Cochran Lab
Cochran Lab
PUBLICATIONS

2017

Mong S.K., Cochran F.V., Yu H., Graziano Z., Lin Y.S., Cochran J.R. and Pentelute B. (2017) Heterochiral Knottin Protein: Folding and Solution Structure, Biochemistry 56 (43), 5720–5725. http://pubs.acs.org/doi/abs/10.1021/acs.biochem.7b00722

Mitchell A.C., Alford S.C., Hunter S.A., Kannan, D., Parra Sperberg R.A., Chang C.H., Cochran J.R. (2017) Development of a Protease Biosensor Based on a Dimerization-Dependent Red Fluorescent Protein. In press, ACS Chemical Biology. http://pubs.acs.org/doi/abs/10.1021/acschembio.7b00715

Thayaparan T., Petrovic R.M., Achkova D.Y., Zabinski T., Davies D.M., Klampatsa A., Parente-Pereira A.C., Whilding L.M., van der Stegen S., Woodman N., Sheaff M., Cochran J.R., Spicer J.F., Maher, J. (2017) CAR T-cell immunotherapy of MET-expressing malignant mesothelioma. In Press, OncoImmunology, Published online: 14 Aug 2017. http://dx.doi.org/10.1080/2162402X.2017.1363137

Longwell, C.K., Labanieh, L. Cochran J.R. (2017) High-throughput screening technologies for enzyme engineering. Current Opinion in Biotechnology, 48: 196-202. doi: 10.1016/j.copbio.2017.05.012. Article

Steele, A.N., Cai, L., Truong, V.N., Edwards, B.B., Goldstone, A.B., Eskandari, A., Mitchell, A.C., Marquardt, L.M., Foster, A.A., Cochran, J.R., Heilshorn, S.C., and Woo Y.J. (2017) A novel protein-engineered hepatocyte growth factor analog released via a shear-thinning injectable hydrogel enhances post-infarction ventricular function. Biotechnology & Bioengineering. Jun 2. doi: 10.1002/bit.26345. [Epub ahead of print]. Article

Kwan, B.H., Zhu, E.F., Tzeng, A., Sugito, H.R., Eltahir, A.A., Ma, B., Delaney, M.K., Murphy, P.A., Kauke, M.J., Angelini, A., Momin, N., Mehta, N.K., Maragh, A.M., Hynes, R.O., Dranoff, G., Cochran, J.R., and Wittrup, K.D. (2017) Integrin-targeted cancer immunotherapy elicits protective adaptive immune responses. In Press, Journal of Experimental Methods, DOI: 10.1084/jem.20160831 Article

Kapur, S., Silverman, A.P., Ye, A.Z., Papo, N., Jindal, D. Blumenkranz, M.S., Cochran, J.R. (2017) Engineered ligand-based VEGFR antagonists with increased receptor binding affinity more effectively inhibit angiogenesis. Bioengineering and Translational Medicine. 2(1): 81–91 Article

Kim J.W., Cochran J.R. (2017) Targeting ligand-receptor interactions for development of cancer therapeutics. Current Opinion in Chemical Biology, 38:62-69.Article

Lim S, Glasgow J.E., Filsinger Interrante M., Storm E.M., Cochran J.R. (2017) Dual display of proteins on the yeast cell surface simplifies quantification of binding interactions and enzymatic bioconjugation reactions. Biotechnology Journal. Mar 16. doi: 10.1002/biot.201600696.Article

ACS Chemical BiologyLim S., Chen B., Kariolis M.S., Dimov I.K., Baer T.M., Cochran J.R. (2017) Engineering High Affinity Protein-Protein Interactions Using a High-Throughput Microcapillary Array Platform. ACS Chemical Biology. Feb 17;12(2):336-341. doi: 10.1021/acschembio.6b00794. Article

Hecht, A., Glasgow, J., Jaschke, P.R., Bawazer, L.A., Munson, M.S., Cochran, J.R., Endy, D., Salit, M. (2017) Measurements of translation initiation from all 64 codons in E. coli. Nucleic Acids Research. doi.org/10.1093/nar/gkx070. Article Press release

