UCR

Computer Science and Engineering



Stefano Lonardi, Professor

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Research Interests
Computational molecular biology, data mining, data compression.  
Education
Doctor of Philosophy
Department of Computer Sciences
Purdue University, West Lafayette, IN, USA.
Aug 1996
Aug 2001
Dottorato in Ingegneria Informatica ed Elettronica Industriali
Università degli Studi di Padova, Padova, Italy.
Apr 1995
Feb 1999
Laurea in Scienze dell'Informazione
Università degli Studi di Pisa, Pisa, Italy.
Nov 1987
Apr 1994
Professional Experience
Professor, Department of Computer Science & Engineering, University of California, Riverside, CA, USA Jul 2011
present
Associate Professor, Department of Computer Science & Engineering, University of California, Riverside, CA, USA Jul 2007
Jun 2011
Assistant Professor, Department of Computer Science & Engineering, University of California, Riverside, CA, USA Jul 2001
Jun 2007
Research Assistant, Purdue Research Foundation, Department of Computer Science, Purdue University, West Lafayette, IN, USA Aug 1999
May 2001
Research Scientist, Celera Genomics, Informatics Research dept., under the supervision of Prof. Gene Myers, Rockville, MD, USA May 1999
Aug 1999
Visiting Research Scholar, Department of Computer Science, Purdue University, West Lafayette, IN, USA Aug 1997
May 1999
Consultant, Project Gamma-plan (geometric modeling), Gamma Lab, Dipartimento di Neurochirurgia, University of Verona, Italy Aug 1995
Dec 1995
Awards
IEEE Fellow (Computer Society) 2016
NSF CAREER Award 2005
Student Research Award, Purdue University 2000
Students Graduated
Anton Polishko (PhD 2014, Computer Science, Entrapreneur) 2014
Sara Nasseri (MS 2014, Computer Science, with Western Digital) 2014
Matthew Alpert (BS, Computer Science, currently with Turtle Rock Studios) 2013
Denise Duma (PhD, Computer Science, currently with Baylor College of Medicine) 2013
Mo Cao (MS, Computer Science, currently with Xangati) 2012
Burair Alsaihati (MS, Computer Science, currently with Joint Center for Genomics Research, KACST) 2011
Elena Harris (PhD, Computer Science, currently Assistant Professor at Cal State, Chico) 2010
Neeti Pokhriyal (MS, Computer Science, currently PhD student at University at Buffalo) 2009
Vladimir Vacic (PhD, Computer Science, currently Bioinformatics Scientist at New York Genome Center) 2008
Yonghui Wu (PhD, Computer Science, currently with Google, Mountain View, CA) 2008
Serdar Bozdag (PhD, Computer Science, currently Assistant Professor at Marquette University) 2008
Jie Zheng (PhD, Computer Science, currently Assistant Professor at Nanyang Tech. Univ., Singapore) 2006
Qiaofeng Yang (PhD, GGB, currently with Bloomberg, NY) 2006
Vi Pham (MS, Computer Science) 2006
San Nguyen (MS, Computer Science, currently with Raytheon) 2006
George Hsu (MS, Computer Science) 2005
Yu Luo (MS, Computer Science, currently with Nationwideauction.com) 2004
Hongwei Ji (MS, Computer Science, currently with EBSCO Publishing) 2004
Kun Yan (MS, Computer Science) 2004
Funding
NSF, "Algorithms for Genome Assembly of Ultra-deep Sequencing Data", $499,000 role: PI 2015-2018
UCR seed grant,, "An in vivo System to Monitor the 4D Mammalian Nucleome", $70,000 role: coPI (with F.Sladek, K.Le Roch) 2015-2016
UCOP, "Intro to Computing I and II, UCR CS 10V and 12V", $50,000 - role: coPI (with F.Vahid, K.Miller, B.Linard) 2014-2015
NIH, "Acquisition of a Scalable Storage Cluster for Data Intensive NIH Research", $592,816 - role: senior personnel (with T. Girke and others) 2014-2015
NSF, "III:Medium:Algorithms and Software Tools for Epigenetic Research", NSF Information Integration and Informatics, $994,370 - role: PI (with K. Le Roch). 2013-2016
US-AID, "Feed the Future Innovation Lab: Advanced Tools for Breeding Climate-Resilient Cowpeas", $4,972,542 - role: coPI (with T.Close, P.Roberts) 2013-2018
UCR Innovative Use of Information Technology in Teaching, "Ultra-Interactive Animated Web Learning", $34,500 - role: coPI (with F.Vahid, K.Miller, and B.Linard) 2013-2014
UCR Chancellor's Strategic Initiatives: Bootstrapping the UCR Center for Computational Entomology", $60,000 - role: coPI (with E.Keogh and C.Shelton) 2011-2012
ABI Innovation: Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing, NSF Advances in Biological Informatics, $428,635 - role: PI (with T. Close) 2011-2014
Understanding the role of nucleosomes turnover in the malaria parasite infection, NIH R01, $1,839,568 - role : coI (with K. Le Roch) 2010-2014
ProLiFiC: Cyber-Genetic Provenance, Lineage, Forensics and Classification, DARPA Cyber Genome Program, $1,800,000 (UCR appropriation about $210,000) - role: subcontract PI (with S.Evans, J.Morrison, E.Keogh, I.Neamtiu) 2010-2011
Advancing the Barley Genome, USDA Cooperative State Research, Education, and Extension Service (USDA CSREES), The Agriculture and Food Research Initiative Program $1,000,000 - role: coPI (with T.Close, G.J.Muehlbauer and J.Bennetzen) 2009-2011
MRI: Acquisition of an Ultra Low-Latency Multiprocessor System with On-Board Hardware Accelerators, NSF Major Research Instrumentation, $330,000 - role: Senior Personnel (with L.Bhuyan, W.Najjar, and G.Ciardo) 2006-2008
Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement, USDA Cooperative State Research, Education, and Extension Service (USDA CSREES) $5,000,000 (UCR appropriation about $406,864) - role: coPI (with G.Muehlbauer, T.Close, and other 28 coPIs) 2006-2010
CAREER: Combinatorial Algorithms for Pattern Discovery with Applications to Data Mining and Computational Biology, NSF Science and Engineering Information Integration and Informatics, $414,277 - role: PI 2005-2010
Coupling Expressed Sequences and Bacterial Artificial Chromosome Resources to Access the Barley Genome, NSF plant genome research project, $2,497,294 - role: coPI (with T.Close and T.Jiang) 2003-2008
HarvEST: A portable EST database viewer, USDA/Plant Genome Program/Bioinformatics and Data Management, $335,000 - role: coPI (with T. Close) 2002-2005
Journal Papers

