| Year |
Citation |
Score |
| 2019 |
Pan W, Jiang T, Lonardi S. OMGS: Optical Map-Based Genome Scaffolding. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31794680 DOI: 10.1089/Cmb.2019.0310 |
0.312 |
|
| 2019 |
Herniter IA, Lo R, Muñoz-Amatriaín M, Lo S, Guo YN, Huynh BL, Lucas M, Jia Z, Roberts PA, Lonardi S, Close TJ. Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.). Frontiers in Plant Science. 10: 1346. PMID 31708953 DOI: 10.3389/Fpls.2019.01346 |
0.315 |
|
| 2019 |
Ardakany AR, Ay F, Lonardi S. Selfish: discovery of differential chromatin interactions via a self-similarity measure. Bioinformatics (Oxford, England). 35: i145-i153. PMID 31510653 DOI: 10.1093/Bioinformatics/Btz362 |
0.364 |
|
| 2019 |
Schwartz C, Cheng JF, Evans R, Schwartz CA, Wagner JM, Anglin S, Beitz A, Pan W, Lonardi S, Blenner M, Alper HS, Yoshikuni Y, Wheeldon I. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica. Metabolic Engineering. PMID 31216436 DOI: 10.1016/J.Ymben.2019.06.007 |
0.313 |
|
| 2019 |
Lonardi S, Muñoz-Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen J, Schulman AH, Zhu T, Luo MC, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, et al. The genome of cowpea (Vigna unguiculata [L.] Walp.). The Plant Journal : For Cell and Molecular Biology. PMID 31017340 DOI: 10.1111/Tpj.14349 |
0.396 |
|
| 2018 |
Pan W, Lonardi S. Accurate Detection of Chimeric Contigs via Bionano Optical Maps. Bioinformatics (Oxford, England). PMID 30295726 DOI: 10.1093/Bioinformatics/Bty850 |
0.341 |
|
| 2017 |
McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, ... Lonardi S, et al. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biology. 18: 182. PMID 28934964 DOI: 10.1186/S13059-017-1299-7 |
0.37 |
|
| 2017 |
Alhakami H, Mirebrahim H, Lonardi S. A comparative evaluation of genome assembly reconciliation tools. Genome Biology. 18: 93. PMID 28521789 DOI: 10.1186/S13059-017-1213-3 |
0.329 |
|
| 2017 |
Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, ... ... Lonardi S, et al. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Scientific Data. 4: 170044. PMID 28448065 DOI: 10.1038/Sdata.2017.44 |
0.391 |
|
| 2017 |
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, ... ... Lonardi S, et al. A chromosome conformation capture ordered sequence of the barley genome. Nature. 544: 427-433. PMID 28447635 DOI: 10.1038/Nature22043 |
0.376 |
|
| 2016 |
Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, ... ... Lonardi S, et al. Genome resources for climate-resilient cowpea, an essential crop for food security. The Plant Journal : For Cell and Molecular Biology. PMID 27775877 DOI: 10.1111/Tpj.13404 |
0.362 |
|
| 2016 |
Hahn L, Leimeister CA, Ounit R, Lonardi S, Morgenstern B. rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison. Plos Computational Biology. 12: e1005107. PMID 27760124 DOI: 10.1371/Journal.Pcbi.1005107 |
0.385 |
|
| 2016 |
Ounit R, Lonardi S. Higher classification sensitivity of short metagenomic reads with CLARK-S. Bioinformatics (Oxford, England). PMID 27540266 DOI: 10.1093/Bioinformatics/Btw542 |
0.313 |
|
| 2016 |
Harris EY, Ounit R, Lonardi S. BRAT-nova: Fast and accurate mapping of bi-sulfite-treated reads. Bioinformatics (Oxford, England). PMID 27153660 DOI: 10.1093/Bioinformatics/Btw226 |
0.375 |
|
| 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 |
0.368 |
|
| 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 |
0.374 |
|
| 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 |
0.403 |
|
| 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 |
0.37 |
|
| 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 |
0.386 |
|
| 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 |
0.363 |
|
| 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 |
0.359 |
|
| 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 |
0.351 |
|
| 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 |
0.409 |
|
| 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 |
0.429 |
|
| 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 |
0.366 |
|
| 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 |
0.37 |
|
| 2012 |
Mirebrahim H, Lonardi S, Roch KL, Ponts N. Reference guided assembly of heterogeneous DNA sequencing data sets to improve the quality of P. falciparum DD2 genome F1000research. 3. DOI: 10.7490/F1000Research.1092110.1 |
