JUMP TO

2018

Nilvebrandt, J. & Sidhu, S. S. (2018) Construction of synthetic antibody phage-display libraries. Methods Mol. Biol. 1701, 45-60.
Abstract on PubMed

2017

Shi, M., Flores, B., Li, P., Gillings, N., McMillan, K. L., Ye, J., Huang, L. J., Sidhu, S. S., Zhong, Y.-P., Grompe, M. T., Streeter, P. R., Moe O. W. & Hu, M. C. (2017) Effects of erythropoietin receptor activity on angiogenesis, tubular injury and fibrosis in acute kidney injury: a "U-shaped" relationship. Am. J. Physiol. Renal Physiol. [Nov 29 Epub ahead of print].
Abstract on PubMed

Canny, M. D., Moatti, N., Wan, L. C. K., Fradet-Turcotte, A., Krasner, D., Mateos-Gomez, P. A., Zimmermann, M., Orthwein, A., Juang, Y. C., Zhang, W., Noordermeer, S. M., Seclen, E., Wilson, M. D., Vorobyov, A., Munro, M., Ernst, A., Ng, T. F., Cho, T., Cannon, P. M., Sidhu, S. S., Sicheri, F. & Durocher. D. (2017) Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency. Nat. Biotechnol. [Nov 27 Epub ahead of print].
Abstract on PubMed

Zhang, H., Liu, K., Izumi, N., Huang, H., Ding, D., Ni, Z., Sidhu, S. S., Chen, C., Tomari, Y. & Min, J. (2017) Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2. Proc. Natl. Acad. Sci. USA 114, 12483-88.
Abstract on PubMed

Rissland, O. S., Subtelny, A. O., Wang, M., Lugowski, A., Nicholson, B., Laver, J. D., Sidhu, S. S., Smibert, C. A., Lipshitz, H. D. & Bartel, D. P. (2017) The influence of microRNAs and poly(A) tail length on endogenous mRNA-protein complexes. Genome Biol. 18, 211.
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Gabrielsen, M., Buetow, L., Nakasone, M. A., Ahmed, S. F., Sibbet, G. J., Smith, B. O., Zhang, W.*, Sidhu, S. S.* & Huang, D. T.*. (2017) A general strategy for discovery of inhibitors and activators of RING and U-box E3 ligases with ubiquitin variants. Mol. Cell 68, 456-70. (*Co-corresponding authors)
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Ghosh, E., Srivastava. A., Baidya, M., Kumari, P., Dwivedi, H., Nidhi, K., Ranjan, R., Dogra, S., Koide, A., Yadav, P. M., Sidhu, S. S., Koide, S. & Shukla, A. K. (2017) A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis. Nat. Nanotechnol. [Oct 2 Epub ahead of print]
Abstract on PubMed

Miersch, S., Kuruganti, S., Walter, M. R. & Sidhu, S. S. (2017) A panel of synthetic antibodies that selectively recognize and antagonize members of the interferon alpha family. Protein Eng. Des. Sel. 30, 697-704.
Abstract on PubMed

Teyra, J., Huang, H., Jain, S., Guan, X., Dong, A., Liu, Y., Tempel, W., Min, J., Tong, Y., Kim, P. M., Bader, G. D. & Sidhu, S. S. (2017) Comprehensive analysis of the human SH3 domain family reveals a wide variety of non-canonical specificities. Structure 25, 1598-1610.
Abstract on PubMed

Han, Z., Sagum, C. A., Takizawa, F., Ruthel, G., Berry, C. T., Kong, J., Sunyer, J. O., Freedman, B. D., Bedford, M. T., Sidhu, S. S., Sudol, M. & Harty, R. N. (2017) Ubiquitin Ligase WWP1 Interacts with Ebola Virus VP40 to Regulate Egress. J. Virol. 91, e00812-17.
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Apel, A. R., Hoban, K., Chuartzman, S., Tonikian, R., Sidhu, S. S., Schuldiner, M., Wendland, B. & Prosser, D. (2017) Syp1 regulates the clathrin-mediated and clathrin-independent endocytosis of multiple cargo proteins through a novel sorting motif. Mol. Biol. Cell 28, 2434-48.
Abstract on PubMed

Zhang, W., Sartori, M. A., Makhnevych, T., Federowicz, K. E., Dong, X., Liu, L., Nim, S., Dong, A., Yang, J., Li, Y., Haddad, D., Ernst, A., Heerding, D., Tong, Y., Moffat, J. & Sidhu, S. S. (2017) Generation and validation of intracellular ubiquitin variant inhibitors for USP7 and USP10. J. Mol. Biol. 429, 3546-60.
Abstract on PubMed

Zhang, W., Bailey-Elkin, B. A., Knaap, R. C. M., Khare, B., Dalebout, T. J., Johnson, G. G., van Kasteren, P. B., McLeish, N. J., Gu, J., He, W., Kikkert, M., Mark, B. L. & Sidhu, S. S. (2017) Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. PLoS Pathog. 13, e1006372.
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Ling, B., Watt, K., Banerjee, S., Newsted, D., Truesdell, P., Adams, J., Sidhu, S. S. & Craig, A. W. (2017) A novel immunotherapy targeting MMP-14 limits hypoxia, immune suppression and metastasis in triple-negative breast cancer models. Oncotarget 8, 58372-85.
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Gorelik, M. & Sidhu, S. S. (2017) Specific targeting of the deubiquitinase and E3 ligase families with engineered ubiquitin variants. Bioeng. Transl. Med. 2, 31-42.
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Qazi, M. A., Vora, P., Venugopal, C., Sidhu, S. S., Moffat, J., Swanton, C. & Singh, S. K. (2017) Intratumoral heterogeneity: Pathways to treatment resistance and relapse in human glioblastoma. Ann. Oncol. 28, 1448-56.
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Miersch, S., Maruthachalam, B. V., Geyer, C. R. & Sidhu, S. S. (2017) Structure-Directed and Tailored Diversity Synthetic Antibody Libraries Yield Novel Anti-EGFR Antagonists. ACS Chem. Biol. 12, 1381-9.
Abstract on PubMed

Manczyk, N., Yates, B.P., Veggiani, G., Ernst, A., Sicheri, F. & Sidhu, S. S. (2017) Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif. Protein Sci. 26, 1060-9.
Abstract on PubMed

Liu, H., Saxena, A., Sidhu, S. S. & Wu, D. (2017) Fc engineering for developing therapeutic bispecific antibodies and novel scaffolds. Front. Immunol. 8, 38.
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Huang, H., Kaneko, T., Sidhu, S. S., Li, S. S. (2017) Creation of phosphotyrosine superbinders by directed evolution of an SH2 domain. Methods Mol. Biol. 1555, 225-54.
Abstract on PubMed

Liang, J., Sagum, C. A., Bedford, M. T., Sidhu, S. S., Sudol, M., Han, Z. & Harty, R. N. (2017) Chaperone-mediated autophagy protein BAG3 negatively regulates Ebola and Marburg VP40-Mediated Egress. PLoS Pathog. 13, e1006132.
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Leung, I., Jarvik, N. & Sidhu, S. (2017) A Highly Diverse and Functional Naïve Ubiquitin Variant Library for Generation of Intracellular Affinity Reagents. J. Mol. Biol. 429, 115-27.
Abstract on PubMed

