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Journal
Papers
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(36)
(35)
T.J.Close, P.R.Bhat, S.Lonardi, Y.Wu,
N.Rostoks, L.Ramsay, A.Druka, N.Stein, J.T.Svensson,
S.Wanamaker, S.Bozdag, M.L.Roose, M.J.Moscou,
S.Chao, R.Varshney, P.Szucs, K.Sato, P.M.Hayes,
D.E.Matthews, A.Kleinhofs, G.J.Muehlbauer,
J.DeYoung, D.F.Marshall, K.Madishetty, R.D.Fenton,
P.Condamine, A.Graner, R.Waugh,
"Development and Implementation of High-Throughput SNP Genotyping
in Barley'', to appear in BMC Genomics, 2009.
(34)
D.Bogunovic, D.W.O'Neill, I.Belitskaya-Levy, V.Vacic, Y.-L.Yu,
S.Adams, F.Darvishian, R.Berman, R.Shapiro,
A.Pavlick, S.Lonardi, J.Zavadil, I.Osman and N.Bhardwaj,
"Immune profile and mitotic index of metastatic melanoma
lesions enhance TNM staging in predicting patient survival",
to appear in Proceedings of the National Academy of Sciences (PNAS), 2009.
(33) V.Vacic, L.M.Iakoucheva, S.Lonardi,
P.Radivojac, "Graphlet Kernels for Prediction of Functional
Residues in Protein Structures", to appear in Journal
Computational Biology, 2009.
(32) L.Liu, Y.Wu, S.Lonardi, T.Jiang,
"Efficient Genome-Wide TagSNP Selection across Populations
via the Linkage Disequilibrium Criterion", to appear in
Journal Computational Biology, 2009.
(31) S.Bozdag, T.Close, S.Lonardi, "A
Compartmentalized Approach to the Assembly of Physical
Maps", BMC Bioinformatics, 10:217, 2009.
(30) Y.Wu, P.Bhat, T.J.Close, S.Lonardi,
"Efficient and accurate construction of genetic linkage maps
from the minimum spanning tree of a graph",
PLOS Genetics, 4(10):e1000212, 2008.
(29) Y.Wu, S.Lonardi, "A Linear-time
Algorithm for Predicting Functional Annotations from
Protein-Protein Interaction Networks",
Journal of Bioinformatics and Computational Biology,
vol.6, no.6, 2008.
(28) N.G.Portney, Y.Wu, L.K.Quezada,
S.Lonardi, M.Ozkan, "Length-based Encoding of Binary Data in
DNA", Langmuir, vol.24, no.5, pp.1631-1616,
2008.
(27) Y.Wu, L.Liu, T.Close, S.Lonardi,
"Deconvoluting BAC-gene relationships using a physical map",
Journal of Bioinformatics and Computational Biology,
vol.6, no.3, pp.603-622, 2008.
(26) H. Jin, V. Vacic, T. Girke,
S. Lonardi, J.-K. Zhu, "Small RNAs and the regulation of
cis-natural antisense transcripts in Arabidopsis.", BMC
Molecular Biology, 9:6, 2007.
(25) V.Vacic, V.N.Uversky, A.K.Dunker,
S.Lonardi, "Composition Profiler: A tool for discovery and
visualization of amino acid composition differences", BMC
Bioinformatics, 8:211, 2007.
(24) S.Lonardi, W.Szpankowski, M.D.Ward,
"Error Resilient LZ'77 Data Compression: Algorithms,
Analysis, and Experiments'', IEEE Transactions on
Information Theory, vol.53, no.5, pp.1799-1813,
2007.
(23) J.Li, E.Keogh, S.Lonardi,
"Experiencing SAX: a Novel Symbolic Representation of Time
Series", Data Mining and Knowledge Discovery, vol.15,
no.2, pp.107-144, 2007.
(22) E.Keogh, S.Lonardi,
C.A.Ratanamahatana, L.Wei, S.-H.Lee, J.Handley,
"Compression-based data mining of sequential data",
Data Mining and Knowledge Discovery,
vol.14, no.1, pp.99-129, 2007.
(21) S.Lonardi, J.Lin, E.Keogh,
B.Chiu, "Efficient Discovery of Unusual Patterns in Time
Series", New Generation Computing,
Special issue on Knowledge Discovery from Data Streams,
vol.25, pp.61-94, 2007.
(20) Q.Yang, S.Lonardi, "A Parallel
Algorithm for Clustering Protein-Protein Interaction
Networks", International Journal of Data Mining and
Bioinformatics, vol.1, no.3, pp.241-247,
2007.