Kariolis M.S., Miao Y.R., Diep A., Nash S.E., Olcina M.M., Jiang D., Jones D.S., Kapur S., Mathews I.I., Koong A.C., Rankin E.B., Cochran J.R., Giaccia A.J. (2017) Inhibition of the GAS6/AXL pathway augments the efficacy of chemotherapies. Journal of Clinical Investigation. 127(1):183-198. doi: 10.1172/JCI85610. [Epub ahead of print] Article

2016

Moynihan K.D., Opel C.F., Szeto G.L., Tzeng A., Zhu E.F., Engreitz J.M., Williams R.T., Rakhra K., Zhang M.H., Rothschilds A.M., Kumari S., Kelly R.L., Kwan B.H., Abraham W., Hu K., Mehta N.K., Kauke M.J., Suh H., Cochran J.R., Lauffenburger D.A., Wittrup K.D., Irvine D.J. (2016) Eradication of large established tumors in mice by combination immunotherapy that engages innate and adaptive immune responses. Nature Medicine, 22(12):1402-1410. doi: 10.1038/nm.4200. Article

Trends in Pharmacological SciencesKintzing, J.R., Filsinger Interrante, M.V., Cochran, J.R. (2016) Emerging strategies for developing next-generation protein therapeutics for cancer treatment. Trends in Pharmacological Sciences, 37(12):993-1008. doi: 10.1016/j.tips.2016.10.005. Article

Kintzing, J.R. and Cochran, J.R. (2016) Engineered knottin peptides as diagnostics, therapeutics, and drug delivery vehicles. Current Opinion in Chemical Biology. Sep 16;34:143-150. doi: 10.1016/j.cbpa.2016.08.022. [Epub ahead of print] Article

Hunter, S.A. and Cochran, J.R. (2016) Cell-binding assays for determining the affinity of protein-protein interactions: Technologies and considerations. Methods in Enzymology 580:21-44. doi: 10.1016/bs.mie.2016.05.002. Article

Angewante Chemie Int Ed Engl.Cox, N., Kintzing, J.R., Smith, M., Grant, G.A., and Cochran, J.R. (2016) Integrin-targeting knottin peptide-drug conjugates are potent inhibitors of tumor cell proliferation. Angew Chem Int Ed Engl. (Communication) 55(34):9894-7. Article. Press release.
*Highlighted as a VIP (Very Important Paper) designated to less than 5% of all articles published in the journal

Molecular Cancer TherapeuticsCurrier N.V., Ackerman S.E., Kintzing J.R., Chen R., Filsinger Interrante M., Steiner A., Sato A.K., Cochran J.R. Targeted drug delivery with an integrin-binding knottin-Fc-MMAF conjugate produced by cell-free protein synthesis. Molecular Cancer Therapeutics.15(6):1291-300. doi: 10.1158/1535-7163.MCT-15-0881. Article. Press release. Highlight.

Glasgow J.E., Salit M.L., Cochran J.R. (2016) In vivo site-specific protein tagging with diverse amines using an engineered sortase variant. Journal of the American Chemical Society. 138(24):7496-9. doi: 10.1021/jacs.6b03836. Article.

Suarez, S.L., Muñoz, A., Mitchell, A.C., Braden, R.L., Luob, C., Cochran, J.R., Almutairi, A., Christman, K.L. (2016) Degradable acetalated dextran microparticles for tunable release of an engineered hepatocyte growth factor fragment, ACS Biomaterials Science & Engineering, 2 (2), 197-204. 10.1021/acsbiomaterials.5b00335. Article

Chen, B., Lim, S., Kannan, A., Alford, S.C., Sunden, F., Herschlag, D., Dimov, I., Baer, T.M., Cochran, J.R. (2016) High-throughput analysis and protein engineering using microcapillary arrays. Nature Chemical Biology, 12, 76-81. doi:10.1038/nchembio.1978.
Article. Press release. News & Views

