Stefano Lonardi

According to our database, Stefano Lonardi authored at least 108 papers between 1998 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2023

RAmbler: de novo genome assembly of complex repetitive regions.

Sakshar Chakravarty, Glennis Logsdon, Stefano Lonardi

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2021

Reference-agnostic representation and visualization of pan-genomes.

Qihua Liang, Stefano Lonardi

BMC Bioinform., 2021

Prediction of histone post-translational modifications using deep learning.

Dipankar Ranjan Baisya, Stefano Lonardi

Bioinform., 2021

2020

OMGS: Optical Map-Based Genome Scaffolding.

Weihua Pan, Tao Jiang, Stefano Lonardi

J. Comput. Biol., 2020

DeeplyEssential: a deep neural network for predicting essential genes in microbes.

Md. Abid Hasan, Stefano Lonardi

BMC Bioinform., 2020

2019

Accurate detection of chimeric contigs via Bionano optical maps.

Weihua Pan, Stefano Lonardi

Bioinform., 2019

Selfish: discovery of differential chromatin interactions via a self-similarity measure.

Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi

Bioinform., 2019

2018

Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.

Weihua Pan, Steve Wanamaker, Audrey M. V. Ah-Fong, Howard S. Judelson, Stefano Lonardi

Bioinform., 2018

mClass: Cancer Type Classification with Somatic Point Mutation Data.

Md. Abid Hasan, Stefano Lonardi

Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017

ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks.

Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik, Karine G. Le Roch, Stefano Lonardi

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps.

Abbas Roayaei Ardakany, Stefano Lonardi

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

2016

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern

PLoS Comput. Biol., 2016

Higher classification sensitivity of short metagenomic reads with CLARK-<i>S</i>.

Rachid Ounit, Stefano Lonardi

Bioinform., 2016

BRAT-nova: fast and accurate mapping of bisulfite-treated reads.

Elena Yavorska Harris, Rachid Ounit, Stefano Lonardi

Bioinform., 2016

2015

FHAST: FPGA-Based Acceleration of Bowtie in Hardware.

Edward B. Fernandez, Jason R. Villarreal, Stefano Lonardi, Walid A. Najjar

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Using the minimum description length to discover the intrinsic cardinality and dimensionality of time series.

Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh

Data Min. Knowl. Discov., 2015

<i>De novo</i> meta-assembly of ultra-deep sequencing data.

Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi

Bioinform., 2015

When less is more: 'slicing' sequencing data improves read decoding accuracy and <i>de novo</i> assembly quality.

Stefano Lonardi, Seyed Hamid Mirebrahim, Steve Wanamaker, Matthew Alpert, Gianfranco Ciardo, Denisa Duma, Timothy J. Close

Bioinform., 2015

Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers.

Rachid Ounit, Stefano Lonardi

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads.

Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

2014

Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining.

Haifen Chen, Stefano Lonardi, Jie Zheng

Comput. Biol. Chem., 2014

PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads.

Anton Polishko, Evelien M. Bunnik, Karine G. Le Roch, Stefano Lonardi

BMC Bioinform., 2014

CLARK, accurate and efficient classification of DNA sequences.

Rachid Ounit, Timothy J. Close, Steve Wanamaker, Stefano Lonardi

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

De novo assembly of ultra-deep sequencing data.

Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013

A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map.

Serdar Bozdag, Timothy J. Close, Stefano Lonardi

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space.

Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna R. Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close

PLoS Comput. Biol., 2013

Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing.

Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert, Timothy J. Close, Gianfranco Ciardo, Stefano Lonardi

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012

MDL-based time series clustering.

Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi, Scott Evans

Knowl. Inf. Syst., 2012

NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model.

Anton Polishko, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi

Bioinform., 2012

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.

Elena Yavorska Harris, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi

Bioinform., 2012

Multithreaded FPGA acceleration of DNA sequence mapping.

Edward Fernandez, Walid A. Najjar, Stefano Lonardi, Jason R. Villarreal

Proceedings of the IEEE Conference on High Performance Extreme Computing, 2012

2011

Accurate Construction of Consensus Genetic Maps via Integer Linear Programming.

Yonghui Wu, Timothy J. Close, Stefano Lonardi

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space

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

CoRR, 2011

Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data.

Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi, Scott Evans

Proceedings of the 11th IEEE International Conference on Data Mining, 2011

Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL.

Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh

Proceedings of the 11th IEEE International Conference on Data Mining, 2011

String Matching in Hardware Using the FM-Index.

Edward Fernandez, Walid A. Najjar, Stefano Lonardi

Proceedings of the IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011

Towards Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL.

Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh

Proceedings of the Algorithmic Probability and Friends. Bayesian Prediction and Artificial Intelligence, 2011

2010

Data Mining in Bioinformatics: Selected Papers from BIOKDD.

Stefano Lonardi, Jake Yue Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Graphlet Kernels for Prediction of Functional Residues in Protein Structures.

Vladimir Vacic, Lilia M. Iakoucheva, Stefano Lonardi, Predrag Radivojac

J. Comput. Biol., 2010

Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion.

Lan Liu, Yonghui Wu, Stefano Lonardi, Tao Jiang

J. Comput. Biol., 2010

BRAT: bisulfite-treated reads analysis tool.

Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi

Bioinform., 2010

Exploration of Short Reads Genome Mapping in Hardware.

Edward Fernandez, Walid A. Najjar, Elena Yavorska Harris, Stefano Lonardi

Proceedings of the International Conference on Field Programmable Logic and Applications, 2010

2009

A compartmentalized approach to the assembly of physical maps.

Serdar Bozdag, Timothy J. Close, Stefano Lonardi

BMC Bioinform., 2009

CPM's 20th Anniversary: A Statistical Retrospective.

Elena Yavorska Harris, Thierry Lecroq, Gregory Kucherov, Stefano Lonardi

Proceedings of the Combinatorial Pattern Matching, 20th Annual Symposium, 2009

2008

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.

Raffaele Giancarlo, Stefano Lonardi

Theor. Comput. Sci., 2008

BIOKDD 2008: a workshop report on data mining in bioinformatics.

Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi

SIGKDD Explor., 2008

Deconvoluting BAC-Gene Relationships Using a Physical Map.

Yonghui Wu, Lan Liu, Timothy J. Close, Stefano Lonardi

J. Bioinform. Comput. Biol., 2008

A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks.

Yonghui Wu, Stefano Lonardi

J. Bioinform. Comput. Biol., 2008

Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming.

Serdar Bozdag, Timothy J. Close, Stefano Lonardi

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

A Probabilistic Model for Small RNA Flowgram Matching.

Vladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi

Proceedings of the Biocomputing 2008, 2008

2007

Error Resilient LZ'77 Data Compression: Algorithms, Analysis, and Experiments.

Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward

IEEE Trans. Inf. Theory, 2007

A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks.

Qiaofeng Yang, Stefano Lonardi

Int. J. Data Min. Bioinform., 2007

Experiencing SAX: a novel symbolic representation of time series.

Jessica Lin, Eamonn J. Keogh, Li Wei, Stefano Lonardi

Data Min. Knowl. Discov., 2007

Compression-based data mining of sequential data.

Eamonn J. Keogh, Stefano Lonardi, Chotirat Ann Ratanamahatana, Li Wei, Sang-Hee Lee, John C. Handley

Data Min. Knowl. Discov., 2007

Composition Profiler: a tool for discovery and visualization of amino acid composition differences.

Vladimir Vacic, Vladimir N. Uversky, A. Keith Dunker, Stefano Lonardi

BMC Bioinform., 2007

Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data.

Yonghui Wu, Prasanna Bhat, Timothy J. Close, Stefano Lonardi

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Clock-frequency assignment for multiple clock domain systems-on-a-chip.

Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid

Proceedings of the 2007 Design, Automation and Test in Europe Conference and Exposition, 2007

Two-level microprocessor-accelerator partitioning.

Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid

Proceedings of the 2007 Design, Automation and Test in Europe Conference and Exposition, 2007

Interactive presentation: Soft-core processor customization using the design of experiments paradigm.

David Sheldon, Frank Vahid, Stefano Lonardi

Proceedings of the 2007 Design, Automation and Test in Europe Conference and Exposition, 2007

2006

Finding biclusters by random projections.

Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang

Theor. Comput. Sci., 2006

Efficient Discovery of Unusual Patterns in Time Series.

Stefano Lonardi, Jessica Lin, Eamonn J. Keogh, Bill Yuan-chi Chiu

New Gener. Comput., 2006

Efficient information compression in sensor networks.

Song Lin, Vana Kalogeraki, Dimitrios Gunopulos, Stefano Lonardi

Int. J. Sens. Networks, 2006

A Bit Level Representation for Time Series Data Mining with Shape Based Similarity.

Anthony J. Bagnall, Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Stefano Lonardi, Gareth J. Janacek

Data Min. Knowl. Discov., 2006

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.

Jie Zheng, Jan T. Svensson, Kavitha Madishetty, Timothy J. Close, Tao Jiang, Stefano Lonardi

BMC Bioinform., 2006

Intelligent Icons: Integrating Lite-Weight Data Mining and Visualization into GUI Operating Systems.

Eamonn J. Keogh, Li Wei, Xiaopeng Xi, Stefano Lonardi, Jin Shieh, Scott Sirowy

Proceedings of the 6th IEEE International Conference on Data Mining (ICDM 2006), 2006

Online Information Compression in Sensor Networks.

Song Lin, Vana Kalogeraki, Dimitrios Gunopulos, Stefano Lonardi

Proceedings of IEEE International Conference on Communications, 2006

Error-Resilient LZW Data Compression.

Yonghui Wu, Stefano Lonardi, Wojciech Szpankowski

Proceedings of the 2006 Data Compression Conference (DCC 2006), 2006

A Compression-Boosting Transform for Two-Dimensional Data.

Qiaofeng Yang, Stefano Lonardi, Avraham A. Melkman

Proceedings of the Algorithmic Aspects in Information and Management, 2006

2005

Assignment of Orthologous Genes via Genome Rearrangement.

Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang

IEEE ACM Trans. Comput. Biol. Bioinform., 2005

Integrating Lite-Weight but Ubiquitous Data Mining into GUI Operating Systems.

Li Wei, Eamonn J. Keogh, Xiaopeng Xi, Stefano Lonardi

J. Univers. Comput. Sci., 2005

Visualizing and discovering non-trivial patterns in large time series databases.

Jessica Lin, Eamonn J. Keogh, Stefano Lonardi

Inf. Vis., 2005

A Data Compression Technique for Sensor Networks with Dynamic Bandwidth Allocation.

Song Lin, Dimitrios Gunopulos, Vana Kalogeraki, Stefano Lonardi

Proceedings of the 12th International Symposium on Temporal Representation and Reasoning (TIME 2005), 2005

Assumption-Free Anomaly Detection in Time Series.

Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana

Proceedings of the 17th International Conference on Scientific and Statistical Database Management, 2005

Time-series Bitmaps: a Practical Visualization Tool for Working with Large Time Series Databases.

Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana

Proceedings of the 2005 SIAM International Conference on Data Mining, 2005

A Novel Bit Level Time Series Representation with Implication of Similarity Search and Clustering.

Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Anthony J. Bagnall, Stefano Lonardi

Proceedings of the Advances in Knowledge Discovery and Data Mining, 2005

Dot Plots for Time Series Analysis.

Dragomir Yankov, Eamonn J. Keogh, Stefano Lonardi, Ada Wai-Chee Fu

Proceedings of the 17th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2005), 2005

A Compression-Boosting Transform for 2D Data.

Qiaofeng Yang, Stefano Lonardi

Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

Applying LVQ Techniques to Compress Historical Information in Sensor Networks.

Song Lin, Dimitrios Gunopulos, Stefano Lonardi, Vana Kalogeraki

Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

A Parallel Algorithm for Clustering Protein-Protein Interaction Networks.

Qiaofeng Yang, Stefano Lonardi

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

A Practical Tool for Visualizing and Data Mining Medical Time Series.

Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana, Helga Van Herle

Proceedings of the 18th IEEE Symposium on Computer-Based Medical Systems (CBMS 2005), 2005

Discovery of Repetitive Patterns in DNA with Accurate Boundaries.

Jie Zheng, Stefano Lonardi

Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005

Computing the Assignment of Orthologous Genes via Genome Rearrangement.

Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang

Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

2004

Computational Biology.

Stefan Kurtz, Stefano Lonardi

Proceedings of the Handbook of Data Structures and Applications., 2004

On average sequence complexity.

Svante Janson, Stefano Lonardi, Wojciech Szpankowski

Theor. Comput. Sci., 2004

Verbumculus and the Discovery of Unusual Words.

Alberto Apostolico, Fang-Cheng Gong, Stefano Lonardi

J. Comput. Sci. Technol., 2004

Augmenting LZ-77 with authentication and integrity assurance capabilities.

Mikhail J. Atallah, Stefano Lonardi

Concurr. Pract. Exp., 2004

Efficient selection of unique and popular oligos for large EST databases.

Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi

Bioinform., 2004

VizTree: a Tool for Visually Mining and Monitoring Massive Time Series Databases.

Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom

Proceedings of the (e)Proceedings of the Thirtieth International Conference on Very Large Data Bases, VLDB 2004, Toronto, Canada, August 31, 2004

Visually mining and monitoring massive time series.

Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom

Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2004

Towards parameter-free data mining.

Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana

Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2004

Error resilient LZ'77 scheme and its analysis.

Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward

Proceedings of the 2004 IEEE International Symposium on Information Theory, 2004

Gridding and Compression of Microarray Images.

Stefano Lonardi, Yu Luo

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

We Have Seen the Future, and It Is Symbolic.

Eamonn J. Keogh, Jessica Lin, Stefano Lonardi, Bill Yuan-chi Chiu

Proceedings of the ACSW Frontiers 2004, 2004 ACSW Workshops, 2004

2003

Monotony of Surprise and Large-Scale Quest for Unusual Words.

Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi

J. Comput. Biol., 2003

Authentication of LZ-77 Compressed Data.

Mikhail J. Atallah, Stefano Lonardi

Proceedings of the 2003 ACM Symposium on Applied Computing (SAC), 2003

Probabilistic discovery of time series motifs.

Bill Yuan-chi Chiu, Eamonn J. Keogh, Stefano Lonardi

Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Washington, DC, USA, August 24, 2003

A symbolic representation of time series, with implications for streaming algorithms.

Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Bill Yuan-chi Chiu

Proceedings of the 8th ACM SIGMOD workshop on Research issues in data mining and knowledge discovery, 2003

Joint Source-Channel LZ'77 Coding.

Stefano Lonardi, Wojciech Szpankowski

Proceedings of the 2003 Data Compression Conference (DCC 2003), 2003

2002

A speed-up for the commute between subword trees and DAWGs.

Alberto Apostolico, Stefano Lonardi

Inf. Process. Lett., 2002

Finding surprising patterns in a time series database in linear time and space.

Eamonn J. Keogh, Stefano Lonardi, Bill Yuan-chi Chiu

Proceedings of the Eighth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2002

Mining Motifs in Massive Time Series Databases.

Pranav Patel, Eamonn J. Keogh, Jessica Lin, Stefano Lonardi

Proceedings of the 2002 IEEE International Conference on Data Mining (ICDM 2002), 2002

Analysis of Secondary Structure Elements of Proteins Using Indexing Techniques.

Concettina Guerra, Stefano Lonardi, Giuseppe Zanotti

Proceedings of the 1st International Symposium on 3D Data Processing Visualization and Transmission (3DPVT 2002), 2002

2000

Off-line compression by greedy textual substitution.

Alberto Apostolico, Stefano Lonardi

Proc. IEEE, 2000

Efficient Detection of Unusual Words.

Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi, Xuyan Xu

J. Comput. Biol., 2000

Compression of Biological Sequences by Greedy Off-Line Textual Substitution.

Alberto Apostolico, Stefano Lonardi

Proceedings of the Data Compression Conference, 2000

1999

Fractal image approximation and orthogonal bases.

Stefano Lonardi, Paolo Sommaruga

Signal Process. Image Commun., 1999

Linear Global Detectors of Redundant and Rare Substrings.

Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi

Proceedings of the Data Compression Conference, 1999

1998

Some Theory and Practice of Greedy Off-Line Textual Substitution.

Alberto Apostolico, Stefano Lonardi

Proceedings of the Data Compression Conference, 1998