(19) S.Lin, V.Kalogeraki, D.Gunopulos,
S.Lonardi, "Efficient Information Compression in Sensor
Networks", International Journal on Sensor Networks,
Special Issue on Recent Developments in Wireless Sensor
Networks, vol.1, no.3/4, pp.229-240, 2006.
(18) S.Lonardi, W.Szpankowski, Q.Yang,
"Finding Biclusters by Random Projections",
Theoretical Computer Science, vol.368, no.3, pp.217-230, 2006.
(17) A.Bagnall, C.A.Ratanamahatana,
E.Keogh, S.Lonardi, G.Janacek, "A Bit Level
Representation for Time Series Data Mining with Shape
Based Similarity", Data Mining and Knowledge
Discovery, vol.13, no.1, pp.11-40, 2006.
(16) J.Zheng, J.T.Svensson, K.Madishetty, T.J.Close,
T.Jiang, S.Lonardi, "Oligospawn: a web-based tool for
the design of overgo probes from large unigene
databases", BMC Bioinformatics, 7:7,
2006.
(15) Y.Luo, S.Lonardi, "Storage
and Transmission of Microarray Images", Drug Discovery
Today, vol.10, no.23/24, pp.1689-1695, 2005.
(14) L.Wei, E.Keogh, X.Xi, S.Lonardi,
"Intelligent Icons: Integrating Lite-Weight Visualization
and Data Mining into Operating Systems", Journal of
Universal Computer Science, Special Issue on Visual Data
Mining, J.S.Aguilar-Ruiz (ed.), vol.11, no.11,
pp.1820-1834, 2005.
(13) X.Chen, J.Zheng, Z.Fu, P.Nan, Y.Zhong,
S.Lonardi, T.Jiang, "Assignment of orthologous genes
via genome rearrangement", IEEE Transactions on
Computational Biology and Bioinformatics, vol. 2, no. 4,
pp. 302-315, 2005.
(12) J.Lin, E.Keogh, S.Lonardi, "Visualizing
and Discovering Non-Trivial Patterns In Large Time Series
Databases", Information Visualization, vol.4,
no.2, pp.61-82, 2005.
(11) S.Janson, S.Lonardi,
W.Szpankowski, "On Average Sequence Complexity",
Theoretical Computer Science, vol.326, no.1-3, pp.213-227, 2004.
(10) J.Zheng, T.Close, T.Jiang,
S.Lonardi, "Efficient Selection of Unique and Popular
Oligos for Large EST Databases", Bioinformatics, vol.20, no.13,
pp.2101-2112, 2004.
(9) A.Apostolico, F.Gong, S.Lonardi,
"Verbumculus and the Discovery of Unusual Words",
Journal of Computer and Science Technology (special
issue in Bioinformatics), vol.19, no.1, pp.22-41,
2004.
(8) M.Atallah, S.Lonardi, "Augmenting
LZ-77 with Authentication and Integrity Assurance
Capabilities", Concurrency and
Computation: Practice and Experience, vol.16,
no.11, pp.1063-1076, 2004.
(7) A.Apostolico, M.E.Bock, S.Lonardi,
"Monotony of surprise and large-scale quest for unusual
words", Journal of Computational Biology, vol.10,
no.2/3, pp.283-311, 2003.
(6) A.Apostolico, S.Lonardi,"A
Speed-up for the Commute between Subword Trees and DAWGs",
Information Processing Letters,
vol.83, no.3, 159-161, 2002.
(5) A.Apostolico, S.Lonardi,
"Off-line Compression by Greedy Textual Substitution",
Proceedings of the IEEE, vol.88, no.11, 1733-1744,
2000.
(4) A.Apostolico, M.E.Bock,
S.Lonardi, X.Xu, "Efficient Detection of Unusual
Words", Journal of Computational Biology, vol.7,
no.1/2, 71-94, 2000.
(3) E.W.Myers, G.G.Sutton, A.L.Delcher,
I.M.Dew, D.P.Fasulo, M.J.Flanigan, S.A.Kravitz,
C.M.Mobarry, K.H.J.Reinert, K.A.Remington, E.L.Anson,
R.A.Bolanos, H.-H. Chou, C.M.Jordan, A.L.Halpern,
S.Lonardi, E.M.Beasley, R.C.Brandon, L.Chen,
P.J.Dunn, Z.Lai, Y.Liang, D.R.Nusskern, M.Zhan, Q.Zhang,
X.Zheng, G.M.Rubin, M.D.Adams, J.C.Venter, "A Whole-Genome
Assembly of Drosophila", Science, vol.287, no.5461,
2196-2204, 2000.