Tong, J., Cao, B., Martyn, G. D., Krieger, J. R., Taylor, P., Yates, B., Sidhu, S. S., Li, S. S. C., Mao, X. & Moran, M. F. (2017) Protein-phosphotyrosine proteome profiling by superbinder-SH2 domain affinity purification mass spectrometry, sSH2-AP-MS. Proteomics 17, issue 6.
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Steinhart, Z., Pavlovic, Z., Chandrashekhar, M., Hart, T., Wang, X., Zhang, X., Robitaille, M., Brown, K. R., Jaksani, S., Overmeer, R., Boj, S. F., Adams, J., Pan, J., Clevers, H., Sidhu, S., Moffat, J. & Angers, S. (2017) Genome-wide CRISPR screens reveal a Wnt-FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors. Nat. Med. 23, 60-8.
Abstract on PubMed

2016

Stolz, A., Putyrski, M., Kutle, I., Huber, J., Wang, C., Major, V., Sidhu, S. S., Youle, R. J., Rogov, V. V., Dötsch, V., Ernst, A. & Dikic, I. (2016) Fluorescence‐based ATG8 sensors monitor localization and function of LC3/GABARAP proteins. EMBO J. 36, 549-64.
Abstract on PubMed

Zhang, W., Ben-David, M. & Sidhu, S. S. (2016) Engineering cell signaling modulators from native protein-protein interactions. Curr. Opin. Struct. Biol. 45, 25-35.
Abstract on PubMed

Nilvebrant, J., Tessier, P. M. & Sidhu, S. S. (2016) Engineered autonomous human variable domains. Curr. Pharm. Des. 22, 6527-37.
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Yamaguchi, M., VanderLinden, R., Weissmann, F., Qiao, R., Dube, P., Brown, N. G., Haselbach, D., Zhang, W., Sidhu, S. S., Peters, J. M., Stark, H. & Schulman, B. A. (2016) Cryo-EM of Mitotic Checkpoint Complex-Bound APC/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation. Mol. Cell 63, 593-607.
Abstract on PubMed

Miersch, S. & Sidhu, S. S. (2016) Intracellular targeting with engineered proteins.
F1000Res 5, 1947.
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Han, Z., Sagum, C. A., Bedford, M. T., Sidhu, S. S., Sudol, M. & Harty, R. N. (2016) ITCH E3 ubiquitin ligase interacts with Ebola virus VP40 to regulate budding. J. Virol. 90, 9163-71.
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Gray, A. C., Sidhu, S. S., Chandrasekera, P. C., Hendriksen, C. F. & Borrebaeck, C. A. (2016) Animal-based antibodies: Obsolete. Science 353, 452-3.
Abstract on PubMed

Gray, A. C., Sidhu, S. S., Chandrasekera, P. C., Hendriksen, C. F. & Borrebaeck, C. A. (2016) Animal-Friendly Affinity Reagents: Replacing the Needless in the Haystack. Trends Biotechnol. 34, 960-9.
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Leung, I., Dekel, A., Shifman, J. M. & Sidhu, S. S. (2016) Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21. Proc. Natl. Acad. Sci. USA 113, 8705-10.
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Banh, R., Iorio, C., Marcotte, R., Xu, Y., Cojocari, D., Rahman, A. A., Pawling, J., Zhang, W., Sinha, A., Rose, C., Isasa, M., Zhang, S., Wu, R., Virtanen, C., Hitomi, T., Habu, T., Sidhu, S., Koizumi, A., Wilkins, S., Kislinger, T., Gygi, S., Schofield, C., Dennis, J., Wouters, B. & Neel, B. (2016) PTP1B controls non-mitochondrial oxygen consumption by regulating RNF213 to promote tumour survival during hypoxia. Nat. Cell Biol. 18, 803-13.
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Hershey, D. M., Browne, P. J., Iavarone, A. T., Teyra, J., Lee, E. H., Sidhu, S. S. & Komeili, A. (2016) Magnetite Biomineralization in Magnetospirillum magneticum is Regulated by a Switch-like Behavior in the HtrA Protease MamE. J. Biol. Chem. 291, 17941-52.
Abstract on PubMed

Brown, N. G., VanderLinden, R., Watson, E. R., Weissmann, F., Ordureau, A., Wu, K.-P., Zhang, W., Yu, S., Mercredi, P. Y., Harrison, J. S., Davidson, I. F., Qiao, R., Lu, Y., Dube, P., Brunner, M. R., Grace, C. R. R., Miller, D. J., Haselbach, D., Jarvis, M.A., Yamaguchi, M., Yanishevski, D., Petzold, G., Sidhu, S. S., Kuhlman, B., Kirschner, M. W., Harper, J. W., Peters, J.-M., Stark, H. & Schulman, B. A. (2016) Dual architectures regulate multiubiquitination and ubiquitin chain elongation for a RING E3. Cell 165, 1440-53.
Abstract on PubMed

Gakhal, A. K., Jensen, T. J., Bozoky, Z., Roldan, A., Lukacs, G. L., Forman-Kay, J., Riordan, J. R. & Sidhu, S. S. (2016) Development and characterization of synthetic antibodies binding to the cystic fibrosis conductance regulator. MAbs. 16, 1-10.
Abstract on PubMed

Gorelik, M., Orlicky, S., Sartori, M. A., Tang, X., Marcon, E., Kurinov, I., Greenblatt, J. F., Tyers, M., Moffat, J., Sicheri, F. & Sidhu, S. S. (2016) Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface. Proc. Natl. Acad. Sci. USA 113, 3527-32.
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Zhang, W., Wu, K.-P., Sartori, M. A., Kamadurai, H. B., Ordureau, A., Jiang, C., Mercredi, P. Y., Murchie, R., Hu, J., Persaud, A., Mukherjee, M., Li, N., Doye, A., Walker, J. R., Sheng, Y., Hao, Z., Li, Y., Brown, K. R., Lemichez, E., Chen, J., Tong, Y., Harper, J. W., Moffat, J., Rotin, D., Schulman, B. A. & Sidhu, S. S. (2016) System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes. Mol. Cell 62, 121-36.
Abstract on PubMed

Na, H., Laver, J. D., Jeon, J., Singh, F., Ancevicius, K., Fan, Y., Cao, W. X., Nie, K., Yang, Z., Luo, H., Wang, M., Rissland, O., Westwood, J. T., Kim, P. M., Smibert, C. A., Lipshitz, H. D. & Sidhu, S. S. (2016) A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes. RNA 22, 636-55.
Abstract on PubMed

Arita, Y., Allen, S., Chen, G., Zhang, W., Wang, Y., Owen, A., Dentinger, P. & Sidhu, S. (2016) Rapid isolation of peptidic inhibitors of the solute carrier family transporters OATP1B1 and OATP1B3 by cell-based phage display selections. Biochem. Biophys. Res. Commun. 473, 370-6.
Abstract on PubMed

Garrido-Urbani, S., Garg, P., Ghossoub, R., Arnold, R., Lembo, F., Sundell, G. N., Kim, P. M., Lopez, M., Zimmermann, P., Sidhu, S. S. & Ivarsson, Y. (2016) Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. FEBS Lett. 590, 3-12.
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Uppalapati, M., Lee, D. J., Mandal, K., Li, H., Miranda, L. P., Lowitz, J., Kenney, J., Adams, J. J., Ault-Riche, D., Kent, S. B.H. & Sidhu, S. S. (2016) A Potent D-protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable and Longer-Circulating In Vivo. ACS Chem. Biol. 11, 1058-65.
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Uchime, O., Dai, Z., Biris, N., Lee, D., Sidhu, S. S., Li, S., Lai, J. R. & Gavathiotis, E. (2016) Synthetic antibodies inhibit Bcl-2-associated X protein (BAX) through blockade of the N-terminal activation site J. Biol. Chem. 291, 89-102.
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Kuruganti, S., Miersch, S., Deshpande, A., Speir, J. A., Harris, B. D., Schriewer, J. M., Buller, R. M., Sidhu, S. S. & Walter, M. R. (2016) Cytokine Activation by Antibody Fragments Targeted to Cytokine-Receptor Signaling Complexes. J. Biol. Chem. 291, 447-61.
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Adams, J. J., Narayanan, S., Birnbaum, M.E., Sidhu, S. S., Blevins, S. J., Gee, M. H., Sibener, L. V., Baker, B. M., Kranz, D. M. & Garcia, K. C. (2016) Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nat. Immunol. 17, 87-94.
Abstract on PubMed

