Stefano Lonardi

121 papers A* 9A 4B 21C 12Misc 3Journal 58Unranked 13

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	AbAffinity: A Large Language Model for Predicting Antibody Binding Affinity against SARS-CoV-2. CoRR Faisal Bin Ashraf, Animesh Ray, Stefano Lonardi
2025	J	`jnl`	Predicting Antibody-Antigen Interactions with Structure-Aware LLMs: Insights from SARS-CoV-2 Variants. J. Chem. Inf. Model. Faisal Bin Ashraf, Vinz Angelo Madrigal, Stefano Lonardi
2025	J	`jnl`	Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model. Briefings Bioinform. Saleh Sereshki, Stefano Lonardi
2025	J	`jnl`	Prediction of DNA Methylation With Long-Range State-Space Models. IEEE Trans. Comput. Biol. Bioinform. Hao Feng, Sakshar Chakravarty, Stefano Lonardi
2025	—	`conf`	Towards optimal selection of ultra-deep sequencing reads for de novo genome assembly. BCB Sakshar Chakravarty, Stefano Lonardi
2023	—	`conf`	RAmbler: de novo genome assembly of complex repetitive regions. BCB Sakshar Chakravarty, Glennis Logsdon, Stefano Lonardi
2021	J	`jnl`	Prediction of histone post-translational modifications using deep learning. Bioinform. Dipankar Ranjan Baisya, Stefano Lonardi
2021	J	`jnl`	Reference-agnostic representation and visualization of pan-genomes. BMC Bioinform. Qihua Liang, Stefano Lonardi
2020	J	`jnl`	DeeplyEssential: a deep neural network for predicting essential genes in microbes. BMC Bioinform. Md. Abid Hasan, Stefano Lonardi
2020	J	`jnl`	OMGS: Optical Map-Based Genome Scaffolding. J. Comput. Biol. Weihua Pan, Tao Jiang, Stefano Lonardi
2019	J	`jnl`	Accurate detection of chimeric contigs via Bionano optical maps. Bioinform. Weihua Pan, Stefano Lonardi
2019	B	`conf`	OMGS: Optical Map-Based Genome Scaffolding. RECOMB Weihua Pan, Tao Jiang, Stefano Lonardi
2019	J	`jnl`	Selfish: discovery of differential chromatin interactions via a self-similarity measure. Bioinform. Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi
2018	J	`jnl`	Novo&Stitch: accurate reconciliation of genome assemblies via optical maps. Bioinform. Weihua Pan, Steve Wanamaker, Audrey M. V. Ah-Fong, Howard S. Judelson, Stefano Lonardi
2018	—	`conf`	mClass: Cancer Type Classification with Somatic Point Mutation Data. RECOMB-CG Md. Abid Hasan, Stefano Lonardi
2017	C	`conf`	Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps. WABI Abbas Roayaei Ardakany, Stefano Lonardi
2017	C	`conf`	ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks. WABI Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik, Karine G. Le Roch, Stefano Lonardi
2016	J	`jnl`	BRAT-nova: fast and accurate mapping of bisulfite-treated reads. Bioinform. Elena Yavorska Harris, Rachid Ounit, Stefano Lonardi
2016	J	`jnl`	Higher classification sensitivity of short metagenomic reads with CLARK- Bioinform. Rachid Ounit, Stefano Lonardi
2016	J	`jnl`	rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison. PLoS Comput. Biol. Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern
2015	J	`jnl`	FHAST: FPGA-Based Acceleration of Bowtie in Hardware. IEEE ACM Trans. Comput. Biol. Bioinform. Edward B. Fernandez, Jason R. Villarreal, Stefano Lonardi, Walid A. Najjar
2015	C	`conf`	Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers. WABI Rachid Ounit, Stefano Lonardi
2015	C	`conf`	Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. WABI Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi
2015	J	`jnl`	Using the minimum description length to discover the intrinsic cardinality and dimensionality of time series. Data Min. Knowl. Discov. Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh
2015	J	`jnl`	When less is more: 'slicing' sequencing data improves read decoding accuracy and Bioinform. Stefano Lonardi, Seyed Hamid Mirebrahim, Steve Wanamaker, Matthew Alpert, Gianfranco Ciardo, Denisa Duma, Timothy J. Close
2014	—	`conf`	CLARK, accurate and efficient classification of DNA sequences. BCB Rachid Ounit, Timothy J. Close, Steve Wanamaker, Stefano Lonardi
2014	—	`conf`	De novo assembly of ultra-deep sequencing data. BCB Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi
2014	J	`jnl`	Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. Comput. Biol. Chem. Haifen Chen, Stefano Lonardi, Jie Zheng
2014	J	`jnl`	PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. BMC Bioinform. Anton Polishko, Evelien M. Bunnik, Karine G. Le Roch, Stefano Lonardi
