Stefano Lonardi, Ph.D. - Publications

Affiliations: 
2001 Purdue University, West Lafayette, IN, United States 
Area:
Computer Science, Genetics

77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Lu XM, Bunnik EM, Pokhriyal N, Nasseri S, Lonardi S, Le Roch KG. Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum. Bmc Genomics. 16: 1005. PMID 26607328 DOI: 10.1186/s12864-015-2214-9  0.44
2015 Fernandez EB, Villarreal J, Lonardi S, Najjar WA. FHAST: FPGA-Based Acceleration of Bowtie in Hardware. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 973-81. PMID 26451812 DOI: 10.1109/TCBB.2015.2405333  0.44
2015 Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, et al. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal : For Cell and Molecular Biology. PMID 26252423 DOI: 10.1111/tpj.12959  0.44
2015 Mirebrahim H, Close TJ, Lonardi S. De novo meta-assembly of ultra-deep sequencing data. Bioinformatics (Oxford, England). 31: i9-16. PMID 26072514 DOI: 10.1093/bioinformatics/btv226  0.44
2015 Lonardi S, Mirebrahim H, Wanamaker S, Alpert M, Ciardo G, Duma D, Close TJ. When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. Bioinformatics (Oxford, England). 31: 2972-80. PMID 25995232 DOI: 10.1093/bioinformatics/btv311  0.44
2015 Ounit R, Wanamaker S, Close TJ, Lonardi S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. Bmc Genomics. 16: 236. PMID 25879410 DOI: 10.1186/s12864-015-1419-2  0.44
2015 Ounit R, Lonardi S. Higher classification accuracy of short metagenomic reads by discriminative spaced k-mers Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9289: 286-295. DOI: 10.1007/978-3-662-48221-6_21  0.44
2015 Duma D, Cordero F, Beccuti M, Ciardo G, Close TJ, Lonardi S. Scrible: Ultra-accurate error-correction of pooled sequenced reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9289: 162-174. DOI: 10.1007/978-3-662-48221-6_12  0.44
2014 Dhall S, Do DC, Garcia M, Kim J, Mirebrahim SH, Lyubovitsky J, Lonardi S, Nothnagel EA, Schiller N, Martins-Green M. Generating and reversing chronic wounds in diabetic mice by manipulating wound redox parameters. Journal of Diabetes Research. 2014: 562625. PMID 25587545 DOI: 10.1155/2014/562625  0.44
2014 Polishko A, Bunnik EM, Le Roch KG, Lonardi S. PuFFIN--a parameter-free method to build nucleosome maps from paired-end reads. Bmc Bioinformatics. 15: S11. PMID 25252810 DOI: 10.1186/1471-2105-15-S9-S11  0.44
2014 Bunnik EM, Polishko A, Prudhomme J, Ponts N, Gill SS, Lonardi S, Le Roch KG. DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum. Bmc Genomics. 15: 347. PMID 24885191 DOI: 10.1186/1471-2164-15-347  0.44
2014 Pottorff M, Roberts PA, Close TJ, Lonardi S, Wanamaker S, Ehlers JD. Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp]. Bmc Genomics. 15: 328. PMID 24885083 DOI: 10.1186/1471-2164-15-328  0.44
2014 Chen H, Lonardi S, Zheng J. Deciphering histone code of transcriptional regulation in malaria parasites by large-scale data mining. Computational Biology and Chemistry. 50: 3-10. PMID 24581698 DOI: 10.1016/j.compbiolchem.2014.01.002  0.44
2014 Ounit R, Close T, Wanamaker S, Lonardi S. CLARK, accurate and efficient classification of DNA sequences Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 602. DOI: 10.1145/2649387.2662449  0.44
2014 Hu B, Rakthanmanon T, Hao Y, Evans S, Lonardi S, Keogh E. Using the minimum description length to discover the intrinsic cardinality and dimensionality of time series Data Mining and Knowledge Discovery. 29: 358-399. DOI: 10.1007/s10618-014-0345-2  0.44
2013 Ponts N, Fu L, Harris EY, Zhang J, Chung DW, Cervantes MC, Prudhomme J, Atanasova-Penichon V, Zehraoui E, Bunnik EM, Rodrigues EM, Lonardi S, Hicks GR, Wang Y, Le Roch KG. Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum. Cell Host & Microbe. 14: 696-706. PMID 24331467 DOI: 10.1016/j.chom.2013.11.007  0.44
2013 Bozdag S, Close TJ, Lonardi S. A graph-theoretical approach to the selection of the minimum tiling path from a physical map. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 352-60. PMID 23929859 DOI: 10.1109/TCBB.2013.26  0.44
