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Stefano Lonardi
Person information
- affiliation: University of California, Riverside, Department of Computer Science and Engineering, CA, USA
- affiliation (PhD): Purdue University, West Lafayette, IN, USA
- affiliation (PhD): University of Padua, Italy
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2020 – today
- 2023
- [c60]Sakshar Chakravarty
, Glennis Logsdon
RAmbler: de novo genome assembly of complex repetitive regions. BCB 2023: 13:1 - 2021
- [j54]Dipankar Ranjan Baisya
Prediction of histone post-translational modifications using deep learning. Bioinform. 36(24): 5610-5617 (2021) - [j53]Qihua Liang
Reference-agnostic representation and visualization of pan-genomes. BMC Bioinform. 22(1): 502 (2021) - 2020
- [j52]Md. Abid Hasan, Stefano Lonardi:
DeeplyEssential: a deep neural network for predicting essential genes in microbes. BMC Bioinform. 21-S(14): 367 (2020) - [j51]Weihua Pan, Tao Jiang
OMGS: Optical Map-Based Genome Scaffolding. J. Comput. Biol. 27(4): 519-533 (2020)
2010 – 2019
- 2019
- [j50]Weihua Pan, Stefano Lonardi
Accurate detection of chimeric contigs via Bionano optical maps. Bioinform. 35(10): 1760-1762 (2019) - [j49]Abbas Roayaei Ardakany, Ferhat Ay
Selfish: discovery of differential chromatin interactions via a self-similarity measure. Bioinform. 35(14): i145-i153 (2019) - [c59]Weihua Pan, Tao Jiang, Stefano Lonardi
OMGS: Optical Map-Based Genome Scaffolding. RECOMB 2019: 190-207 - 2018
- [j48]Weihua Pan, Steve Wanamaker, Audrey M. V. Ah-Fong, Howard S. Judelson, Stefano Lonardi
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps. Bioinform. 34(13): i43-i51 (2018) - [c58]Md. Abid Hasan, Stefano Lonardi
mClass: Cancer Type Classification with Somatic Point Mutation Data. RECOMB-CG 2018: 131-145 - 2017
- [c57]Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik
ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks. WABI 2017: 19:1-19:16 - [c56]Abbas Roayaei Ardakany, Stefano Lonardi
Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps. WABI 2017: 22:1-22:11 - 2016
- [j47]Elena Yavorska Harris, Rachid Ounit, Stefano Lonardi
BRAT-nova: fast and accurate mapping of bisulfite-treated reads. Bioinform. 32(17): 2696-2698 (2016) - [j46]Rachid Ounit, Stefano Lonardi
Higher classification sensitivity of short metagenomic reads with CLARK-S. Bioinform. 32(24): 3823-3825 (2016) - [j45]Lars Hahn
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison. PLoS Comput. Biol. 12(10) (2016) - 2015
- [j44]Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi
De novo meta-assembly of ultra-deep sequencing data. Bioinform. 31(12): 9-16 (2015) - [j43]Stefano Lonardi
When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. Bioinform. 31(18): 2972-2980 (2015) - [j42]Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi
Using the minimum description length to discover the intrinsic cardinality and dimensionality of time series. Data Min. Knowl. Discov. 29(2): 358-399 (2015) - [j41]Edward B. Fernandez, Jason R. Villarreal, Stefano Lonardi
FHAST: FPGA-Based Acceleration of Bowtie in Hardware. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 973-981 (2015) - [c55]Denise Duma, Francesca Cordero
Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. WABI 2015: 162-174 - [c54]Rachid Ounit
Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers. WABI 2015: 286-295 - 2014
- [j40]Anton Polishko, Evelien M. Bunnik
PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. BMC Bioinform. 15(S-9): S11 (2014) - [j39]Haifen Chen, Stefano Lonardi
Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. Comput. Biol. Chem. 50: 3-10 (2014) - [c53]Rachid Ounit, Timothy J. Close, Steve Wanamaker, Stefano Lonardi
CLARK, accurate and efficient classification of DNA sequences. BCB 2014: 602 - [c52]Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi:
De novo assembly of ultra-deep sequencing data. BCB 2014: 609 - 2013
- [j38]Stefano Lonardi
Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLoS Comput. Biol. 9(4) (2013) - [j37]Serdar Bozdag, Timothy J. Close, Stefano Lonardi
A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map. IEEE ACM Trans. Comput. Biol. Bioinform. 10(2): 352-360 (2013) - [c51]Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert, Timothy J. Close, Gianfranco Ciardo, Stefano Lonardi
Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing. WABI 2013: 70-84 - 2012
- [j36]Anton Polishko, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi
NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model. Bioinform. 28(12): 242-249 (2012) - [j35]Elena Yavorska Harris, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi
BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinform. 28(13): 1795-1796 (2012) - [j34]Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi
MDL-based time series clustering. Knowl. Inf. Syst. 33(2): 371-399 (2012) - [c50]Edward Fernandez, Walid A. Najjar
Multithreaded FPGA acceleration of DNA sequence mapping. HPEC 2012: 1-6 - 2011
- [j33]Yonghui Wu, Timothy J. Close, Stefano Lonardi
Accurate Construction of Consensus Genetic Maps via Integer Linear Programming. IEEE ACM Trans. Comput. Biol. Bioinform. 8(2): 381-394 (2011) - [c49]Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh:
Towards Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. Algorithmic Probability and Friends 2011: 184-197 - [c48]Edward Fernandez, Walid A. Najjar
String Matching in Hardware Using the FM-Index. FCCM 2011: 218-225 - [c47]Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi
Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data. ICDM 2011: 547-556 - [c46]Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi
Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. ICDM 2011: 1086-1091 - [i1]Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Timothy J. Close:
Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space. CoRR abs/1112.4438 (2011) - 2010
- [j32]Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi
BRAT: bisulfite-treated reads analysis tool. Bioinform. 26(4): 572-573 (2010) - [j31]Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi
BRAT: bisulfite-treated reads analysis tool. Bioinform. 26(19): 2499 (2010) - [j30]Lan Liu, Yonghui Wu, Stefano Lonardi
Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion. J. Comput. Biol. 17(1): 21-37 (2010) - [j29]Vladimir Vacic
Graphlet Kernels for Prediction of Functional Residues in Protein Structures. J. Comput. Biol. 17(1): 55-72 (2010) - [j28]Stefano Lonardi
Data Mining in Bioinformatics: Selected Papers from BIOKDD. IEEE ACM Trans. Comput. Biol. Bioinform. 7(2): 195-196 (2010) - [c45]Edward Fernandez, Walid A. Najjar
Exploration of Short Reads Genome Mapping in Hardware. FPL 2010: 360-363 - [e1]Edgar Chávez
String Processing and Information Retrieval - 17th International Symposium, SPIRE 2010, Los Cabos, Mexico, October 11-13, 2010. Proceedings. Lecture Notes in Computer Science 6393, Springer 2010, ISBN 978-3-642-16320-3 [contents]
2000 – 2009
- 2009
- [j27]Serdar Bozdag, Timothy J. Close, Stefano Lonardi
A compartmentalized approach to the assembly of physical maps. BMC Bioinform. 10 (2009) - [c44]Elena Yavorska Harris, Thierry Lecroq
CPM's 20th Anniversary: A Statistical Retrospective. CPM 2009: 1-11 - 2008
- [j26]Yonghui Wu, Lan Liu, Timothy J. Close, Stefano Lonardi
Deconvoluting BAC-Gene Relationships Using a Physical Map. J. Bioinform. Comput. Biol. 6(3): 603-622 (2008) - [j25]Yonghui Wu, Stefano Lonardi:
A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks. J. Bioinform. Comput. Biol. 6(6): 1049-1065 (2008) - [j24]Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi:
BIOKDD 2008: a workshop report on data mining in bioinformatics. SIGKDD Explor. 10(2): 51-53 (2008) - [j23]Raffaele Giancarlo, Stefano Lonardi
Foreword: Special issue in honor of the 60th Birthday of Professor Alberto Apostolico: Work is for people who do not know how to: SAIL - String Algorithms, Information and Learning. Theor. Comput. Sci. 395(2-3): 135-136 (2008) - [c43]Vladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi:
A Probabilistic Model for Small RNA Flowgram Matching. Pacific Symposium on Biocomputing 2008: 75-86 - [c42]Serdar Bozdag, Timothy J. Close, Stefano Lonardi
Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. WABI 2008: 148-161 - 2007
- [j22]Vladimir Vacic
Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinform. 8 (2007) - [j21]Eamonn J. Keogh, Stefano Lonardi
Compression-based data mining of sequential data. Data Min. Knowl. Discov. 14(1): 99-129 (2007) - [j20]Jessica Lin, Eamonn J. Keogh, Li Wei, Stefano Lonardi