2013	J	`jnl`	A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map. IEEE ACM Trans. Comput. Biol. Bioinform. Serdar Bozdag, Timothy J. Close, Stefano Lonardi
2013	C	`conf`	Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing. WABI Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert, Timothy J. Close, Gianfranco Ciardo, Stefano Lonardi
2013	J	`jnl`	Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLoS Comput. Biol. 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
2012	J	`jnl`	BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinform. Elena Yavorska Harris, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi
2012	J	`jnl`	MDL-based time series clustering. Knowl. Inf. Syst. Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi, Scott Evans
2012	—	`conf`	Multithreaded FPGA acceleration of DNA sequence mapping. HPEC Edward Fernandez, Walid A. Najjar, Stefano Lonardi, Jason R. Villarreal
2012	J	`jnl`	NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model. Bioinform. Anton Polishko, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi
2011	J	`jnl`	Accurate Construction of Consensus Genetic Maps via Integer Linear Programming. IEEE ACM Trans. Comput. Biol. Bioinform. Yonghui Wu, Timothy J. Close, Stefano Lonardi
2011	J	`jnl`	Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space CoRR 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
2011	A*	`conf`	Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. ICDM Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh
2011	Misc	`conf`	String Matching in Hardware Using the FM-Index. FCCM Edward Fernandez, Walid A. Najjar, Stefano Lonardi
2011	A*	`conf`	Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data. ICDM Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi, Scott Evans
2011	—	`conf`	Towards Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. Algorithmic Probability and Friends Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh
2010	J	`jnl`	BRAT: bisulfite-treated reads analysis tool. Bioinform. Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi
2010	J	`jnl`	BRAT: bisulfite-treated reads analysis tool. Bioinform. Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi
2010	J	`jnl`	Data Mining in Bioinformatics: Selected Papers from BIOKDD. IEEE ACM Trans. Comput. Biol. Bioinform. Stefano Lonardi, Jake Yue Chen
2010	J	`jnl`	Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion. J. Comput. Biol. Lan Liu, Yonghui Wu, Stefano Lonardi, Tao Jiang
2010	B	`conf`	Exploration of Short Reads Genome Mapping in Hardware. FPL Edward Fernandez, Walid A. Najjar, Elena Yavorska Harris, Stefano Lonardi
2010	J	`jnl`	Graphlet Kernels for Prediction of Functional Residues in Protein Structures. J. Comput. Biol. Vladimir Vacic, Lilia M. Iakoucheva, Stefano Lonardi, Predrag Radivojac
2010	C	`ed.`	String Processing and Information Retrieval - 17th International Symposium, SPIRE 2010, Los Cabos, Mexico, October 11-13, 2010. Proceedings SPIRE Edgar Chávez, Stefano Lonardi
2009	J	`jnl`	A compartmentalized approach to the assembly of physical maps. BMC Bioinform. Serdar Bozdag, Timothy J. Close, Stefano Lonardi
2009	B	`conf`	CPM's 20th Anniversary: A Statistical Retrospective. CPM Elena Yavorska Harris, Thierry Lecroq, Gregory Kucherov, Stefano Lonardi
2008	J	`jnl`	A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks. J. Bioinform. Comput. Biol. Yonghui Wu, Stefano Lonardi
2008	Misc	`conf`	A Probabilistic Model for Small RNA Flowgram Matching. Pacific Symposium on Biocomputing Vladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi
2008	J	`jnl`	BIOKDD 2008: a workshop report on data mining in bioinformatics. SIGKDD Explor. Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi
2008	C	`conf`	Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. WABI Serdar Bozdag, Timothy J. Close, Stefano Lonardi
2008	J	`jnl`	Deconvoluting BAC-Gene Relationships Using a Physical Map. J. Bioinform. Comput. Biol. Yonghui Wu, Lan Liu, Timothy J. Close, Stefano Lonardi
2008	J	`jnl`	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. Raffaele Giancarlo, Stefano Lonardi
2007	C	`conf`	A Compartmentalized Approach to the Assembly of Physical Maps. BIBE Serdar Bozdag, Timothy J. Close, Stefano Lonardi
2007	J	`jnl`	A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks. Int. J. Data Min. Bioinform. Qiaofeng Yang, Stefano Lonardi
