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Shalloway, David I
Greater Philadelphia Professor of Biological Sciences
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With a PhD in theoretical physics and over twenty years experience in experimental biological research, it is not surprising that my current research is in computational biology, with a focus on protein structure prediction and analysis. Similarly, I am particularly interested in the training of both our undergraduate and graduate biology students at the interface between biology, mathematics, physics and computation. Through Computing and Information Science I am engaged in promoting computational biology at Cornell.
Research Areas
- biochemistry
- biophysics (Applied Engineering Physics)
- biophysics (CALS)
- breast cancer
- cancer research
- cell biology
- computational biology
- computer science
- molecular biology
- new life sciences
Websites
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- Research
- Publications
- Teaching
- Service
- Background
- Other
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Affiliations
Research
research overview
- I have two research progrms: The first is in computational biology and includes the development of new algorithms for clustering in biological data analysis, kinetics of cell development, and analysis of the SELEX process. I am also collaborating in a computational astrobiology project to examine the possibility of the development of life in the hydrocarbon seas of Titan. The second is on the role of PTPalpha in human cancer, including the development of pilot therapeutics and diagnostics
other area(s) of concentration/expertise
- Computational Biology
keywords
- astrobiology
- biochemistry
- carcinogenesis
- cell biology
- computational biology
- signal transduction
submitted impact statement
Publications
individual publications
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academic article
- Multiplexed microcolumn-based process for efficient selection of RNA aptamers.. Analytical Chemistry. 2013
- Activation of Src and transformation by a RPTPα splice mutant found in human tumors. EMBO Journal. 30:3200-3211. 2011
- Extracellular domain dependence of PTPalpha transforming activity. Genes to Cells. 15:711-724. 2010
- Stem cell dynamics in mouse hair follicles: a story from cell division counting and single cell lineage tracing. Cell Cycle. 9:1504-1510. 2010
- Efficient uncertainty minimization for spectral macrostate data clustering. Physical Review E. 80. 2009
- Selective apoptosis of estrogen receptor-negative breast and colon cancer cell lines by PTPα and Src RNAi. International Journal of Cancer. 122:1999-2007. 2008
- Tyrosine phosphatase PTPalpha regulates focal adhesion remodeling through Rac1 activation. American Journal of Physiology Cell Physiology. 294. 2008
- Extending molecular dynamics timescales with milestoning: Example of complex kinetics in a solvated peptide. J. Chem. Phys.. 126. 2007
- Efficiently computing the first passage time generating function by steady-state relaxation. J. Chem. Phys.. 124. 2006
- ESR study of dynamic structure of cell plasma membranes. Biophysical Journal. 84. 2003
- Macrostate data clustering. Physical Review E. 67:056704. 2003
- Tracing synonymous codon-secondary structure correlations through evolution. Journal of Molecular Evolution. 56:473-484. 2003
- Mitotic activation of protein-tyrosine phosphatase alpha and regulation of its Src-mediated transforming activity by its sites of protein kinase C phosphorylation. Journal of Biological Chemistry. 277:21922-219299. 2002
- Physical and functional interaction between the transcriptional cofactor CBP and the KH domain protein Sam68. Mol Cancer Res. 1:48-55. 2002
- Non-radioactive determination of Ras-GTP levels using ARIA. Methods in Enzymology. 333:333-342. 2001
- Qmol: a program for molecular visualization on Windows-based PCs. Journal of Molecular Graphics and Modelling. 19:557-559. 2001
- Top-down free-energy minimization on protein potential energy landscapes. Proceedings at the National Academy of Science USA. 98:6098-6103. 2001
- Two mechanisms activate PTPα during mitosis. EMBO Journal. 20:6037-6049. 2001
- A phosphotyrosine displacement mechanism for activation of Src by PTPα. EMBO Journal. 19:964-978. 2000
- Shadow mass and the relationship between velocity and momentum in symplectic numerical integration. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 61:4587-4592. 2000
- Temperature-dependent reaction coordinates. J Chem Phys. 112:5539-5545. 2000
- Characterization of Raf-1 activation in mitosis. Journal of Biological Chemistry. 274:4430-4439. 1999
- Macrostate dissection of thermodynamic Monte Carlo integrals. Advances in Chemical Physics. 105:273-310. 1999
