Stefano Lonardi, Professor
| Download my most up-to-date CV | |||
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Research
Interests
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Computational molecular biology, data mining, data compression. | ||
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Education
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Doctor of Philosophy Department of Computer Sciences Purdue University, West Lafayette, IN, USA. |
Aug 1996 Aug 2001 |
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| Dottorato in Ingegneria
Informatica ed Elettronica Industriali Università degli Studi di Padova, Padova, Italy. |
Apr 1995 Feb 1999 |
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| Laurea in Scienze
dell'Informazione Università degli Studi di Pisa, Pisa, Italy. |
Nov 1987 Apr 1994 |
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Professional Experience
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Professor, Department of Computer Science & Engineering, University of California, Riverside, CA, USA | Jul 2011 present |
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| Associate Professor, Department of Computer Science & Engineering, University of California, Riverside, CA, USA | Jul 2007 Jun 2011 |
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| Assistant Professor, Department of Computer Science & Engineering, University of California, Riverside, CA, USA | Jul 2001 Jun 2007 |
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| Research Assistant, Purdue Research Foundation, Department of Computer Science, Purdue University, West Lafayette, IN, USA | Aug 1999 May 2001 |
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| Research Scientist, Celera Genomics, Informatics Research dept., under the supervision of Prof. Gene Myers, Rockville, MD, USA | May 1999 Aug 1999 |
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| Visiting Research Scholar, Department of Computer Science, Purdue University, West Lafayette, IN, USA | Aug 1997 May 1999 |
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| Consultant, Project Gamma-plan (geometric modeling), Gamma Lab, Dipartimento di Neurochirurgia, University of Verona, Italy | Aug 1995 Dec 1995 |
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Awards
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NIH Director's Transformative Research Award | 2021 | |
| AAAS Fellow | 2018 | ||
| ACM Distinguished Scientist | 2017 | ||
| IEEE Fellow (Computer Society) | 2016 | ||
| NSF CAREER Award | 2005 | ||
| Student Research Award, Purdue University | 2000 | ||
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Students Graduated
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Dipankar Baisya (PhD, Computer Science, Applied Scientist at Amazon Science, Seattle, WA) | 2021 | |
| Qihua Liang (PhD, Genomics-Genetics-Bioinformatics, Bioinformatics Scientist at Zymergen, Emeryville, CA) | 2020 | ||
| Md. Abid Hasan (PhD, Computer Science, Principal Scientist at Roche Sequencing) | 2019 | ||
| Abbas Roayaei (PhD, Computer Science, Post-doc at La Jolla Institute for Immunology) | 2019 | ||
| Weihua Pan (PhD, Computer Science, Post-doc at Carnegie Mellon University) | 2019 | ||
| Hind Alhakami (PhD, Computer Science, Scientist at Dovetail Genomics) | 2017 | ||
| Rachid Ounit (PhD, Computer Science, CTO at Biotia) | 2017 | ||
| Seyed Hamid Mirebrahim (PhD, Computer Science, Principal Scientist at Roche Sequencing) | 2015 | ||
| Anton Polishko (PhD, Computer Science, CTO at Zulloo Inc) | 2014 | ||
| Sara Nasseri (MS, Computer Science, with Western Digital) | 2014 | ||
| Matthew Alpert (BS, Computer Science, with Turtle Rock Studios) | 2013 | ||
| Denise Duma (PhD, Computer Science, with Baylor College of Medicine) | 2013 | ||
| Mo Cao (MS, Computer Science, with Xangati) | 2012 | ||
| Burair Alsaihati (MS, Computer Science, with Joint Center for Genomics Research, KACST) | 2011 | ||
| Elena Harris (PhD, Computer Science, Assistant Professor at Cal State, Chico) | 2010 | ||
