Education and Biography

Ph.D. in Mathematics, University of California, Berkeley, 1998

B.A. in Mathematics, San Jose State University, 1992

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Publications

• Cimermancic P, Weinkam P, Rettenmaier JT, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ONA, Mitchell JC, Wells JA, et al. (2016) CryptoSite: Expanding the druggable proteome by characterization and prediction of cryptic binding sites. (in press).
• Alsop JD, Mitchell JC (2015) Interolog interfaces in protein docking. Proteins 83:1940–6. [3] Hatano H, Shaw J, Marquardt KR, Zhang Z, Gauthier L, Chanteux S, Rossi B, Li D, Mitchell JC, Kollnberger S (2015) The D0 immunoglobulin-like domain plays a central role for the stronger binding of KIR3DL2 to B27 free heavy chain dimers. J Immunol 194:1591–601.
• Lohman LC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich A, Stefely JA, Sukumar S, LunaSnchez M, Jochem A, et al. (2014) Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proc Natl Acad Sci U S A 111:E4697–705.
• Shen QT, Schuh AL, Zheng Y, , Quinney K, Hanna M, Mitchell JC, Otegui MS, Ahlquist P, Cui Q, et al. (2014) Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly. J Cell Biol 206:763–77.
• Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E, Schmitz C, van Dijk M, Bonvin AMJJ, Eisenstein M, et al. (2014) Blind prediction of interfacial water positions in CAPRI. Proteins: Structure, Function, and Bioinformatics 82:620–32.
• Zhu X, Ericksen SS, Demerdash ONA, Mitchell JC (2013) Data-driven models for protein interaction and design. Proteins: Structure, Function, and Bioinformatics 81:2221–2228.
• Demerdash ONA, Mitchell JC (2013) Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind. Proteins 81:1919–1930.
• Zhu X, Ericksen SE, Mitchell JC (2013) DBSI: DNA binding site identifier. Nucl Acid Res Methods 41:e160.
• Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JPGLM, Trellet M, Bonvin AMJJ, Cui M, et al. (2013) Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins: Structure, Function, and Bioinformatics 81:1980– 1987.
• Pattnaik BR, Tokarz S, Asuma M, Schroeder T, Sharma A, Mitchell JC, Edwards AO, Pillers DM (2012) Snowflake vitreoretinal degeneration (SVD) mutation of human Kir7.1 (R162W) is a non-functional channel. PLoS ONE 8:e71744.
• Demerdash ONA, Mitchell JC (2012) Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis. Proteins 80:1766–1779.
• Fleishman SJ, Whitehead TA, Strauch E, Corn JE, Qin S, Zhou H, Mitchell JC, Demerdash ONA, et al, Baker D (2011) Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol 414:289–302.
• Mitchell JC, Rutkoski TJ, Bannen RM, G N Phillips J (2011) Designing thermophilic proteins: A structurebased computational approach. In: Sen S, Nilsson L, editors, Thermostable Proteins: Structural Stability and Design, CRC Press. pp. 105–116. 
• Zhu X, Mitchell JC (2011) KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density and plasticity features. Proteins 79:2671–2683.
• Lall R, Donohue T, Marino S, Mitchell JC (2011) Optimizing ethanol production selectivity. Math Comp Modell 53:1363–1373.
• Demerdash ONA, Buyan A, Mitchell JC (2010) ReplicOpter: A replicate optimizer for flexible docking. Proteins 78:3156–3165.
• Dufour YS, Wesenberg GE, Tritt AJ, Glasner JD, Perna N, Mitchell JC, Donohue TJ (2010) chipD: A web tool to design oligonucleotide probes for high-density tiling arrays. Nuc Acid Res 38:W321–W325.
• Demerdash ONA, Daily M, Mitchell JC (2009) Structure-based predictive models for allosteric hot spots. PLoS Comp Biol 5:e1000531.
• Dynerman D, Butzlaff EA, Mitchell JC (2009) CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation. J Comp Biol 16:523–537.
