All Publications

Silberstein JL, Du J, Kun-Wei C, Frank JA, Mathews II, Kim YB, You J, Lu Q, Liu J, Philips EA, Liu P, Rao E, Fernandez D, Rodriguez GE, Kong XP, Wang J, Cochran JR. (2024). Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function. PNAS

McIntosh BJ, Hartmann GG, Yamada-Hunter SA, Liu P, Williams CF, Sage J, Cochran JR. (2023). An engineered interleukin-11 decoy cytokine inhibits receptor signaling and proliferation in lung adenocarcinoma. Bioeng Transl Med

Miller CL, Sagiv-Barfi I, Neuhöfer P, Czerwinski DK, Bertozzi CR, Cochran JR, Levy R. (2023). Targeted TLR9 Agonist Elicits Effective Antitumor Immunity against Spontaneously Arising Breast Tumors. J Immunol

Hollander MJ, Malaker SA, Riley NM, Perez I, Abney NM, Gray MA, Maxson JE, Cochran JR, Bertozzi CR. (2023) Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. J Biol Chem

Zeng L, Liu Y, Nguyenla XH, Abbott TR, Han M, Zhu Y, Chemparathy A, Lin X, Chen X, Wang H, Rane DA, Spatz JM, Jain S, Rustagi A, Pinsky B, Zepeda AE, Kadina AP, Walker JA 3rd, Holden K, Temperton N, Cochran JR, Barron AE, Connolly MD, Blish CA, Lewis DB, Stanley SA, La Russa MF, Qi LS. (2022) Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro. Nature Communications

Grosskopf AK, Labanieh L, Klysz DD, Roth GA, Xu P, Adebowale O, Gale EC, Jons CK, Klich JH, Yan J, Maikawa CL, Correa S, Ou BS, d’Aquino AI, Cochran JR, Chaudhuri O, Mackall CL, Appel EA. (2022) Delivery of CAR-T cells in a transient injectable stimulatory hydrogel niche improves treatment of solid tumors. Science Advances

Labanieh L, Majzner RG, Klysz, D, Sotillo E, Fisher CJ, Vilches-Moure JG, Pacheco KZB, Malipatlolla M, Xu P, Hui JH, Murty T, Theruvath J, Mehta N, Yamada-Hunter SA, Weber EW, Heitzeneder S, Parker KR, Satpathy AT, Chang HY, Lin MZ, Cochran JR, Mackall CL. (2022) Enhanced safety and efficacy of protease-regulated CAR-T cell receptors. Cell.

Theruvath J, Menard M, Smith BAH, Linde MH, Coles GL, Dalton GN, Wu W, Kiru L, Delaidelli A, Sotillo E, Silberstein JL, Geraghty AC, Banuelos A, Radosevich MT, Dhingra S, Heitzeneder S, Tousley A, Lattin J, Xu P, Huang J, Nasholm N, He A, Kuo TC, Sangalang ERB, Pons J, Barkal A, Brewer RE, Marjon KD, Vilches-Moure JG, Marshall PL, Fernandes R, Monje M, Cochran JR, Sorensen PH, Daldrup-Link HE, Weissman IL, Sage J, Majeti R, Bertozzi CR, Weiss WA, Mackall CL, Majzner RG. (2022) Anti-GD2 synergizes with CD47 blockade to mediate tumor eradication. Nat Med.

Miller CL, Sagiv-Barfi I, Neuhöfer P, Czerwinski DK, Artandi SE, Bertozzi CR, Levy R, Cochran JR. (2022) Systemic delivery of a targeted synthetic immunostimulant transforms the immune landscape for effective tumor regression. Cell Chem. Bio.

Wirz OF, Röltgen K, Stevens BA, Pandey S, Sahoo MK, Tolentino L, Verghese M, Nguyen K, Hunter M, Snow TT, Singh AR, Blish CA, Cochran JR, Zehnder JL, Nadeau KC, Pinsky BA, Pham TD, Boyd SD. (2021) Use of Outpatient-Derived COVID-19 Convalescent Plasma in COVID-19 Patients Before Seroconversion. Front Immunol.

