Eng Des Sel 2014 Oct
Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding. D'Angelo S, Ferrara F, Naranjo L, Erasmus MF, Hraber P, Bradbury ARM Frontiers in immunology 29568296 Front Immunol 2018
The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires. D'Angelo S, Glanville J, Ferrara F, Naranjo L, Gleasner CD, Shen X, Bradbury AR, Kiss C mAbs 24423623 MAbs 2014 Jan-Feb
Recombinant renewable polyclonal antibodies. Ferrara F, D'Angelo S, Gaiotto T, Naranjo L, Tian H, Gräslund S, Dobrovetsky E, Hraber P, Lund-Johansen F, Saragozza S, Sblattero D, Kiss C, Bradbury AR mAbs 25530082 MAbs 2015
An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network. Jha RK, Gaiotto T, Bradbury AR, Strauss CE Protein engineering, design & selection : PEDS 24632761 Protein Eng Des Sel 2014 Apr
Phage display technology for human monoclonal antibodies. Deantonio C, Cotella D, Macor P, Santoro C, Sblattero D Methods in molecular biology (Clifton, N.J.) 24037846 Methods Mol Biol 2014
Ligand-targeted theranostic nanomedicines against cancer. Yao VJ, D'Angelo S, Butler KS, Theron C, Smith TL, Marchiò S, Gelovani JG, Sidman RL, Dobroff AS, Brinker CJ, Bradbury ARM, Arap W, Pasqualini R Journal of controlled release : official journal of the Controlled Release Society 26772878 J Control Release 2016 Oct 28
Enzymatic fabrication of high-density RNA arrays. Wu CH, Holden MT, Smith LM Angewandte Chemie (International ed. in English) 25339581 Angew Chem Int Ed Engl 2014 Dec 1
Synthetic aptamer-polymer hybrid constructs for programmed drug delivery into specific target cells. Oh SS, Lee BF, Leibfarth FA, Eisenstein M, Robb MJ, Lynd NA, Hawker CJ, Soh HT Journal of the American Chemical Society 25290917 J Am Chem Soc 2014 Oct 22
Real-time, aptamer-based tracking of circulating therapeutic agents in living animals. Ferguson BS, Hoggarth DA, Maliniak D, Ploense K, White RJ, Woodward N, Hsieh K, Bonham AJ, Eisenstein M, Kippin TE, Plaxco KW, Soh HT Science translational medicine 24285484 Sci Transl Med 2013 Nov 27
Particle display: a quantitative screening method for generating high-affinity aptamers. Wang J, Gong Q, Maheshwari N, Eisenstein M, Arcila ML, Kosik KS, Soh HT Angewandte Chemie (International ed. in English) 24644057 Angew Chem Int Ed Engl 2014 May 5
Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers. Broderick AH, Carter MC, Lockett MR, Smith LM, Lynn DM ACS applied materials & interfaces 23237360 ACS Appl Mater Interfaces 2013 Jan 23
Aptamer-based cell imaging reagents capable of fluorescence switching. Jung YK, Woo MA, Soh HT, Park HG Chemical communications (Cambridge, England) 25182171 Chem Commun (Camb) 2014 Oct 21
Carbon Substrates: A Stable Foundation for Biomolecular Arrays. Lockett MR, Smith LM Annual review of analytical chemistry (Palo Alto, Calif.) 26048550 Annu Rev Anal Chem (Palo Alto Calif) 2015
Selection strategy to generate aptamer pairs that bind to distinct sites on protein targets. Gong Q, Wang J, Ahmad KM, Csordas AT, Zhou J, Nie J, Stewart R, Thomson JA, Rossi JJ, Soh HT Analytical chemistry 22624874 Anal Chem 2012 Jun 19
Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution. Ahmad KM, Xiao Y, Soh HT Nucleic acids research 23042245 Nucleic Acids Res 2012 Dec
The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell BS, Kendziorski C, Attie AD PLoS genetics 27935966 PLoS Genet 2016 Dec
Controlling the function of DNA nanostructures with specific trigger sequences. Deborggraeve S, Dai JY, Xiao Y, Soh HT Chemical communications (Cambridge, England) 23192255 Chem Commun (Camb) 2013 Jan 14
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM BMC genomics 25149441 BMC Genomics 2014 Aug 22
MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers. Jiang P, Meyer S, Hou Z, Propson NE, Soh HT, Thomson JA, Stewart R Bioinformatics (Oxford, England) 24872422 Bioinformatics 2014 Sep 15
Integrated electrochemical microsystems for genetic detection of pathogens at the point of care. Hsieh K, Ferguson BS, Eisenstein M, Plaxco KW, Soh HT Accounts of chemical research 25785632 Acc Chem Res 2015 Apr 21
Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents. Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JA PloS one 23967247 PLoS One 2013
In vitro selection of shape-changing DNA nanostructures capable of binding-induced cargo release. Oh SS, Plakos K, Xiao Y, Eisenstein M, Soh HT ACS nano 24168267 ACS Nano 2013 Nov 26