(60) M. Munoz-Amatriain, S. Lonardi, M.-C. Luo, K. Madishetty, J. Svensson, M. Moscou, S. Wanamaker, T. Jiang, A. Kleinhofs, G. Muehlbauer, R. Wise, N. Stein, Y. Ma, E. Rodriguez, D. Kudrna, P. Bhat, S. Chao, P. Condamine, S. Heinen, J. Resnik, R. Wing, H. Witt, M. Alpert, M. Beccuti, S. Bozdag, F. Cordero, H. Mirebrahim, R. Ounit, Y. Wu, F. You, J. Zheng, H. Simkova, J. Dolezel, J. Grimwood, J. Schmutz, D. Duma, L. Altschmied, T. Blake, P. Bregitzer, L. Cooper, M. Dilbirligi, A. Falk, L. Feiz, A. Graner, P. Gustafson, P. Hayes, P. Lemaux, J. Mammadov, T. Close, "Sequencing of 15,622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome", The Plant Journal, to appear, 2015.

(59) S.Lonardi, H.Mirebrahim, S.Wanamaker, M.Alpert, G.Ciardo, D.Duma, T.J.Close, "When Less is More: Slicing Sequencing Data Improves Read Decoding Accuracy and De Novo Assembly Quality", Bioinformatics, vol.31, no.18, pp. 2972-2980, 2015.

(58) H.Mirebrahim, T.J.Close, S.Lonardi, "De Novo Meta-Assembly of Ultra-deep Sequencing Data Bioinformatics", Bioinformatics, vol.31, no.12, i9-i16, 2015.

(57) E.B.Fernandez, J.Villarreal, S.Lonardi, W.A.Najjar, FHAST: FPGA-based acceleration of Bowtie in hardware, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.12, no.5, pp.973-981, 2015.

