Gray, Jeffrey

Associate Professor
Dept Of Chemical And Biomolecular Engrg

Maryland Hall 208
3400 N Charles St
(410) 516-5313
jgray@jhu.edu

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News

ChemBE’s Jeff Gray wins AIChE’s Himmelblau Award

July 13, 2016

Jeffrey Gray, professor in the Department of Chemical and Biomolecular Engineering, has been selected as this year’s recipient of the American Institute for Chemical Engineers’ David Himmelblau Award for Innovations in Computer-Based Chemical Engineering Education. This prestigious award is bestowed annually by AIChE’s Computing & Systems Technology Division to a person or group making new […]

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Student researchers collaborate virtually with help of open-source software

July 29, 2015

A summer research internship for undergraduates is not only helping them learn to build new lifesaving drug molecules and create new biofuels—it’s also testing the concept of a virtual research community. The Johns Hopkins Institute for NanoBioTechnology—with the help of a $200,000, two-year grant from the National Science Foundation—has launched a first-of-its-kind training program in […]

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About

Education
  • Ph.D. 2000, University of Texas
  • Other Bachelor's Degree (B.S.E.) 1994, University of Michigan
Awards
  • 2015:  AIMBE Fellow
  • 2015:  Centennial Lecturer
  • 2015:  Plenary Lecturer
  • 2011:  F. Stuart Hodgson Faculty Scholar
  • 2011:  Fisher Award for Undergraduate Research in Cancer - M.-Y. Lee (*student advised by Jeff Gray)
  • 2010:  NSF Graduate Research Fellowship - R. Harrison (To attend Oxford; *Undergraduate advised by J. Gray)
  • 2010:  NSF Graduate Research Fellowship Honorable Mention - S. Schrier (Attending MIT; *Undergraduate advised by J. Gray)
  • 2010:  Provost's Undergraduate Research Award - M.-Y. Lee (*Student Advised by Jeff Gray)
  • 2009:  NSF CAREER Award
  • 2008:  JHU Center for Educational Resources Technology Fellowship - J.D. Bagert & Julian Rosenberg - 2008 (*Student Advised by Jeff Gray)
  • 2007:  Genentech Second Place Poster Award - 1st International Conference on Biomolecular Engineering - D. Masica - 2007 (*Student advised by Jeff Gray)
  • 2007:  NIH Ruth L. Kirschstein Graduate Fellowship - M. Berrondo - 2007-2011 (*Student advised by Jeff Gray)
  • 2007:  Provost's Undergraduate Research Award - E. Kim - 2007 (*Student Advised by Jeff Gray)
  • 2006:  JHU Alumni Association Excellence in Teaching Award
  • 2006:  Undergraduate lab members Elizabeth Specht and Sarah Schrier shared an Elenora Streb Muly Award
  • 2005:  Beckman Foundation Young Investigator Award
  • 2005:  Intel Science Talent Search Finalist awarded to lab member Ryan Harrison (12th grade student)
  • 2003:  Nominee (disqualified due to young age) for JHU Whiting School teaching award
  • 2002:  International Society for Computational Biology travel fellowship
  • 2001:  NIH K01 Mentored Quantitative Research Fellowship in Genomics
  • 2000:  University of Texas Outstanding Doctoral Dissertation - Honorable Mention
Presentations
  • "RosettaCarbohydrates: Expanding the computational tools available to glycoscientists", Society for Glycobiology Annual Meeting.  San Francisco.  2015
  • "Toward the Rational Design of Antibodies with Improved Therapeutic Potential", Society for Glycobiology Annual Meeting.  San Francisco.  2015
  • "Proteins Dancing the Texas Two-Step", Centennial Lecture Series.  Austin, TX.  December 1, 2015
  • "Modeling chiral recognition between amino acids and vaterite surfaces", AIChE Annual Meeting.  Salt Lake City.  2015
  • "Toward Structure Prediction and Design of Protein Glycosylations", AIChE Annual Meeting.  Salt Lake City.  2015
  • "How Proteins Dance with their Partners", Inaugural Professorial Lecture.  Baltimore, MD.  2015
  • "RosettaCarbohydrates: Expanding the Computational Tools Available to Glycoscientists", RosettaCon XIII.  Leavenworth, WA.  2015
  • "The origin of CDR H3 structural diversity", RosettaCon XIII.  Leavenworth, WA.  2015
  • "Teaching Biomolecular Structure Prediction and Design with PyRosetta", Biochemical and Molecular Engineering XIX.  Puerto Vallarta, Mexico.  2015
  • "Toward structure prediction and design of protein glycosylations", Biochemical and Molecular Engineering XIX.  Puerto Vallarta, Mexico.  2015
  • "Design and Structure Prediction of Proteins that Control Biomineralization", “From Biomineralization to Materials Science” Seminar Series.  Dresden, Germany.  2015
  • "Producing physically realistic structural models with RosettaAntibody", Americas Antibody Congress.  San Diego.  2015
  • "Rosetta-MPDock: A novel computational tool for protein-protein docking within the membrane bilayer", Biophysical Society Annual Meeting.  Baltimore, MD.  2015
  • "The origin of CDR H3 structural diversity", Biophysical Society Annual Meeting.  Baltimore, MD.  2015
  • "Docking and design of oligosaccharides, glycoproteins, and glycolipids: Expanding the computational tools available to glycoscientists", Joint Meeting of the Society for Glycobiology and the Japanese Society of Carbohydrate Research.  Honolulu.  November 19, 2014
  • "Computational Molecular Biophysics: Design Your Future", Grace Hopper Celebration of Women in Computing.  Pheonix, AZ.  October 8, 2014
  • "Chiral acidic amino acids induce biomineral chirality: Effects of L- and D- Asp and Glu on calcium carbonate (vaterite) growth", Gordon Research Conference on Biomineralization.  New London, NH.  2014
  • "Computational design of peptides to control calcite growth", Gordon Research Conference on Biomineralization.  New London, NH.  2014
  • "Experimental characterization of peptides to control calcite growth", Gordon Research Conference on Biomineralization.  New London, NH.  2014
  • "Computational Design of Peptides to Control Calcite Growth", Gordon Research Conference on Biomineralization.  New London, NH.  August 20, 2014
  • "Diversity Efforts within the Rosetta Commons", Rosetta Conference.  Leavenworth, WA.  August 1, 2014
  • "Applying Rosetta to Antibody Loop Modeling and Docking", Protein Engineering Summit (PEGS).  Boston, MA.  May 6, 2014