2013 Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Bhat PR, Wu Y, Ciardo G, Alsaihati B, Ma Y, Wanamaker S, Resnik J, Bozdag S, Luo MC, Close TJ. Combinatorial pooling enables selective sequencing of the barley gene space. Plos Computational Biology. 9: e1003010. PMID 23592960 DOI: 10.1371/journal.pcbi.1003010  0.44
2013 Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, Lonardi S, Zhu JK, Liu R, Jin H. Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Molecular Plant. 6: 704-15. PMID 23505223 DOI: 10.1093/mp/sst051  0.44
2013 Hu B, Rakthanmanon T, Hao Y, Evans S, Lonardi S, Keogh E. Towards discovering the intrinsic cardinality and dimensionality of time series using MDL Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7070: 184-197. DOI: 10.1007/978-3-642-44958-1-14  0.44
2013 Duma D, Wootters M, Gilbert AC, Ngo HQ, Rudra A, Alpert M, Close TJ, Ciardo G, Lonardi S. Accurate decoding of pooled sequenced data using compressed sensing Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8126: 70-84. DOI: 10.1007/978-3-642-40453-5_7  0.44
2012 Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491: 711-6. PMID 23075845 DOI: 10.1038/nature11543  0.44
2012 Polishko A, Ponts N, Le Roch KG, Lonardi S. NORMAL: accurate nucleosome positioning using a modified Gaussian mixture model. Bioinformatics (Oxford, England). 28: i242-9. PMID 22689767 DOI: 10.1093/bioinformatics/bts206  0.44
2012 Harris EY, Ponts N, Le Roch KG, Lonardi S. BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics (Oxford, England). 28: 1795-6. PMID 22563065 DOI: 10.1093/bioinformatics/bts264  0.44
2012 Fernandez EB, Najjar WA, Lonardi S, Villarreal J. Multithreaded FPGA acceleration of DNA sequence mapping 2012 Ieee Conference On High Performance Extreme Computing, Hpec 2012. DOI: 10.1109/HPEC.2012.6408669  0.44
2012 Rakthanmanon T, Keogh EJ, Lonardi S, Evans S. MDL-based time series clustering Knowledge and Information Systems. 33: 371-399. DOI: 10.1007/s10115-012-0508-7  0.44
2011 Harris EY, Ponts N, Le Roch KG, Lonardi S. Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite. Bmc Genomics. 12: 601. PMID 22165844 DOI: 10.1186/1471-2164-12-601  0.44
2011 Ponts N, Harris EY, Lonardi S, Le Roch KG. Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence? Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 716-24. PMID 20708104 DOI: 10.1016/j.meegid.2010.08.002  0.44
2011 Wu Y, Close TJ, Lonardi S. Accurate construction of consensus genetic maps via integer linear programming. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 381-94. PMID 20479505 DOI: 10.1109/TCBB.2010.35  0.44
2011 Hu B, Rakthanmanon T, Hao Y, Evans S, Lonardi S, Keogh E. Discovering the intrinsic cardinality and dimensionality of time series using MDL Proceedings - Ieee International Conference On Data Mining, Icdm. 1086-1091. DOI: 10.1109/ICDM.2011.54  0.44
2011 Rakthanmanon T, Keogh EJ, Lonardi S, Evans S. Time series epenthesis: Clustering time series streams requires ignoring some data Proceedings - Ieee International Conference On Data Mining, Icdm. 547-556. DOI: 10.1109/ICDM.2011.146  0.44
2011 Fernandez E, Najjar W, Lonardi S. String matching in hardware using the FM-Index Proceedings - Ieee International Symposium On Field-Programmable Custom Computing Machines, Fccm 2011. 218-225. DOI: 10.1109/FCCM.2011.55  0.44
2010 Lonardi S, Chen J. Data mining in bioinformatics: selected papers from BIOKDD. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 195-6. PMID 20458778 DOI: 10.1109/TCBB.2010.28  0.44
2010 Vacic V, Iakoucheva LM, Lonardi S, Radivojac P. Graphlet kernels for prediction of functional residues in protein structures. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 55-72. PMID 20078397 DOI: 10.1089/cmb.2009.0029  0.44
2010 Liu L, Wu Y, Lonardi S, Jiang T. Efficient genome-wide TagSNP selection across populations via the linkage disequilibrium criterion. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 21-37. PMID 20078395 DOI: 10.1089/cmb.2007.0228  0.44
2010 Ponts N, Harris EY, Prudhomme J, Wick I, Eckhardt-Ludka C, Hicks GR, Hardiman G, Lonardi S, Le Roch KG. Nucleosome landscape and control of transcription in the human malaria parasite. Genome Research. 20: 228-38. PMID 20054063 DOI: 10.1101/gr.101063.109  0.44