(2) S.Lonardi, P.Sommaruga, "Fractal
Image Compression and Orthogonal Basis", Image
Communication, vol.14, no.5, 413-423, 1999.
(1) R.Foroni, J.Hoch, G.Giri, A.Pasoli,
M.Gerosa, A.Pasqualin, A.Nicolato, E.Piovan, P.Zampieri,
E.Bortolazzi, S.Lonardi, "Shape recovery and volume
calculation from biplane angiography in the stereotactic
radiosurgery treatment of arteriovenous malformation" in
International Journal of Radiation Oncology, Biology and
Physics, vol.35, no.3, 565-577, 1996.
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Conference Papers
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(47)
(46) E.Y.Harris, T.Lecroq, G.Kucherov,
S.Lonardi, "CPM's 20th anniversary: A statistical
retrospective'', Proceedings of Symposium on
Combinatorial Pattern Matching (CPM'09), LNCS 5577,
pp. 1-11, Lille, France, 2009 (invited paper).
(45) S.Bozdag, T.Close, S.Lonardi,
"Computing the Minimal Tiling Path from a Physical Map by
Integer Linear Programming", Proceedings of the Workshop
on Algorithms in Bioinformatics (WABI'08), LNBI 5251,
pp.148-161, Universitat Karlsruhe, Germany,
2008.
(44) Y.Wu, T.J.Close, S.Lonardi, "On
the accurate construction of consensus genetic maps",
Proceedings of LSS Computational Systems Bioinformatics
Conference (CSB'08), pp.285--296, Stanford, CA,
2008.
(43) V.Vacic, H.Jin, J.-K.Zhu,
S.Lonardi, "A probabilistic method small RNA flowgram
matching", Proceedings of Pacific Symposium on
Biocomputing (PSB'08), pp.75-86, Hawaii,
2008.
(42) S.Bozdag, T.Close, S.Lonardi, "A
compartmentalized approach to the assembly of physical
maps", Proceedings of IEEE International Symposium on
Bioinformatics and Bioengineering (BIBE'07),
pp.218-225, Boston, MA, 2007.
(41) Y.Wu, S.Lonardi, "A Linear-time
Algorithm for Predicting Functional Annotations from
Protein-Protein Interaction Networks", Proceedings of
the Workshop on Data Mining in Bioinformatics
(BIOKDD'07), pp.35-41, San Jose, CA, 2007.
(40) Q.Yang, S.Lonardi, "A Graph
Decomposition Approach to the Identification of Network
Building Modules", Proceedings of the Workshop on Data
Mining in Bioinformatics (BIOKDD'07), pp.50-59, San
Jose, CA, 2007.
(39) Y.Wu, P.Bhat, T.J.Close,
S.Lonardi, "Efficient and accurate construction of genetic
linkage maps from noisy and missing genotyping data",
Proceedings of the Workshop on Algorithms in
Bioinformatics (WABI'07), LNBI 4645, pp.395-406,
Philadelphia, PA, 2007.
(38) L.Liu, Y.Wu, S.Lonardi, T.Jiang,
"Efficient Algorithms for Genome-Wide TagSNP Selection
across Populations via the Linkage Disequilibrium
Criterion", Proceedings of LSS Computational Systems
Bioinformatics Conference (CSB'07), pp.67-78,
Stanford, CA, 2007.
(37) Y.Wu, L.Liu, T.Close, S.Lonardi,
"Deconvoluting the BAC-gene relationships using a physical
map", Proceedings of LSS Computational Systems
Bioinformatics Conference (CSB'07), pp.203--214,
Stanford, CA, 2007.
(36) D.Shelton, F.Vahid, S.Lonardi,
"Soft-core Processor Customization using the Design of
Experiments Paradigm'', Proceedings of Design,
Automation and Test in Europe (DATE'07), pp.821-826,
Nice, France.
(35) S.Sirowy, Y.Wu, S.Lonardi,
F.Vahid, "Two Level Microprocessor-Accelerator
Partitioning", Proceedings of Design,
Automation and Test in Europe (DATE'07), pp.313-318,
Nice, France.
(34) S.Sirowy, Y.Wu, F.Vahid,
S.Lonardi, "Clock-Frequency Partitioning for Multiple
Clock Domains Systems-on-a-Chip",
Proceedings of Design, Automation and Test in
Europe (DATE'07), pp.397-402, Nice, France.
(33) E.Keogh, L.Wei, X.Xi, S.Lonardi,
J.Shieh, S.Sirowy, "Intelligent Icons: Integrating
Lite-Weight Data Mining and Visualization into GUI
Operating Systems", Proceedings of the
IEEE International Conference on Data Mining (ICDM'06),
pp.912-916, Hong Kong.
