{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T18:54:58Z","timestamp":1775069698848,"version":"3.50.1"},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1707-8","type":"journal-article","created":{"date-parts":[[2017,6,2]],"date-time":"2017-06-02T11:55:20Z","timestamp":1496404520000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing"],"prefix":"10.1186","volume":"18","author":[{"given":"Marek","family":"Palkowski","sequence":"first","affiliation":[]},{"given":"Wlodzimierz","family":"Bielecki","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,6,2]]},"reference":[{"issue":"1","key":"1707_CR1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1137\/0135006","volume":"35","author":"R Nussinov","year":"1978","unstructured":"Nussinov R, Pieczenik G, Griggs JR, Kleitman DJ. Algorithms for loop matchings. SIAM J Appl Math. 1978; 35(1):68\u201382.","journal-title":"SIAM J Appl Math"},{"key":"1707_CR2","volume-title":"IPDPS Workshops","author":"L Liu","year":"2011","unstructured":"Liu L, Wang M, Jiang J, Li R, Yang G. Efficient nonserial polyadic dynamic programming on the cell processor. In: IPDPS Workshops. Anchorage, Alaska: IEEE: 2011. p. 460\u201371."},{"key":"1707_CR3","volume-title":"Proceedings of the Fourteenth Annual ACM Symposium on Parallel Algorithms and Architectures. SPAA \u201902,","author":"F Almeida","year":"2002","unstructured":"Almeida F, et al. Optimal tiling for the rna base pairing problem. In: Proceedings of the Fourteenth Annual ACM Symposium on Parallel Algorithms and Architectures. SPAA \u201902,New York: ACM: 2002. p. 173\u201382. doi: 10.1145\/564870.564901 ."},{"key":"1707_CR4","volume-title":"SC 2006 Conference, Proceedings of the ACM\/IEEE","author":"G Tan","year":"2006","unstructured":"Tan G, Feng S, Sun N. Locality and parallelism optimization for dynamic programming algorithm in bioinformatics. In: SC 2006 Conference, Proceedings of the ACM\/IEEE. Tampa: IEEE, Conference Location: 2006. p. 41\u20131."},{"key":"1707_CR5","volume-title":"Proceedings of the 2008 International Conference on Application-Specific Systems, Architectures and Processors. ASAP \u201908,","author":"A Jacob","year":"2008","unstructured":"Jacob A, Buhler J, Chamberlain RD. Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs. In: Proceedings of the 2008 International Conference on Application-Specific Systems, Architectures and Processors. ASAP \u201908,Washington: IEEE Computer Society: 2008. p. 191\u20136. doi: 10.1109\/ASAP.2008.4580177 ."},{"key":"1707_CR6","volume-title":"UNAFold","year":"2008","unstructured":"Markham NR, Zuker M. In: Keith JM, (ed).UNAFold. Totowa, NJ: Humana Press; 2008, pp. 3\u201331."},{"key":"1707_CR7","volume-title":"Proceedings of the 2009 ACM Symposium on Applied Computing. SAC \u201909,","author":"A Mathuriya","year":"2009","unstructured":"Mathuriya A, Bader DA, Heitsch CE, Harvey SC. Gtfold: A scalable multicore code for rna secondary structure prediction. In: Proceedings of the 2009 ACM Symposium on Applied Computing. SAC \u201909,New York: ACM: 2009. p. 981\u20138."},{"key":"1707_CR8","volume-title":"Field-Programmable Custom Computing Machines (FCCM), 2010 18th IEEE Annual Int. Symp. On","author":"AC Jacob","year":"2010","unstructured":"Jacob AC, Buhler JD, Chamberlain RD. Rapid rna folding: Analysis and acceleration of the zuker recurrence. In: Field-Programmable Custom Computing Machines (FCCM), 2010 18th IEEE Annual Int. Symp. On. Charlotte: IEEE, Conference Location: 2010. p. 87\u201394."