• Yershova A, Jain S, LaValle SM, Mitchell JC (2009) Generating uniform incremental grids on SO(3) using the Hopf fibration. International Journal of Robotics Research :doi:10.1177/0278364909352700.
• Bannen RM, Suresh V, Wright SJ, G N Phillips J, Mitchell JC (2008) Optimal design of thermostable proteins. Bioinformatics 24:2339–2343.
• Mitchell JC (2008) Discrete uniform sampling of rotation groups using successive orthogonal images. SIAM J Sci Comp 30:525–547.
• Darnell SJ, Legault L, Mitchell JC (2008) KFC server: Interactive forecasting of protein interaction hot spots. Nuc Acid Res 36:W265–W269.
• Lall R, Mitchell JC (2007) Metal-reduction kinetics in Shewanella. Bioinformatics 23:2754–2759.
• Darnell SJ, Page D, Mitchell JC (2007) Automated decision-tree approach to predicting protein-protein interaction hot spots. Proteins 68:813–823. 
• Marcia RF, Mitchell JC, Rosen JB (2007) Multi-funnel optimization using Gaussian underestimation. Journal of Global Optimization 39:39–48.
• Marcia RF, Mitchell JC, Wright SJ (2007) Global optimization in protein docking using convex underestimation and semidefinite programming. Optimization Methods and Software 22:803–811. 
• Lynch KL, Gerona RRL, Larsen EC, Marcia RF, Mitchell JC, Martin TFJ (2007) Synaptotagmin C2A loop 2 mediates Ca2+-dependent SNARE interactions essential for Ca2+-triggered vesicle exocytosis. Mol Biol Cell 18:4957–4968. (Feature article).
• Kedlaya RH, Bhat KMR, Mitchell JC, Darnell SJ, Setaluri V (2006) Trp1 interacting PDZ-domain protein GIPC forms oligomers and is localized to intracellular vesicles in human melanocytes. Arch Bioc Biophys 454:160–169.
• Rutkoski TJ, Kurten EL, Mitchell JC, Raines RT (2005) Disruption of shape-complementarity markers to create cytotoxic variants of ribonuclease A. J Mol Biol 354:41–54.
• Marcia RF, Mitchell JC, Rosen JB (2005) Iterative convex quadratic approximation for global optimization in protein docking. Comp Opt Appl 32:285–297.
• Zbilut JP, Giuliani A, Colosimo A, Mitchell JC, Colafranceschi M, Marwan N, Jr CLW, Uversky VN (2004) Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins: A computational approach. J Proteome Res 3:1243–1253.
• Zbilut JP, Mitchell JC, Giuliani A, Colosimo A, Marwan N, Webber Jr CL (2004) Singular hydrophobicity patterns and net charge: A mesoscopic principle for protein aggregation/folding. Physica A 343:348–358.
• Mitchell JC, Shahbaz S, Ten Eyck LF (2004) Interfaces in molecular docking. Molecular Simulation 30:97– 106.
• Law DH, Ten Eyck LF, Katzenelson O, Tsigelny I, Roberts VA, Pique ME, Mitchell JC (2003) Finding needles in haystacks: Re-ranking dot results using shape complementarity, cluster analysis and biological information. Proteins 52:33–40.
• Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF (2001) Protein docking using continuum electrostatics and geometric fit. Protein Engineering 14:105–113.
• Mitchell JC, Kerr R, Ten Eyck LF (2001) Rapid atomic density methods for molecular shape characterization. J Mol Graph Model 19:324–329. 
• Mitchell JC, Phillips AT, Rosen JB, Ten Eyck LF (2000) A coupled scanning and optimization scheme for molecular docking. In: Floudas CA, Pardalos PM, editors, Optimization in Molecular Biology and Computational Chemistry. Klewer Academic Publishers, pp. 190–207.
• Mitchell JC, Phillips AT, Rosen JB, Ten Eyck LF (1999) Coupled optimization in protein docking. In: Istrail S, Pevzner P, Waterman M, editors, Proceedings of the Third Annual Conference in Computational Biology (RECOMB99). ACM Press, New York, pp. 180–184.D. Vural, J. C. Smith, and L. Petridis. Dynamics of the Lignin Glass Transition. Phys. Chem. Chem. Phys. 2018, 20, 20504-20512