Hu, M.-C., Shi, M., Zhang, J., Addo, T., Cho, H. J., Barker, S. L., Ravikumar, P., Gillings, N., Bian, A., Sidhu, S. S., Kuro-o, M. & Moe, O. W. (2016) Renal Production, Uptake, and Handling of Circulating alpha-Klotho. J. Am. Soc. Nephrol. 27, 79-90.
Abstract on PubMed

2015

Hart, T., Chandrashekhar, M., Aregger, M., Steinhart, Z., Brown, K. R., MacLeod, G., Mis, M., Zimmermann, M., Fradet-Turcotte, A., Sun, S., Mero, P., Dirks, P., Sidhu, S., Roth, F. P., Rissland, O. S., Durocher, D., Angers, S. & Moffat, J. (2015) High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell 163, 1515-26.
Abstract on PubMed

Mattera, R., Guardia, C. M., Sidhu, S. & Bonifacino, J. S. (2015) Bivalent Motif-Ear Interactions Mediate the Recruitment of the Accessory Protein Tepsin by the AP-4 Adaptor Complex. J. Biol. Chem. 290, 30736-49.
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Huang, H., Economopoulos, N. O., Liu, B. A., Uetrecht, A., Gu, J., Jarvik, N., Nadeem, V., Pawson, T., Moffat, J., Miersch, S. & Sidhu, S. S. (2015) Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. Protein Sci. 24, 1890-900.
Abstract on PubMed

Van Deventer, J. A., Kelly, R. L., Rajan, S., Wittrup, K. D. & Sidhu, S. S. (2015) A switchable yeast display/secretion system. Protein Eng. Des. Sel. 28, 317-25. Cover feature.
Abstract on PubMed

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, R. J., Lai, D., Griffin, C., Li, Z., Vizeacoumar, F. J., Dong, D., Campbell, E., Anderson, S., Zhong, N., Gräslund, S., Koide, S., Moffat, J., Sidhu, S., Kossiakoff, A. & Wells, J. (2015) A high through-put platform for recombinant antibodies to folded proteins. Mol. Cell. Proteomics 14, 2833-47.
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Zhong, N., Loppnau, P., Seitova, A., Ravichandran, M., Fenner, M., Jain, H., Bhattacharya, A., Hutchinson, A., Paduch, M., Lu, V., Olszewski, M., Kossiakoff, A. A., Dowdell, E., Koide, A., Koide, S., Huang, H., Nadeem, V., Sidhu, S. S., Greenblatt, J. F., Marcon, E., Arrowsmith, C. H., Edwards, A., M. & Gräslund, S. (2015) Optimizing production of antigens and Fabs in the context of generating recombinant antibodies to human proteins. PLoS One 10, e0120481.
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Marcon, E., Jain, H., Bhattacharya, A., Guo, H., Phanse, S., Pu, S., Byram, G., Collins, B. C., Dowdell, E., Fenner, M., Guo, X., Hutchinson, A., Kennedy, J. J., Krastins, B., Larsen, B., Lin, Z.-Y., Lopez, M. F., Loppnau, P., Miersch, S., Nguyen, T., Olsen, J. B., Paduch, M., Ravichandran, M., Seitova, A., Vadali, G., Vogelsang, M. S., Whiteaker, J. R., Zhong, G., Zhong, N., Zhao, L., Aebersold, R., Arrowsmith, C. H., Emili, A., Frappier, L., Gingras, A.-C., Gstaiger, M., Paulovich, A. G., Koide, S., Kossiakoff, A. A., Sidhu, S. S., Wodak, S. J., Gräslund, S., Greenblatt, J. F. & Edwards, A. M. (2015) Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat. Methods 12, 725-31.
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Laver, J. D., Li, X., Ray, D., Cook, K. B., Hahn, N. A., Nabeel-Shah, S., Kekis, M., Luo, H., Marsolais, A. J., Fung, K. Y., Hughes, T. R., Westwood, J. T., Sidhu, S. S., Morris, Q., Lipshitz, H. D. & Smibert, C. A. (2015) Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biol. 16, 94.
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Chen, G., Gorelik, L., Simon, K. J., Pavlenco, A., Cheung, A., Brickelmaier, M., Chen, L. L., Jin, P., Weinreb, P. H. & Sidhu, S. S. (2015) Synthetic antibodies and peptides recognizing progressive multifocal leukoencephalopathy-specific point mutations in polyomavirus JC capsid viral protein 1. MAbs. 7, 681-92.
Abstract on PubMed

Luz, D., Chen, G., Maranhão, A. Q., Rocha, L. B., Sidhu, S. & Piazza, R. M. (2015) Development and characterization of recombinant antibody fragments that recognize and neutralize in vitro Stx2 Toxin from Shiga Toxin-producing Escherichia coli. PLoS One 10, e0120481.
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Fellouse, F. A. & Sidhu, S. (2015) Synthetic Antibody Libraries. In “Phage display in drug discovery and Biotechnology, Second Edition” (S. S. Sidhu & C. R. Geyer, Eds.), Chapter 18, pp 495-520, CRC Press, Boca Raton, FL.

Tomic, J., McLaughlin, M., Hart, T., Sidhu, S. & Moffat, J. (2015) Leveraging Synthetic Phage-Antibody Libraries for Panning on the Mammalian Cell Surface. In “Phage display in drug discovery and Biotechnology, Second Edition” (S. S. Sidhu & C. R. Geyer, Eds.), Chapter 5, pp 113-22, CRC Press, Boca Raton, FL.

Miersch, S., Li, Z., Hanna, R., McLaughlin, M. E., Hornsby, M., Matsuguchi, T., Paduch, M., Sääf, A., Wells, J., Koide, S., Kossiakoff, A. & Sidhu, S. S. (2015) Scalable high throughput selection from phage-displayed synthetic antibody libraries. J. Vis. Exp. 95, Immunology and Infection, January 17 [video 51492].
Abstract on PubMed

Boyle, A. J., Cao, P. J., Hedley, D. W., Sidhu, S. S., Winnik, M. A. & Reilly, R. M. (2015) MicroPET/CT imaging of patient-derived pancreatic cancer xenografts implanted subcutaneously or orthotopically in NOD-scid mice using 64Cu-NOTA-panitumumab F(ab')2 fragments. Nucl. Med. Biol. 42, 71-7.
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Barker, S. L., Pastor, J., Carranza, D., Quiñones, H., Griffith, C., Goetz, R., Mohammadi, M., Ye, J., Zhang, J., Hu, M. C., Kuro-O, M., Moe, O. W. & Sidhu, S. S. (2015) The demonstration of αKlotho deficiency in human chronic kidney disease with a novel synthetic antibody. Nephrol. Dial. Transplant. 30, 223-33.
Abstract on PubMed