(32) Q.Yang, G.Siganos, M.Faloutsos, S.Lonardi,
"Evolution versus Intelligent Design: Comparing the
Topology of Protein-Protein Interaction Networks to
the Internet", in Proceedings of LSS Computational Systems
Bioinformatics Conference (CSB'06), pp.299-310,
Stanford, CA, 2006.
(31) Q.Yang, S.Lonardi, A.Melkman, "A
compression-boosting transform for two-dimensional data",
Proceedings of Second International Conference on
Algorithmic Aspects in Information and Management
(AAIM'06), LNCS 4041, pp.126-137, Hong Kong, China,
2006.
(30) S.Lin, V.Kalogeraki, D.Gunopulos,
S.Lonardi, "Online Information Compression in Sensor
Networks", Proceedings of the IEEE
International Conference on Communications (ICC'06),
2006.
(29) Y. Wu, S.Lonardi,
W.Szpankowski, "Error-Resilient LZW Data Compression",
Proceedings of the IEEE Data Compression
Conference (DCC'06), pp.193-202, Snowbird, Utah, 2006.
(28) D.Yankov, E.Keogh, S.Lonardi, "Dot
Plots for Time Series Analysis",
Proceedings of IEEE International Conference on Tools
with Artificial Intelligence (ICTAI'05), pp.159-168, Hong Kong,
China.
(27) J.Zheng, S.Lonardi,
"Discovery of repetitive patterns in DNA with accurate
boundaries", Proceedings of IEEE International
Symposium on BioInformatics and BioEngineering
(BIBE'05), pp.105-112, Minneapolis, Minnesota.
(26) L.Wei, N.Kumar, V.Lolla, E.Keogh,
S.Lonardi, C.A.Ratanamahatana, "Assumption-Free
Anomaly Detection in Time Series", Proceedings of the
International Statistical and Scientific Database
Management Conference (SSDBM'05), pp.237-240, Santa
Barbara, CA.
(25) L.Wei, N.Kumar, V.N.Lolla, E.Keogh,
S.Lonardi, C.A.Ratanamahatana, H.Van Herle, "A
Practical Tool for Visualizing and Data Mining Medical
Time Series", Proceedings of IEEE International
Symposium on Computer-Based Medical Systems (CBM'05),
pp.341-346, Dublin, Ireland.
(24) C.A.Ratanamahatana, E.Keogh,
A.J.Bagnall, S.Lonardi, "A Novel Bit Level Time Series
Representation with Implications for Similarity Search and
Clustering", Proceedings of
Pacific-Asia Conference on Knowledge Discovery and Data
Mining, (PAKDD'05), LNAI 3518, pp.771-777, Hanoi,
Vietnam, 2005.
(23) N.Kumar, N.Lolla, E.Keogh,
S.Lonardi, C.A.Ratanamahatana, L.Wei, "Time-series
Bitmaps: A Practical Visualization Tool for working with
Large Time Series Databases", Proceedings of
SIAM Conference in Data Mining, (SDM'05), pp.531-535, Newport
Beach, CA, 2005
(22) X.Chen, J.Zheng, Z.Fu, P.Nan,
Y.Zhong, S.Lonardi, T.Jiang, "Computing the
assignment of orthologous genes via genome rearrangement",
Proceedings of Asia-Pacific Bioinformatics
Conference (APBC'05), pp.363-378, Singapore, Jan 2005.
(21) E.Keogh, S.Lonardi,
C.A.Ratanamahatana, "Towards Parameter-Free Data Mining",
Proceedings of ACM Conference on Knowledge Discovery and
Data Mining (KDD'04), pp.206-215, Seattle, WA,
2004.
(20) J.Lin, E.Keogh, S.Lonardi,
J.P.Lankford, D.M.Nystrom, "Visually Mining and Monitoring Massive
Time Series", Proceedings of ACM Conference on
Knowledge Discovery and Data Mining (KDD'04),
pp.460-469, Seattle, WA, 2004.
(19) J.Lin, E.Keogh, S.Lonardi,
J.P.Lankford, D.M.Nystrom, "VizTree: a Tool for Visually
Mining and Monitoring Massive Time Series Databases",
Proceedings of International Conference on Very
Large Data Bases (VLDB'04), pp.1269-1272, Toronto,
Canada, 2004.
(18) S.Lonardi,
Y.Luo, "Gridding and Compression of Microarray Images",
Proceedings of IEEE Computational Systems Bioinformatics
Conference (CSB'04), pp.122-130, Stanford, CA, 2004.