2007	A	`conf`	Clock-frequency assignment for multiple clock domain systems-on-a-chip. DATE Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid
2007	J	`jnl`	Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinform. Vladimir Vacic, Vladimir N. Uversky, A. Keith Dunker, Stefano Lonardi
2007	J	`jnl`	Compression-based data mining of sequential data. Data Min. Knowl. Discov. Eamonn J. Keogh, Stefano Lonardi, Chotirat Ann Ratanamahatana, Li Wei, Sang-Hee Lee, John C. Handley
2007	C	`conf`	Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. WABI Yonghui Wu, Prasanna Bhat, Timothy J. Close, Stefano Lonardi
2007	J	`jnl`	Error Resilient LZ'77 Data Compression: Algorithms, Analysis, and Experiments. IEEE Trans. Inf. Theory Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward
2007	J	`jnl`	Experiencing SAX: a novel symbolic representation of time series. Data Min. Knowl. Discov. Jessica Lin, Eamonn J. Keogh, Li Wei, Stefano Lonardi
2007	A	`conf`	Interactive presentation: Soft-core processor customization using the design of experiments paradigm. DATE David Sheldon, Frank Vahid, Stefano Lonardi
2007	A	`conf`	Two-level microprocessor-accelerator partitioning. DATE Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid
2006	J	`jnl`	A Bit Level Representation for Time Series Data Mining with Shape Based Similarity. Data Min. Knowl. Discov. Anthony J. Bagnall, Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Stefano Lonardi, Gareth J. Janacek
2006	C	`conf`	A Compression-Boosting Transform for Two-Dimensional Data. AAIM Qiaofeng Yang, Stefano Lonardi, Avraham A. Melkman
2006	J	`jnl`	Efficient Discovery of Unusual Patterns in Time Series. New Gener. Comput. Stefano Lonardi, Jessica Lin, Eamonn J. Keogh, Bill Yuan-chi Chiu
2006	J	`jnl`	Efficient information compression in sensor networks. Int. J. Sens. Networks Song Lin, Vana Kalogeraki, Dimitrios Gunopulos, Stefano Lonardi
2006	B	`conf`	Error-Resilient LZW Data Compression. DCC Yonghui Wu, Stefano Lonardi, Wojciech Szpankowski
2006	J	`jnl`	Finding biclusters by random projections. Theor. Comput. Sci. Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang
2006	A*	`conf`	Intelligent Icons: Integrating Lite-Weight Data Mining and Visualization into GUI Operating Systems. ICDM Eamonn J. Keogh, Li Wei, Xiaopeng Xi, Stefano Lonardi, Jin Shieh, Scott Sirowy
2006	J	`jnl`	OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BMC Bioinform. Jie Zheng, Jan T. Svensson, Kavitha Madishetty, Timothy J. Close, Tao Jiang, Stefano Lonardi
2006	—	`conf`	Online Information Compression in Sensor Networks. ICC Song Lin, Vana Kalogeraki, Dimitrios Gunopulos, Stefano Lonardi
2005	B	`conf`	A Compression-Boosting Transform for 2D Data. DCC Qiaofeng Yang, Stefano Lonardi
2005	C	`conf`	A Data Compression Technique for Sensor Networks with Dynamic Bandwidth Allocation. TIME Song Lin, Dimitrios Gunopulos, Vana Kalogeraki, Stefano Lonardi
2005	B	`conf`	A Novel Bit Level Time Series Representation with Implication of Similarity Search and Clustering. PAKDD Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Anthony J. Bagnall, Stefano Lonardi
2005	—	`conf`	A Parallel Algorithm for Clustering Protein-Protein Interaction Networks. CSB Workshops Qiaofeng Yang, Stefano Lonardi
2005	B	`conf`	A Practical Tool for Visualizing and Data Mining Medical Time Series. CBMS Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana, Helga Van Herle
2005	B	`conf`	Applying LVQ Techniques to Compress Historical Information in Sensor Networks. DCC Song Lin, Dimitrios Gunopulos, Stefano Lonardi, Vana Kalogeraki
2005	J	`jnl`	Assignment of Orthologous Genes via Genome Rearrangement. IEEE ACM Trans. Comput. Biol. Bioinform. Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
2005	B	`conf`	Assumption-Free Anomaly Detection in Time Series. SSDBM Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana
2005	B	`conf`	Computing the Assignment of Orthologous Genes via Genome Rearrangement. APBC Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
2005	C	`conf`	Discovery of Repetitive Patterns in DNA with Accurate Boundaries. BIBE Jie Zheng, Stefano Lonardi
2005	B	`conf`	Dot Plots for Time Series Analysis. ICTAI Dragomir Yankov, Eamonn J. Keogh, Stefano Lonardi, Ada Wai-Chee Fu
2005	J	`jnl`	Integrating Lite-Weight but Ubiquitous Data Mining into GUI Operating Systems. J. Univers. Comput. Sci. Li Wei, Eamonn J. Keogh, Xiaopeng Xi, Stefano Lonardi
