\begin{thebibliography}{10}


\bibitem{bottou10}
L.~Bottou.
\newblock {Large-Scale Machine Learning with Stochastic Gradient Descent}.
\newblock In Y.~Lechevallier and G.~Saporta, editors, {\em Proceedings of the
  19th International Conference on Computational Statistics (COMPSTAT'2010)},
  pages 177--187, Paris, France, August 2010. Springer.

\bibitem{breiman01}
L.~Breiman.
\newblock Random forests.
\newblock {\em Machine Learning}, 45(1):5--32, 2001.

\bibitem{cole05}
R.~Cole, D.~Shasha, and X.~Zhao.
\newblock Fast window correlations over uncooperative time series.
\newblock In R.~Grossman, R.~J. Bayardo, and K.~P. Bennett, editors, {\em KDD},
  pages 743--749. ACM, 2005.

\bibitem{gutierrez08}
R.~A. Gutierrez, L.~Lejay, A.~Dean, F.~Chiaromonte, D.~E. Shasha, and G.~M.
  Coruzzi.
\newblock {Qualitative network models and genome-wide expression data define
  carbon/nitrogen-responsive molecular machines in Arabidopsis}, Jan. 2007.

\bibitem{kimmel06}
Z.~Kimmel, D.~Shasha, A.~Turchin, and R.~A. Greenes.
\newblock {State-Based Clinical Decision Support (SBCDS)}, June 2006.

\bibitem{krouk10}
G.~Krouk, P.~Mirowski, Y.~LeCun, D.~Shasha, and G.~Coruzzi.
\newblock Predictive network modeling of the high-resolution dynamic plant
  transcriptome in response to nitrate.
\newblock {\em Genome Biology}, 11(R123), December 2010.

\bibitem{natale10}
R.~D. Natale, A.~Ferro, R.~Giugno, M.~Mongiov\`{\i}, A.~Pulvirenti, and
  D.~Shasha.
\newblock {SING: Subgraph search In Non-homogeneous Graphs}, 2010.

\bibitem{Pandit07}
S.~Pandit, D.~H. Chau, S.~Wang, and C.~Faloutsos.
\newblock Netprobe: a fast and scalable system for fraud detection in online
  auction networks, 2007.

\bibitem{recupero08}
D.~R. Recupero, R.~A. Gutiérrez, and D.~Shasha.
\newblock {Graphclust: A Method for Clustering Database of Graphs}.

\bibitem{shalev09}
S.~Shalev-Shwartz and A.~Tewari.
\newblock Stochastic methods for l $_1$ regularized loss minimization.
\newblock In A.~P. Danyluk, L.~Bottou, and M.~L. Littman, editors, {\em ICML},
  volume 382 of {\em ACM International Conference Proceeding Series}, page 117.
  ACM, 2009.

\bibitem{zhao05}
X.~Zhao, X.~Zhang, T.~Neylon, and D.~Shasha.
\newblock Incremental methods for simple problems in time series: Algorithms
  and experiments, 2005.

\bibitem{zhu03}
Y.~Zhu and D.~Shasha.
\newblock {\em High performance discovery in time series: Techniques and case
  studies}, June~16 2003.


\bibitem{chen10}
Huang-Wen Chen, Sunayan Bandyopadhyay, Dennis E. Shasha, and
Kenneth D. Birnbaum 
\newblock Estimation of genome-wide redundancy in Arabidopsis thaliana,
BMC Evolutionary Biology 2010, 10:357; doi:10.1186/1471-2148-10-357

\bibitem{elastic10}
X. Zhang, D. Shasha, Y. Song and J. T. L. Wang,
\newblock Fast Elastic Peak Detection for Mass Spectrometry Data Mining,
IEEE Transactions on Knowledge and Data Engineering,
Issue 99.
November 29, 2010, doi: 10.1109/TKDE.2010.238

\bibitem{virtplant10}
Manpreet S. Katari, Steve D. Nowicki, Felipe F. Aceituno, Damion Nero, 
Jonathan Kelfer, Lee Parnell Thompson, Juan M. Cabello, 
Rebecca S. Davidson, Arthur P. Goldberg, 
Dennis E. Shasha, Gloria M. Coruzzi, and Rodrigo A. Gutierrez, 
\newblock VirtualPlant: a software platform to support system biology research
Plant Physiology 152:500-515 (2010)

\bibitem{interact09}
Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A. Cruikshank,
Dennis Shasha, Gloria M. Coruzzi, Rodrigo A. Guitierrez
\newblock
A Systems Approach Uncovers Restrictions for Signal
Interactions Regulating Genome-wide Responses to
Nutritional Cues in Arabidopsis
PLOS Computational Biology
March 2009, volume 5, issue 3

