Stefano Lonardi

ORCID

Publication Activity (10 Years)

Years Active: 1998-2023
Publications (10 Years): 15

Top Venues

Publications

Sakshar Chakravarty, Glennis Logsdon, Stefano Lonardi
RAmbler: de novo genome assembly of complex repetitive regions. BCB (2023)
Dipankar Ranjan Baisya, Stefano Lonardi
Prediction of histone post-translational modifications using deep learning. Bioinform. 36 (24) (2021)
Qihua Liang, Stefano Lonardi
Reference-agnostic representation and visualization of pan-genomes. BMC Bioinform. 22 (1) (2021)
Weihua Pan, Tao Jiang, Stefano Lonardi
OMGS: Optical Map-Based Genome Scaffolding. J. Comput. Biol. 27 (4) (2020)
Md. Abid Hasan, Stefano Lonardi
DeeplyEssential: a deep neural network for predicting essential genes in microbes. BMC Bioinform. (14) (2020)
Weihua Pan, Stefano Lonardi
Accurate detection of chimeric contigs via Bionano optical maps. Bioinform. 35 (10) (2019)
Weihua Pan, Tao Jiang, Stefano Lonardi
OMGS: Optical Map-Based Genome Scaffolding. RECOMB (2019)
Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi
Selfish: discovery of differential chromatin interactions via a self-similarity measure. Bioinform. 35 (14) (2019)
Md. Abid Hasan, Stefano Lonardi
mClass: Cancer Type Classification with Somatic Point Mutation Data. RECOMB-CG (2018)
Weihua Pan, Steve Wanamaker, Audrey M. V. Ah-Fong, Howard S. Judelson, Stefano Lonardi
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps. Bioinform. 34 (13) (2018)
Abbas Roayaei Ardakany, Stefano Lonardi
Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps. WABI (2017)
Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik, Karine G. Le Roch, Stefano Lonardi
ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks. WABI (2017)
Rachid Ounit, Stefano Lonardi
. Bioinform. 32 (24) (2016)
Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison. PLoS Comput. Biol. 12 (10) (2016)
Elena Yavorska Harris, Rachid Ounit, Stefano Lonardi
BRAT-nova: fast and accurate mapping of bisulfite-treated reads. Bioinform. 32 (17) (2016)
Rachid Ounit, Stefano Lonardi
Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers. WABI (2015)
Stefano Lonardi, Seyed Hamid Mirebrahim, Steve Wanamaker, Matthew Alpert, Gianfranco Ciardo, Denisa Duma, Timothy J. Close
assembly quality. Bioinform. 31 (18) (2015)
Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi
meta-assembly of ultra-deep sequencing data. Bioinform. 31 (12) (2015)
Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh
Using the minimum description length to discover the intrinsic cardinality and dimensionality of time series. Data Min. Knowl. Discov. 29 (2) (2015)
Edward B. Fernandez, Jason R. Villarreal, Stefano Lonardi, Walid A. Najjar
FHAST: FPGA-Based Acceleration of Bowtie in Hardware. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (5) (2015)
Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi
Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. WABI (2015)
Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi
De novo assembly of ultra-deep sequencing data. BCB (2014)
Anton Polishko, Evelien M. Bunnik, Karine G. Le Roch, Stefano Lonardi
PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. BMC Bioinform. 15 (S-9) (2014)
Rachid Ounit, Timothy J. Close, Steve Wanamaker, Stefano Lonardi
CLARK, accurate and efficient classification of DNA sequences. BCB (2014)
Haifen Chen, Stefano Lonardi, Jie Zheng
Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. Comput. Biol. Chem. 50 (2014)
Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert, Timothy J. Close, Gianfranco Ciardo, Stefano Lonardi
Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing. WABI (2013)
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
Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLoS Comput. Biol. 9 (4) (2013)
Serdar Bozdag, Timothy J. Close, Stefano Lonardi
A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (2) (2013)
Elena Yavorska Harris, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi
BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinform. 28 (13) (2012)
Edward Fernandez, Walid A. Najjar, Stefano Lonardi, Jason R. Villarreal
Multithreaded FPGA acceleration of DNA sequence mapping. HPEC (2012)
Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi, Scott Evans
MDL-based time series clustering. Knowl. Inf. Syst. 33 (2) (2012)
Anton Polishko, Nadia Ponts, Karine G. Le Roch, Stefano Lonardi
NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model. Bioinform. 28 (12) (2012)
Thanawin Rakthanmanon, Eamonn J. Keogh, Stefano Lonardi, Scott Evans
Time Series Epenthesis: Clustering Time Series Streams Requires Ignoring Some Data. ICDM (2011)
Edward Fernandez, Walid A. Najjar, Stefano Lonardi
String Matching in Hardware Using the FM-Index. FCCM (2011)
Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh
Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. ICDM (2011)
Bing Hu, Thanawin Rakthanmanon, Yuan Hao, Scott Evans, Stefano Lonardi, Eamonn J. Keogh
Towards Discovering the Intrinsic Cardinality and Dimensionality of Time Series Using MDL. Algorithmic Probability and Friends (2011)
Yonghui Wu, Timothy J. Close, Stefano Lonardi
Accurate Construction of Consensus Genetic Maps via Integer Linear Programming. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (2) (2011)
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
Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space CoRR (2011)
Stefano Lonardi, Jake Yue Chen
Data Mining in Bioinformatics: Selected Papers from BIOKDD. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (2) (2010)
Vladimir Vacic, Lilia M. Iakoucheva, Stefano Lonardi, Predrag Radivojac
Graphlet Kernels for Prediction of Functional Residues in Protein Structures. J. Comput. Biol. 17 (1) (2010)
Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi
BRAT: bisulfite-treated reads analysis tool. Bioinform. 26 (19) (2010)
Elena Yavorska Harris, Nadia Ponts, Aleksandr Levchuk, Karine G. Le Roch, Stefano Lonardi
BRAT: bisulfite-treated reads analysis tool. Bioinform. 26 (4) (2010)
Lan Liu, Yonghui Wu, Stefano Lonardi, Tao Jiang
Efficient Genome-Wide TagSNP Selection Across Populations via the Linkage Disequilibrium Criterion. J. Comput. Biol. 17 (1) (2010)
Edward Fernandez, Walid A. Najjar, Elena Yavorska Harris, Stefano Lonardi
Exploration of Short Reads Genome Mapping in Hardware. FPL (2010)
Elena Yavorska Harris, Thierry Lecroq, Gregory Kucherov, Stefano Lonardi
CPM's 20th Anniversary: A Statistical Retrospective. CPM (2009)
Serdar Bozdag, Timothy J. Close, Stefano Lonardi
A compartmentalized approach to the assembly of physical maps. BMC Bioinform. 10 (2009)
Yonghui Wu, Lan Liu, Timothy J. Close, Stefano Lonardi
Deconvoluting BAC-Gene Relationships Using a Physical Map. J. Bioinform. Comput. Biol. 6 (3) (2008)
Vladimir Vacic, Hailing Jin, Jian-Kang Zhu, Stefano Lonardi
A Probabilistic Model for Small RNA Flowgram Matching. Pacific Symposium on Biocomputing (2008)
Yonghui Wu, Stefano Lonardi
A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks. J. Bioinform. Comput. Biol. 6 (6) (2008)
Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi
BIOKDD 2008: a workshop report on data mining in bioinformatics. SIGKDD Explor. 10 (2) (2008)
