Some Theory and Practice of Greedy Off-Line Textual Substitution. - Alberto Apostolico; Stefano Lonardi (Data Compression Conference, 1998)

Linear Global Detectors of Redundant and Rare Substrings. - Alberto Apostolico; Mary Ellen Bock; Stefano Lonardi (Data Compression Conference, 1999)

Fractal image approximation and orthogonal bases. - Stefano Lonardi; Paolo Sommaruga (Signal Process. Image Commun., 1999)

Compression of Biological Sequences by Greedy Off-Line Textual Substitution. - Alberto Apostolico; Stefano Lonardi (Data Compression Conference, 2000)

Efficient Detection of Unusual Words. - Alberto Apostolico; Mary Ellen Bock; Stefano Lonardi; Xuyan Xu (J. Comput. Biol., 2000)

Off-line compression by greedy textual substitution. - Alberto Apostolico; Stefano Lonardi (Proc. IEEE, 2000)

Analysis of Secondary Structure Elements of Proteins Using Indexing Techniques. - Concettina Guerra; Stefano Lonardi; Giuseppe Zanotti (3DPVT, 2002)

Mining Motifs in Massive Time Series Databases. - Pranav Patel; Eamonn J. Keogh; Jessica Lin 001; Stefano Lonardi (ICDM, 2002)

Finding surprising patterns in a time series database in linear time and space. - Eamonn J. Keogh; Stefano Lonardi; Bill Yuan-chi Chiu (KDD, 2002)

A speed-up for the commute between subword trees and DAWGs. - Alberto Apostolico; Stefano Lonardi (Inf. Process. Lett., 2002)

Joint Source-Channel LZ'77 Coding. - Stefano Lonardi; Wojciech Szpankowski (DCC, 2003)

A symbolic representation of time series, with implications for streaming algorithms. - Jessica Lin 001; Eamonn J. Keogh; Stefano Lonardi; Bill Yuan-chi Chiu (DMKD, 2003)

Probabilistic discovery of time series motifs. - Bill Yuan-chi Chiu; Eamonn J. Keogh; Stefano Lonardi (KDD, 2003)

Authentication of LZ-77 Compressed Data. - Mikhail J. Atallah; Stefano Lonardi (SAC, 2003)

Monotony of Surprise and Large-Scale Quest for Unusual Words. - Alberto Apostolico; Mary Ellen Bock; Stefano Lonardi (J. Comput. Biol., 2003)

We Have Seen the Future, and It Is Symbolic. - Eamonn J. Keogh; Jessica Lin 001; Stefano Lonardi; Bill Yuan-chi Chiu (ACSW, 2004)

Gridding and Compression of Microarray Images. - Stefano Lonardi; Yu Luo (CSB, 2004)

Error resilient LZ'77 scheme and its analysis. - Stefano Lonardi; Wojciech Szpankowski; Mark Daniel Ward (ISIT, 2004)

Towards parameter-free data mining. - Eamonn J. Keogh; Stefano Lonardi; Chotirat (Ann) Ratanamahatana (KDD, 2004)

Visually mining and monitoring massive time series. - Jessica Lin 001; Eamonn J. Keogh; Stefano Lonardi; Jeffrey P. Lankford; Donna M. Nystrom (KDD, 2004)

VizTree: a Tool for Visually Mining and Monitoring Massive Time Series Databases. - Jessica Lin 001; Eamonn J. Keogh; Stefano Lonardi; Jeffrey P. Lankford; Donna M. Nystrom (VLDB, 2004)

Efficient selection of unique and popular oligos for large EST databases. - Jie Zheng 002; Timothy J. Close; Tao Jiang 001; Stefano Lonardi (Bioinform., 2004)

Augmenting LZ-77 with authentication and integrity assurance capabilities. - Mikhail J. Atallah; Stefano Lonardi (Concurr. Pract. Exp., 2004)

Verbumculus and the Discovery of Unusual Words. - Alberto Apostolico; Fang-Cheng Gong; Stefano Lonardi (J. Comput. Sci. Technol., 2004)

On average sequence complexity. - Svante Janson; Stefano Lonardi; Wojciech Szpankowski (Theor. Comput. Sci., 2004)

Computational Biology. - Stefan Kurtz; Stefano Lonardi (Handbook of Data Structures and Applications, 2004)