Ren, L., Willet, A. H., Roberts-Galbraith, R. H., McDonald, N. A., Feoktistova, A., Chen, J. S., Huang, H., Guillen, R., Boone, C., Sidhu, S. S., Beckley, J. R. & Gould, K. L. (2015) The Cdc15 and Imp2 SH3 domains cooperatively scaffold a network of proteins that redundantly ensure efficient cell division in fission yeast. Mol. Biol. Cell 26, 256-69.
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2014

Jeon, J., Nim, S., Teyra, J., Datti, A., Wrana, J. L., Sidhu, S. S., Moffat, J. & Kim, P. M. (2014) A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. Genome Med. 6, 57.
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Ernst, A., Appleton, B. A., Ivarsson, Y., Zhang, Y., Gfeller, D., Wiesmann, C & Sidhu, S. S. (2014) A structural portrait of the PDZ domain family. J. Mol. Biol. 426, 3509-19.
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Chen, G., Koellhoffer, J. F., Zak, S. E., Frei, J. C., Liu, N., Long, H., Yi, W., Nagar, K., Pan, G., Chandran, K., Dye, J. M., Sidhu, S. S. & Lai, J. R. (2014) Synthetic Antibodies with a Human Framework that Protect Mice from Lethal Sudan Ebolavirus Challenge. ACS Chem. Biol. 9, 2263-73.
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Shukla, A. K., Westfield, G. H., Xiao, K., Reis, R. I., Huang, L. Y., Tripathi-Shukla, P., Qian, J., Li, S., Blanc, A., Oleskie, A. N., Dosey, A. M., Su, M., Liang, C. R., Gu, L. L., Shan, J. M., Chen, X., Hanna, R., Choi, M., Yao, X. J., Klink, B. U., Kahsai, A. W., Sidhu, S. S., Koide, S., Penczek, P. A., Kossiakoff, A. A., Woods Jr, V. L., Kobilka, B. K., Skiniotis, G. & Lefkowitz, R. J. (2014) Visualization of arrestin recruitment by a G-protein-coupled receptor. Nature 512, 218-22.
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Ni, Z., Xu, C., Guo, X., Hunter, G. O., Kuznetsova, O. V., Tempel, W., Marcon, E., Zhong, G., Guo, H., Kuo, W. H., Li, J., Young, P., Olsen, J. B., Wan, C., Loppnau, P., El Bakkouri, M., Senisterra, G. A., He, H., Huang, H., Sidhu, S. S., Emil, A., Murphy, S., Mosley, A. L., Arrowsmith, C. H., Min, J. & Greenblatt, J. F. (2014) RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Nat. Struct. Mol. Biol. 21, 686-95.
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Murciano-Calles, J., McLaughlin, M. E., Erijman, A., Hooda, Y., Chakravorty, N., Martinez, J. C., Shifman, J. M., Sidhu, S. S. (2014) Alteration of the C-terminal ligand specificity of the Erbin PDZ domain by allosteric mutational effects. J. Mol. Biol. 426, 3500-8.
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Gfeller, D., Ernst, A., Jarvik, N., Sidhu, S. S. & Bader, G. D. (2014) Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs. PLoS One 9, e94507.
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Adams, J. J. & Sidhu, S. S. (2014) Synthetic antibody technologies. Curr. Opin. Struct. Biol. 24C, 1-9.
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Abu-Odeh, M., Bar-Mag, T., Huang, H., Kim, T., Salah, Z., Abdeen, S. K., Sudol, M., Reichmann, D., Sidhu, S. S., Kim, P. M. & Aqeilan, R. I. (2014) Characterizing WW Domain Interactions of Tumor Suppressor WWOX Reveals its Association with Multiprotein Networks. J. Biol. Chem. 28, 8865-80.
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Ivarsson, Y., Arnold, R., McLaughlin, M., Nim, S., Joshi, R., Ray, D., Liu, B., Teyra, J., Pawson, T., Moffat, J., Li, S.-S., Sidhu, S. S. & Kim, P. M. (2014) Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes. Proc. Natl. Acad. Sci. USA 111, 2542-7.
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Chen, G. & Sidhu, S. S. (2014) Design and generation of synthetic antibody libraries for phage display. Methods Mol. Biol. 1131, 113-31.
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Liu, P., Cai, Z., Kang, J. W., Boyle, A. J., Adams, J., Lu, Y., Mbong, G. N., Sidhu, S. S., Reilly, R. M. & Winnik, M. A. (2014) Intracellular Routing in Breast Cancer Cells of Streptavidin-Conjugated Trastuzumab Fab Fragments Linked to Biotinylated Doxorubicin-Functionalized Metal Chelating Polymers. Biomacromolecules 15, 715-25.
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Yu, C. G., Tonikian. R., Felsensteiner, C., Jhingree, J. R., Desveaux, D., Sidhu, S. S. & Harris, T. J. (2014) Peptide binding properties of the three PDZ domains of bazooka (Drosophila par-3). PLoS One 9, e86412.
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Huang, H., Ceccarelli, D. F., Orlicky, S., St-Cyr, D. J., Ziemba, A., Garg, P., Plamondon, S., Auer, M., Sidhu, S. S., Marinier, A., Kleiger, G., Tyers, M. & Sicheri, F. (2014) E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin. Nat. Chem. Biol. 10, 156-63.
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Zhang, W. & Sidhu, S. S. (2014) Development of inhibitors in the ubiquitin cascade. FEBS Lett. 588, 356-67.
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Adams, J. J., Nelson, B. & Sidhu, S. S. (2014) Recombinant genetic libraries and human monoclonal antibodies. Methods Mol. Biol. 1060, 149-70.
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2013

Reshetnyak, A. V., Nelson, B., Shi, X., Boggon, T.J., Pavlenco, A., Mandel-Bausch, E. M., Tome, F., Suzuki, Y., Sidhu, S. S., Lax, I. & Schlessinger, J. (2013) Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region. Proc. Natl. Acad. Sci. USA 110, 17832-7.
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Owen, S. C., Patel, N., Logie, J., Pan, G., Persson, H., Moffat, J., Sidhu, S. S. & Shoichet, M. S. (2013) Targeting HER2+ breast cancer cells: Lysosomal accumulation of anti-HER2 antibodies is influenced by antibody binding site and conjugation to polymeric nanoparticles. J. Control. Release. 172, 395-404.
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Ernst, A. & Sidhu, S. S. (2013) Engineering ubiquitin to modulate the ubiquitin proteasome system. Cell Cycle 12, 1651-2.
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Hu, M.-C., Shi, M., Cho, H. J., Zhang, J., Pavlenco, A., Sidhu, S. S., Huang, L. J.-S. & Moe, O. W. (2013) The erythropoietin receptor is a downstream effector of Klotho-induced cytoprotection. Kidney Int. 84, 468-81.
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Xin, X., Gfeller, D., Cheng, J., Tonikian, R, Sun, L., Guo, A., Lopez, L., Pavlenco, A., Akintobi, A., Zhang, Y., Rual, J. F., Currell, B., Seshagiri, S., Hao, T., Yang, X., Shen, Y. A., Salehi-Ashtiani, K., Li, J., Cheng, A. T., Bouamalay, D., Lugari, A., Hill, D. E., Grimes, M. L, Drubin, D. G., Grant, B. D., Vidal, M., Boone, C., Sidhu, S. S. & Bader, G. D. (2013) SH3 interactome conserves general function over specific form. Mol. Syst. Biol. 9, 652.
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Ma, X., Barthelemy, P. A., Rouge, L., Wiesmann, C. & Sidhu, S. S. (2013) Design of Synthetic Autonomous VH Domain Libraries and Structural Analysis of a VH Domain Bound to Vascular Endothelial Growth Factor. J. Mol. Biol. 425, 2247-59.
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Findlay, G. M., Smith, M. J., Lanner, F., Hsiung, M. S., Gish, G. D., Petsalaki, E., Cockburn, K., Kaneko, T., Huang, H, Bagshaw, R. D., Ketela, T., Tucholska, M., Taylor, L., Botwell, D. D., Moffat, J., Ikura, M., Li, S. S., Sidhu, S. S., Rossant, J. & Pawson, T. (2013) Interaction domains of Sos1/Grb2 are finely tuned for cooperative control of embryonic stem cell fate. Cell 152, 1008-20.
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McLaughlin, M. E. & Sidhu, S. S. (2013) Engineering and analysis of peptide-recognition domain specificities by phage display and deep sequencing. Methods Enzymol. 523, 327-49.
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Ernst, A., Avvakumov, G., Tong, J., Fan, Y., Zhao, Y., Alberts, P., Persaud, A., Walker, J. R., Neculai, A. M., Neculai, D., Vorobyov, A., Garg, P., Beatty, L., Chan, P. K., Juang, Y. C., Landry, M. C., Yeh, C., Zeqiraj, E., Karamboulas, K., Allali-Hassani, A., Vedadi, M., Tyers, M., Moffat, J., Sicheri, F., Pelletier, L., Durocher, D., Raught, B., Rotin, D., Yang, J., Moran, M. F., Dhe-Paganon S. & Sidhu, S. S. (2013) A Strategy for Modulation of Enzymes in the Ubiquitin System. Science 339, 590-5.
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Rojas, G., Pupo, A., Leon, K., Avellanet, J., Carmenate, T. & Sidhu, S. (2013) Deciphering the molecular bases of the biological effects of antibodies against Interleukin-2: a versatile platform for fine epitope mapping. Immunobiology 218, 105-13.
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2012