\bibitem{diego08}
Diego Reforgiato, Rodrigo Gutierrez, Dennis Shasha
\newblock GraphClust: A Method for Clustering Databases of Graphs
Journal of Information and Knowledge Management (JIKM)
Volume:  7, Issue: 4 (December 2008)
Page 231 - 241
http://www.worldscinet.com/cgi-bin/details.cgi?id=jsname:jikm\&type=current

\bibitem{thum08}
Karen E Thum, Michael J Shin, Rodrigo Gutierrez, Indrani Mukherjee, Manpreet S
Katari, Damion Nero, Dennis Shasha and Gloria M Coruzzi
\newblock An integrated genetic, genomic 
and systems approach defines gene networks
 regulated by the interaction of light and 
carbon signaling pathways in Arabidopsis"
BMC Systems Biology 2008, 2:31 (04 Apr 2008)

\bibitem{carbnit07}
Gutierrez, R.A.,  Lejay, L., Chiaromonte, 
F., Shasha, D.E., Coruzzi, G.M. (2007) 
\newblock Qualitative network 
models and genome-wide expression data 
define carbon/nitrogen-responsive molecular machines in Arabidopsis.  
Genome Biol.: 8, pp. R7. "Must read" Factor 6 in the Faculty of 1000.

\bibitem{graphfind07}
A. Ferro, R. Giugno, M. Mongiovi, A. Pulvirenti, D. Skripin, D.  Shasha,
\newblock GraphFind: Enhancing Graph Searching by Low Support Data Mining
Techniques
BMC Bioinformatics, vol. 8 ISSN: 1471-2105, 2007.

\bibitem{usingsungear07}
Rodrigo A. Gutiérrez, Miriam L. Gifford, Chris Poultney, Rongchen Wang, 
Dennis E. Shasha, Gloria M. Coruzzi and Nigel M. Crawford
\newblock Insights into the genomic nitrate response using
genetics and the Sungear software system
JXB Advance Access published online on April 29, 2007 
Journal of Experimental Botany, doi:10.1093/jxb/erm079 

\bibitem{sungear07}
Christopher S. Poultney, Rodrigo A. Gutirrez, Manpreet S. Katari, 
Miriam L. Gifford, W. Bradford Paley, Gloria M.  Coruzzi and Dennis E. Shasha
\newblock Sungear: Interactive visualization and functional analysis 
of genomic datasets
Bioinformatics, 2007; Jan 15;23(2):259-61
doi: 10.1093/bioinformatics/btl496

\bibitem{sysbio05}
Rodrigo Gutierrez, Dennis Shasha, and Gloria Coruzzi,
\newblock Systems Biology for the Virtual Plant
Plant Physiology, June 2005, vol. 38, pp. 550-554.

\bibitem{combdesign04}
Laurence V. Lejay, Dennis E. Shasha, Peter M. Palenchar, Andrei Y.
Kouranov,
Alexis A. Cruikshank, Michael F. Chou, Gloria M. Coruzzi
\newblock Adaptive Combinatorial Design to explore Large Experimental Spaces:
approach and validation
Systems Biology, volume 1, issue 2, December 2004, pp. 206-212.

\bibitem{birnbaum03}
Kenneth Birnbaum, Dennis E. Shasha, Jean Y. Wang, 
Jee W. Jung, Georgina M. Lambert, David W. Galbraith, and Philip N. Benfey
\newblock A gene
expression map of the Arabidopsis root
Science, Dec 12 2003: 1956-1960 
(A review article in the Research Focus section of Trends in Biotechnology
called the article 
``At the end of 2003, the root biology community was blessed with what
has become today already a historical paper that described for the 
first time a genome wide expression analysis 
of Arabidopsis root development [2].'') 

\bibitem{traittogene03}
Mitchell Levesque, Dennis Shasha, Wook Kim, 
Michael G. Surette, and Philip N. Benfey
\newblock Trait-To-Gene: A Computational Method for 
Predicting the Function of Uncharacterized Genes
{\em Current Biology}, vol. 13, 129-133, January 21, 2003.
Discussed in:
http://www.the-scientist.com/yr2003/jun/hot\_030603.html

\bibitem{timeseries04}
Alberto Lerner, Dennis Shasha, Zhihua Wang, Xiaojian Zhao,
Yunyue Zhu
\newblock Fast Algorithms for Time Series with Applications
to Finance, Physics, Music, Biology and other Suspects
ACM Sigmod 2004, pp. 965-968.

\bibitem{burst03}
Yunyue Zhu and Dennis Shasha
\newblock Efficient Elastic Burst Detection in Data Streams
The Ninth ACM SIGKDD International Conference on
 Knowledge Discovery and Data Mining
 KDD-2003
24 August 2003 - 27 August 2003
\end{thebibliography}