(17) S.Janson, S.Lonardi,
W.Szpankowski, "On Average Sequence Complexity",
Proceedings of Symposium on Combinatorial Pattern
Matching (CPM'04), LNCS 3109, pp.74-88, Istanbul,
Turkey, 2004.
(16) S.Lonardi, W.Szpankowski, Q.Yang,
"Finding biclusters by random projections",
Proceedings of Symposium on Combinatorial Pattern
Matching (CPM'04), LNCS 3109, pp.102-116, Istanbul, Turkey, 2004.
(15) S.Lonardi, W.Szpankowski, M.Ward,
"Error Resilient LZ'77 and its Analysis", Proceedings of
IEEE International Symposium on Information Theory
(ISIT'04), p.56, Chicago, IL, 2004.
(14) B.Chiu, E.Keogh, S.Lonardi,
"Probabilistic Discovery of Time Series Motifs", Proceedings
of the ACM Conference on Knowledge Discovery and Data
Mining, (KDD'03), pp.493-498, Washington, DC,
2003.
(13) J.Lin, E.Keogh, S.Lonardi, and
B.Chiu, "Symbolic Representation of Time Series, with
Implications for Streaming Algorithms", Proceedings of the
ACM SIGMOD Workshop on Research Issues in Data Mining and
Knowledge Discovery, pp.2-11, San Diego, CA,
2003.
(12) J.Zheng, T.Close, T.Jiang,
S.Lonardi, "Efficient Selection of Unique and Popular
Oligos for Large EST Databases", Proceedings of Symposium
on Combinatorial Pattern Matching (CPM'03), LNCS 2676,
pp.384-401, Morelia, Mexico, 2003.
(11) S.Lonardi, W.Szpankowski,
"Joint Source-Channel LZ'77 Coding", Proceedings of the
IEEE Data Compression Conference (DCC'03),
pp.273-283, Snowbird, Utah, 2003.
(10) M.J.Atallah, S.Lonardi,
"Authentication of LZ-77 compressed data", Proceedings of
ACM Symposium on Applied Computing (SAC'03),
pp.282-287, Melbourne, FL, 2003.
(9) P.Patel, E.Keogh, J.Lin,
S.Lonardi, "Mining Motifs in Massive Time Series
Databases.", Proceedings of IEEE International
Conference on Data Mining (ICDM'02), pp.370-377,
Maebashi City, Japan, 2002.
(8) J.Lin, E.Keogh, S.Lonardi,
P.Patel, "Finding motifs in time series", Proceedings of
2nd Workshop on Temporal Data Mining, pp.53-68, at
the 8th ACM SIGKDD International Conference on Knowledge
Discovery and Data Mining, Edmonton, Alberta, Canada,
2002.
(7) C.Guerra, S.Lonardi, G.Zanotti,
"Analysis of Secondary Structure Elements of Proteins Using
Indexing Techniques", Proceedings of 1st
International Symposium on 3D Data Processing Visualization
and Transmission (3DPVT'02), pp.812-823, Padova, Italy,
2002.
(6) E.Keogh, S.Lonardi, B.Chiu,
"Finding Surprising Patterns in a Time Series Database in
Linear Time and Space", Proceedings of ACM
SIGKDD International Conference on Knowledge Discovery and
Data Mining (KDD '02), pp.550-556, Edmonton, Alberta,
Canada, 2002.
(5) A.Apostolico, M.E.Bock, S.Lonardi,
"Monotony of surprise and large-scale quest for unusual
words", Proceedings of ACM Annual International
Conference on Research in Computational Molecular
Biology (RECOMB'02), pp.22-31, Washington, DC,
2002.
(4) A.Apostolico, S.Lonardi,
"Compression of Biological Sequences by Greedy Off-line
Textual Substitution", Proceedings of IEEE Data
Compression Conference (DCC'00), pp.143-152, Snowbird,
Utah, March 27-30, 2000.
(3) A.Apostolico, M.E.Bock, S.Lonardi,
"Linear Global Detectors of Redundant and Rare Substrings",
Proceedings of IEEE Data Compression Conference
(DCC'99), pp.168-177, Snowbird, Utah, 1999.
(2) A.Apostolico, S.Lonardi, "Some
Theory and Practice of Greedy Off-Line Textual
Substitution", Proceedings of Data Compression
Conference (DCC'98), pp.119-128, Snowbird, Utah,
1998.
(1) S.Lonardi, A.Sperduti, A.Starita,
"Encoding pyramids by Labeling RAAM", Proceedings of
IEEE Workshop on Neural Networks for Signal
Processing, pp.651-660, Ermioni, Greece 1994.
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