(56) R.Ounit, S.Wanamaker, T.J.Close, S.Lonardi, "CLARK: Fast and Accurate Classification of Metagenomic and Genomic Sequences using Discriminative Kmers", BMC Genomics, vol.236, no.16, 2015.

(55) B.Hu, T.Rakthanmanon, Y.Hao, S.Evans, S.Lonardi, E.Keogh, "Using the Minimum Description Length to Discover the Intrinsic Cardinality and Dimensionality of Time Series", Data Mining and Knowledge Discovery, vol.29, no.2, pp.358–399, 2015.

(54) S.Dhall, D.C.Do, M.Garcia, J.Kim, H.Mirebrahim, J.Lyubovitsky, S.Lonardi, E.A.Nothnagel, N.L.Schiller, M.Martins-Green, Generating and Reversing Chronic Wounds in Diabetic Mice by Manipulating Wound Redox Parameters", Journal of Diabetes Research, vol.2014, p.562625, 2014.

(53) A.Polishko, E.M.Bunnik, K.G.Le Roch, S.Lonardi, "PuFFIN: A Parameter-free Method to Build Nucleosome Maps from Paired-end Reads", BMC Bioinformatics vol.15, Suppl.9, S11, 2014.

(52) H.Chen, S.Lonardi, J.Zheng, "Deciphering Histone Code of Transcriptional Regulation in Malaria Parasites by Large-scale Data Mining", Computational Biology and Chemistry, vol.50, pp.3-10, 2014

(51) E.M.Bunnik, A.Polishko, J.Prudhomme, N.Ponts, S.S.Gill, S.Lonardi, K.G.LeRoch, "DNA-encoded Nucleosome Occupancy is Associated with Transcription Levels in the Human Malaria Parasite Plasmodium falciparum", BMC Genomics, vol.15, no.347, 2014

(50) M.Pottorff, P.A.Roberts, T.J.Close, S.Lonardi, S.Wanamaker, J.D.Ehlers, "Identification of Candidate Genes and Molecular Markers for Heat-induced Brown Discoloration of Seed Coats in Cowpea [Vigna unguiculata (L.) Walp]", BMC Genomics, vol.15, no.328, 2014

(49) N.Ponts, L.Fu, E.Y.Harris, J.Zhang, D.-W.D.Chung, E.Bunnik, M.C.Cervantes, J.Prudhomme, V.Atanasova-Penichon, E.Zehraoui, E.M.Rodrigues, S.Lonardi, G.R.Hicks, Y.Wang, K.G.Le Roch, "Genome-scale discovery of DNA methylations in the human malaria parasite", Cell Host and Microbe, vol. 14, no. 6, pp. 696-706, 2013.

(48) S.Bozdag, T.Close, S.Lonardi, "A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.14, no.6, pp.696-706, 2013.

(47) X.Zhang, Y.Lii, Z.Wu, A.Polishko, H.Zhang, V.Chinnusamy, S.Lonardi, J.K. Zhu, R.Liu, H.Jin, "Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues", Molecular Plant, vol.6, no.3, pp.704-715, 2013.

(46) S.Lonardi, D.Duma, M.Alpert, F.Cordero, M.Beccuti, P.R.Bhat, Y.Wu, G.Ciardo, B.Alsaihati, Y.Ma, S.Wanamaker, J.Resnik, S.Bozdag, M.-C.Luo, T.J.Close, "Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space", PLoS Computational Biology, vol.9, pp.e1003010, 2013.

(45) N.Stein, A.Graner, A.Himmelbach, B.Steuernagel, D.Schulte, M.Mascher, N.Poursarebani, R.Zhou, R.Ariyadasa, T.Schmutzer, U.Scholz, H.Gundlach, K.Mayer, M.Spannagl, M.Pfeifer, M.Martis, T.Nussbaumer, A.Druka, D.Marshall, H.Liu, J.Morris, J.Russell, M.Bayer, J.Brown, P.Hedley, R.Waugh, Bujun Shi, P.Langridge, J.Svensson, J.Resnik, K.Madishetty, M.Moscou, P.Bhat, S.Wannamaker, T.Close, Y.Ma, D.Duma, F.Cordero, G.Ciardo, M.Beccuti, M.Alpert, S.Lonardi, H.Berges, A.Korol, Z.Frenkel, M.Groth, M.Felder, M.Platzer, S.Taudien, A.Schulman, C.Moisy, J.Tanskanen, T.Matsumoto, T.Tanaka, K.Sato, G.Fincher, D.Swarbreck, D.Sampath, M.Caccamo, M.Febrer, S.Ayling, R.Wing, G.Muehlbauer, A.Zuccolo, F.Cattonaro, M.Morgante, S.Scalabrin, S.Radovic, V.Vendramin, J.Poland, R.Wise, "A physical, genetical and functional sequence assembly of the barley genome", Nature, vol.491, no.7426, pp.711-716, 2012.