Experiencing SAX: a novel symbolic representation of time series. Data Min. Knowl. Discov. 15(2): 107-144 (2007) - [j19]Qiaofeng Yang, Stefano Lonardi
A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks. Int. J. Data Min. Bioinform. 1(3): 241-247 (2007) - [j18]Stefano Lonardi
Error Resilient LZ'77 Data Compression: Algorithms, Analysis, and Experiments. IEEE Trans. Inf. Theory 53(5): 1799-1813 (2007) - [c41]Serdar Bozdag, Timothy J. Close, Stefano Lonardi
A Compartmentalized Approach to the Assembly of Physical Maps. BIBE 2007: 218-225 - [c40]Scott Sirowy, Yonghui Wu, Stefano Lonardi
Two-level microprocessor-accelerator partitioning. DATE 2007: 313-318 - [c39]Scott Sirowy, Yonghui Wu, Stefano Lonardi
Clock-frequency assignment for multiple clock domain systems-on-a-chip. DATE 2007: 397-402 - [c38]David Sheldon, Frank Vahid, Stefano Lonardi
Interactive presentation: Soft-core processor customization using the design of experiments paradigm. DATE 2007: 821-826 - [c37]Yonghui Wu, Prasanna Bhat, Timothy J. Close, Stefano Lonardi
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. WABI 2007: 395-406 - 2006
- [j17]Jie Zheng
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BMC Bioinform. 7: 7 (2006) - [j16]Anthony J. Bagnall, Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Stefano Lonardi
A Bit Level Representation for Time Series Data Mining with Shape Based Similarity. Data Min. Knowl. Discov. 13(1): 11-40 (2006) - [j15]Song Lin, Vana Kalogeraki
Efficient information compression in sensor networks. Int. J. Sens. Networks 1(3/4): 229-240 (2006) - [j14]Stefano Lonardi
Efficient Discovery of Unusual Patterns in Time Series. New Gener. Comput. 25(1): 61-93 (2006) - [j13]Stefano Lonardi
Finding biclusters by random projections. Theor. Comput. Sci. 368(3): 217-230 (2006) - [c36]Qiaofeng Yang, Stefano Lonardi
A Compression-Boosting Transform for Two-Dimensional Data. AAIM 2006: 126-137 - [c35]Yonghui Wu, Stefano Lonardi
Error-Resilient LZW Data Compression. DCC 2006: 193-202 - [c34]Song Lin, Vana Kalogeraki
Online Information Compression in Sensor Networks. ICC 2006: 3371-3376 - [c33]Eamonn J. Keogh, Li Wei, Xiaopeng Xi, Stefano Lonardi
Intelligent Icons: Integrating Lite-Weight Data Mining and Visualization into GUI Operating Systems. ICDM 2006: 912-916 - 2005
- [j12]Jessica Lin, Eamonn J. Keogh, Stefano Lonardi
Visualizing and discovering non-trivial patterns in large time series databases. Inf. Vis. 4(2): 61-82 (2005) - [j11]Li Wei, Eamonn J. Keogh, Xiaopeng Xi, Stefano Lonardi:
Integrating Lite-Weight but Ubiquitous Data Mining into GUI Operating Systems. J. Univers. Comput. Sci. 11(11): 1820-1834 (2005) - [j10]Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi
Assignment of Orthologous Genes via Genome Rearrangement. IEEE ACM Trans. Comput. Biol. Bioinform. 2(4): 302-315 (2005) - [c32]Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang:
Computing the Assignment of Orthologous Genes via Genome Rearrangement. APBC 2005: 363-378 - [c31]Jie Zheng, Stefano Lonardi
Discovery of Repetitive Patterns in DNA with Accurate Boundaries. BIBE 2005: 105-112 - [c30]Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi
A Practical Tool for Visualizing and Data Mining Medical Time Series. CBMS 2005: 341-346 - [c29]Qiaofeng Yang, Stefano Lonardi
A Parallel Algorithm for Clustering Protein-Protein Interaction Networks. CSB Workshops 2005: 174-177 - [c28]Song Lin, Dimitrios Gunopulos, Stefano Lonardi, Vana Kalogeraki
Applying LVQ Techniques to Compress Historical Information in Sensor Networks. DCC 2005: 468 - [c27]Qiaofeng Yang, Stefano Lonardi:
A Compression-Boosting Transform for 2D Data. DCC 2005: 492 - [c26]Dragomir Yankov, Eamonn J. Keogh, Stefano Lonardi
Dot Plots for Time Series Analysis. ICTAI 2005: 159-168 - [c25]Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Anthony J. Bagnall, Stefano Lonardi:
A Novel Bit Level Time Series Representation with Implication of Similarity Search and Clustering. PAKDD 2005: 771-777 - [c24]Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana:
Time-series Bitmaps: a Practical Visualization Tool for Working with Large Time Series Databases. SDM 2005: 531-535 - [c23]Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana:
Assumption-Free Anomaly Detection in Time Series. SSDBM 2005: 237-240 - [c22]Song Lin, Dimitrios Gunopulos