Marin BM, Porath KA, Jain S, Kim M, Conage-Pough JE, Oh JH, Miller CL, Talele S, Kitange GJ, Tian S, Burgenske DM, Mladek AC, Gupta SK, Decker PA, McMinn MH, Stopka SA, Regan MS, He L, Carlson BL, Bakken K, Burns TC, Parney IF, Giannini C, Agar NYR, Eckel-Passow JE, Cochran JR, Elmquist WF, Vaubel RA, White FM, Sarkaria JN. (2021) Heterogeneous delivery across the blood-brain barrier limits the efficacy of an EGFR-targeting antibody drug conjugate in glioblastoma. Neuro-Oncology.

Hunter SA, McIntosh BJ , Shi Y, Parra Sperberg RA, Funatogawa C, Labanieh L, Soon E, Wastyk HC, Mehta N, Carter C, Hunter T, Cochran JR. (2021) An engineered ligand trap inhibits leukemia inhibitory factor as pancreatic cancer treatment strategy. Nat. Comm. Bio.

Bell BN, Powell AE, Rodriguez C, Cochran JR, Kim PS. (2021) Neutralizing antibodies targeting the SARS-CoV-2 receptor binding domain isolated from a naïve human antibody library. Protein Sci.

Ahn G, Banik SM, Miller CL, Riley NM, Cochran JR, Bertozzi CR. (2021) LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation. Nat Chem Bio.

Theruvath J, Menard M, Smith BAH, Linde MH, Coles GL, Wu W, Kiru L, Delaidelli A, Silberstein JL, Banuelos A, Dhingra S, Sotillo E, Heitzeneder S, Tousley A, Lattin J, Xu P, Huang J, Nasholm N, Dalton GN, He A, Kuo TC, Sangalang ERB, Pons J, Barkal A, Brewer R, Marjon KD, Marshall PL, Fernandes R, Cochran JR, Sorensen PH, Daldrup-Link HE, Weissman IL, Sage J, Majeti R, Bertozzi CR, Weiss WA, Mackall CL, Majzner RG. (2021) Anti-GD2 antibody disrupts GD2:Siglec-7 interactions and synergizes with CD47 blockade to mediate tumor eradication. bioRxiv [preprint].

Bhamidipati K, Silberstein JL, Chaichian Y, Baker MC, Lanz TV, Zia A, Racheed YS, Cochran JR, and Robinson WH. (2021) CD52 Is Elevated on B cells of SLE Patients and Regulates B Cell Function. Front Immunol.

Longwell CK, Hanna S, Hartrampf N, Parra Sperberg RA, Huang P, Pentelute BL, and Cochran JR. (2020) Identification of N-Terminally Diversified GLP-1R Agonists Using Saturation Mutagenesis and Chemical Design. ACS Chem Bio.

Röltgen K, Powell AE, Wirz OF, Stevens BA, Hogan CA, Najeeb J, Hunter M, Wang H, Sahoo MK, Huang CH, Yamamoto F, Manohar M, Manalac J, Otrelo-Cardoso AR, Pham RD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Jardetzky TS, Zehnder JL, Wang TT, Narasimhan B, Gombar S, Tibshirani R, Nadeau KC, Kim PS, Pinsky BA, and Boyd SD. (2020) Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Science Immunology 5(54).

Murty S, Labanieh L, Murty T, Gowrishankar G, Haywood T, Alam IS, Beinat C, Robinson E, Aalipour A, Klysz DD, Cochran JR, Majzner RG, Mackall CL, Gambhir SS. (2020) PET reporter gene imaging and ganciclovir-mediated ablation of chimeric antigen receptor T-cells in solid tumors. Cancer Res.

Mehta N, Maddineni S, Kelly RL, Lee RB, Hunter SA, Silberstein JL, Parra Sperberg RA, Miller CL, Rabe A, Labanieh L, Cochran, JR. (2020) An engineered antibody binds a distinct epitope and is a potent inhibitor of murine and human VISTA. Sci Rep 10, 15171.

Su Y, Walker JR, Park Y, Smith TP, Liu LX, Hall MP, Labanieh L, Hurst R, Wang DC, Encell LP, Kim N, Zhang F, Kay MA, Casey KM, Majzner RG, Cochran JR, Mackall CL, Kirkland TA, Lin MZ. (2020) Novel NanoLuc substrates enable bright two-population bioluminescence imaging in animals. Nature Methods 2020 Jul 13.

Kim JW, Marquez CP, Sperberg RAP, Wu J, Bae WG, Huang PS, Sweet-Cordero EA, Cochran JR. (2020) Engineering a potent receptor superagonist or antagonist from a novel IL-6 family cytokine ligand. Proc Natl Acad Sci USA. 2020 Jun 23;117 (25):14110-14118. Press Release.