Persson, H., Ye, W., Wernimont, A., Adams, J. J., Lam, R. & Sidhu, S. S. (2012) CDR-H3 Diversity is Not Required For Antigen Recognition by Synthetic Antibodies. J. Mol. Biol. 425, 803-11.
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Ahmed, S. M., Thériault, B. L., Uppalapati, M., Chiu, C. W., Gallie, B. L., Sidhu, S. S. & Angers, S. (2012) KIF14 negatively regulates Rap1a-Radil signaling during breast cancer progression. J. Cell Biol. 199, 951-67.
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Miersch, S. & Sidhu, S. S. (2012) Immunology: Evolving superkines for selectivity. Nat. Chem. Biol. 8, 955-6.
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Koellhoffer, J. F., Chen, G., Sandesara, R. G., Bale, S. Saphire, E. O., Chandran, K., Sidhu, S. S. & Lai, J. R. (2012) Two synthetic antibodies that recognize and neutralize distinct proteolytic forms of the Ebola virus envelope glycoprotein. Chembiochem. 13, 2549-57.
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Orava, E. W., Jarvik, N., Shek, Y. L., Sidhu, S. S. & Gariepy, J. (2013) A short DNA Aptamer that Recognizes TNFα and blocks its activity in vitro. ACS Chem. Biol. 8, 170-8.
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Kaneko, T., Huang, H., Cao, X., Li, X., Li, C., Voss, C., Sidhu, S. S. & Li, S. S. (2012) Superbinder SH2 domains act as antagonists of cell signaling. Sci. Signal. 5, ra68.
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Mandal, K., Uppalapati, M., Ault-Riche, D., Kenney, J., Lowitz, J., Sidhu, S. S., Kent, S. B. (2012) Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography. Proc. Natl. Acad. Sci. USA 109, 14779-84.
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Miller, K. R, Koide, A., Leung, B., Fitzsimmons, J., Yoder, B., Yuan, H., Jay, M., Sidhu, S. S., Koide, S. & Collins, E. J. (2012) T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment. PLoS One 7, e43746.
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Tonikian, R. & Sidhu, S. S. (2012) Selecting and purifying autonomous human variable heavy (VH) domains. Methods Mol. Biol. 911, 327-53.
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Zalatan, J. G, Coyle, S. M., Rajan, S., Sidhu, S. S. & Lim, W. A. (2012) Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation. Science 337, 1218-22.
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Miersch, S. & Sidhu, S. S. (2012) Synthetic antibodies: concepts, potential and practical considerations. Methods 57, 486-98.
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Nelson, B. & Sidhu, S. S. (2012) Synthetic antibody libraries. Methods Mol. Biol. 899, 27-41.
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Geyer, C. R., McCafferty, J., Dübel, S., Bradbury, A. R. & Sidhu, S. S. (2012) Recombinant antibodies and in vitro selection technologies. Methods Mol. Biol. 901, 11-32.
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Teyra, J., Sidhu, S. S. & Kim, P. M. (2012) Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains. FEBS Lett. 586, 2613-7.
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Sidhu, S. S. (2012) Antibodies for All: The Case for Genome-wide Affinity Reagents. FEBS Lett. 586, 2778-9.
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Karauzum, H.*, Chen, G.*, Abaandou, L., Mahmoudieh, M., Boroun, A. R., Shulenin, S., Devi, V. S., Stavale, E., Warfield, K. L., Zeitlin, L., Roy, C. J., Sidhu, S. S. & Aman, M. J. (2012) Synthetic human monoclonal antibodies towards staphylococcal enterotoxin B (SEB) protective against toxic shock syndrome. J. Biol. Chem. 287, 25203-15. * equal contribution
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Laver, J. D., Ancevicius, K., Sollazzo, P., Westwood, J. T., Sidhu, S. S., Lipshitz, H. D. & Smibert, C. A. (2012) Synthetic antibodies as tools to probe RNA-binding protein function. Molec. Biosyst. 8, 1650-7.
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Kim, T., Tyndel, M. S., Huang, H., Sidhu, S. S., Bader, G. D., Gfeller, D. & Kim, P. M. (2012) MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucl. Acids Res. 40, e47.
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McCluskey, A. J., Bolewska-Pedyczak, E., Jarvik, N., Chen, G., Sidhu, S. S. & Gariépy, J. (2012) Charged and hydrophobic surfaces on the a chain of shiga-like toxin 1 recognize the C-terminal domain of ribosomal stalk proteins. PLoS One 7, e31191.
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Rajan, S. & Sidhu, S. S. (2012) Simplified synthetic antibody libraries. Methods Enzymol. 502: 3-23.
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2011

Huang, H. & Sidhu, S. S. (2011) Studying binding specificities of peptide recognition modules by high-throughput phage display selections. Methods Mol. Biol. 781, 87-97.
Abstract on PubMed