},{"key":"1707_CR9","unstructured":"Mullapudi RT, Bondhugula U. Tiling for dynamic scheduling In: Rajopadhye S, Verdoolaege S, editors. Proceedings of the 4th International Workshop on Polyhedral Compilation Techniques. Vienna, Austria: 2014. http:\/\/impact.gforge.inria.fr\/impact2014\/papers\/impact2014-mullapudi.pdf ."},{"issue":"6","key":"1707_CR10","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1145\/1379022.1375595","volume":"43","author":"U Bondhugula","year":"2008","unstructured":"Bondhugula U, Hartono A, Ramanujam J, Sadayappan P. A practical automatic polyhedral parallelizer and locality optimizer. SIGPLAN Not. 2008; 43(6):101\u201313. doi: 10.1145\/1379022.1375595 .","journal-title":"SIGPLAN Not."},{"key":"1707_CR11","unstructured":"Griebl M. Automatic Parallelization of Loop Programs for Distributed Memory Architectures: University of Passau; 2004. Habilitation thesis."},{"key":"1707_CR12","volume-title":"Proceedings of the 13th ACM SIGARCH Int. Conf. on Supercomputing","author":"A Lim","year":"1999","unstructured":"Lim A, Cheong GI, Lam MS. An affine partitioning algorithm to maximize parallelism and minimize communication. In: Proceedings of the 13th ACM SIGARCH Int. Conf. on Supercomputing. Portland: ACM Press: 1999. p. 228\u201337."},{"issue":"4","key":"1707_CR13","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1142\/S0129626497000401","volume":"7","author":"J Xue","year":"1997","unstructured":"Xue J. On tiling as a loop transformation. Parallel Process Lett. 1997; 7(4):409\u2013424.","journal-title":"Parallel Process Lett"},{"key":"1707_CR14","unstructured":"Wonnacott D, Jin T, Lake A. Automatic tiling of \u201cmostly-tileable\u201d loop nests. In: IMPACT 2015: 5th International Workshop on Polyhedral Compilation Techniques. Amsterdam: 2015. http:\/\/impact.gforge.inria.fr\/impact2015\/papers\/impact2015-wonnacott.pdf ."},{"issue":"9","key":"1707_CR15","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1016\/j.parco.2012.06.001","volume":"38","author":"W Bielecki","year":"2012","unstructured":"Bielecki W, Palkowski M, Klimek T. Free scheduling for statement instances of parameterized arbitrarily nested affine loops. Parallel Comput. 2012; 38(9):518\u201332.","journal-title":"Parallel Comput"},{"key":"1707_CR16","volume-title":"Computational Science \u2013 ICCS 2009. Lecture Notes in Computer Science,","author":"G Rizk","year":"2009","unstructured":"Rizk G, Lavenier D. Gpu accelerated rna folding algorithm In: Allen G, Nabrzyski J, Seidel E, van Albada G, Dongarra J, Sloot PA, editors. Computational Science \u2013 ICCS 2009. Lecture Notes in Computer Science,Baton Rouge, LA, USA: Springer: 2009. p. 1004\u20131013."},{"key":"1707_CR17","volume-title":"Proceedings of the 23rd ACM Symposium on Parallelism in Algorithms and Architectures. SPAA \u201911,","author":"Y Tang","year":"2011","unstructured":"Tang Y, Chowdhury RA, Kuszmaul BC, Luk CK, Leiserson CE. The pochoir stencil compiler. In: Proceedings of the 23rd ACM Symposium on Parallelism in Algorithms and Architectures. SPAA \u201911,New York: ACM: 2011. p. 117\u201328. doi: 10.1145\/1989493.1989508 ."},{"issue":"8","key":"1707_CR18","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1016\/j.jpdc.2010.01.004","volume":"70","author":"A Stivala","year":"2010","unstructured":"Stivala A, Stuckey PJ, Garcia de la Banda M, Hermenegildo M, Wirth A. Lock-free parallel dynamic programming. J Parallel Distrib Comput. 