Mitchell A.C., Briquez P.S., Hubbell J.A., Cochran J.R. (2016) Engineering growth factors for regenerative medicine applications. Acta Biomaterialia. 30:1-12 doi: 10.1016/j.actbio.2015.11.007. Article

2015

Cherf, G.M. and Cochran, J.R. (2015) Applications of yeast surface display for protein engineering, Methods in Molecular Biology, 1319: 155-75. doi: 10.1007/978-1-4939-2748-7_8. Article

Zheng L.L., Vanchinathan V., Dalal R., Noolandi J., Waters D.J., Hartmann L., Cochran J.R., Frank C.W., Yu C.Q., Ta C.N. (2015) Biocompatibility of poly(ethylene glycol) and poly(acrylic acid) interpenetrating network hydrogel by intrastromal implantation in rabbit cornea. Journal of Biomedical Materials Research A. 103(10):3157-65. doi: 10.1002/jbm.a.35453. Article

Parke-Houben R., Fox C.H., Zheng L.L., Waters D.J., Cochran J.R., Ta C.N., Frank C.W. (2015) Interpenetrating polymer network hydrogel scaffolds for artificial cornea periphery. Journal of Materials Science: Materials in Medicine. 26(2), 107. Article

Sonnenberg, S., Rane, A.A., Liu, C.J., Rao, N., Agmon, G., Suarez, S., Wang, R., Munoz, A., Bajaj, V., Zhang, S., Braden, R., Schup-Magoffin, P.J., Kwan, O.L., DeMaria, A.N., Cochran, J.R., Christman, K.L. (2015) Delivery of an engineered HGF fragment in an extracellular matrix-derived hydrogel prevents negative LV remodeling post-myocardial infarction, Biomaterials. 45, 56-63. Article

Kim, J.W., Cochran, F.V., and Cochran, J.R. (2015) A chemically cross-linked knottin dimer binds integrins with picomolar affinity and inhibits tumor cell migration and proliferation. Journal of the American Chemical Society (Communication), 137 (1), 6-9. Article

2014

Liu, C. J., Jones, D. S., Tsai, P.C., Venkataramana, A. and Cochran, J.R. (2014) An engineered dimeric fragment of hepatocyte growth factor is a potent c-MET agonist. FEBS Letters, 588, 4831-4837 Article

Kariolis, M.S., Miao, Y.R., Jones, D.S., Kapur, S., Mathews, I.I., Giaccia. A.J., Cochran, J.R. (2014) An Engineered Axl ‘decoy receptor’ effectively silences the Gas6-Axl signaling axis. Nature Chemical Biology, 10(11), 977-83. doi:10.1038/nchembio.1636
Article | Press release | SF Chronicle | NBC News

Ackerman, S.E., Wilson, C.M., Kahn, S.A., Kintzing, J.R., Jindal, D.A., Cheshier, S., Grant, G.A., Cochran, J.R. (2014) A bioengineered peptide that localizes to and illuminates medulloblastoma: A new tool with potential or fluorescence-guided surgical resection. Cureus 6(9): e207. doi:10.7759/cureus.207    Article 
**Winner of the Grand Prize for Scientific Acclaim-- ZEISS & Cureus Intraoperative Fluorescence Publishing Competition**

Ackerman, S.E., Currier, N.V., Bergen, J.M., and Cochran, J.R. (2014) Cystine-knot peptides: emerging tools for cancer imaging and therapy. Expert Opinion in Proteomics, 11, 561-572, doi: 10.1586/14789450.2014.932251 Article

Liu, C. J. and Cochran, J.R. (2014) “Engineering Multivalent and Multispecific Protein Therapeutics”, in Engineering in Translational Medicine, Weibo Cai, ed., Springer, Chapter 14, page 365-396 Article

2013

Moore, S. J., Hayden Gephart, M.G., Bergen, J.M., Su, Y.S., Rayburn, H., Scott, M. P., Cochran, J.R. (2013) Engineered knottin peptide enables noninvasive optical imaging of intracranial medulloblastoma. Proceedings of the National Academy of Science, 110(36):14598-603. doi: 10.1073/pnas.1311333110 Article | Press Release