Serdar Bozdag, Timothy J. Close, Stefano Lonardi
Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. WABI (2008)
Raffaele Giancarlo, Stefano Lonardi
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. 395 (2-3) (2008)
Eamonn J. Keogh, Stefano Lonardi, Chotirat Ann Ratanamahatana, Li Wei, Sang-Hee Lee, John Handley
Compression-based data mining of sequential data. Data Min. Knowl. Discov. 14 (1) (2007)
Qiaofeng Yang, Stefano Lonardi
A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks. Int. J. Data Min. Bioinform. 1 (3) (2007)
Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward
Error Resilient LZ'77 Data Compression: Algorithms, Analysis, and Experiments. IEEE Trans. Inf. Theory 53 (5) (2007)
Vladimir Vacic, Vladimir N. Uversky, A. Keith Dunker, Stefano Lonardi
Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinform. 8 (2007)
Yonghui Wu, Prasanna Bhat, Timothy J. Close, Stefano Lonardi
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. WABI (2007)
Serdar Bozdag, Timothy J. Close, Stefano Lonardi
A Compartmentalized Approach to the Assembly of Physical Maps. BIBE (2007)
David Sheldon, Frank Vahid, Stefano Lonardi
Interactive presentation: Soft-core processor customization using the design of experiments paradigm. DATE (2007)
Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid
Two-level microprocessor-accelerator partitioning. DATE (2007)
Jessica Lin, Eamonn J. Keogh, Li Wei, Stefano Lonardi
Experiencing SAX: a novel symbolic representation of time series. Data Min. Knowl. Discov. 15 (2) (2007)
Scott Sirowy, Yonghui Wu, Stefano Lonardi, Frank Vahid
Clock-frequency assignment for multiple clock domain systems-on-a-chip. DATE (2007)
Yonghui Wu, Stefano Lonardi, Wojciech Szpankowski
Error-Resilient LZW Data Compression. DCC (2006)
Anthony J. Bagnall, Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Stefano Lonardi, Gareth J. Janacek
A Bit Level Representation for Time Series Data Mining with Shape Based Similarity. Data Min. Knowl. Discov. 13 (1) (2006)
Stefano Lonardi, Jessica Lin, Eamonn J. Keogh, Bill Yuan-chi Chiu
Efficient Discovery of Unusual Patterns in Time Series. New Gener. Comput. 25 (1) (2006)
Eamonn J. Keogh, Li Wei, Xiaopeng Xi, Stefano Lonardi, Jin Shieh, Scott Sirowy
Intelligent Icons: Integrating Lite-Weight Data Mining and Visualization into GUI Operating Systems. ICDM (2006)
Song Lin, Vana Kalogeraki, Dimitrios Gunopulos, Stefano Lonardi
Efficient information compression in sensor networks. Int. J. Sens. Networks 1 (3/4) (2006)
Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang
Finding biclusters by random projections. Theor. Comput. Sci. 368 (3) (2006)
Qiaofeng Yang, Stefano Lonardi, Avraham A. Melkman
A Compression-Boosting Transform for Two-Dimensional Data. AAIM (2006)
Song Lin, Vana Kalogeraki, Dimitrios Gunopulos, Stefano Lonardi
Online Information Compression in Sensor Networks. ICC (2006)
Jie Zheng, Jan T. Svensson, Kavitha Madishetty, Timothy J. Close, Tao Jiang, Stefano Lonardi
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BMC Bioinform. 7 (2006)
Qiaofeng Yang, Stefano Lonardi
A Parallel Algorithm for Clustering Protein-Protein Interaction Networks. CSB Workshops (2005)
Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana, Helga Van Herle
A Practical Tool for Visualizing and Data Mining Medical Time Series. CBMS (2005)
Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
Computing the Assignment of Orthologous Genes via Genome Rearrangement. APBC (2005)
Jie Zheng, Stefano Lonardi
