| 2019 | RECOMB | OMGS: Optical Map-Based Genome Scaffolding. | Weihua Pan, Tao Jiang, Stefano Lonardi |
| 2018 | RECOMB | mClass: Cancer Type Classification with Somatic Point Mutation Data. | Md. Abid Hasan, Stefano Lonardi |
| 2017 | WABI | Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps. | Abbas Roayaei Ardakany, Stefano Lonardi |
| 2017 | WABI | ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks. | Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik, Karine G. Le Roch, Stefano Lonardi |
| 2015 | WABI | Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. | Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi |
| 2015 | WABI | Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers. | Rachid Ounit, Stefano Lonardi |
| 2013 | WABI | 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 |
| 2011 | FCCM | String Matching in Hardware Using the FM-Index. | Edward Fernandez, Walid A. Najjar, Stefano Lonardi |
| 2011 | ICDM | Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. | Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh |
| 2011 | ICDM | Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data. | Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi, Scott Evans |
| 2010 | FPL | Exploration of Short Reads Genome Mapping in Hardware. | Edward Fernandez, Walid A. Najjar, Elena Yavorska Harris, Stefano Lonardi |
| 2009 | CPM | CPM's 20th Anniversary: A Statistical Retrospective. | Elena Yavorska Harris, Thierry Lecroq, Gregory Kucherov, Stefano Lonardi |
| 2008 | PSB | A Probabilistic Model for Small RNA Flowgram Matching. | Vladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi |
| 2008 | WABI | Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. | Serdar Bozdag, Timothy J. Close, Stefano Lonardi |
| 2007 | BIBE | A Compartmentalized Approach to the Assembly of Physical Maps. | Serdar Bozdag, Timothy J. Close, Stefano Lonardi |
| 2007 | DATE | Interactive presentation: Soft-core processor customization using the design of experiments paradigm. | David Sheldon, Frank Vahid, Stefano Lonardi |
| 2007 | DATE | Two-level microprocessor-accelerator partitioning. | Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid |
| 2007 | DATE | Clock-frequency assignment for multiple clock domain systems-on-a-chip. | Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid |
| 2007 | WABI | Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. | Yonghui Wu, Prasanna Bhat, Timothy J. Close, Stefano Lonardi |
| 2006 | AAIM | A Compression-Boosting Transform for Two-Dimensional Data. | Qiaofeng Yang, Stefano Lonardi, Avraham A. Melkman |
| 2006 | DCC | Error-Resilient LZW Data Compression. | Yonghui Wu, Stefano Lonardi, Wojciech Szpankowski |
| 2006 | ICDM | 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 |
| 2005 | APBC | Computing the Assignment of Orthologous Genes via Genome Rearrangement. | Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang |
| 2005 | BIBE | Discovery of Repetitive Patterns in DNA with Accurate Boundaries. | Jie Zheng, Stefano Lonardi |
| 2005 | CBMS | 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 |
| 2005 | DCC | Applying LVQ Techniques to Compress Historical Information in Sensor Networks. | Song Lin, Dimitrios Gunopulos, Stefano Lonardi, Vana Kalogeraki |
| 2005 | DCC | A Compression-Boosting Transform for 2D Data. | Qiaofeng Yang, Stefano Lonardi |
| 2005 | ICTAI | Dot Plots for Time Series Analysis. | Dragomir Yankov, Eamonn J. Keogh, Stefano Lonardi, Ada Wai-Chee Fu |
| 2005 | PAKDD | 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 |
| 2005 | SDM | 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 |
| 2005 | SSDBM | Assumption-Free Anomaly Detection in Time Series. | Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana |
| 2005 | TIME | A Data Compression Technique for Sensor Networks with Dynamic Bandwidth Allocation. | Song Lin, Dimitrios Gunopulos, Vana Kalogeraki, Stefano Lonardi |
| 2004 | CPM | On the Average Sequence Complexity. | Svante Janson, Stefano Lonardi, Wojciech Szpankowski |
| 2004 | CPM | Finding Biclusters by Random Projections. | Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang |
| 2004 | DCC | On the Average Sequence Complexity. | Svante Janson, Stefano Lonardi, Wojciech Szpankowski |
| 2004 | ISIT | Error resilient LZ'77 scheme and its analysis. | Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward |
| 2004 | KDD | Towards parameter-free data mining. | Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana |
| 2004 | KDD | Visually mining and monitoring massive time series. | Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom |
| 2004 | VLDB | 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 |
| 2003 | CPM | Efficient Selection of Unique and Popular Oligos for Large EST Databases. | Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi |
| 2003 | DCC | Joint Source-Channel LZ'77 Coding. | Stefano Lonardi, Wojciech Szpankowski |
| 2003 | KDD | Probabilistic discovery of time series motifs. | Bill Yuan-chi Chiu, Eamonn J. Keogh, Stefano Lonardi |
| 2003 | SAC | Authentication of LZ-77 Compressed Data. | Mikhail J. Atallah, Stefano Lonardi |
| 2002 | ICDM | Mining Motifs in Massive Time Series Databases. | Pranav Patel, Eamonn J. Keogh, Jessica Lin, Stefano Lonardi |
| 2002 | KDD | Finding surprising patterns in a time series database in linear time and space. | Eamonn J. Keogh, Stefano Lonardi, Bill Yuan-chi Chiu |
| 2002 | RECOMB | Monotony of surprise and large-scale quest for unusual words. | Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi |
| 2000 | DCC | Compression of Biological Sequences by Greedy Off-Line Textual Substitution. | Alberto Apostolico, Stefano Lonardi |
| 1999 | DCC | Linear Global Detectors of Redundant and Rare Substrings. | Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi |
| 1998 | DCC | Some Theory and Practice of Greedy Off-Line Textual Substitution. | Alberto Apostolico, Stefano Lonardi |