Kariolis, M.S., Kapur, S., and Cochran, J.R. (2013) Beyond antibodies: using biological principles to guide the development of next-generation protein therapeutics. Curr Opin Biotechnol. 24(6):1072-7. doi: 10.1016/j.copbio.2013.03.017 Article

Moore, S. J., Leung, C. L., Norton, H.K., and Cochran, J. R. (2013) Engineering Agatoxin, a cystine-knot peptide from spider venom, as a molecular probe for in vivo tumor imaging, PLoS ONE, 8, e60498. Article

Myung, D., Kourtis, L., Noolandi, J., Cochran, J., Ta, C.N., and Frank C.W. (2013) "Surface Modification of High-Strength Interpenetrating Network Hydrogels for Biomedical Device Applications," Chapter 10, pp 407-446, in Handbook of Biofunctional Surfaces, Wolfgang Knoll, ed., Pan Stanford Publishing.

Jiang, H., Moore, S. J., Liu, S., Liu, H., Miao, Z., Cochran, F.V., Liu, Y., Tian, M. Cochran J.R., Zhang, H., and Cheng, Z. (2013) A novel radiofluorinated agouti-related protein for tumor angiogenesis imaging. Amino Acids. 44(2):673-81. doi: 10.1007/s00726-012-1391-y. Article


2012

Moore, S. J., Leung, C. L., and Cochran, J. R. (2012) Knottins: Disulfide-bonded Therapeutic and Diagnostic Peptides. Drug Discovery Today: Technologies, 9, e3-e11. Article

Jiang, L., Miao, Z., Kimura, R. H., Silverman, A. P., Ren, G., Liu, H., Lu, H., Cochran, J. R., Cheng, Z. (2012) 111In-labeled cystine-knot peptides based on the Agouti-related protein for targeting tumor angiogenesis.  Journal of Biomedicine and Biotechnology. Article ID 368075, doi:10.1155/2012/368075. Article

Charalel, R.A., Engberg, K., Noolandi, J., Cochran, J.R., Frank, C.W., Ta, C.N. (2012) Diffusion of Protein Through the Human Cornea. Ophthalmic Research. 48, 50-55. Article

Moore, S. J. and Cochran, J. R. (2012) Engineering Knottins as Novel Binding Agents. Methods in Enzymology. 503, 223-251. Article


2011

Jones., D. S., Tsai, P.C, and Cochran, J. R. (2011) Engineering hepatocyte growth factor fragments with high stability and activity as Met receptor agonists and antagonists. Proceedings of the National Academy of Science. 108, 13035-40. Article

Papo, N., Silverman, A. P., Lahti, J. L., and Cochran, J. R. (2011) Antagonistic VEGF variants engineered to simultaneously bind to and inhibit VEGFR2 and alphav beta3 integrin. Proceedings of the National Academy of Science. 108, 14067-72. Article | Press Release

Kimura, R. H., Jones, D. S., Jiang, L., Miao, Z., Cheng, Z., and Cochran, J. R. (2011) Functional Mutation of Multiple Solvent-Exposed Loops in the Ecballium elaterium Trypsin Inhibitor-II Cystine Knot Miniprotein. PLoS ONE, 6, e16112. Article

Silverman, A. P., Kariolis, M. S., and Cochran, J. R. (2011) Cystine-Knot Peptides Engineered With Specificities for alphaiib beta3 or alphaiib beta3 and alphav beta3 Integrins are Potent Inhibitors of Platelet Aggregation. Journal of Molecular Recognition. 24, 127-135. Article

Lahti, J. L., Lui, B. H., Beck, S. E., Lee, S. S., Ly, D. P., Longaker, M. T., Yang, G. P., and Cochran, J. R. (2011) Engineered Epidermal Growth Factor Mutants with Faster Binding On-Rates Correlate with Enhanced Receptor Activation. FEBS Letters. 585, 1135-1139. Article

Lui, B. H., Cochran, J. R., and Swartz, J. R. (2011) Discovery of improved EGF agonists using a novel in vitro screening platform. Journal of Molecular Biology. 413, 406-415. Article