(44) T.Rakthanmanon, E.Keogh, S.Lonardi, S.Evans, "MDL-Based Time Series Clustering", Knowledge and Information Systems, vol.31, vol.33, no.2, pp.371-399, 2012.

(43) E.Y.Harris, N.Ponts, K.G.Le Roch, S.Lonardi, "BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads'', Bioinformatics, vol.28, no.13, pp.1795-1796, 2012..

(42) A.Polishko, N.Ponts, K.G.Le Roch, S.Lonardi, "NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model", Bioinformatics, vol.28, no.12, pp.i242-i249, 2012.

(41) E.Y.Harris, N.Ponts, K.G.Le Roch, S.Lonardi, "Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite", BMC Genomics, 12:601, 2011.

(40) M.Munoz-Amatriain, M.J.Moscou, P.R.Bhat, J.T.Svensson, J.Bartos, P.Suchankova, H.Simkova, T.R.Endo, R.D.Fenton, Y.Wu, S.Lonardi, A.M.Castillo, S.Chao, L.Cistue, A.Cuesta-Marcos, K.Forrest, M.J.Hayden, P.M.Hayes, R.D.Horsley, A.Kleinhofs, D.Moody, K.Sato, M.P.Valles, B.B.H.Wulff, G.J.Muehlbauer, J.Dolezel, T.J.Close, "An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers", The Plant Genome, vol.4, no.3, pp.238-249, 2011.

(39) N.Ponts, E.Y.Harris, S.Lonardi, K.Le Roch, "Nucleosome Occupancy at Transcription Start Sites in the Human Malaria Parasite: A Hard-wired Evolution of Virulence?", Infection, Genetics and Evolution, vol.11, no.4, pp.716-724, 2011.

(38) Y.Wu, T.J.Close, S.Lonardi, "Accurate Construction of Consensus Genetic Maps via Integer Linear Programming", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no.2, pp.381-394, 2011.

(37) E.Y.Harris, N.Ponts, A.Levchuk, K.G.Le Roch, S.Lonardi, "BRAT: Bisulfite-treated Reads Analysis Tool", Bioinformatics, vol.26, no.4, pp.572-573, 2010.

(36) N.Ponts, E.Y.Harris, J.Prudhomme, I.Wick, C.Eckhardt-Ludka, G.Hicks, G.Hardiman, S.Lonardi, and K.Le Roch, "Nucleosome landscape and control of transcription in the human malaria parasite", Genome Research, vol.20, pp.228-238, 2010.

(35) V.Vacic, L.M.Iakoucheva, S.Lonardi, P.Radivojac, "Graphlet Kernels for Prediction of Functional Residues in Protein Structures", Journal Computational Biology, vol.17, no.1, pp.55-72, 2010.

(34) L.Liu, Y.Wu, S.Lonardi, T.Jiang, "Efficient Genome-Wide TagSNP Selection across Populations via the Linkage Disequilibrium Criterion", Journal Computational Biology, vol.17, no.1, pp.21-37, 2010.

(33) 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'', BMC Genomics, 10:582, 2009.

(32) 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", Proceedings of the National Academy of Sciences (PNAS), vol.106, no.48, pp.20429--20434, 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.

Books and Book Chapters

(5) E. Chavez, S. Lonardi, "Proceedings of 17th International Symposium on String Processing and Information Retrieval (SPIRE 2010)", Lecture Notes in Computer Science 6393, Los Cabos, Mexico, 2010.

(4) J.Chen, S.Lonardi, "Biological Data Mining", Chapman and Hall/CRC Press, 2009.

(3) S.Lonardi, J.Y.Chen, M.Zaki, "Proceedings of 8th International Workshop on Data Mining in Bioinformatics (BIOKDD 2008)", held in conjunction with SIGKDD conference, August 2008, Las Vegas, NV, ACM Press.

