Information Brochure (pdf) - Physiology and Neurobiology ...

The research in my laboratory is aimed at uncovering,
understanding, predicting, and visualizing the
“words” hidden within biological sequence data as
well as disseminating this information to the greater
biological research community. Accomplishing
this task requires a multidisciplinary approach that
integrates computational algorithm development,
experimental method refinement, and web-based
software design. As such, sample projects in my
laboratory involve, i) the improvement of the existing
motif-x and scan-x web tools for motif extraction
and prediction, ii) the development of experimental
assays to decipher enzymatic specificity
at the sequence motif level, and iii) the creation of
sequence motif visualization software.
Finally, armed with our knowledge of protein
sequence motifs, my laboratory seeks to use this
information to “read” viral proteomes in an effort to
understand the molecular mechanisms by which
viruses hijack cells, thus leading us closer toward
the goal of developing rationally-designed therapeutic
agents against these important human
pathogens.
Sample sequence motif of the insulin receptor kinase (InsR).
Selected Publications
Schwartz D., Green B., Carmichael L.E., & Parrish C.R. (2002).
The canine minute virus (minute virus of canines) is a distinct
parvovirus that is most similar to bovine parvovirus. Virology 302,
219-23.
Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D.,
Marsischky G., Roelofs J., Finley D., & Gygi S.P. (2003). A
proteomics approach to understanding protein ubiquitination. Nat
Biotechnology 21, 921-6.
Shimura H., Schwartz D., Gygi S.P., & Kosik K.S. (2004). CHIP-
Hsc70 complex ubiquitinates phosphorylated tau and enhances
cell survival. J Biol Chem 279, 4869-76.
Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen
J., Li J., Cohn M.A., Cantley L.C., & Gygi S.P. (2004). Large-scale
characterization of HeLa cell nuclear phosphoproteins. Proc Natl
Acad Sci U S A 101, 12130-5.
Ballif B.A., Villen J., Beausoleil S.A., Schwartz D., & Gygi S.P.
(2004). Phosphoproteomic analysis of the developing mouse
brain. Mol Cell Proteomics 3, 1093-101.
Schwartz D. and Gygi S.P. (2005). An iterative statistical
approach to the identification of protein phosphorylation motifs
from large-scale data sets. Nat Biotechnology 23, 1391-8.
Chiang C.W., Derti A., Schwartz D., Chou M.F., Hirschhorn J.N.,
& Wu C.T. (2008). Ultraconserved elements: analyses of dosage
sensitivity, motifs and boundaries. Genetics 180, 2277-93.
Schwartz D., Chou M.F., & Church G.M. (2009). Predicting
protein post-translational modifications using meta-analysis of
proteome scale data sets. Mol Cell Proteomics 8, 365-79.
Grimsrud P.A., den Os D., Wenger C.D., Swaney D.L., Schwartz
D., Sussman M.R., Ane J.M., & Coon J.J. (2010). Large-scale
phosphoprotein analysis in Medicago truncatula roots provides
insight into in vivo kinase activity in legumes. Plant Physiol 152,
19-28.
Prisic S., Dankwa S., Schwartz D., Chou M.F., Locasale J.W.,
Kang C.M., Bemis G., Church G.M., Steen H., & Husson R.N.
(2010). Extensive phosphorylation with overlapping specificity
by Mycobacterium tuberculosis serine/threonine protein kinases.
Proc Natl Acad Sci U S A 107, 7521-6.
Schwartz D. and Church G.M. (2010). Collection and motifbased
prediction of phosphorylation sites in human viruses. Sci.
Signal. 3, rs2.
Ballif B.A., Cao Z., Schwartz D., Carraway K.L., & Gygi S.P.
(2006). Identification of 14-3-3 substrates from embryonic murine
brain. J Proteome Res 5, 2372-9.