| Neeti Pokhriyal (MS, Computer Science, PhD student at University at Buffalo) | 2009 | ||
| Vladimir Vacic (PhD, Computer Science, Bioinformatics Scientist at 23andme) | 2008 | ||
| Yonghui Wu (PhD, Computer Science, with Google, Mountain View, CA) | 2008 | ||
| Serdar Bozdag (PhD, Computer Science, Assistant Professor at Marquette University) | 2008 | ||
| Jie Zheng (PhD, Computer Science, Assistant Professor at Nanyang Tech. Univ., Singapore) | 2006 | ||
| Qiaofeng Yang (PhD, GGB, with Bloomberg, NY) | 2006 | ||
| Vi Pham (MS, Computer Science) | 2006 | ||
| San Nguyen (MS, Computer Science, with Raytheon) | 2006 | ||
| George Hsu (MS, Computer Science) | 2005 | ||
| Yu Luo (MS, Computer Science, with Nationwideauction.com) | 2004 | ||
| Hongwei Ji (MS, Computer Science, with EBSCO Publishing) | 2004 | ||
| Kun Yan (MS, Computer Science) | 2004 | ||
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Funding
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NSF, "Data-driven engineering of the thermotolerant yeast Kluyveromyces marxianus, $1,499,991 – role: coPI (with I. Wheeldon, N. Da Silva, and Argonne National Laboratory) | 2022-2025 | |
| NIH, "Director’s Transformative Research Award: Rapid response for pandemics: single cell sequencing and deep learning to predict antibody sequences against an emerging antigen", $3.2M, role: coPD (with A. Ray, J. Hernandez, M. H. Sazinsky) | 2021-2026 | ||
| DOE, "Establishing the thermotolerant yeast Kluyveromyces marxianus as a host for biobased fuels and chemicals production", $1,499,999, role: coPI (with I. Wheeldon, N. Da Silva) | 2018-2021 | ||
| NSF, "Improving de novo Genome Assembly using Optical Maps", $499,978, role: sole PI | 2018-2021 | ||
| NSF, "BREAD: Advancing the Cowpea Genome for Food Security", $1,587,345 role: coPI (with T. Close et al) | 2016-2020 | ||
| NSF, "Algorithms for Genome Assembly of Ultra-deep Sequencing Data", $499,000 role: PI | 2015-2019 | ||
| 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) | 2013-2019 | ||
| 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 | ||
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Journal
Papers
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(87) Q. Liang, M. Munoz-Amatriain, S. Shu, S. Lo, X. Wu, J. W. Carlson, P. Davidson, D. M. Goodstein, J. Phillips, N. M. Janis, E. J. Lee, C. N. Liang, P. L. Morrell, A. D. Farmer, P. Xu, T. J. Close, S. Lonardi, "A view of the pan-genome of domesticated cowpea (Vigna unguiculata [L.] Walp.)", The Plant Genome, no. e20319, 2023 (86) A. Ramesh, V. Trivedi, S. Lee, A. Tafrishi, C. Schwartz, A. Mohseni, M. Li, S. Lonardi, I. Wheeldon, "acCRISPR: An activity-correction method for improving the accuracy of CRISPR screens", Communication Biology,, 2023 (85) S. Sereshki, N. Lee, M. Omirou, D. Fasoula, S. Lonardi, "On the Prediction of non-CG DNA Methylation using Machine Learning", NAR Genomics and Bioinformatics, vol. 5, no. 2, 2023 (84) P. Singh, S. Lonardi, Q. Liang, P. Vydyam, E. Khabirova, T. Fang, S. Gihaz, J. Thekkiniath, M. Munshi, S. Abel, G. Batugedara, M. Gupta, X. M. Lu, T. Lenz, S. Chakravarty, E. Cornillot, Y. Hu, W. Ma, L. M. Gonzalez, S. Sanchez, A. Sanchez-Flores, K. Estrada, O. S. Harb, K. G. L. Roch, C. B. Mamoun, "Babesia duncani multi-omics identifies virulence factors and drug targets", Nature Microbiology, vol. 8, pp. 845–859, 2023 (83) D. Baisya, A. Ramesh, C. Schwartz, S. Lonardi, I. Wheeldon, "Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica", Nature Communications, vol. 13, no. 922, 2022 (82) M. E. H. Matson, Q. Liang, S. Lonardi, H. S. Judelson, "Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the phytopathogen Phytophthora infestans revealed using its first chromosome- scale assembly", PLOS Pathogens, vol. 18, no. 10, e1010869, 2022 (81) Q. Liang, S. Lonardi, "Reference-agnostic Representation and Visualization of Pan-genomes", BMC Bioinformatics, vol. 22, no. 502, 2021 (80) A. R. Ardakany, H. T. Gezer, S. Lonardi, F. Ay, "Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation", Genome