Stefano Lonardi

According to our database1, Stefano Lonardi authored at least 104 papers between 1998 and 2020.

Collaborative distances:

Awards

IEEE Fellow

IEEE Fellow 2016, "For contributions to computational biology and data mining".

Timeline

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In proceedings 
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Bibliography

2020
DeeplyEssential: a deep neural network for predicting essential genes in microbes.
BMC Bioinform., 2020

2019
Accurate detection of chimeric contigs via Bionano optical maps.
Bioinform., 2019

Selfish: discovery of differential chromatin interactions via a self-similarity measure.
Bioinform., 2019

OMGS: Optical Map-Based Genome Scaffolding.
Proceedings of the Research in Computational Molecular Biology, 2019

2018
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.
Bioinform., 2018

mClass: Cancer Type Classification with Somatic Point Mutation Data.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017
ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks.
Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps.
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.
PLoS Comput. Biol., 2016

Higher classification sensitivity of short metagenomic reads with CLARK-<i>S</i>.
Bioinform., 2016

BRAT-nova: fast and accurate mapping of bisulfite-treated reads.
Bioinform., 2016

2015
FHAST: FPGA-Based Acceleration of Bowtie in Hardware.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Using the minimum description length to discover the intrinsic cardinality and dimensionality of time series.
Data Min. Knowl. Discov., 2015

<i>De novo</i> meta-assembly of ultra-deep sequencing data.
Bioinform., 2015

When less is more: 'slicing' sequencing data improves read decoding accuracy and <i>de novo</i> assembly quality.
Bioinform., 2015

Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads.
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.
Comput. Biol. Chem., 2014

PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads.
BMC Bioinform., 2014

CLARK, accurate and efficient classification of DNA sequences.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

De novo assembly of ultra-deep sequencing data.
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.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space.
PLoS Comput. Biol., 2013

Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

2012
MDL-based time series clustering.
Knowl. Inf. Syst., 2012

NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model.
Bioinform., 2012

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
Bioinform., 2012

Multithreaded FPGA acceleration of DNA sequence mapping.
Proceedings of the IEEE Conference on High Performance Extreme Computing, 2012

2011
Accurate Construction of Consensus Genetic Maps via Integer Linear Programming.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space
CoRR, 2011

Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data.
Proceedings of the 11th IEEE International Conference on Data Mining, 2011

Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL.
Proceedings of the 11th IEEE International Conference on Data Mining, 2011

String Matching in Hardware Using the FM-Index.
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.
Proceedings of the Algorithmic Probability and Friends. Bayesian Prediction and Artificial Intelligence, 2011

2010
Data Mining in Bioinformatics: Selected Papers from BIOKDD.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Graphlet Kernels for Prediction of Functional Residues in Protein Structures.
J. Comput. Biol., 2010

Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion.
J. Comput. Biol., 2010

BRAT: bisulfite-treated reads analysis tool.
Bioinform., 2010

Exploration of Short Reads Genome Mapping in Hardware.
Proceedings of the International Conference on Field Programmable Logic and Applications, 2010

2009
A compartmentalized approach to the assembly of physical maps.
BMC Bioinform., 2009

CPM's 20th Anniversary: A Statistical Retrospective.
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.
Theor. Comput. Sci., 2008

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

Deconvoluting BAC-Gene Relationships Using a Physical Map.
J. Bioinform. Comput. Biol., 2008

A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks.
J. Bioinform. Comput. Biol., 2008

Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming.
Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

A Probabilistic Model for Small RNA Flowgram Matching.
Proceedings of the Biocomputing 2008, 2008

2007
Error Resilient LZ'77 Data Compression: Algorithms, Analysis, and Experiments.
IEEE Trans. Inf. Theory, 2007

A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks.
Int. J. Data Min. Bioinform., 2007

Experiencing SAX: a novel symbolic representation of time series.
Data Min. Knowl. Discov., 2007

Compression-based data mining of sequential data.
Data Min. Knowl. Discov., 2007

Composition Profiler: a tool for discovery and visualization of amino acid composition differences.
BMC Bioinform., 2007

Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Clock-frequency assignment for multiple clock domain systems-on-a-chip.
Proceedings of the 2007 Design, Automation and Test in Europe Conference and Exposition, 2007

Two-level microprocessor-accelerator partitioning.
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.
Proceedings of the 2007 Design, Automation and Test in Europe Conference and Exposition, 2007

2006
Finding biclusters by random projections.
Theor. Comput. Sci., 2006

Efficient Discovery of Unusual Patterns in Time Series.
New Gener. Comput., 2006

Efficient information compression in sensor networks.
Int. J. Sens. Networks, 2006

