SMART - Singapore MIT Alliance for Research and Technology

Singapore-MIT Alliance for Research & Technology

Biosystems and Micromechanics

BioSystems and Micromechanics (BioSyM) Inter-Disciplinary Research Group

Bruce Tidor
Professor of Biological Engineering and Computer Science, MIT
Co-Director, Computational and Systems Biology Initiative, MIT

http://groups.csail.mit.edu/tidor/

Positions

  • 2005 – co-Director, Computational and Systems Biology Initiative, MIT
  • 2005 – Professor of Biological Engineering & Computer Science, MIT
  • 2005 – 2007 Associate Chair of the Faculty, MIT
  • 2002 – 2007 Graduate Program Director, Computational and Systems Biology, MIT
  • 2001 – 2005 Associate Professor of Bioengineering & Computer Science, MIT
  • 1999 – 2001 Associate Professor of Chemistry, MIT
  • 1994 – 1999 Assistant Professor of Chemistry, MIT
  • 1990 – 1994 Whitehead Fellow, Whitehead Institute for Biomedical Research

Honors

  • American Association for the Advancement of Science, Fellow (2009)
  • Marshall Scholar (1983 – 1985)
  • Leonard T. Skeggs Chair for Whitehead Fellows (1992 – 1994)
  • Paul M. Cook Career Development Chair (1996 – 1999)
  • Alfred P. Sloan Research Fellow (1999 – 2001)
  • Cecil H. Green Professorship (2002 – 2004)

Selected peer-reviewed publications

  • D. Machado, R.S. Costa, E.C. Ferreira, I. Rocha, and B. Tidor. Exploring the gap between dynamic and constraint-based models of metabolism. Metab. Eng. 14: 112–119 (2012) PMID 22306209.
  • D.J. Huggins, W. Sherman, and B. Tidor. Rational approaches to improving selectivity in drug design. J. Med. Chem. 55: 1424–1444 (2012) PMID: 22239221
  • D.J. Huggins and B. Tidor. Systematic placement of structural water molecules for improved scoring of protein–ligand interactions. Protein Eng. Des. Sel. 24: 777–789 (2011) PMID: 21771870.
  • X.N. Wei, B.C. Han, J.X. Zhang, X.H. Liu, C.Y. Tan, Y.Y. Jiang, B.C. Low, B. Tidor, and Y. Z. Chen.  An integrated mathematical model of thrombin-, histamine-and VEGF-mediated signalling in endothelial permeability.  BMC Syst. Biol. 5: 112 (2011) PMCID: PMC3149001.
  • N. Bahl, R. Du, I. Winarsih, B. Ho, L. Tucker-Kellogg, B. Tidor, J.L. and Ding. Delineation of lipopolysaccharide (LPS)-binding sites on hemoglobin. J. Biol. Chem. 286:37793–37803 (2011) PMID: 21900232.
  • D. Machado, R.S. Costa, M. Rocha, E.C. Ferreira, B. Tidor, and I. Rocha. Modeling formalisms in systems biology. AMB Express 5:45 (2011) PMID: 22141422.
  • E. Leonard, P.K. Ajikumar, K. Thayer, W.H. Xiao, J.D. Mo, B. Tidor, G. Stephanopoulos, and K.L. Prather. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc. Natl. Acad. Sci. U.S.A. 107:13654–13659 (2010) PMCID: PMC2922259.
  • D.R. Hagen, J.F. Apgar, D.K. Witmer, F.M. White, and B. Tidor. Reply to Comment on "Sloppy models, parameter uncertainty, and the role of experimental design".  Mol. Biosyst. 7: 2523--2524 (2011) PMID: 21701723.
  • X.N. Wei, B.C. Han, J.X. Zhang, X.H. Liu, C.Y. Tan, Y.Y. Jiang, B.C. Low, B. Tidor, and Y. Z. Chen.  An integrated mathematical model of thrombin-, histamine-and VEGF-mediated signalling in endothelial permeability.  BMC Syst. Biol. 5: 112 (2011) PMID: 21756365.
  • L. Huang, C.Q. Pan, B. Li, L. Tucker-Kellogg, B. Tidor, Y. Chen, and B.C. Low.  Simulating EGFR-ERK signaling control by scaffold proteins KSR and MP1 reveals differential ligand-sensitivity co-regulated by Cbl-CIN85 and endophilin. PLoS One 6: e22933 (2011) PMID: 21829671.
  • M.N. Nalam, A. Ali, M.D. Altman, G.S. Reddy, S. Chellappan, V. Kairys, A. Ozen, H. Cao, M.K. Gilson, B. Tidor, T.M. Rana, and C.A. Schiffer. Evaluating the substrate-envelope hypothesis: Structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J. Virol. 84:5368–5378 (2010) PMCID: PMC2863851.
  • J.F. Apgar, D.K. Witmer, F.M. White, and B. Tidor. Sloppy models, parameter uncertainty, and the role of experimental design. Mol. Biosyst. 6:1890–1900 (2010) PMID: 20556289.
  • M.L. Radhakrishnan and B. Tidor. Cellular level models as tools for cytokine design. Biotechnol. Prog. 26:919–937 (2010) PMID: 20568274.
  • E. Leonard, P.K. Ajikumar, K. Thayer, W.H. Xiao, J.D. Mo, B. Tidor, G. Stephanopoulos, and K.L. Prather. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc. Natl. Acad. Sci. U.S.A. 107:13654–13659 (2010) PMCID: PMC2922259.
  • B.M. King and B. Tidor. MIST: Maximum information spanning trees for dimension reduction of biological data sets. Bioinformatics 25: 1165–1172 (2009)
  • J.E. Toettcher, A. Loewer, G.J. Ostheimer, M.B. Yaffe, B. Tidor, G. Lahav. Distinct mechanisms act in concert to mediate cell cycle arrest. Proc. Natl. Acad. Sci. U.S.A. 106: 785–790 (2009)
  • S.L. Sazinsky, R.G. Ott, N.W. Silver, B. Tidor, J.V. Ravetch, K.D. Wittrup. Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors. Proc. Natl. Acad. Sci. U.S.A. 105: 20167–20172 (2008) PMID: 19074274.
  • M.D. Altman, A. Ali, G.S.K.K. Reddy, M.N.L. Nalam, S.G. Anjum, H. Cao, S. Chellappan, V. Kairys, M.X. Fernandes, M.K. Gilson, C.A. Schiffer, T.M. Rana, and B. Tidor.  HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J. Am. Chem. Soc. 130: 6099–6113 (2008)
  • Lippow SM, Wittrup KD, Tidor B. Computational design of antibody affinity improvement beyond in vivo maturation. Nature Biotechnol 2007; 25: 1171–1176.
  • Altman MD, Bardhan JP, Tidor B, White JK. FFTSVD: A fast, multiscale boundary-element method solver suitable for Bio-MEMS and biomolecule simulation. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 2006; 25: 274–284.
  • Sarkar CA, Lowenhaupt C, Horan T, Boone T, Tidor B, Lauffenburger DA. Increased lifetime and enhanced potency using pH-activated “histidine switching”. Nature Biotechnol 2002; 20: 908–913.