Biology, vol. 21, no. 256, 2020 (79) D. R. Baisya, S. Lonardi, "Prediction of Histone Post-translational Modifications using Deep Learning", Bioinformatics,vol. 36, no. 24, pp. 5610–5617, 2020 (78) Md A. Hasan, S. Lonardi, "DeeplyEssential: A Deep Neural Network for Predicting Essential Genes in Microbes", BMC Bioinformatics, vol. 21, no. 367, 2020. (77) W. Pan, T. Jiang, S. Lonardi, "OMGS: Optical Map-based Genome Scaffolding", Journal of Computational Biology, vol. 27, no. 4, pp. 519-533, 2020. (76) A. R. Ardakany, F. Ay, S. Lonardi, "Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure", Bioinformatics, vol. 35, no. 14, pp. i145-i153, 2019. (75) I. A. Herniter, R. Lo, M. Munoz-Amatriain, S. Lo, Y.-N. Guo, B.-L. Huynh, M. R. Lucas, Z. Jia, P. A. Roberts, S. Lonardi, T. Close, "Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)", Frontiers in Plant Science, vol. 10, p. 1346, 2019. (74) S. Lonardi, M. Munoz-Amatriain, Q. Liang, S. Shu, S. Wanamaker, S. Lo, J. Tanskanen, A. Schulman, T. Zhu, M.-C. Luo, H. Alhakami, R. Ounit, A. Hasan, J. Verdier, P. Roberts, J. Santos, A. Ndeve, J. Dolezel, J. Vrana, S. Hokin, A. Farmer, S. Cannon, T. Close, "The Genome of Cowpea (Vigna unguiculata L. Walp.)", The Plant Journal, vol. 98, no. 5, pp. 767-782, 2019. (73) C. Schwartz, J.-F. Cheng, R. Evans, C. A. Schwartz, J. M. Wagner, S. Anglin, A. Beitz, W. Pan, S. Lonardi, M. Blenner, H. S.Alper, Y. Yoshikuni, I. Wheeldon, "Validating Genome-wide CRISPR-Cas9 Function Improves Screening in the Oleaginous Yeast Yarrowia lipolytica", Metabolic Engineering, vol. 55, pp. 102-110, 2019. (72) W. Pan, S. Lonardi, "Accurate Detection of Chimeric Contigs via Bionano Optical Maps", Bioinformatics, vol.35, no.10, pp.1760-1762, 2019. (71) W. Pan, S. Wanamaker, A. Ah-Fong, H. Judelson, S. Lonardi, "Novo&Stitch: Accurate Reconciliation of Genome Assemblies via Optical Maps", Bioinformatics, vol.34, no.13, p.i43-i51, 2018. (70) B.-L. Huynh, J. Ehlers, B. E. Huang, M. Munoz-Amatriain, S. Lonardi , J. Santos, A. Ndeve, B. Batieno, O. Boukar, N. Cisse, I. Drabo, C. Fatokun, F. Kusi, R. Agyare, Y. - N. Guo, I. Herniter, S. Lo, S. Wanamaker, S. Xu, T. Close, P. Roberts, "A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.)", The Plant Journal, vol.92, no.6, p.1129-1142, 2018. (69) H. Alhakami, H. Mirebrahim, S. Lonardi, "A Comparative Evaluation of Genome Assembly Reconciliation Tools", Genome Biology, vol.18, no.1, p.93, 2017. (68) L. S. Beier, A. Himmelbach, C. Colmsee, X.-Q. Zhang, R. A. Barrero, Q. Zhang, L. Li, M. Bayer, D. Bolser, S. Taudien, M. Groth, M. Felder, A. Hastie, H. Simkova, H. Stankova, J. Vrana, S. Chan, M. Munoz-Amatriain, R. Ounit, S. Wanamaker, T. Schmutzer, L. Aliyeva-Schnorr, S. Grasso, J. Tanskanen, D. Sampath, D. Heavens, S. Cao, B. Chapman, F. Dai, Y. Han, H. Li, X. Li, C. Lin, J. K. McCooke, C. Tan, S. Wang, S. Yin, G. Zhou, J. A. Poland, M. I. Bellgard, A. Houben, J. Dolezel, S. Ayling, S. Lonardi , P. Langridge, G. J. Muehlbauer, P. Kersey, M. D. Clark, M. Caccamo, A. H. Schulman, M. Platzer, T. J. Close, M. Hansson, G. Zhang, I. Braumann, C. Li, R. Waugh, U. Scholz, N. Stein, M. Mascher, "Construction of a Map-based Reference Genome Sequence for Barley, Hordeum vulgare", Scientific Data (Nature), vol.4, p.170044, 2017. (67) M. Mascher, H. Gundlach, A. Himmelbach, S. Beier, S. O. Twardziok, T. Wicker, V. Radchuk, C. Dockter, P. E. Hedley, J. Russell, M. Bayer, L. Ramsay, H. Liu, G. Haberer, X.