Yip, K. Y., Utz, L., Sitwell, S., Hu, X., Sidhu, S. S., Turk, B. E., Gerstein, M. B. & Kim, P. M. (2011) Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. BMC Biol. 9, 53.
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Bahudhanapati, H., Zhang, Y., Sidhu, S. S. & Brew, K. (2011) Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): Identification of selective inhibitors of collagenase-1 (MMP-1). J. Biol. Chem. 286, 31761-70.
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Colwill, K.; Renewable Protein Binder Working Group; In vitro Antibody Consortium, Persson, H., Jarvik, N. E., Wyrzucki, A., Wojcik, J., Koide, A., Kossiakoff, A. A., Koide, S., Sidhu, S. S., Dyson, M. R., Pershad, K., Pavlovic, J. D., Karatt-Vellatt, A., Schofield, D. J., Kay, B. K., McCafferty, J., Mersmann, M., Meier, D., Mersmann, J., Helmsing, S., Hust, M., Dübel, S.; Monash Antibody Technologies Facility, Berkowicz, S., Freemantle, A., Spiegel, M., Sawyer, A., Layton, D., Nice, E.; Pawson Laboratory, Dai, A., Rocks, O., Williton, K., Fellouse, F. A., Hersi, K., Pawson, T.; Human Protein Atlas, Nilsson, P., Sundberg, M., Sjöberg, R., Sivertsson, A., Schwenk, J. M., Takanen, J. O., Hober, S., Uhlén, M.; Structural Genomics Consortium, Dahlgren, L. G., Flores, A., Johansson, I., Weigelt, J., Crombet, L., Loppnau, P., Kozieradzki, I., Cossar, D., Arrowsmith, C. H., Edwards, A. M. & Gräslund, S. (2011) A roadmap to generate renewable protein binders to the human proteome. Nat. Methods 8, 551-8.
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Gfeller, D., Butty, F., Wierzbicka, M., Verschueren, E., Vanhee, P., Huang, H., Ernst, A., Dar, N., Stagljar, I., Serrano, L., Sidhu, S. S., Bader, G. D. & Kim, P. M. (2011) The multiple-specificity landscape of modular peptide recognition domains. Mol. Syst. Biol. 7, 484.
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Qazi, O., Rani, M., Gnanam, A. J., Cullen, T. W., Stead, C. M., Kensing, H., McCaul, K., Ngugi, S., Prior, J. L., Lipka, A., Nagy, J. M., Gregory, C. W., Judy, B. M., Harding, S. V., Titball, R. W., Sidhu, S. S., Trent, M. S., Kitto, G. B., Torres, A., Estes, D. M., Iverson, B., Georgiou, G. & Brown, K. A. (2011) Development of reagents and assays for the detection of pathogenic Burkholderia species. Faraday Discuss. 149, 23-36.
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Bradbury, A. R., Sidhu, S. S., Dübel, S., & McCafferty, J. (2011) Beyond natural antibodies: the power of in vitro display technologies. Nat. Biotechnol. 29, 245-54.
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Kaneko, T., Sidhu, S. S. & Li, S. S. (2011) Evolving specificity from variability for protein interaction domains. Trends Biochem. Sci. 36, 183-90.
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Koldobskaya, Y., Duguid, E. M., Shechner, D. M., Suslov, N. B., Ye, J., Sidhu, S. S., Bartel, D. P., Koide, S., Kossiakoff, A. A. & Piccirilli, J. A. (2011) A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat. Struct. Mol. Biol. 18, 100-6.
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2010

Oka, T., Remue, E., Meerschaert, K., Vanloo, B., Boucherie, C., Gfeller, D., Bader, G. D., Sidhu, S. S., Vandekerckhove, J., Gettemans, J. & Sudol, M. (2010) Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling. Biochem. J. 432, 461-72.
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Ernst, A., Gfeller, D., Kan, Z., Seshagiri, S., Kim, P. M., Bader, G.D. & Sidhu, S. S. (2010) Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol. Biosyst. 6, 1782-90.
Abstract on PubMed

Fisher, R. D., Ultsch, M., Lingel, A., Schaefer, G., Shao, L., Birtalan, S., Sidhu, S. S. & Eigenbrot, C. (2010) Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine. J. Mol. Biol. 402, 217-29.
Abstract on PubMed

Lam, H. Y. K., Kim, P. M., Mok, J., Tonikian, R., Sidhu, S. S., Turk, B. E., Snyder, M. & Gerstein, M. B. (2010) MOTIPS: Automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics. 11, 243.
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Birtalan, S., Fisher, R. D. & Sidhu, S. S. (2010) The functional capacity of the natural amino acids for molecular recognition. Mol. Biosyst. 6, 1186-94.
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2009

Pal, G. & Sidhu, S. S. (2009) Mapping protein function by combinatorial mutagenesis. In “Computational protein-protein interactions” (R. Nussinov & G. Schreiber, Eds.), pp 57-86, CRC Press, Boca Raton, FL.

Ernst, A. & Sidhu, S. S. (2009) Phage Display. In “Protein Engineering and Design” (S. Park and J. Cochran, Eds), pp1-22, Taylor and Francis: Boca Raton.

Li, B., Xi, H., Diehl, L., Lee, W. P., Sturgeon, L., Chinn, J., DeForge, L., Kelley, R. F., Wiesmann, C., van Lookeren Campagne, M. & Sidhu, S. S. (2009) Improving therapeutic efficacy of a complement receptor by structure-based affinity maturation. J. Biol. Chem. 284, 35605-11.
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Tonikian, R., Xin, X., Toret, C. P., Gfeller, D., Landgraf, C., Panni, S., Paoluzi, S., Castagnoli, L, Currell, B., Seshagiri, S., Yu, H. Winsor, B., Vidal, M., Davidson, A. R., Gerstein, M. B., Bader, G. D., Volkmer, R., Cesarini, G., Drubin, D. G., Kim, P. M., Sidhu, S. S. & Boone, C. (2009) Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 7, e1000218.
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Ernst, A., Sazinsky, S. L., Hui, S., Currell, B., Dharsee, M., Seshagiri, S., Bader, G. D. & Sidhu, S. S. (2009) Rapid evolution of functional complexity in a domain family. Sci. Signal. 2, ra50.
Abstract on PubMed

Uysal, S., Vasquez, V., Esaiki, K., Fellouse, F. A., Sidhu, S. S., Koide, S., Perozo, E. & Kossiakoff, A. A. (2009) Crystal structure of full-length KcsA in its closed conformation. Proc. Natl. Acad. Sci. USA 106, 6644-9.
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Koide, S. & Sidhu, S. S. (2009) The importance of being tyrosine: Lessons in molecular recognition from minimalist synthetic binding proteins. ACS Chem. Biol. 4, 325-34.
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Zhang, Y., Appleton, B. A., Wiesmann, C., Lau, T., Costa, M., Hannoush, R. N. & Sidhu, S. S. (2009) Inhibition of Wnt/b-catenin signaling by peptides that target dishevelled PDZ domains. Nat. Chem. Biol. 5, 217-9.
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Gao, J., Sidhu, S. S. & Wells, J. A. (2009) Two-state selection of conformation-specific antibodies. Proc. Natl. Acad. Sci. USA 106, 3071-6.
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2008

Tonikian, R., Zhang, Y., Sazinsky, S. L., Currell, B., Yeh, J. -H., Reva, B., Held, H. A., Appleton, B. A., Evangelista, M., Wu, Y., Xin, X., Chan, A. C., Seshagiri, S., Sander, C., Lasky, L. A., Boone, C., Bader, G. D. & Sidhu, S. S. (2008) A specificity map for the PDZ domain family. PLoS Biol. 6, e239.
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Newton, K., Matsumoto, M. L., Wertz, I. E., Kirkpatrick, D. S., Lill, J. R., Tan, J., Dugger, D., Gordon, N., Sidhu, S. S., Fellouse, F. A., Komuves, L., French, D. M., Ferrando, R. E., Lam, C., Compaan, D., Yu, C., Bosanac, I., Hymowitz, S. G., Kelly, R. F. & Dixit, V. M. (2008) Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell 134, 668-78.
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Gilbreth, R. N, Esaki, K., Koide, A., Sidhu, S. S. & Koide, S. (2008) A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J. Mol. Biol. 381, 407-18.
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Michnick, S. W. & Sidhu, S. S. (2008) Submitting antibodies to binding arbitration. Nat. Chem. Biol. 4, 326-9.
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Yeh, J.-H., Sidhu, S. S. & Chan, A. C. (2008) Regulation of a late phase of T cell polarity and effector functions by Crtam. Cell 132, 846-59.
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Birtalan, S., Zhang, Y., Fellouse, F. A., Shao, L., Schaefer, G. & Sidhu, S. S. (2008) The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. J. Mol. Biol. 337, 1518-28.
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Barthelemy, P. A., Raab, H., Appleton, B. A., Bond, C. J., Wu, P., Wiesmann, C. & Sidhu, S. S. (2008) Comprehensive analysis of the factors contributing to the stability and solubility of autonomous human VH domains. J. Biol. Chem. 138, 3639-54.
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2007