2010 Harris EY, Ponts N, Levchuk A, Roch KL, Lonardi S. BRAT: bisulfite-treated reads analysis tool. Bioinformatics (Oxford, England). 26: 572-3. PMID 20031974 DOI: 10.1093/bioinformatics/btp706  0.44
2010 Fernandez E, Najjar W, Harris E, Lonardi S. Exploration of short reads genome mapping in hardware Proceedings - 2010 International Conference On Field Programmable Logic and Applications, Fpl 2010. 360-363. DOI: 10.1109/FPL.2010.78  0.44
2010 Harris EY, Ponts N, Levchuk A, Le Roch K, Lonardi S. Corrigendum to BRAT: Bisulfite-treated reads analysis tool, [Bioinformatics, (2010) 26(4), 572-573] Bioinformatics. 26: 2499. DOI: 10.1093/bioinformatics/btq494  0.44
2010 Chavez E, Lonardi S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6393. DOI: 10.1007/978-3-642-16321-0  0.44
2009 Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, et al. Development and implementation of high-throughput SNP genotyping in barley. Bmc Genomics. 10: 582. PMID 19961604 DOI: 10.1186/1471-2164-10-582  0.44
2009 Bogunovic D, O'Neill DW, Belitskaya-Levy I, Vacic V, Yu YL, Adams S, Darvishian F, Berman R, Shapiro R, Pavlick AC, Lonardi S, Zavadil J, Osman I, Bhardwaj N. Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival. Proceedings of the National Academy of Sciences of the United States of America. 106: 20429-34. PMID 19915147 DOI: 10.1073/pnas.0905139106  0.44
2009 Bozdag S, Close TJ, Lonardi S. A compartmentalized approach to the assembly of physical maps. Bmc Bioinformatics. 10: 217. PMID 19604400 DOI: 10.1186/1471-2105-10-217  0.44
2009 Harris EY, Lecroq T, Kucherov G, Lonardi S. CPM's 20th anniversary: A statistical retrospective Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5577: 1-11. DOI: 10.1007/978-3-642-02441-2_1  0.44
2008 Wu Y, Close TJ, Lonardi S. On the accurate construction of consensus genetic maps. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7: 285-96. PMID 19642288  0.44
2008 Lonardi S, Chen J. International Workshop on Data Mining in Bioinformatics (BIOKDD) 2007. Introduction. Journal of Bioinformatics and Computational Biology. 6: v-vi. PMID 19248302  0.44
2008 Wu Y, Lonardi S. A linear-time algorithm for predicting functional annotations from PPI networks. Journal of Bioinformatics and Computational Biology. 6: 1049-65. PMID 19090017  0.44
2008 Wu Y, Bhat PR, Close TJ, Lonardi S. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. Plos Genetics. 4: e1000212. PMID 18846212 DOI: 10.1371/journal.pgen.1000212  0.44
2008 Wu Y, Liu L, Close TJ, Lonardi S. Deconvoluting BAC-gene relationships using a physical map. Journal of Bioinformatics and Computational Biology. 6: 603-22. PMID 18574865 DOI: 10.1142/S0219720008003564  0.44
2008 Portney NG, Wu Y, Quezada LK, Lonardi S, Ozkan M. Length-based encoding of binary data in DNA. Langmuir : the Acs Journal of Surfaces and Colloids. 24: 1613-6. PMID 18229963 DOI: 10.1021/la703235y  0.44
2008 Vacic V, Jin H, Zhu JK, Lonardi S. A probabilistic method for small RNA flowgram matching. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 75-86. PMID 18229677  0.44
2008 Jin H, Vacic V, Girke T, Lonardi S, Zhu JK. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. Bmc Molecular Biology. 9: 6. PMID 18194570 DOI: 10.1186/1471-2199-9-6  0.44
2008 Giancarlo R, Lonardi S. 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 Theoretical Computer Science. 395: 135-136. DOI: 10.1016/j.tcs.2008.01.016  0.44
2008 Bozdag S, Close TJ, Lonardi S. Computing the minimal tiling path from a physical map by integer linear programming Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5251: 148-161. DOI: 10.1007/978-3-540-87361-7_13  0.44
2008 Wu Y, Lonardi S. A linear-time algorithm for predicting functionsl annotations from PPI networks Journal of Bioinformatics and Computational Biology. 6: 104-1065.  0.44
2007 Yang Q, Lonardi S. A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks. International Journal of Data Mining and Bioinformatics. 1: 241-7. PMID 18399073 DOI: 10.1504/IJDMB.2007.011611  0.44
2007 Wu Y, Liu L, Close TJ, Lonardi S. Deconvoluting the BAC-gene relationships using a physical map. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 6: 203-14. PMID 17951825  0.44
