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Dr. Lisa
Tucker-Kellogg
Lee Kuan Yew Postdoctoral Fellow
Faculty Member of the Singapore-MIT
Alliance
Department of Computer Science
National University of Singapore
Singapore
117590
Office: NUS Room #COM1-03-24
Phone: (+65) 6516-2865
Departmental Fax: (+65) 6779-4580
Personal Fax: 1-419-502-0572
Email: tucker [at] comp [dot] "nus.edu.sg"
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Research
Interests
COMPUTATIONAL
SYSTEMS BIOLOGY
Constructing
computational models of redox regulation in apoptotic and survival pathways.
Parameter estimation for kinetic models of cellular signaling pathways.
- Decomposition, Discretization, and Probabilistic
Graphical Models as tools for approaching the problem of Parameter
Estimation. Relevant work: “Composing Globally Consistent Pathway
Parameter Estimates through Belief Propagation.” Workshop on
Algorithms for BioInformatics (2007) 420-430. Ongoing work with student Nim
Tri Hieu, and in collaboration with Jacob White at MIT.
- The role of LY29 and LY30 in sensitizing cancer cells
to TRAIL-induced apoptosis, in collaboration with Shazib Pervaiz in
Physiology. We used computational
modeling to guide when and where to measure, towards finding some blips in
the apoptotic cascade. This ongoing project has a conference
paper (Comp.Sys.Bioinf. Conference 2009) here: http://csb2009.org/pdf/076ShiTuckerKellog.pdf This topic is inspired by the
papers: “LY294002 and LY303511 sensitize tumor cells to
drug-induced apoptosis via intracellular hydrogen peroxide production
independent of the phosphoinositide 3-kinase-Akt pathway.” Cancer
Research 2005 65:6264, and “LY303511 amplifies TRAIL-induced
apoptosis in tumor cells…” by Poh, Huang, Hirpara and
Pervaiz.
- The role of Superoxide in cell survival signaling.
Drugs that promote accumulation of superoxide also promote activation of
Akt, a kinase that promotes survival. In collaboration with Marie-Véronique
Clément in Biochemistry, we hypothesize reactions that might be
involved, model their dynamics, and seek to design more focused
experiments that can help confirm the original hypotheses. Inspired by
the paper: “Phosphorylation of the survival kinase Akt by
superoxide…” by Lim and Clement in Free Radic Biol Med
42:1178.
- Activation kinetics of plasmin and TGF-beta. This ongoing work is in collaboration
with a large team, particularly Hanry Yu in Physiology.
COMPUTATIONAL STRUCTURAL BIOLOGY (Previously my main focus)
- Automated analysis of flexibility in protein
structures. ONGOING WORK: Algorithmic development of pFlexAna and
adapting the ideas of pFlexAna to additional problems such as visualization
of molecular dynamics trajectories. See “pFlexAna: Detecting
Conformational Changes in Remotely Related Proteins.” By Nigham,
Tucker-Kellogg, Mihalek, Verma, and Hsu. Nucleic Acids Research, 2008 July 1; 36: W246–W251.
- [Older Work] Systematic Conformational Search. "De
novo determination of peptide structure with solid-state magic-angle
spinning NMR spectroscopy." By by Rienstra, Tucker-Kellogg,
Jaroniec, Hohwy, Tidor, Lozano-Pérez, Griffin. PROC. NATL. ACAD.
SCI. USA, 2002 Aug 6: 99(16): 10260-5.
- [Older Work] X-ray crystallography towards better
understanding protein-DNA binding. "Engrailed Gln50 - Lys
homeodomain-DNA complex at 1.9 A resolution: structural basis for
enhanced affinity and altered specificity" by Tucker-Kellogg,
Rould, Chambers, Ades, Sauer, and Pabo. STRUCTURE, Vol. 5, No. 8, pp.
1047-1054, 1997. PMID: 9309220
- [Older Work] Virus shell assembly. "Local rule-based
theory of virus shell assembly" by Berger, Shor, Tucker-Kellogg,
King. PROC. NATL. ACAD. SCI. USA Vol. 91, pp.7732-7736, 1994. PMID:
8052652
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