Ye, J.-D., Tereshko, V., Frederiksen, J. K., Koide, A., Fellouse, F. A., Sidhu, S. S., Koide, S., Kossiakoff, A. A. & Piccirilli, J. A. (2007) Antibodies that bind RNA: selection and co-crystallization. Proc. Natl. Acad. Sci. USA. 105, 82-7.
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Alto, N. M., Weflen, A. W., Rardin, M. J., Yarar, D., Lazar, C. S., Tonikian, R., Koller, A., Taylor, S. S., Boone, C., Sidhu, S. S., Schmid, S. L., Hecht, G. A. & Dixon, J. E. (2007) The type III effector EspF coordinates membrane trafficking by the spatiotemporal activation of two eukaryotic signaling pathways. J. Cell Biol. 178, 1265-78.
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Sidhu, S. S. & Koide, S. (2007) Phage display for engineering and analyzing protein interaction interfaces. Curr. Opin. Struct. Biol. 17, 481-7.
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Fellouse, F. A., Esaki, K., Birtalan, S., Raptis, J., Cancasci, V. J., Koide, A., Jhurani, P., Vasser, M., Wiesmann, C., Kossiakoff, A. A., Koide, S. & Sidhu, S. S. (2007) High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J. Mol. Biol. 373, 924-40.
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Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., Wiesmann, C., Skelton, N. J. & Sidhu, S. S. (2007) Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Sci. 16, 2454-71.
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Zhang, Y., Appleton, B. A., Wu, P., Wiesmann, C. & Sidhu, S. S. (2007) Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain. Protein Sci. 16, 1738-50.
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Tonikian, R., Zhang, Y., Boone, C. & Sidhu, S. S. (2007) Identifying specificity profiles for peptide binding modules with phage-displayed peptide libraries. Nat. Protoc. 2, 1368-86.
Abstract on PubMed

Gupta, R., Kus, B., Fladd, C., Wasmuth, J., Tonikian, R., Sidhu, S. S., Krogan, N. J., Parkinson, J. & Rotin, D. (2007) Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol. Syst. Biol. 3, 116.
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Sidhu, S. S. & Kossiakoff, A. A. (2007) Exploring and designing protein function with restricted diversity. Curr. Opin. Chem. Biol. 11, 347-54.
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Sidhu, S. S. (2007) Full-length antibodies on display. Nat. Biotechnol. 25, 537-8.
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Fellouse, F. A. & Sidhu, S. S. (2007) Making antibodies in bacteria. In “Making and using antibodies” (G. C. Howard & M. R. Kaser, Eds.), pp157-180, CRC Press, Boca Raton, FL.

Sidhu, S. S., Feld, B. K. & Weiss, G. A. (2007) M13 bacteriophage coat proteins engineered for improved phage display. Methods Mol. Biol. 352, 205-19.
Abstract on PubMed

2006

Sidhu, S. S. & Fellouse, F. A. (2006) Synthetic therapeutic antibodies. Nat. Chem. Biol. 12, 682-8.
Abstract on PubMed

Li, B., Totpal, K., Russell, S., Yeh, S., Wong, W. L., Cochran, A., Ashkenazi, A., Hymowitz, S & Sidhu, S. S. (2006) Activation of the proapoptotic death receptor DR5 by oligomeric peptide and antibody agonists. J. Mol. Biol. 361, 522-36.
Abstract on PubMed

Pal, G., Kouadio, J. -L., Artis, D. R., Kossiakoff, A. A. & Sidhu, S. S. (2006) Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J. Biol. Chem. 281, 22378-85. JBC paper of the week. Cover feature in ASBMB Today (October, 2006).
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Appleton, B. A., Zhang, Y., Wu, P., Yin, J. P., Hunziker, W., Skelton, N. J. Sidhu, S. S. & Wiesmann, C. (2006) Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1: Insights into determinants of PDZ domain specificity. J. Biol. Chem. 281, 22312-20.
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Zhang, Y., Yeh, S., Appleton, B. A., Held, H. A., Kausalya, J. P., Phua , D. C. Y., Wong, W. L., Lasky, L. A., Wiesmann, C., Hunziker, W. & Sidhu, S. S. (2006) Convergent and divergent ligand specificity amongst the PDZ domains of the LAP and zonula occludens (ZO) families. J. Biol. Chem. 281, 22299-311.
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Fellouse, F. A., Barthelemy, P. A., Kelley, R. F. & Sidhu, S. S. (2006) Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code. J. Mol. Biol. 357, 100-14.
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Fellouse, F. A. & Sidhu, S. S. (2006) Synthetic antibody libraries. In “Phage display in drug discovery and Biotechnology” (S. S. Sidhu, Ed.), pp 709-740, CRC Press, Boca Raton, FL.

2005

Pal, G., Fong, S.-Y., Kossiakoff, A. A. & Sidhu, S. S. (2005) Alternative views of functional protein binding epitopes obtained by combinatorial shotgun scanning mutagenesis. Protein Sci. 14, 2405-13.
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Fellouse, F. A., Li, B., Compaan, D. M., Peden, A. A., Hymowitz, S. G. & Sidhu, S. S. (2005) Molecular recognition by a binary code. J. Mol. Biol. 348, 1153-62. Cover feature.
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Bond, C., Wiesmann, C., Marsters, J. C. & Sidhu, S. S. (2005) A structure-based database of antibody variable domain diversity. J. Mol. Biol. 348, 699-709.
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Pal, G., Ultsch, M. H., Clark, P. C., Currell, B., Kossiakoff, A. A. & Sidhu, S. S. (2005) Intramolecular cooperativity in a protein binding site assessed by combinatorial shotgun scanning mutagenesis. J. Mol. Biol. 347, 489-94.
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Lasky, L. A., Skelton, N. J. & Sidhu, S. S. (2005) PDZ domains: Intracellular mediators of carboxy-terminal protein recognition and scaffolding. In “Modular protein domains” (G. Cesarini, M. Gimona, M. Sudol & M. Yaffe, Eds.), pp 257-278, Wiley-VCH Inc., Germany.