Computing the Assignment of Orthologous Genes via Genome Rearrangement. - Xin Chen 037; Jie Zheng 002; Zheng Fu; Peng Nan; Yang Zhong; Stefano Lonardi; Tao Jiang 001 (APBC, 2005)

Discovery of Repetitive Patterns in DNA with Accurate Boundaries. - Jie Zheng 002; Stefano Lonardi (BIBE, 2005)

A Practical Tool for Visualizing and Data Mining Medical Time Series. - Li Wei 001; Nitin Kumar 002; Venkata Nishanth Lolla; Eamonn J. Keogh; Stefano Lonardi; Chotirat (Ann) Ratanamahatana; Helga Van Herle (CBMS, 2005)

A Parallel Algorithm for Clustering Protein-Protein Interaction Networks. - Qiaofeng Yang; Stefano Lonardi (CSB Workshops, 2005)

Applying LVQ Techniques to Compress Historical Information in Sensor Networks. - Song Lin; Dimitrios Gunopulos; Stefano Lonardi; Vana Kalogeraki (DCC, 2005)

A Compression-Boosting Transform for 2D Data. - Qiaofeng Yang; Stefano Lonardi (DCC, 2005)

Dot Plots for Time Series Analysis. - Dragomir Yankov; Eamonn J. Keogh; Stefano Lonardi; Ada Wai-Chee Fu (ICTAI, 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 (PAKDD, 2005)

Time-series Bitmaps: a Practical Visualization Tool for Working with Large Time Series Databases. - Nitin Kumar 002; Venkata Nishanth Lolla; Eamonn J. Keogh; Stefano Lonardi; Chotirat (Ann) Ratanamahatana (SDM, 2005)

Assumption-Free Anomaly Detection in Time Series. - Li Wei 001; Nitin Kumar 002; Venkata Nishanth Lolla; Eamonn J. Keogh; Stefano Lonardi; Chotirat (Ann) Ratanamahatana (SSDBM, 2005)

A Data Compression Technique for Sensor Networks with Dynamic Bandwidth Allocation. - Song Lin; Dimitrios Gunopulos; Vana Kalogeraki; Stefano Lonardi (TIME, 2005)

Visualizing and discovering non-trivial patterns in large time series databases. - Jessica Lin 001; Eamonn J. Keogh; Stefano Lonardi (Inf. Vis., 2005)

Integrating Lite-Weight but Ubiquitous Data Mining into GUI Operating Systems. - Li Wei 001; Eamonn J. Keogh; Xiaopeng Xi; Stefano Lonardi (J. Univers. Comput. Sci., 2005)

Assignment of Orthologous Genes via Genome Rearrangement. - Xin Chen 037; Jie Zheng 002; Zheng Fu; Peng Nan; Yang Zhong; Stefano Lonardi; Tao Jiang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

A Compression-Boosting Transform for Two-Dimensional Data. - Qiaofeng Yang; Stefano Lonardi; Avraham A. Melkman (AAIM, 2006)

Error-Resilient LZW Data Compression. - Yonghui Wu; Stefano Lonardi; Wojciech Szpankowski (DCC, 2006)

Online Information Compression in Sensor Networks. - Song Lin; Vana Kalogeraki; Dimitrios Gunopulos; Stefano Lonardi (ICC, 2006)

Intelligent Icons: Integrating Lite-Weight Data Mining and Visualization into GUI Operating Systems. - Eamonn J. Keogh; Li Wei 001; Xiaopeng Xi; Stefano Lonardi; Jin Shieh; Scott Sirowy (ICDM, 2006)

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. - Jie Zheng 002; Jan T. Svensson; Kavitha Madishetty; Timothy J. Close; Tao Jiang 001; Stefano Lonardi (BMC Bioinform., 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)

Efficient information compression in sensor networks. - Song Lin; Vana Kalogeraki; Dimitrios Gunopulos; Stefano Lonardi (Int. J. Sens. Networks, 2006)

Efficient Discovery of Unusual Patterns in Time Series. - Stefano Lonardi; Jessica Lin 001; Eamonn J. Keogh; Bill Yuan-chi Chiu (New Gener. Comput., 2006)

Finding biclusters by random projections. - Stefano Lonardi; Wojciech Szpankowski; Qiaofeng Yang (Theor. Comput. Sci., 2006)