-Q. Zhang, Q. Zhang, R. A. Barrero, L. Li, S. Taudien, M. Groth, M. Felder, A. Hastie, H. Simkova, H. Stankova, J. Vrana, S. Chan, M. Munoz-Amatriain, R. Ounit, S. Wanamaker, D. Bolser, C. Colmsee, T. Schmutzer, L. Aliyeva-Schnorr, S. Grasso, J. Tanskanen, A. Chailyan, D. Sampath, D. Heavens, L. Clissold, S. Cao, B. Chapman, F. Dai, Y. Han, H. Li, X. Li, C. Lin, J. K. McCooke, C. Tan, P. Wang, S. Wang, S. Yin, G. Zhou, J. A. Poland, M. I. Bellgard, L. Borisjuk, A. Houben, J. Dolezel, S. Ayling, S. Lonardi , P. Kersey, P. Langridge, G. J. Muehlbauer, M. D. Clark, M. Caccamo, A. H. Schulman, K. F. Mayer, M. Platzer, T. J. Close, U. Scholz, M. Hansson, G. Zhang, I. Braumann, M. Spannagl, C. Li, R. Waugh, N. Stein, "A Chromosome Conformation Capture Ordered Sequence of the Barley Genome", Nature, vol.544, pp.427-433, 2017. (66) A. McIntyre, R. Ounit, E. Afshinnekoo, R. Prill, E. Henaff, N. Alexander, S. Minot, D. Danko, J. Foox, S. Ahsanuddin, S. Tighe, N. Hasan, P. Subramanian, K. Moffat, S. Lonardi , S. Levy, N. Greenfield, R. Colwell, G. Rosen, C. Mason, "Comprehensive benchmarking and ensemble approaches for metagenomic classifiers", Genome Biology, vol.18, no.1, p.182, 2017. (65) L. Hahn, C.-A. Leimeister, R. Ounit, S. Lonardi, B. Morgenstern, "Rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison", PLoS Computational Biology, vol.12, no.10, e1005107, 2016. (64) E. Y. Harris, R. Ounit, S. Lonardi, "BRAT-nova: Fast and Accurate Mapping of Bisulfite-treated Reads", Bioinformatics, vol. 32, no. 17, pp. 2696-2698, 2016. (63) M. Munoz-Amatriain, H. Mirebrahim, P. Xu, S. I. Wanamaker, M. Luo, H. Alhakami, M. Alpert, I. Atokple, B. J. Batieno, O. Boukar, S. Bozdag, N. Cisse, I. Drabo, J. D. Ehlers, A. Farmer, C. Fatokun, Y. Q. Gu, Y.-N. Guo, B.-L. Huynh, S. A. Jackson, F. Kusi, C. T. Lawley, M. R. Lucas, Y. Ma, M. P. Timko, J. Wu, F. You, P. A. Roberts, S. Lonardi, T. J. Close, "Genome Resources for Climate-resilient Cowpea, an Essential Crop for Food Security", The Plant Journal, vol.89, no.5, pp.1042-1054, 2016. (62) R.Ounit, S.Lonardi, "Higher Classification Sensitivity of Short Metagenomic Reads with CLARK-S", Bioinformatics, vol.32, no.24, pp.3823-3825, 2016. (61) 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, vol.89, no.5, pp. 1042-1054, 2016. (60) X. M. Lu, E. Bunnik, N. Pokhriyal, S. Nasseri, S. Lonardi, K. L. Roch, "Analysis of Nucleosome Positioning Landscapes Enables Gene Discovery in the Human Malaria Parasite Plasmodium falciparum", BMC Genomics, vol. 16, no. 1005, 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. |
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Books and Book Chapters
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(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. |
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Conference Papers
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(67) S. Chakravarty, G. Logsdon, S. Lonardi, "RAmbler: de novo genome assembly of complex repetitive regions", Proceedings of ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB), Houston, TX, 2023. (66) A. R. Ardakany, F. Ay, S. Lonardi, "Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure", Proceedings of Conference on Intelligent Systems for Molecular Biology (ISMB), Basel, Switzerland, 2019. (65) W. Pan, T. Jiang, S. Lonardi, "OMGS: Optical Map-based Genome Scaffolding", Proceedings of Conference on Research in Computational Molecular Biology (RECOMB), Washington, DC, 2019. (64) Md Abid Hasan, S. Lonardi, "mClass: Cancer Type Classification with Somatic Point Mutation Data", Proceedings of RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG), Magog-Orford, Canada, 2018. (63) W. Pan, S. Wanamaker, A. Ah-Fong, H. Judelson, S. Lonardi, "Novo&Stitch: Accurate Reconciliation of Genome Assemblies via Optical Maps", Proceedings of Conference on Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, 2018. (62) A.R.Ardakany, S.Lonardi, "Efficient and Accurate Detection of Topologically Associating Domains from Contact Map", Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), 22:1-22:11, Boston, MA, 2017. (61) A.Polishko, M.A.Hasan, W.Pan, E.Bunnik, K.L.Roch, S. Lonardi, "ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks", Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), 19:1-9:16,Boston, MA, 2017. (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, 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", in Proceedings of Solomonoff 85th Memorial Conference, pp.184-197,, 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. |