2010; 70(8):839\u201348.","journal-title":"J Parallel Distrib Comput"},{"key":"1707_CR19","volume-title":"Finding Free Schedules for RNA Secondary Structure Prediction, Springer Int. Publishing, Rutkowski et al., Artificial Intelligence and Soft Computing: ICAISC 2016, Poland, Proceedings, Part II","author":"M Palkowski","year":"2016","unstructured":"Palkowski M. Finding Free Schedules for RNA Secondary Structure Prediction, Springer Int. Publishing, Rutkowski et al., Artificial Intelligence and Soft Computing: ICAISC 2016, Poland, Proceedings, Part II. Zakopane: Springer International Publishing; 2016, pp. 179\u201388."},{"key":"1707_CR20","volume-title":"An exact method for analysis of value-based array data dependences","year":"1994","unstructured":"Pugh W, Wonnacott D. In: Banerjee U, Gelernter D, Nicolau A, Padua D, (eds).An exact method for analysis of value-based array data dependences. Berlin, Heidelberg: Springer; 1994, pp. 546\u201366."},{"key":"1707_CR21","unstructured":"Kelly W, Maslov V, Pugh W, Rosser E, Shpeisman T, Wonnacott D. The omega library interface guide. Technical report, College Park, MD, USA 1995."},{"issue":"4","key":"1707_CR22","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1515\/amcs-2016-0065","volume":"26","author":"W Bielecki","year":"2016","unstructured":"Bielecki W, Palkowski M. Tiling of arbitrarily nested loops by means of the transitive closure of dependence graphs. Int J Appl Math Comput Sci (AMCS). 2016; 26(4):919\u2013939.","journal-title":"Int J Appl Math Comput Sci (AMCS)"},{"issue":"2","key":"1707_CR23","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s10878-014-9740-2","volume":"30","author":"W Bielecki","year":"2015","unstructured":"Bielecki W, Kraska K, Klimek T. Using basis dependence distance vectors in the modified floyd\u2013warshall algorithm. J Comb Optim. 2015; 30(2):253\u201375.","journal-title":"J Comb Optim"},{"key":"1707_CR24","volume-title":"PACT\u201913 IEEE International Conference on Parallel Architecture and Compilation Techniques","author":"C Bastoul","year":"2004","unstructured":"Bastoul C. Code generation in the polyhedral model is easier than you think. In: PACT\u201913 IEEE International Conference on Parallel Architecture and Compilation Techniques. Juan-les-Pins: IEEE Computer Society: 2004. p. 7\u201316."},{"key":"1707_CR25","unstructured":"Verdoolaege S. Integer set library - manual, Technical report 2016. http:\/\/isl.gforge.inria.fr\/manual.pdf . Accessed 27 May 2017."},{"issue":"4","key":"1707_CR26","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/BF01407876","volume":"15","author":"M Wolfe","year":"1986","unstructured":"Wolfe M. Loops skewing: The wavefront method revisited. Int J Parallel Programm. 1986; 15(4):279\u201393.","journal-title":"Int J Parallel Programm"},{"key":"1707_CR27","unstructured":"OpenMP Architecture Review Board. OpenMP Application Program Interface Version 4.5. 2015. http:\/\/www.openmp.org\/wp-content\/uploads\/openmp-4.5.pdf . Accessed 27 May 2017."},{"issue":"3","key":"1707_CR28","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1145\/2896389","volume":"38","author":"U Bondhugula","year":"2016","unstructured":"Bondhugula U, Acharya A, Cohen A. The pluto+ algorithm: A practical approach for parallelization and locality optimization of affine loop nests. ACM Trans Program Lang Syst. 2016; 38(3):12\u201311232. doi: 10.1145\/2896389 .","journal-title":"ACM Trans Program Lang Syst"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1707-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,25]],"date-time":"2019-09-25T12:59:46Z","timestamp":1569416386000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1707-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,2]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1707"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1707-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6,2]]},"article-number":"290"}}