Interactive presentation: Soft-core processor customization using the design of experiments paradigm. - David Sheldon; Frank Vahid; Stefano Lonardi (DATE, 2007)

Two-level microprocessor-accelerator partitioning. - Scott Sirowy; Yonghui Wu; Stefano Lonardi; Frank Vahid (DATE, 2007)

Clock-frequency assignment for multiple clock domain systems-on-a-chip. - Scott Sirowy; Yonghui Wu; Stefano Lonardi; Frank Vahid (DATE, 2007)

Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. - Yonghui Wu; Prasanna Bhat; Timothy J. Close; Stefano Lonardi (WABI, 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)

Compression-based data mining of sequential data. - Eamonn J. Keogh; Stefano Lonardi; Chotirat Ann Ratanamahatana; Li Wei 001; Sang-Hee Lee 003; John C. Handley (Data Min. Knowl. Discov., 2007)

Experiencing SAX: a novel symbolic representation of time series. - Jessica Lin 001; Eamonn J. Keogh; Li Wei 001; Stefano Lonardi (Data Min. Knowl. Discov., 2007)

A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks. - Qiaofeng Yang; Stefano Lonardi (Int. J. Data Min. Bioinform., 2007)

Error Resilient LZ'77 Data Compression: Algorithms, Analysis, and Experiments. - Stefano Lonardi; Wojciech Szpankowski; Mark Daniel Ward (IEEE Trans. Inf. Theory, 2007)

A Probabilistic Model for Small RNA Flowgram Matching. - Vladimir Vacic; Hailing Jin; Jian-Kang Zhu; Stefano Lonardi (Pacific Symposium on Biocomputing, 2008)

Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (WABI, 2008)

A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks. - Yonghui Wu; Stefano Lonardi (J. Bioinform. Comput. Biol., 2008)

Deconvoluting BAC-Gene Relationships Using a Physical Map. - Yonghui Wu; Lan Liu 001; Timothy J. Close; Stefano Lonardi (J. Bioinform. Comput. Biol., 2008)

BIOKDD 2008: a workshop report on data mining in bioinformatics. - Jake Y. Chen; Mohammed Javeed Zaki; Stefano Lonardi (SIGKDD Explor., 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)

CPM's 20th Anniversary: A Statistical Retrospective. - Elena Yavorska Harris; Thierry Lecroq; Gregory Kucherov; Stefano Lonardi (CPM, 2009)

A compartmentalized approach to the assembly of physical maps. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (BMC Bioinform., 2009)

Exploration of Short Reads Genome Mapping in Hardware. - Edward Fernandez; Walid A. Najjar; Elena Yavorska Harris; Stefano Lonardi (FPL, 2010)

BRAT: bisulfite-treated reads analysis tool. - Elena Yavorska Harris; Nadia Ponts; Aleksandr Levchuk; Karine G. Le Roch; Stefano Lonardi (Bioinform., 2010)

Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion. - Lan Liu 001; Yonghui Wu; Stefano Lonardi; Tao Jiang 001 (J. Comput. Biol., 2010)

Graphlet Kernels for Prediction of Functional Residues in Protein Structures. - Vladimir Vacic; Lilia M. Iakoucheva; Stefano Lonardi; Predrag Radivojac (J. Comput. Biol., 2010)

Data Mining in Bioinformatics: Selected Papers from BIOKDD. - Stefano Lonardi; Jake Yue Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Towards Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. - Bing Hu 001; Thanawin Rakthanmanon; Yuan Hao; Scott Evans; Stefano Lonardi; Eamonn J. Keogh (Algorithmic Probability and Friends, 2011)

String Matching in Hardware Using the FM-Index. - Edward Fernandez; Walid A. Najjar; Stefano Lonardi (FCCM, 2011)

Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. - Bing Hu 001; Thanawin Rakthanmanon; Yuan Hao; Scott Evans; Stefano Lonardi; Eamonn J. Keogh (ICDM, 2011)

Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data. - Thanawin Rakthanmanon; Eamonn J. Keogh; Stefano Lonardi; Scott Evans (ICDM, 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; et al. (CoRR, 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)

Multithreaded FPGA acceleration of DNA sequence mapping. - Edward Fernandez; Walid A. Najjar; Stefano Lonardi; Jason R. Villarreal (HPEC, 2012)