Jiang, L., Miao, Z., Kimura, R. H., Liu, H., Cochran, J.R., Culter, C.S., Bao, A., Li, P., and Cheng, Z. (2011) Preliminary evaluation of (177)Lu-labeled knottin peptides for integrin receptor-targeted radionuclide therapy. Eur J Nucl Med Mol Imaging. 38, 613-22. Article

Liu, S., Liu, H., Ren, G., Kimura, R.H., Cochran, J.R., Cheng, Z. (2011) PET imaging of Integrin Positive Tumors using 18F-labeled knottin peptides. Theranostics. 1, 403-12. Article

Hartmann, L., Watanabe, K., Zheng, L.L., Kim, C-Y., Beck, S. E., Huie, P., Noolandi, J., Cochran, J. R., Ta, C.N., Frank, C.W. (2011) Toward the Development of an Artifical Cornea: Improved Stability of Interpenetrating Polymer Networks. Journal of Biomedical Materials Research: Part B -- Applied Biomaterials. 98B, 8-17.

Lui, B. H., and Cochran, J. R. (2011) “Rational and Combinatorial Methods for Creating Designer Protein Interfaces”, in Comprehensive Biomaterials, Ducheyne, Healy, Hutmacher, Grainger, and Kirkpatrick, eds., Elsevier. October 2011. Book


2010

Science in Translational MedicineCochran, J.R. (2010) Engineered Proteins Pull Double Duty. Science Translational Medicine, 2, 17ps5. Article

Cochran, F.V., and Cochran, J.R. (2010) Phage Display and Molecular Imaging: Expanding Fields of Vision in Living Subjects. Biotechnology and Genetic Engineering Reviews. 27, 57-94. Article

Atmaja, B., Lui, B.H., Hu, Y., Beck, S. E., Frank, C. W., and Cochran, J.R. (2010) Targeting of Cancer Cells Using Quantum Dot-Polypeptide Hybrid Assemblies that Function as Molecular Imaging Agents and Carrier Systems. Advanced Functional Materials. 20, 4091-97. Article

Kimura, R. H., Miao, Z., Cheng, Z., Gambhir, S. S., Cochran, J. R. (2010) A Dual-Labeled Knottin Peptide for PET and Near-Infrared Fluorescence Imaging of Integrin Expression in Living Subjects. Bioconjugate Chemistry, 21, 436-44. Article

Nielsen, C.H., Kimura, R. H. Withofs, N., Tran, P.T., Miao, Z., Cochran, J.R., Cheng, Z., Felsher, D., Kjaer, A., Willmann, J. K., Gambhir, S.S. (2010) PET Imaging of Tumor Neovascularization in a Transgenic Mouse Model Using a Novel 64-Cu-DOTA-Knottin Peptide. Cancer Research, 70, 9022-30. Article

Willmann, J. K., Kimura, R. H., Deshpande, N., Lutz, A. M., J., Cochran, J. R., and Gambhir, S. S. (2010) Targeted Contrast-Enhanced Ultrasound Imaging of Tumor Angiogenesis with Contrast Microbubbles Conjugated to Integrin-Binding Knottin Peptides. Journal of Nuclear Medicine, 51, 433-40. Article | Press Release

Jiang, L., Kimura, R. H., Miao, Z., Silverman, A. P., Ren, G., Liu, H. G., Li, P. Y., Gambhir, S. S., Cochran, J. R.†, and Cheng, Z.† (2010) Evaluation of a 64Cu-Labeled Cystine-Knot Peptide Based on Agouti Related Protein for PET Imaging of Tumors Expressing alphav beta3 Integrin. Journal of Nuclear Medicine, 51, 251-8. †co-corresponding authors. Article


2009

Lahti, J. L., Silverman, A. P., Cochran, J. R. (2009) Interrogation and Prediction of Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein. PLoS Computational Biology, 5, e1000499. Article