- KH Domain Integrity Is Required for Wild-Type Localization of Sam68. Experimental Cell Research. 241:84-95. 1998
- Specific correlations between relative synonymous codon usage and protein secondary structure. J Mol Biol. 281:31-48. 1998
- Variational calculation of macrostate transition rates. J Chem Phys. 109:1670-1686. 1998
- Association between v-Src and protein kinase C delta in v-Src-transformed fibroblasts. Journal of Biological Chemistry. 272:13275-13280. 1997
- Finding transition states using contangency curves. J Chem Phys. 106:10099-10104. 1997
- Heteronuclear NMR studies of the combined SH3-SH2 domains of pp60c-src. The effects of phosphopeptide binding. Biochemistry. 36:14561-14571. 1997
- Oncoprotein signalling pathways and mitosis. Cellular Signalling. 9:249-255. 1997
- Phosphorylation of the Src substrate Sam68 by Cdc2 during mitosis. Oncogene. 15:1247-1254. 1997
- Specificity and determinants of Sam68 RNA binding. Journal of Biological Chemistry. 272:27274-27280. 1997
- Src: more than the sum of its parts. Trends Cell Biol. 7:215-217. 1997
- Cell cycle-dependent activation of Ras. Current Biology. 6:1621-1627. 1996
- Characterizing large correlated fluctuations of macromolecular conformations in torsion-angle space using the multivariate wrapped-Gaussian distribution. Polymer. 37:1805-1813. 1996
- Macrostates of classical stochastic systems. J Chem Phys. 105:9986-10007. 1996
- Spatial interpolation methods for integrating Newton's equation in multiple dimensions. J Comp Phys. 129:87-100. 1996
- Src and the control of cell division. Bio Essays. 18:9-11. 1996
- Autophosphorylation of purified c-Src at its primary negative regulation site. Journal of Biological Chemistry. 270:25729-25732. 1995
- Characterizing large correlated fluctuations of peptide conformations in torsion angle space. Polymer Pre. 36:636-637. 1995
- Functional interaction between c-Src and its mitotic target, Sam 68. Journal of Biological Chemistry. 270:10120-10124. 1995
- Raf-1 is activated during mitosis. Journal of Biological Chemistry. 270:26742-26745. 1995
- Transformation of mouse cells by wild-type mouse c-Src. Oncogene. 10:401-405. 1995
- A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing. J Global Optimization. 4:171-186. 1994
- Accessibility of the c-src SH2-domain for binding is increased during mitosis. Journal of Biological Chemistry. 269:10247-10251. 1994
- An RNA-binding protein associated with Src through its SH2 and SH3 domains in mitosis. Nature. 368:867-871. 1994
- Differential effect of phosphorylation and substrate modulation on tau's ability to promote microtubule growth and nucleation. Journal of Biological Chemistry. 269:11776-11782. 1994
- Direct interaction of v-Src with the focal adhesion kinase mediated by the SH2 domain. Molecular Biology of the Cell. 5:413-421. 1994
- Hierarchical characterization of energy landscapes using Gaussian packet states. J Chem Phys. 101:9844-9857. 1994
- Optimization methods for computing global minima of nonconvex potential energy functions. J Global Optimization. 4:117-133. 1994
- Src signalling in mitosis: SH2 and SH3 domain-directed association with a tyrosine-phosphorylated RNA binding protein. FASEB Journal. 8. 1994
- Tyrosine dephosphorylation of pp60c-src is stimulated by a serine/threonine phosphatase inhibitor. Oncogene. 9:1947-1955. 1994
- Aluminum interaction with human brain tau protein phosphorylation by various kinases. J Environ Sci Health B. 28:763-777. 1993
- Aluminum-induced nonenzymatic phospho-incorporation into human tau and other proteins. Journal of Biological Chemistry. 268:11976-11981. 1993
- Differential localization patterns of myristoylated and nonmyristoylated c-src proteins in interphase and mitotic c-src overexpressor cells. J Cell Sci. 105:613-628. 1993
- Gap junctional communication and neoplastic transformation. Crit Rev Oncogenesis. 4:541-558. 1993
- Isotropic effective energy simulated annealing searches for low energy molecular cluster states. Comput Optim Applic. 2:145-170. 1993
- Mitogenic activation of the Ras guanine nucleotide exchange factor in NIH 3T3 cells involves protein tyrosine phosphorylation. Proceedings at the National Academy of Science USA. 90:8504-8508. 1993
- Myristylation is required for Tyr-527 dephosphorylation and activation of pp60c-src in mitosis. Molecular and Cellular Biology. 13:1464-1470. 1993
- The cell cycle and c-Src. Curr Opin Genet Devel. 3:26-34. 1993
- Application of the renormalization group to deterministic global minimization of molecular conformation energy functions. J Global Optimiz. 2:281-311. 1992
- Phosphorylation of tau protein by purified p34cdc28 and a related protein kinase from neurofilaments. Journal of Biological Chemistry. 267:19705-19709. 1992