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. - Elena Yavorska Harris; Nadia Ponts; Karine G. Le Roch; Stefano Lonardi (Bioinform., 2012)

NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model. - Anton Polishko; Nadia Ponts; Karine G. Le Roch; Stefano Lonardi (Bioinform., 2012)

MDL-based time series clustering. - Thanawin Rakthanmanon; Eamonn J. Keogh; Stefano Lonardi; Scott Evans (Knowl. Inf. Syst., 2012)

Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing. - Denisa Duma; Mary Wootters; Anna C. Gilbert; Hung Q. Ngo 001; Atri Rudra; Matthew Alpert; Timothy J. Close; Gianfranco Ciardo; Stefano Lonardi (WABI, 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; et al. (PLoS Comput. Biol., 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)

De novo assembly of ultra-deep sequencing data. - Seyed Hamid Mirebrahim; Timothy J. Close; Stefano Lonardi (BCB, 2014)

CLARK, accurate and efficient classification of DNA sequences. - Rachid Ounit; Timothy J. Close; Steve Wanamaker; Stefano Lonardi (BCB, 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)

Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. - Haifen Chen; Stefano Lonardi; Jie Zheng 002 (Comput. Biol. Chem., 2014)

Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. - Denise Duma; Francesca Cordero; Marco Beccuti; Gianfranco Ciardo; Timothy J. Close; Stefano Lonardi (WABI, 2015)

Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers. - Rachid Ounit; Stefano Lonardi (WABI, 2015)

When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. - Stefano Lonardi; Seyed Hamid Mirebrahim; Steve Wanamaker; Matthew Alpert; Gianfranco Ciardo; Denisa Duma; Timothy J. Close (Bioinform., 2015)

De novo meta-assembly of ultra-deep sequencing data. - Seyed Hamid Mirebrahim; Timothy J. Close; Stefano Lonardi (Bioinform., 2015)

Using the minimum description length to discover the intrinsic cardinality and dimensionality of time series. - Bing Hu 001; Thanawin Rakthanmanon; Yuan Hao; Scott Evans; Stefano Lonardi; Eamonn J. Keogh (Data Min. Knowl. Discov., 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)

BRAT-nova: fast and accurate mapping of bisulfite-treated reads. - Elena Yavorska Harris; Rachid Ounit; Stefano Lonardi (Bioinform., 2016)

Higher classification sensitivity of short metagenomic reads with CLARK-S. - Rachid Ounit; Stefano Lonardi (Bioinform., 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)

Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps. - Abbas Roayaei Ardakany; Stefano Lonardi (WABI, 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 (WABI, 2017)

mClass: Cancer Type Classification with Somatic Point Mutation Data. - Md. Abid Hasan; Stefano Lonardi (RECOMB-CG, 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)

Selfish: discovery of differential chromatin interactions via a self-similarity measure. - Abbas Roayaei Ardakany; Ferhat Ay; Stefano Lonardi (Bioinform., 2019)

Accurate detection of chimeric contigs via Bionano optical maps. - Weihua Pan; Stefano Lonardi (Bioinform., 2019)

DeeplyEssential: a deep neural network for predicting essential genes in microbes. - Md. Abid Hasan; Stefano Lonardi (BMC Bioinform., 2020)

OMGS: Optical Map-Based Genome Scaffolding. - Weihua Pan; Tao Jiang 001; Stefano Lonardi (J. Comput. Biol., 2020)

Prediction of histone post-translational modifications using deep learning. - Dipankar Ranjan Baisya; Stefano Lonardi (Bioinform., 2021)

Reference-agnostic representation and visualization of pan-genomes. - Qihua Liang; Stefano Lonardi (BMC Bioinform., 2021)

RAmbler: de novo genome assembly of complex repetitive regions. - Sakshar Chakravarty; Glennis Logsdon; Stefano Lonardi (BCB, 2023)

Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model. - Saleh Sereshki; Stefano Lonardi (Briefings Bioinform., 2025)

Predicting Antibody-Antigen Interactions with Structure-Aware LLMs: Insights from SARS-CoV-2 Variants. - Faisal Bin Ashraf; Vinz Angelo Madrigal; Stefano Lonardi (J. Chem. Inf. Model., 2025)