0.35 |
|
| 2012 |
Svensson J T, Xu J, Zheng J, Witt H, Condamine P, Wanamaker S, Madishetty K, You F, Luo M, Roose M, Jiang T, Cui X, Lonardi S, Close T. Coupling expressed sequences and bacterial artificial chromosome resources to access the barley genome Czech Journal of Genetics and Plant Breeding. 41: 219-219. DOI: 10.17221/6179-Cjgpb |
0.327 |
|
| 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 |
0.316 |
|
| 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 |
0.345 |
|
| 2011 |
Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, Suchánková P, Šimková H, Endo TR, Fenton RD, Lonardi S, Castillo AM, Chao S, Cistué L, Cuesta-Marcos A, Forrest KL, et al. An Improved Consensus Linkage Map of Barley Based on Flow-Sorted Chromosomes and Single Nucleotide Polymorphism Markers The Plant Genome. 4: 238-249. DOI: 10.3835/Plantgenome2011.08.0023 |
0.309 |
|
| 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 |
0.312 |
|
| 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 |
0.333 |
|
| 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 |
0.39 |
|
| 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 |
0.331 |
|
| 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 |
0.332 |
|
| 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 DOI: 10.1142/S0219720008003916 |
0.318 |
|
| 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 |
0.353 |
|
| 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 |
0.381 |
|
| 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 |
0.326 |
|
| 2008 |
Chen JY, Zaki M, Lonardi S. BIOKDD 2008 Acm Sigkdd Explorations Newsletter. 10: 51-53. DOI: 10.1145/1540276.1540292 |
0.335 |
|
| 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 |
0.302 |
|
| 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 |
0.346 |
|
| 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 |
0.327 |
|
| 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 |
0.323 |
|
| 2006 |
Zheng J, Svensson JT, Madishetty K, Close TJ, Jiang T, Lonardi S. OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. Bmc Bioinformatics. 7: 7. PMID 16401345 DOI: 10.1186/1471-2105-7-7 |
0.335 |
|
| 2006 |
Bagnall A, Ratanamahatana C, Keogh E, Lonardi S, Janacek G. A bit level representation for time series data mining with shape based similarity Data Mining and Knowledge Discovery. 13: 11-40. DOI: 10.1007/S10618-005-0028-0 |
0.339 |
|
| 2005 |
Chen X, Zheng J, Fu Z, Nan P, Zhong Y, Lonardi S, Jiang T. Assignment of orthologous genes via genome rearrangement. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 2: 302-15. PMID 17044168 DOI: 10.1109/Tcbb.2005.48 |
0.423 |
|
| 2005 |
Lin J, Keogh E, Lonardi S. Visualizing and Discovering Non-Trivial Patterns in Large Time Series Databases Information Visualization. 4: 61-82. DOI: 10.1057/Palgrave.Ivs.9500089 |
0.327 |
|
| 2004 |
Zheng J, Close TJ, Jiang T, Lonardi S. Efficient selection of unique and popular oligos for large EST databases. Bioinformatics (Oxford, England). 20: 2101-12. PMID 15059835 DOI: 10.1093/Bioinformatics/Bth210 |
0.379 |
|
| 2004 |
Apostolico A, Gong FC, Lonardi S. Verbumculus and the discovery of unusual words Journal of Computer Science and Technology. 19: 22-41. DOI: 10.1007/Bf02944783 |
0.61 |
|
| 2004 |
Atallah MJ, Lonardi S. Augmenting LZ-77 with authentication and integrity assurance capabilities Concurrency Computation Practice and Experience. 16: 1063-1076. DOI: 10.1002/Cpe.804 |
0.315 |
|
| 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 |
0.619 |
|
| 2002 |
Apostolico A, Lonardi S. A speed-up for the commute between subword trees and DAWGs Information Processing Letters. 83: 159-161. DOI: 10.1016/S0020-0190(01)00327-1 |
0.557 |
|
| 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 |
0.589 |
|
| 2000 |
Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, ... Lonardi S, et al. A whole-genome assembly of Drosophila. Science (New York, N.Y.). 287: 2196-204. PMID 10731133 DOI: 10.1126/Science.287.5461.2196 |
0.386 |
|
| 2000 |
Apostolico A, Lonardi S. Off-line compression by greedy textual substitution Proceedings of the Ieee. 88: 1733-1744. DOI: 10.1109/5.892709 |
0.513 |
|
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