- Regulation of focal adhesion-associated protein tyrosine kinase by both cellular adhesion and oncogenic transformation. Nature. 358:690-692. 1992
- Role of p34cdc2 -mediated phosphorylations in two-step activation of pp60c-src during mitosis. Proceedings at the National Academy of Science USA. 89:7237-7241. 1992
- Substrate-specific modulation of Src-mediated phosphorylation of Ras and caseins by sphingosines and other substrate modulators. Biochim Biophys Acta. 1137:349-355. 1992
- Altered tyrosine 527 phosphorylation and mitotic activation of p60c-src. Nature. 349:172-175. 1991
- GelMetric: Semi-automated electrophoretic mobility analysis. Computer Applic Biosci. 7:109-110. 1991
- Incorporation of the gene for a cell-cell channel protein into transformed cells leads to normalization of growth. J Membr Biol. 124:207-225. 1991
- SMGWS 2: Improved microcomputer-based three-dimensional stereoscopic macromolecular graphics display. Computer Applic Biosci. 7:107-108. 1991
- Selective binding of activated pp60c-src by an immobilized synthetic phosphopeptide modeled on the carboxy terminus of pp60c-src. Proceedings at the National Academy of Science USA. 88:10696-10700. 1991
- Induction of sensitivity to the cytotoxic action of tumor necrosis factor alphaï€ by adenovirus E1A is independent of transformation and transcriptional activation. Journal of Virology. 64:4115-4122. 1990
- Sequence and functional differences between Schmidt-Ruppin D and Schmidt-Ruppin A strains of pp60v-src. Journal of Virology. 64:3545-3550. 1990
- Junctional intercellular communication is cooperatively inhibited by oncogenes in transformation. Oncogene. 4:1161-1168. 1989
- Mutation of amino acids in pp60c-src that are phosphorylated by protein kinases C and A. Molecular and Cellular Biology. 9:2453-2463. 1989
- Purified maturation promoting factor phosphorylates pp60c-src at the sites phosphorylated during fibroblast mitosis. Cell. 57:763-774. 1989
- Regulation by tyrosine kinases: src protein activates various promoters, including c-fos. Molecular and Cellular Biology. 9:2493-2499. 1989
- Role of tumor necrosis factor-alpha in ElA oncogene-induced susceptibility of neoplastic cells to lysis by natural killer cells and activated macrophages. J Immunol. 142:4527-4534. 1989
- Altered phosphorylation and activation of pp60c-src during fibroblast mitosis. Cell. 52:801-810. 1988
- Comparison of the effects of carboxyl terminal truncation and point mutations on pp60c-src activities. Oncogene Res. 3:207-212. 1988
- Microcomputer-based three-dimensional stereoscopic macromolecular graphics display. Computer Appl Biol Sci. 4:193-196. 1988
- Regulation by the autophosphorylation site in overexpressed pp60c-src. Molecular and Cellular Biology. 8:4541-4546. 1988
- The cellular src gene product regulates junctional cell-to-cell communication. Science. 239:398-401. 1988
- v-src mutations outside the carboxyl-coding region are not sufficient to full activate transformation by pp60c-src in NIH 3T3 cells. Molecular and Cellular Biology. 8:704-712. 1988
- Activation and suppression of pp60c-src transforming ability by mutation of its primary sites of tyrosine phosphorylation. Cell. 49:65-73. 1987
- Analysis of polyomavirus middle T antigen transformed rat cell variants expressing different levels of pp60c-src. Journal of Virology. 61:1079-1085. 1987
- Induction by E1A oncogene expression of cellular susceptibility to lysis by TNF. Nature. 330. 1987
- Transfection and amplification of the chicken c-src proto-oncogene in Rat-1 cells. Cell Biol Int Rep. 11:379-388. 1987
- Transformation of NIH 3T3 cells by cotransfection with c-src and nuclear oncogenes. Molecular and Cellular Biology. 7:3582-3590. 1987
- Features of the pp60v-src carboxyl terminus that are required for transformation. Molecular and Cellular Biology. 6:2807-2819. 1986
- Junctional communication is down regulated in cells overexpressing pp60c-src. Journal of Cell Biology. 103. 1986
- Regulation of pp60c-src synthesis by inducible RNA complementary to c-src mRNA in polyoma virus transformed rat cells. Molecular and Cellular Biology. 6:2305-2316. 1986
- Information management in recombinant DNA research. Perspectives in Computing. 5:22-23. 1985
- Overexpressed pp60c-src can induce focus formation without complete transformation of NIH 3T3 cells. Molecular and Cellular Biology. 5:1073-1083. 1985
- Protein kinase C phosphorylates pp60src at a novel site. Cell. 42:849-857. 1985
- Restriction of the in vitro and in vivo tyrosine protein kinase activities of pp60c-src relative to pp60v-src. Molecular and Cellular Biology. 5:2753-2763. 1985
- Overexpression of the c-src protein does not induce transformation of NIH 3T3 cells. Proceedings at the National Academy of Science USA. 81:7071-7075. 1984