2004

Fellouse, F. A., Wiesmann, C. & Sidhu, S. S. (2004) Synthetic antibodies from a four amino acid code: A dominant role for tyrosine in antigen recognition. Proc. Natl. Acad. Sci. USA 101, 12467-72.
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Lee, C. V., Liang, W.-C., Dennis, M. S., Eigenbrot, C., Sidhu, S. S. & Fuh, G. (2004) High affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J. Mol. Biol. 340, 1073-93.
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Skelton, N. J., Schaffer, M. L., Deshayes, K., Blandl, T., Runyon, S., Nakamura, G. & Sidhu, S. S. (2004) Phage display-derived peptide-binding provides structural insight into insulin-like growth factor I function. Spectroscopy 18, 237-49.
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Held, H. A. & Sidhu, S. S. (2004) Comprehensive mutational analysis of the M13 major coat protein: Improved scaffolds for C-terminal phage display. J. Mol. Biol. 340, 587-97.
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Sidhu, S. S., Li, B., Chen, Y., Fellouse, F. A., Eigenbrot, C. & Fuh, G. (2004) Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. J. Mol. Biol. 338, 299-310.
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Lee, C. V., Sidhu, S. S. & Fuh, G. (2004) Bivalent antibody phage display mimics natural immunoglobulins. J. Immunol. Methods 284, 119-32.
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Mattera, R., Ritter, B., Sidhu, S. S., McPherson, P. S. & Bonifacino, J. S. (2004) Definition of the consensus motif recognized by gamma-adaptin ear domains. J. Biol. Chem. 279, 8018-28.
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2003

Weiss, G. A., Roth, T. A., Baldi, P. F. & Sidhu, S. S. (2003) Comprehensive mutagenesis of the C-terminal domain of the M13 gene-3 minor coat protein: The requirements for assembly into the bacteriophage particle. J. Mol. Biol. 332, 777-82.
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Schaffer, M. L., Deshayes, K., Nakamura, G. R., Sidhu, S. S. & Skelton, N. J. (2003) Complex with a phage display-derived peptide provides insight into the function of insulin-like growth factor I. Biochemistry 42, 9324-34.
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Bond, C., Marsters, J. C. Jr. & Sidhu, S. S. (2003) Contributions of CDR3 to VHH domain stability and the design of monobody scaffolds for naïve antibody libraries. J. Mol. Biol. 332, 643-55.
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Pal, G., Kossiakoff, A. A., Sidhu, S. S. (2003) The functional binding epitope of a high affinity variant of human growth hormone mapped by shotgun alanine-scanning mutagenesis: Insights into the mechanisms responsible for improved affinity. J. Mol. Biol. 332, 195-204.
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Sidhu, S. S. & Weiss, G. A. (2003) Constructing phage display libraries by oligonucleotide-directed mutagenesis. In “Phage display: A practical approach” (T. Clackson and H. B. Lowman, Eds.), pp 27-41, Oxford University Press.

Skelton, N. J., Koehler, M. F. T., Zobel, K., Wong, W. L., Yeh, S., Pisabarro, M. T., Yin, J. P., Lasky, L. A. & Sidhu, S. S. (2003) Origins of PDZ domain ligand specificity: Structure determination and mutagenesis of the Erbin PDZ domain. J. Biol. Chem. 278, 7645-54.
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Sidhu, S. S., Bader, G. D. & Boone, C. (2003) Functional genomics of intracellular peptide recognition domains with combinatorial biology methods. Curr. Opin. Chem. Biol. 7, 97-102.
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Sidhu, S. S., Fairbrother, W. J. & Deshayes, K. (2003) Exploring protein-protein interactions with phage display. Chembiochem 4, 14-25. Cover feature.
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2002

Sidhu, S. S. & Weiss, G. A. (2002). DNA-encoded peptide libraries and drug discovery. In “Anticancer drug development” (B. Baguley and D. Kerr, Eds.), pp 237-248, Academic Press, San Diego.

Roth, T. A., Weiss, G. A., Eigenbrot, C. & Sidhu, S. S. (2002). A minimized M13 coat protein defines the requirements for assembly into the bacteriophage particle. J. Mol. Biol. 322, 357-67.
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Laura, R. P., Witt, A. S., Held, H. A., Gerstner, R., Deshayes, K., Koehler, M. F. T., Kosik, K. S., Sidhu, S. S. & Lasky, L. A. (2002). The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of d-catenin and ARVCF. J. Biol. Chem. 277, 12906-14.
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Vajdos, F. F., Adams, C. W., Breece, T. N., Presta, L. G., de Vos, A. M. & Sidhu, S. S. (2002). Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. J. Mol. Biol. 320, 415-28.
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Deshayes, K., Schaffer, M., Skelton, N. J., Nakamura, G., Kadkhodayan, S. & Sidhu, S. S. (2002). Rapid identification of small binding motifs with high-throughput phage display: Discovery of peptidic antagonists of IGF-1. Chem. Biol. 9, 495-505.
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2001

Sidhu, S. S. (2001). Getting what you want from phage display. Trends Microbiol. 9, 565.

Sidhu, S. S. (2001). Phage display: Increasing the rewards from genomic information. Drug Discov. Today 6, 936.
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Sidhu, S. S. (2001). Engineering M13 for phage display. Biomol. Eng. 18, 57-63.
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Pelletier, J. & Sidhu, S. S. (2001). Mapping protein-protein interactions with combinatorial biology methods. Curr. Opin. Biotechnol. 12, 340-7.
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2000 and Earlier

Sidhu, S. S. (2000). Phage display in pharmaceutical biotechnology. Curr. Opin. Biotechnol. 11, 610-6.
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Sidhu, S. S., Lowman, H. B., Cunningham, B. C. & Wells, J. A. (2000). Phage display for selection of novel binding peptides. Methods Enzymol. 328, 333-63.
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Fuh, G. & Sidhu, S. S. (2000). Efficient phage display of polypeptides fused to the carboxy-terminus of the M13 gene-3 minor coat protein. FEBS Lett. 480, 231-4.
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Weiss, G. A., Watanabe, C., Zhong, A., Goddard A. & Sidhu, S. S. (2000). Rapid mapping of protein functional epitopes by combinatorial alanine-scanning. Proc. Natl. Acad. Sci. U.S.A. 97, 8950-4.
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Fuh, G., Pisabarro, M. T., Li, Y., Quan, C., Lasky, L. A. & Sidhu, S. S. (2000). Analysis of PDZ domain-ligand interactions using carboxyl-terminal phage display. J. Biol. Chem. 275, 21486-91.
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Weiss, G. A. & Sidhu, S. S. (2000). Design and evolution of artificial M13 coat proteins. J. Mol. Biol. 300, 213-9.
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Weiss, G. A., Wells, J. A. & Sidhu, S. S. (2000). Mutational analysis of the major coat protein of M13 identifies residues that control protein display. Protein Sci. 9, 647-54.
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Sidhu, S. S., Weiss, G. A. & Wells, J. A. (2000). High copy display of large proteins on phage for functional selections. J. Mol. Biol. 296, 487-95.
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Baardsnes, J., Sidhu, S. S., Macleod, A., Elliott, J., Morden, D., Watson, J. & Borgford, T. J. (1998). Streptomyces griseus protease B - Secretion correlates with the length of the propeptide. J. Bacteriol. 180, 3241-4.
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Sidhu, S. S. & Borgford T. J. (1996). Selection of Streptomyces griseus protease B mutants with desired alterations in primary specificity using a library screening strategy. J. Mol. Biol. 257, 233-45.
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Sidhu, S. S., Kalmar, G. B., Willis, L. G. & Borgford, T. J. (1995). Protease evolution in Streptomyces griseus: Discovery of a novel dimeric enzyme. J. Biol. Chem. 270, 7594-600.
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Sidhu, S. S., Kalmar, G. B., Willis, L. G. & Borgford, T. J. (1994). Streptomyces griseus protease C: A novel enzyme of the chymotrypsin superfamily. J. Biol. Chem. 269, 20167-71.
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Sidhu, S. S., Kalmar, G. B. & Borgford, T. J. (1993). Characterization of the gene encoding the glutamic acid-specific protease of Streptomyces griseus. Biochem. Cell Biol. 71, 454-61.
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