Discovery of Repetitive Patterns in DNA with Accurate Boundaries. BIBE (2005)
Chotirat (Ann) Ratanamahatana, Eamonn J. Keogh, Anthony J. Bagnall, Stefano Lonardi
A Novel Bit Level Time Series Representation with Implication of Similarity Search and Clustering. PAKDD (2005)
Qiaofeng Yang, Stefano Lonardi
A Compression-Boosting Transform for 2D Data. DCC (2005)
Li Wei, Eamonn J. Keogh, Xiaopeng Xi, Stefano Lonardi
Integrating Lite-Weight but Ubiquitous Data Mining into GUI Operating Systems. J. Univers. Comput. Sci. 11 (11) (2005)
Dragomir Yankov, Eamonn J. Keogh, Stefano Lonardi, Ada Wai-Chee Fu
Dot Plots for Time Series Analysis. ICTAI (2005)
Li Wei, Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana
Assumption-Free Anomaly Detection in Time Series. SSDBM (2005)
Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang
Assignment of Orthologous Genes via Genome Rearrangement. IEEE ACM Trans. Comput. Biol. Bioinform. 2 (4) (2005)
Song Lin, Dimitrios Gunopulos, Vana Kalogeraki, Stefano Lonardi
A Data Compression Technique for Sensor Networks with Dynamic Bandwidth Allocation. TIME (2005)
Song Lin, Dimitrios Gunopulos, Stefano Lonardi, Vana Kalogeraki
Applying LVQ Techniques to Compress Historical Information in Sensor Networks. DCC (2005)
Nitin Kumar, Venkata Nishanth Lolla, Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana
Time-series Bitmaps: a Practical Visualization Tool for Working with Large Time Series Databases. SDM (2005)
Jessica Lin, Eamonn J. Keogh, Stefano Lonardi
Visualizing and discovering non-trivial patterns in large time series databases. Inf. Vis. 4 (2) (2005)
Mikhail J. Atallah, Stefano Lonardi
Augmenting LZ-77 with authentication and integrity assurance capabilities. Concurr. Pract. Exp. 16 (11) (2004)
Stefano Lonardi, Yu Luo
Gridding and Compression of Microarray Images. CSB (2004)
Svante Janson, Stefano Lonardi, Wojciech Szpankowski
On the Average Sequence Complexity. CPM (2004)
Stefano Lonardi, Wojciech Szpankowski, Qiaofeng Yang
Finding Biclusters by Random Projections. CPM (2004)
Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom
Visually mining and monitoring massive time series. KDD (2004)
Stefano Lonardi, Wojciech Szpankowski, Mark Daniel Ward
Error resilient LZ'77 scheme and its analysis. ISIT (2004)
Svante Janson, Stefano Lonardi, Wojciech Szpankowski
On the Average Sequence Complexity. Data Compression Conference (2004)
Svante Janson, Stefano Lonardi, Wojciech Szpankowski
On average sequence complexity. Theor. Comput. Sci. 326 (1-3) (2004)
Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
Efficient selection of unique and popular oligos for large EST databases. Bioinform. 20 (13) (2004)
Alberto Apostolico, Fang-Cheng Gong, Stefano Lonardi
Verbumculus and the Discovery of Unusual Words. J. Comput. Sci. Technol. 19 (1) (2004)
Eamonn J. Keogh, Stefano Lonardi, Chotirat (Ann) Ratanamahatana
Towards parameter-free data mining. KDD (2004)
Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Jeffrey P. Lankford, Donna M. Nystrom
VizTree: a Tool for Visually Mining and Monitoring Massive Time Series Databases. VLDB (2004)
Eamonn J. Keogh, Jessica Lin, Stefano Lonardi, Bill Yuan-chi Chiu
We Have Seen the Future, and It Is Symbolic. ACSW (2004)
Jie Zheng, Timothy J. Close, Tao Jiang, Stefano Lonardi
Efficient Selection of Unique and Popular Oligos for Large EST Databases. CPM (2003)
Jessica Lin, Eamonn J. Keogh, Stefano Lonardi, Bill Yuan-chi Chiu
A symbolic representation of time series, with implications for streaming algorithms. DMKD (2003)

Stefano Lonardi.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Stefano Lonardi