(2) J.Y.Chen, S.Lonardi, M.Zaki, "Proceedings of 7th International Workshop on Data Mining in Bioinformatics (BIOKDD 2007)", held in conjunction with SIGKDD conference, August 2007, San Jose, CA, ACM Press.

(1) S.Kurtz, S.Lonardi, "Computational Biology", in Handbook on Data Structures and Applications, Dinesh Mehta and Sartaj Sahni (eds), CRC Press, 2003.

Conference Papers

(60) D.Duma, F.Cordero, M.Beccuti, G.Ciardo, T.J.Close, S.Lonardi, "Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads", Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), pp.162-174, Atlanta, GA, 2015.

(59) R.Ounit, S.Lonardi, "Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers", Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), pp.286-295, Atlanta, GA, 2015.

(58) H. Mirebrahim, T. J. Close, S. Lonardi, "De Novo Meta-Assembly of Ultra-deep Sequencing Data", Proceedings of Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB'15), pp.i9-i16 (Bioinformatics), Dublin, Ireland, 2015

(57) A.Polishko, E.M.Bunnik, K.G.Le Roch, S.Lonardi, "PuFFIN: A Parameter-free Method to Build Nucleosome Maps from Paired-end Reads", Proceedings of RECOMB Workshop on Massively Parallel Sequencing (RECOMB-SEQ'14), Pittsburgh, PA, 2014

(56) H.Chen, S.Lonardi, J.Zheng, "Deciphering Histone Code of Transcriptional Regulation in Malaria Parasites by Large-scale Data Mining", Proceedings of Asia Pacific Bioinformatics Conference (APBC'14), Shanghai, China, 2014

(55) D.Duma, M.Wootters, A.C.Gilbert, H.Q.Ngo, A.Rudra, M.Alpert, T.J.Close, G.Ciardo, S.Lonardi, "Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing", Proceedings of the Workshop on Algorithms in Bioinformatics (WABI'13), pp.70-84, Sophia Antipolis, France.

(54) E.B.Fernandez, W.A.Najjar, S.Lonardi, J.Villarreal, "Multithreaded FPGA Acceleration of DNA Sequence Mapping", to appear in Proceedings of IEEE High Performance Extreme Computing (HPEC'12), Waltham, MA, 2012.

(53) A.Polishko, N.Ponts, K.G.Le Roch, S.Lonardi, "NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model", Proceedings of Annual International Conference on Intelligent Systems for Molecular Biology (ISMB'12), pp.i242-i249, Long Beach, CA, 2012.

(52) T.Rakthanmanon, E.Keogh, S.Lonardi, S.Evans, "Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data", Proceedigs of IEEE International Conference on Data Mining (ICDM'11), pp.547-556, 2011.

(51) B.Hu, T.Rakthanmanon, Y.Hao, S.Evans, S.Lonardi, E.Keogh, "Discovering the Intrinsic Cardinality and Dimensionality of Time Series using MDL", Proceedigs of IEEE International Conference on Data Mining (ICDM'11), pp.1086-1091, 2011.

(50) B.Hu, T.Rakthanmanon, Y.Hao, S.Evans, S.Lonardi, E.Keogh, "Towards Discovering the Intrinsic Cardinality and Dimensionality of Time Series using MDL", to appear in Proceedings of Solomonoff 85th Memorial Conference, LNAI ??, Melbourne, Australia, 2011.

(49) E. Fernandez, W. Najjar, S. Lonardi, "String Matching in Hardware using the FM Index", Proceedings of IEEE International Symposium on Field-Programmable Custom Computing Machines (FCCM'11), pp.218-225, Salt Lake City, Utah, 2011

(48) E. B. Fernandez, E. Harris, W. Najjar, S. Lonardi, "Exploration of Short Reads Mapping in Hardware", Proceedings of International Conference on Field Programmable Logic and Applications (FPL'10), pp.360-363, Milano, Italy, 2010.

(47) N.Pokhriyal, N.Ponts, E.Y.Harris, K.G.Le Roch, and S.Lonardi, "Novel Gene Discovery in the Human Malaria Parasite using Nucleosome Positioning Data", to appear in Proceedings of LSS Computational Systems Bioinformatics Conference (CSB'10), pp.124-135, Stanford, CA, 2010.

(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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