Publications

Journal Articles
  • Lensink, M., authors, 1., Gray, J., Wodak, S. (2016).  Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.  Proteins.  accepted.
  • Leman, J. K., Ulmschneider, M., Gray, J. (2015).  Computational modeling of membrane proteins.  Proteins-Structure Function and Bioinformatics.  83(1).  1-24.
  • Matlahov, I., Iline-Vul, T., Abayev, M., Lee, E. M., Nadav-Tsubery, M., Keinan-Adamsky, K., Gray, J., Goobes, G. (2015).  Interfacial Mineral–Peptide Properties of a Mineral Binding Peptide from Osteonectin and Bone-like Apatite.  Chemistry of Materials.  27(16).  5562-5569.
  • Weitzner, B. D., Dunbrack, R. L., Gray, J. (2015).  The Origin of CDR H3 Structural Diversity.  Structure.
  • Pierre, B., Labonte, J., Xiong, T., Aoraha, E., Williams, A., Shah, V., Chau, E., Helal, K. Y., Gray, J., Kim, J. (2015).  Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein..  Chembiochem : a European journal of chemical biology.  16(16).  2392-402.
  • Alford, R. F., Koehler Leman, J., Weitzner, B. D., Duran, A. M., Tilley, D. C., Elazar, A., Gray, J. (2015).  An Integrated Framework Advancing Membrane Protein Modeling and Design..  PLoS computational biology.  11(9).  e1004398.
  • Jiang, Q., Arnold, S., Heanue, T., Kilambi, K. P., Doan, B., Kapoor, A., Ling, A. Y., Sosa, M. X., Guy, M., Jiang, Q., Burzynski, G., West, K., Bessling, S., Griseri, P., Amiel, J., Fernandez, R. M., Verheij, J. B., Hofstra, R. M., Borrego, S., Lyonnet, S., Ceccherini, I., Gray, J., Pachnis, V., McCallion, A. S., Chakravarti, A. (2015).  Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability..  American journal of human genetics.  96(4).  581-96.
  • Weitzner, B. D., Dunbrack, Jr, R. L., Gray, J. (2015).  The origin of CDR H3 structural diversity..  Structure (London, England : 1993).  23(2).  302-11.
  • Koehler Leman, J., Ulmschneider, M., Gray, J. (2015).  Computational modeling of membrane proteins..  Proteins.  83(1).  1-24.
  • Lensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A. S., Karaca, E., Schmitz, C., Dijk, M., Bonvin, A. M., Eisenstein, M., others. (2014).  Blind prediction of interfacial water positions in CAPRI.  Proteins: Structure, Function, and Bioinformatics.  82(4).  620–632.
  • Weitzner, B. D., Kuroda, D., Marze, N., Xu, J., Gray, J. (2014).  Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization.  Proteins: Structure, Function, and Bioinformatics.  82(8).  1611–1623.
  • Kilambi, K. P., Reddy, K., Gray, J. (2014).  Protein-Protein Docking with Dynamic Residue Protonation States.  PLoS computational biology.  10(12).  e1004018.
  • Xu, J., Tack, D., Hughes, R. A., Ellington, A. D., Gray, J. (2014).  Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex.  Journal of structural biology.  185(2).  215–222.
  • Firnberg, E., Labonte, J., Gray, J., Ostermeier, M. (2014).  A comprehensive, high-resolution map of a gene's fitness landscape..  Molecular Biology and Evolution.  31(6).  1581-92.
  • Chaikind, B., Kilambi, K. P., Gray, J., Ostermeier, M. (2012).  Targeted DNA methylation using an artificially bisected M.HhaI fused to zinc fingers.  PLoS One.  7(9).  e44852.
  • Berrondo, M., Ostermeier, M., Gray, J. (2008).  Structure prediction of domain insertion proteins from structures of individual domains.  Structure.  16(4).  513-27.
Other Publications
  • Roy Burman, S. S., Pacella, M. S., De Yoreo, J. J., Gray, J. (2015).  Characterization of Peptides Designed to Control Crystal Nucleation and Growth.  Biophysical Journal.  108(2).  633a.
  • Labonte, J., Gray, J. (2015).  Docking and Design of Oligosaccharides, Glycoproteins, and Glycolipids.  Biophysical Journal.  108(2).  470a.
  • Leman, J. K., Alford, R. F., Gray, J. (2015).  Rosetta-MPDock: A Novel Computational Tool for Protein-Protein Docking within the Membrane Bilayer.  Biophysical Journal.  108(2).  250a.
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