- Recombinant DNA data management at the restriction and functional site level. Nucleic Acids Research. 12:739-750. 1984
- Molecular Cloning and Characterization of the chicken gene homologous to the transforming gene of Rous sarcoma virus. Cell. 24:531-541. 1981
- Mapping of SV40 DNA replication origin region binding sites for the SV40 T Antigen by protection against exonuclease III digestion. Cell. 20:411-422. 1980
- Renormalization group and infrared behavior of quantum chromodynamics. Phys Rev. D19:1762-1781. 1979
- Dynamically parametrized quantization of local operators in the bag model. Phys Rev. D14:1032-1048. 1976
- Quantization of the bag in two dimensions by Dirac's method. Phys Rev. D11:3545-3564. 1975
- Mass Singularities in an approximation to single-fermion-loop vacuum polarization. Phys Rev. D10:486-492. 1974
- High accuracy precession measurement with an autometric gyro. Astrophys. and Space Science. 10:106-121. 1971
- Amygdaloid lesions and social behavior in the golden hamster. Physiology & Behavior. 5:153-161. 1970
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booksection
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chapter
- Variable-scale coarse-graining in macromolecular global optimization. Large Scale Optimization with Applications to Inverse Problems, Optimal Control and Design, and Molecular and Structural Optimization. 135-161. 1997
- Tracking metastable states to free-energy global minima. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding. 41-64. 1996
- Computer-assisted recombinant DNA design and analysis with MATILDA. Microcomputers in Biochemistry: A Practical Approach. 159-188. 1992
- Packet annealing: a deterministic method for global minimization. Application to molecular conformation. Recent Advances in Global Optimization. 433-477. 1992
- c-Src and mitosis. Ciba Foundation Symposium No. 170, Regulation of the Eukaryotic Cell Cycle. 248-275. 1992
- Mitotic activation of pp60c-src. Accomplishments in Cancer Research. 228-242. 1991
- Oncoprotein kinases in mitosis. Advances in Cancer Research. 185-225. 1991
- Maturation-promoting factor and the regulation of the cell cycle. The Cell Cycle. 53-63. 1989
- Studies on the NIH 3T3 cells sensitized to tumor necrosis factor by the expression of adenovirus E1A oncogene. Monokines and Other Non-Lymphocytic Cytokines. 243-248. 1988
- The cellular src gene: regulation of communication and growth. Gap Junctions. 1988
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document part
-
report
- A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing 1993
- Optimization methods for computing global minima of nonconvex potential energy functions 1993
- Isotropic effective energy simulated annealing searches for low energy molecular cluster states 1992
- Expanding integration and sharing of tools for computational biology 1991
- Macrostates of classical stochastic systems 1999
- Variational calculation of macrostate transition rates 1999
- Wrong policy? 1994
Teaching
teaching overview
- BioBM 834: Mathematical and statistical tools needed to analyze experimental data in molecular biology and genetics using examples from the literature. The goal is to provide a foundation for individual study of the quantitative techniques needed in individual research programs.
- BioBM 838: Scientific Communication and Quantitation in Biochemistry, Molecular and Cell Biology- students are coached in preparing a mock NIH grant proposal and presenting a scientific talk about their reserach; basic statistics is also covered
teaching activities
- BIOMG-8380: Scientific Communication in BMCB - Spring 2013
- BIOMG-4300: Mathematical Analysis and Computational Statistics of the Molecular Cell - Spring 2012
- BIOMG-6300: Mathematical Analysis and Computational Statistics of the Molecular Cell - Spring 2012
- BIOMG-8380: Scientific Communication in BMCB - Spring 2012
Service
service to the profession
- National Institutes of Health Committee Member 2011
- Journal of Chemical Physics Manuscript reviewer 2001 - 2011
- Penn State Biotechnology Institute Member 1987 - 1990
reviewer or editor for
Background
education and training
- Ph.D. in, Massachusetts Institute of Technology 1975
- M.S. in Physics, Stanford University 1970
- Massachusetts Institute of Technology 1969
awards and honors
- NIH Research Career Development Award, 1987
- ACS Junior Faculty Research Award, 1983
- NIH Postdoctoral Fellow, 1981
- NIH Postdoctoral Fellow, 1979
- ACS Postdoctoral Fellow, 1978
- Woodrow Wilson Graduate Fellow, 1969
- Danforth Graduate Fellow, 1969
- NSF Graduate Fellow, 1969
Other
alternate name
- David Shalloway
college
- CALS
research keyword
- astrobiology
- biochemistry
- carcinogenesis
- cell biology
- computational biology
- signal transduction