Accurate zygote-specific discrimination of single-nucleotide polymorphisms using microfluidic electrochemical DNA melting curves. Yang AH, Hsieh K, Patterson AS, Ferguson BS, Eisenstein M, Plaxco KW, Soh HT Angewandte Chemie (International ed. in English) 24520069 Angew Chem Int Ed Engl 2014 Mar 17
Array-based discovery of aptamer pairs. Cho M, Oh SS, Nie J, Stewart R, Radeke MJ, Eisenstein M, Coffey PJ, Thomson JA, Soh HT Analytical chemistry 25495696 Anal Chem 2015 Jan 6
Quantitative selection and parallel characterization of aptamers. Cho M, Soo Oh S, Nie J, Stewart R, Eisenstein M, Chambers J, Marth JD, Walker F, Thomson JA, Soh HT Proceedings of the National Academy of Sciences of the United States of America 24167271 Proc Natl Acad Sci U S A 2013 Nov 12
Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Shortreed MR, Wenger CD, Frey BL, Sheynkman GM, Scalf M, Keller MP, Attie AD, Smith LM Journal of proteome research 26418581 J Proteome Res 2015 Nov 6
In Vitro Selection of pH-Activated DNA Nanostructures. Fong FY, Oh SS, Hawker CJ, Soh HT Angewandte Chemie (International ed. in English) 27809385 Angew Chem Int Ed Engl 2016 Dec 5
General approach for characterizing in vitro selected peptides with protein binding affinity. Larsen AC, Gillig A, Shah P, Sau SP, Fenton KE, Chaput JC Analytical chemistry 24970615 Anal Chem 2014 Aug 5
Development of a full-length human protein production pipeline. Saul J, Petritis B, Sau S, Rauf F, Gaskin M, Ober-Reynolds B, Mineyev I, Magee M, Chaput J, Qiu J, LaBaer J Protein science : a publication of the Protein Society 24806540 Protein Sci 2014 Aug
Comparative analysis of eukaryotic cell-free expression systems. Hartsough EM, Shah P, Larsen AC, Chaput JC BioTechniques 26345507 Biotechniques 2015 Sep
Automated solid-phase synthesis of high capacity oligo-dT cellulose for affinity purification of poly-A tagged biomolecules. Sau SP, Larsen AC, Chaput JC Bioorganic & medicinal chemistry letters 25467163 Bioorg Med Chem Lett 2014 Dec 15
SH3 domains come of age. Kay BK FEBS letters 22683951 FEBS Lett 2012 Aug 14
Improvements to the Kunkel mutagenesis protocol for constructing primary and secondary phage-display libraries. Huang R, Fang P, Kay BK Methods (San Diego, Calif.) 22959950 Methods 2012 Sep
Generating thermal stable variants of protein domains through phage display. Pershad K, Kay BK Methods (San Diego, Calif.) 23276752 Methods 2013 Mar 15
Generating Recombinant Antibodies against Putative Biomarkers of Retinal Injury. Kierny MR, Cunningham TD, Bouhenni RA, Edward DP, Kay BK PloS one 25902199 PLoS One 2015
Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK Antibodies (Basel, Switzerland) 31557992 Antibodies (Basel) 2016 May 2
Construction of an Ultra-Large Phage Display Library by Kunkel Mutagenesis and Rolling Circle Amplification. Huang RR, Kierny M, Volgina V, Iwashima M, Miller C, Kay BK Methods in molecular biology (Clifton, N.J.) 37679621 Methods Mol Biol 2023
Directed evolution of the forkhead-associated domain to generate anti-phosphospecific reagents by phage display. Pershad K, Wypisniak K, Kay BK Journal of molecular biology 22985966 J Mol Biol 2012 Nov 23
Generating FN3-Based Affinity Reagents Through Phage Display. Gorman K, McGinnis J, Kay B Current protocols in chemical biology 29927113 Curr Protoc Chem Biol 2018 Jun
A comparison of phosphospecific affinity reagents reveals the utility of recombinant Forkhead-associated domains in recognizing phosphothreonine-containing peptides. Venegas LA, Pershad K, Bankole O, Shah N, Kay BK New biotechnology 26772725 N Biotechnol 2016 Sep 25
Phosphorylated Gβ is a directional cue during yeast gradient tracking. Abdul-Ganiyu R, Venegas LA, Wang X, Puerner C, Arkowitz RA, Kay BK, Stone DE Science signaling 33975981 Sci Signal 2021 May 11
In vivo elimination of parental clones in general and site-directed mutagenesis. Holland EG, Acca FE, Belanger KM, Bylo ME, Kay BK, Weiner MP, Kiss MM Journal of immunological methods 25523926 J Immunol Methods 2015 Feb
Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step. Huang R, Gorman KT, Vinci CR, Dobrovetsky E, Gräslund S, Kay BK International journal of molecular sciences 26437402 Int J Mol Sci 2015 Sep 30
AXM mutagenesis: an efficient means for the production of libraries for directed evolution of proteins. Holland EG, Buhr DL, Acca FE, Alderman D, Bovat K, Busygina V, Kay BK, Weiner MP, Kiss MM Journal of immunological methods 23680235 J Immunol Methods 2013 Aug 30
Directed Evolution of a Highly Specific FN3 Monobody to the SH3 Domain of Human Lyn Tyrosine Kinase. Huang R, Fang P, Hao Z, Kay BK PloS one 26731115 PLoS One 2016

This page last reviewed on March 13, 2025