Kimura, R. H., Levin, A. M., Cochran, F. V., and Cochran, J. R. (2009) Engineered Cystine Knot Peptides that Bind alphav beta3, alphav beta5, and alpha5 beta1 Integrins with Low Nanomolar Affinity. Proteins: Structure, Function, and Bioinformatics. 77, 359-69. Article

Silverman, A. P., Levin, A. M., Lahti, J. L., and Cochran, J. R. (2009) Engineered Cystine-Knot Peptides That Bind alphav beta3 Integrin with Antibody-Like Affinities. Journal of Molecular Biology, 385, 1064-75. Article

Miao, Z., Ren G., Liu, H., Kimura, R.H., Jiang, L., Cochran, J.R., Gambhir, S.S, Cheng, Z. (2009) An Engineered Knottin Peptide Labeled with 18F for PET Imaging of Integrin Expression. Bioconjugate Chemistry, 20, 2342-7. Article

Kimura, R. H., Cheng, Z., Gambhir, S.S., and Cochran, J. R. (2009) Engineered Knottin Peptides: A New Class of Agents for Imaging Integrin Expression in Living Subjects. Cancer Research, 69, 2435-42. Article | Highlights | GEN News article

Garrett, T.P., Burgess, A.W., Gan, H.K., Luwor, R.B., Cartwright, G., Walker, F., Orchard, S.G., Clayton, A.H., Nice, E.C., Rothacker, J., Catimel, B., Cavenee, W.K., Old, L.J., Stockert, E., Ritter, G., Adams, T.E., Hoyne, P.A., Wittrup, K.D., Chao, G., Cochran, J.R., Luo, C., Lou, M., Huyton, T., Xu, Y., Fairlie, W.D., Yao, S., Scott, A.M., and Johns, T.G. (2009) Antibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR. Proceedings of the National Academy of Science, 106, 5082-7. Article

Myung, D., Farooqui, N., Zheng, L., Koh, W., Gupta, S. Noolandi, J., Cochran, J. R., Frank, C. W., Ta, C. N. (2009) Bioactive Interpenetrating Polymer Network Hydrogels that Support Corneal Surface Epithelial Wound Healing, Journal of Biomedical Materials Research, Part A, 90, 70-81. Article

Lahti, J. L., and Cochran, J. R. (2009) “Yeast Surface Display”, in Therapeutic Antibodies: from Theory to Practice, Zhiqiang An and William Strohl, eds., John Wiley & Sons, Inc. Release date: October 2009. Book

Moore, S. J., Olsen, M. J., Cochran J.R., and Cochran, F.V. (2009) “Cell Surface Display Systems for Protein Engineering” in Protein Engineering and Design, Sheldon J. Park and Jennifer R. Cochran, eds., Taylor and Francis, Boca Raton. Release date: September 25, 2009. Book

Sheldon J. Park and Jennifer R. Cochran, eds. (2009) Protein Engineering and Design, Taylor and Francis, Boca Raton. Release date: September 25, 2009. Book


2008

Jones, D.S., Silverman, A.P., Cochran, J.R. (2008) Developing Therapeutic Proteins by Engineering Ligand-Receptor Interactions. Trends in Biotechnology, 26, 498-505. Article

Myung, D., Duhamel, P.E., Cochran, J. R., Noolandi, J., Ta, C.N., and Frank, C. W. (2008) Development of Hydrogel-Based Keratoprostheses: A Materials Perspective. Biotechnology Progress, 24, 735-741. Article


2007

Hanick, N. A., Rickert, M., Varani, L., Bankovich, A. J., Cochran, J. R., Kim, D. M., Surh, C. D., and Garcia, K. C. (2007) Elucidation of the Interleukin-15 binding site on its alpha receptor by NMR. Biochemistry, 46, 9453-61. Article

Myung, D., Koh, W., Bakri, A., Zhang, F., Marshall, A., Ko, J., Noolandi, J., Carrasco, M., Cochran, J. R., Frank, C. W., Ta, C. N. (2007) Design and Fabrication of an Artificial Cornea Based on a Photolithographically Patterned Hydrogel Construct. Biomedical Microdevices. 9, 911-22. Article

 

back to top