2007 Liu L, Wu Y, Lonardi S, Jiang T. Efficient algorithms for genome-wide tagSNP selection across populations via the linkage disequilibrium criterion. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 6: 67-78. PMID 17951813  0.44
2007 Vacic V, Uversky VN, Dunker AK, Lonardi S. Composition Profiler: a tool for discovery and visualization of amino acid composition differences. Bmc Bioinformatics. 8: 211. PMID 17578581 DOI: 10.1186/1471-2105-8-211  0.44
2007 Lonardi S, Szpankowski W, Ward MD. Error resilient LZ'77 data compression: Algorithms, analysis, and experiments Ieee Transactions On Information Theory. 53: 1799-1813. DOI: 10.1109/TIT.2007.894689  0.44
2007 Sirowy S, Wu Y, Lonardi S, Vahid F. Clock-frequency assignment for multiple clock domain systems-on-a-chip Proceedings -Design, Automation and Test in Europe, Date. 397-402. DOI: 10.1109/DATE.2007.364624  0.44
2007 Sirowy S, Wu Y, Lonardi S, Vahid F. Two-level microprocessor-accelerator partitioning Proceedings -Design, Automation and Test in Europe, Date. 313-318. DOI: 10.1109/DATE.2007.364610  0.44
2007 Sheldon D, Vahid F, Lonardi S. Soft-core processor customization using the design of experiments paradigm Proceedings -Design, Automation and Test in Europe, Date. 821-826. DOI: 10.1109/DATE.2007.364392  0.44
2007 Lin J, Keogh E, Wei L, Lonardi S. Experiencing SAX: A novel symbolic representation of time series Data Mining and Knowledge Discovery. 15: 107-144. DOI: 10.1007/s10618-007-0064-z  0.44
2007 Keogh E, Lonardi S, Ratanamahatana CA, Wei L, Lee SH, Handley J. Compression-based data mining of sequential data Data Mining and Knowledge Discovery. 14: 99-129. DOI: 10.1007/s10618-006-0049-3  0.44
2007 Lonardi S, Lin J, Keogh E, Chiu B. Efficient discovery of unusual patterns in time series New Generation Computing. 25: 61-93. DOI: 10.1007/s00354-006-0004-2  0.44
2007 Wu Y, Bhat P, Close TJ, Lonardi S. Efficient and accurate construction of genetic linkage maps from noisy and missing genotyping data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4645: 395-406.  0.44
2007 Wu Y, Lonardi S. A linear-time algorithm for predicting functional annotations from protein protein interaction networks Proceedings of the Acm Sigkdd International Conference On Knowledge Discovery and Data Mining. 35-41.  0.44
2007 Yang Q, Lonardi S. A decomposition approach for discovering network building blocks Proceedings of the Acm Sigkdd International Conference On Knowledge Discovery and Data Mining. 50-59.  0.44
2006 Yang Q, Siganos G, Faloutsos M, Lonardi S. Evolution versus "intelligent design": comparing the topology of protein-protein interaction networks to the Internet. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 299-310. PMID 17369648  0.44
2006 Lin S, Kalogeraki V, Gunopulos D, Lonardi S. Efficient information compression in sensor networks International Journal of Sensor Networks. 1: 229-240. DOI: 10.1504/IJSNET.2006.012038  0.44
2006 Keogh E, Wei L, Xi A, Lonardi S, Shieh J, Sirowy S. Intelligent icons: Integrating lite-weight data mining and visualization into GUI operating systems Proceedings - Ieee International Conference On Data Mining, Icdm. 912-916. DOI: 10.1109/ICDM.2006.90  0.44
2006 Song L, Kalogeraki V, Gunopulos D, Lonardi S. Online information compression in sensor networks Ieee International Conference On Communications. 7: 3371-3376. DOI: 10.1109/ICC.2006.255237  0.44
2006 Wu Y, Lonardi S, Szpankowski W. Error-resilient LZW data compression Data Compression Conference Proceedings. 193-202. DOI: 10.1109/DCC.2006.33  0.44
2004 Lonardi S, Szpankowski W, Yang Q. Finding biclusters by random projections Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3109: 102-116. DOI: 10.1016/j.tcs.2006.09.023  0.44
2003 Apostolico A, Bock ME, Lonardi S. Monotony of surprise and large-scale quest for unusual words. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 283-311. PMID 12935329 DOI: 10.1089/10665270360688020  0.44
2000 Apostolico A, Bock ME, Lonardi S, Xu X. Efficient detection of unusual words. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 71-94. PMID 10890389 DOI: 10.1089/10665270050081397  0.44
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