A Data Compression Technique for Sensor Networks with Dynamic Bandwidth Allocation. TIME 2005: 186-188 - 2004
- [j9]Jie Zheng
Efficient selection of unique and popular oligos for large EST databases. Bioinform. 20(13): 2101-2112 (2004) - [j8]Mikhail J. Atallah, Stefano Lonardi
Augmenting LZ-77 with authentication and integrity assurance capabilities. Concurr. Pract. Exp. 16(11): 1063-1076 (2004) - [j7]Alberto Apostolico, Fang-Cheng Gong, Stefano Lonardi
Verbumculus and the Discovery of Unusual Words. J. Comput. Sci. Technol. 19(1): 22-41 (2004) - [j6]Svante Janson, Stefano Lonardi
On average sequence complexity. Theor. Comput. Sci. 326(1-3): 213-227 (2004) - [c21]Eamonn J. Keogh, Jessica Lin, Stefano Lonardi, Bill Yuan-chi Chiu:
We Have Seen the Future, and It Is Symbolic. ACSW 2004: 83 - [c20]Svante Janson, Stefano Lonardi, Wojciech Szpankowski:
On the Average Sequence Complexity. CPM 2004: 74-88 - [c19]Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang:
Finding Biclusters by Random Projections. CPM 2004: 102-116 - [c18]Stefano Lonardi, Yu Luo:
Gridding and Compression of Microarray Images. CSB 2004: 122-130 - [c17]Svante Janson, Stefano Lonardi, Wojciech Szpankowski:
On the Average Sequence Complexity. Data Compression Conference 2004: 542 - [c16]Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward:
Error resilient LZ'77 scheme and its analysis. ISIT 2004: 56 - [c15]Eamonn J. Keogh, Stefano Lonardi
Towards parameter-free data mining. KDD 2004: 206-215 - [c14]Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom:
Visually mining and monitoring massive time series. KDD 2004: 460-469 - [c13]Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom:
VizTree: a Tool for Visually Mining and Monitoring Massive Time Series Databases. VLDB 2004: 1269-1272 - [r1]Stefan Kurtz, Stefano Lonardi:
Computational Biology. Handbook of Data Structures and Applications 2004 - 2003
- [j5]Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi
Monotony of Surprise and Large-Scale Quest for Unusual Words. J. Comput. Biol. 10(3/4): 283-311 (2003) - [c12]Jie Zheng, Timothy J. Close, Tao Jiang
Efficient Selection of Unique and Popular Oligos for Large EST Databases. CPM 2003: 384-401 - [c11]Stefano Lonardi
Joint Source-Channel LZ'77 Coding. DCC 2003: 273-282 - [c10]Jessica Lin, Eamonn J. Keogh, Stefano Lonardi
A symbolic representation of time series, with implications for streaming algorithms. DMKD 2003: 2-11 - [c9]Bill Yuan-chi Chiu, Eamonn J. Keogh, Stefano Lonardi
Probabilistic discovery of time series motifs. KDD 2003: 493-498 - [c8]Mikhail J. Atallah, Stefano Lonardi
Authentication of LZ-77 Compressed Data. SAC 2003: 282-287 - 2002
- [j4]Alberto Apostolico, Stefano Lonardi
A speed-up for the commute between subword trees and DAWGs. Inf. Process. Lett. 83(3): 159-161 (2002) - [c7]Concettina Guerra, Stefano Lonardi
Analysis of Secondary Structure Elements of Proteins Using Indexing Techniques. 3DPVT 2002: 812-823 - [c6]Pranav Patel, Eamonn J. Keogh, Jessica Lin, Stefano Lonardi:
Mining Motifs in Massive Time Series Databases. ICDM 2002: 370-377 - [c5]Eamonn J. Keogh, Stefano Lonardi, Bill Yuan-chi Chiu:
Finding surprising patterns in a time series database in linear time and space. KDD 2002: 550-556 - [c4]Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi:
Monotony of surprise and large-scale quest for unusual words. RECOMB 2002: 22-31 - 2000
- [j3]Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi
Efficient Detection of Unusual Words. J. Comput. Biol. 7(1-2): 71-94 (2000) - [j2]Alberto Apostolico, Stefano Lonardi
Off-line compression by greedy textual substitution. Proc. IEEE 88(11): 1733-1744 (2000) - [c3]Alberto Apostolico, Stefano Lonardi:
Compression of Biological Sequences by Greedy Off-Line Textual Substitution. Data Compression Conference 2000: 143-152
1990 – 1999
- 1999
- [j1]Stefano Lonardi
Fractal image approximation and orthogonal bases. Signal Process. Image Commun. 14(5): 413-423 (1999) - [c2]Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi
Linear Global Detectors of Redundant and Rare Substrings. Data Compression Conference 1999: 168-177 - 1998
- [c1]Alberto Apostolico, Stefano Lonardi
Some Theory and Practice of Greedy Off-Line Textual Substitution. Data Compression Conference 1998: 119-128
Coauthor Index
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