2005	A	`conf`	Time-series Bitmaps: a Practical Visualization Tool for Working with Large Time Series Databases. SDM Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana
2005	J	`jnl`	Visualizing and discovering non-trivial patterns in large time series databases. Inf. Vis. Jessica Lin, Eamonn J. Keogh, Stefano Lonardi
2004	J	`jnl`	Augmenting LZ-77 with authentication and integrity assurance capabilities. Concurr. Pract. Exp. Mikhail J. Atallah, Stefano Lonardi
2004	—	`ch.`	Computational Biology. Handbook of Data Structures and Applications Stefan Kurtz, Stefano Lonardi
2004	J	`jnl`	Efficient selection of unique and popular oligos for large EST databases. Bioinform. Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
2004	B	`conf`	Error resilient LZ'77 scheme and its analysis. ISIT Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward
2004	B	`conf`	Finding Biclusters by Random Projections. CPM Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang
2004	—	`conf`	Gridding and Compression of Microarray Images. CSB Stefano Lonardi, Yu Luo
2004	J	`jnl`	On average sequence complexity. Theor. Comput. Sci. Svante Janson, Stefano Lonardi, Wojciech Szpankowski
2004	B	`conf`	On the Average Sequence Complexity. CPM Svante Janson, Stefano Lonardi, Wojciech Szpankowski
2004	B	`conf`	On the Average Sequence Complexity. Data Compression Conference Svante Janson, Stefano Lonardi, Wojciech Szpankowski
2004	A*	`conf`	Towards parameter-free data mining. KDD Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana
2004	J	`jnl`	Verbumculus and the Discovery of Unusual Words. J. Comput. Sci. Technol. Alberto Apostolico, Fang-Cheng Gong, Stefano Lonardi
2004	A*	`conf`	Visually mining and monitoring massive time series. KDD Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom
2004	A*	`conf`	VizTree: a Tool for Visually Mining and Monitoring Massive Time Series Databases. VLDB Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom
2004	—	`conf`	We Have Seen the Future, and It Is Symbolic. ACSW Eamonn J. Keogh, Jessica Lin, Stefano Lonardi, Bill Yuan-chi Chiu
2003	—	`conf`	A symbolic representation of time series, with implications for streaming algorithms. DMKD Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Bill Yuan-chi Chiu
2003	Misc	`conf`	Authentication of LZ-77 Compressed Data. SAC Mikhail J. Atallah, Stefano Lonardi
2003	B	`conf`	Efficient Selection of Unique and Popular Oligos for Large EST Databases. CPM Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
2003	B	`conf`	Joint Source-Channel LZ'77 Coding. DCC Stefano Lonardi, Wojciech Szpankowski
2003	J	`jnl`	Monotony of Surprise and Large-Scale Quest for Unusual Words. J. Comput. Biol. Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi
2003	A*	`conf`	Probabilistic discovery of time series motifs. KDD Bill Yuan-chi Chiu, Eamonn J. Keogh, Stefano Lonardi
2002	J	`jnl`	A speed-up for the commute between subword trees and DAWGs. Inf. Process. Lett. Alberto Apostolico, Stefano Lonardi
2002	—	`conf`	Analysis of Secondary Structure Elements of Proteins Using Indexing Techniques. 3DPVT Concettina Guerra, Stefano Lonardi, Giuseppe Zanotti
2002	A*	`conf`	Finding surprising patterns in a time series database in linear time and space. KDD Eamonn J. Keogh, Stefano Lonardi, Bill Yuan-chi Chiu
2002	A*	`conf`	Mining Motifs in Massive Time Series Databases. ICDM Pranav Patel, Eamonn J. Keogh, Jessica Lin, Stefano Lonardi
2002	B	`conf`	Monotony of surprise and large-scale quest for unusual words. RECOMB Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi
2000	B	`conf`	Compression of Biological Sequences by Greedy Off-Line Textual Substitution. Data Compression Conference Alberto Apostolico, Stefano Lonardi
2000	J	`jnl`	Efficient Detection of Unusual Words. J. Comput. Biol. Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi, Xuyan Xu
2000	J	`jnl`	Off-line compression by greedy textual substitution. Proc. IEEE Alberto Apostolico, Stefano Lonardi
1999	J	`jnl`	Fractal image approximation and orthogonal bases. Signal Process. Image Commun. Stefano Lonardi, Paolo Sommaruga
1999	B	`conf`	Linear Global Detectors of Redundant and Rare Substrings. Data Compression Conference Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi
1998	B	`conf`	Some Theory and Practice of Greedy Off-Line Textual Substitution. Data Compression Conference Alberto Apostolico, Stefano Lonardi