Steele AN, Paulsen MJ, Wang H, Stapleton LM, Lucian HJ, Eskandari A, Hironaka CE, Farry JM, Baker SW, Thakore AD, Jaatinen KJ, Tada Y, Hollander MJ, Williams KM, Seymour AJ, Totherow KP, Yu AC, Cochran JR, Appel EA, Woo YJ. (2020) Multi-phase catheter-injectable hydrogel enables dual-stage protein-engineered cytokine release to mitigate adverse left ventricular remodeling following myocardial infarction in a small animal model and a large animal model. Cytokine. 2020 Mar;127:154974.

Mehta N, Maddineni S, Mathews II, Andres Parra Sperberg R, Huang PS, Cochran JR. (2019) Structure and Functional Binding Epitope of V-domain Ig Suppressor of T Cell Activation. Cell Rep. 2019 28(10):2509-2516.e5. Press Release.

Kim, J.W., Marquez, C.P., Kostyrko, K., Koehne, A.L., Marini, K., Simpson, D.R., Lee, A.G., Leung, S.G., Sayles, L.C., Shrager, J., Ferrer, I., Paz-Ares, L., Gephart, M.H., Vicent, S., Cochran, J.R., Sweet-Cordero, E.A. (2019) Antitumor activity of an engineered decoy receptor targeting CLCF1–CNTFR signaling in lung adenocarcinoma. Nat. Med. 25, 1783–1795. Press Release.

Van Agthoven JF, Shams H, Cochran FV, Alonso JL, Kintzing JR, Garakani K, Adair BD, Xiong JP, Mofrad MRK, Cochran JR, Arnaout MA. (2019) Structural Basis of the Differential Binding of Engineered Knottins to Integrins αVβ3 and α5β1. Structure 27(9):1443-1451.e6.

Mitchell AC, Alford SC, Hunter SA, Kannan D, Parra Sperberg RA, Chang CH, Cochran JR. (2018) Development of a Protease Biosensor Based on a Dimerization-Dependent Red Fluorescent Protein. ACS Chem Biol 13(1):66-72.

Mitchell AC, Kannan D, Hunter SA, Parra Sperberg RA, Chang CH, Cochran JR. (2018) Engineering a potent inhibitor of matriptase from the natural hepatocyte growth factor activator inhibitor type-1 (HAI-1) protein. J Biol Chem. Apr 6;293(14):4969-4980.

Park, S.J., Lui, B.H., and Cochran, J.R. (2017) Rational and combinatorial methods to create designer protein interfaces, chapter in Comprehensive Biomaterials Volume 2, Ducheyne, Healy, Hutmacher, Grainger, and Kirkpatrick, eds., Elsevier.

Thayaparan T, Petrovic RM, Achkova DY, Zabinski T, Davies DM, Klampatsa A, Parente-Pereira AC, Whilding LM, van der Stegen SJ, Woodman N, Sheaff M, Cochran JR, Spicer JF, Maher J. (2017) CAR T-cell immunotherapy of MET-expressing malignant mesothelioma. Oncoimmunology 6(12):e1363137.

Mehta N, Cochran JR. (2017) Beyond Antibodies: Engineered Protein Scaffolds for Therapeutic Development. Methods and Principles in Medicinal Chemistry, Wiley-VCH, chapter in Protein Therapeutics.

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. 

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. ACS Chemical Biology. 

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. OncoImmunology, Published online: 14 Aug 2017.

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

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.

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.

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.

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

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.

Lim 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.

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. 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.

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.

Kintzing, 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.

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.

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.

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. Press release.
**Highlighted as a VIP (Very Important Paper) designated to less than 5% of all articles published in the journal**

Currier 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. 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.

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. 

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. 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.

Cherf, G.M. and Cochran, J.R. (2015) Applications of yeast surface display for protein engineering. Methods in Molecular Biology, 1319: 155-75.

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.

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. 

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. 

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.

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.

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. 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.
**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.

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

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. 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.

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.

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.

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. 

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.

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. 

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

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. 

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. 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. 

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. 

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. 

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. 

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.

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.

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. Comprehensive Biomaterials, Ducheyne, Healy, Hutmacher, Grainger, and Kirkpatrick, eds., Elsevier. October 2011.

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

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.

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. 

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. 

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.

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. 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. 

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.

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. 

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. 

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. 

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. 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. 

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. 

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.

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.

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

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

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. 

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.