A Bit Level Representation for Time Series Data Mining with Shape Based Similarity.
Data Min. Knowl. Discov., 2006

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.
BMC Bioinform., 2006

Intelligent Icons: Integrating Lite-Weight Data Mining and Visualization into GUI Operating Systems.
Proceedings of the 6th IEEE International Conference on Data Mining (ICDM 2006), 2006

Online Information Compression in Sensor Networks.
Proceedings of IEEE International Conference on Communications, 2006

Error-Resilient LZW Data Compression.
Proceedings of the 2006 Data Compression Conference (DCC 2006), 2006

A Compression-Boosting Transform for Two-Dimensional Data.
Proceedings of the Algorithmic Aspects in Information and Management, 2006

2005
Assignment of Orthologous Genes via Genome Rearrangement.
IEEE ACM Trans. Comput. Biol. Bioinform., 2005

Integrating Lite-Weight but Ubiquitous Data Mining into GUI Operating Systems.
J. Univers. Comput. Sci., 2005

Visualizing and discovering non-trivial patterns in large time series databases.
Inf. Vis., 2005

A Data Compression Technique for Sensor Networks with Dynamic Bandwidth Allocation.
Proceedings of the 12th International Symposium on Temporal Representation and Reasoning (TIME 2005), 2005

Assumption-Free Anomaly Detection in Time Series.
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.
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.
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2005

Dot Plots for Time Series Analysis.
Proceedings of the 17th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2005), 2005

A Compression-Boosting Transform for 2D Data.
Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

Applying LVQ Techniques to Compress Historical Information in Sensor Networks.
Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

A Parallel Algorithm for Clustering Protein-Protein Interaction Networks.
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.
Proceedings of the 18th IEEE Symposium on Computer-Based Medical Systems (CBMS 2005), 2005

Discovery of Repetitive Patterns in DNA with Accurate Boundaries.
Proceedings of the Fifth IEEE International Symposium on Bioinformatic and Bioengineering (BIBE 2005), 2005

Computing the Assignment of Orthologous Genes via Genome Rearrangement.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

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

On average sequence complexity.
Theor. Comput. Sci., 2004

Verbumculus and the Discovery of Unusual Words.
J. Comput. Sci. Technol., 2004

Augmenting LZ-77 with authentication and integrity assurance capabilities.
Concurr. Pract. Exp., 2004

Efficient selection of unique and popular oligos for large EST databases.
Bioinform., 2004

VizTree: a Tool for Visually Mining and Monitoring Massive Time Series Databases.
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.
Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2004

Towards parameter-free data mining.
Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2004

Error resilient LZ'77 scheme and its analysis.
Proceedings of the 2004 IEEE International Symposium on Information Theory, 2004

Gridding and Compression of Microarray Images.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

We Have Seen the Future, and It Is Symbolic.
Proceedings of the ACSW Frontiers 2004, 2004 ACSW Workshops, 2004

2003
Monotony of Surprise and Large-Scale Quest for Unusual Words.
J. Comput. Biol., 2003

Authentication of LZ-77 Compressed Data.
Proceedings of the 2003 ACM Symposium on Applied Computing (SAC), 2003

Probabilistic discovery of time series motifs.
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.
Proceedings of the 8th ACM SIGMOD workshop on Research issues in data mining and knowledge discovery, 2003

Joint Source-Channel LZ'77 Coding.
Proceedings of the 2003 Data Compression Conference (DCC 2003), 2003

2002
A speed-up for the commute between subword trees and DAWGs.
Inf. Process. Lett., 2002

Finding surprising patterns in a time series database in linear time and space.
Proceedings of the Eighth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2002

Mining Motifs in Massive Time Series Databases.
Proceedings of the 2002 IEEE International Conference on Data Mining (ICDM 2002), 2002

Analysis of Secondary Structure Elements of Proteins Using Indexing Techniques.
Proceedings of the 1st International Symposium on 3D Data Processing Visualization and Transmission (3DPVT 2002), 2002

2000
Efficient Detection of Unusual Words.
J. Comput. Biol., 2000

Compression of Biological Sequences by Greedy Off-Line Textual Substitution.
Proceedings of the Data Compression Conference, 2000

1999
Fractal image approximation and orthogonal bases.
Signal Process. Image Commun., 1999

Linear Global Detectors of Redundant and Rare Substrings.
Proceedings of the Data Compression Conference, 1999

1998
Some Theory and Practice of Greedy Off-Line Textual Substitution.
Proceedings of the Data Compression Conference, 1998


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