{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,29]],"date-time":"2022-03-29T04:17:24Z","timestamp":1648527444476},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2019,4,23]],"date-time":"2019-04-23T00:00:00Z","timestamp":1555977600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2019,4,23]],"date-time":"2019-04-23T00:00:00Z","timestamp":1555977600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Sign Process Syst"],"published-print":{"date-parts":[[2020,10]]},"DOI":"10.1007\/s11265-019-01452-x","type":"journal-article","created":{"date-parts":[[2019,4,23]],"date-time":"2019-04-23T04:03:18Z","timestamp":1555992198000},"page":"1197-1213","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Towards Accelerated Genome Informatics on Parallel HPC Platforms: The ReneGENE-GI Perspective"],"prefix":"10.1007","volume":"92","author":[{"given":"Santhi","family":"Natarajan","sequence":"first","affiliation":[]},{"given":"Krishna Kumar","family":"N.","sequence":"additional","affiliation":[]},{"given":"Debnath","family":"Pal","sequence":"additional","affiliation":[]},{"given":"S. K.","family":"Nandy","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,4,23]]},"reference":[{"issue":"4","key":"1452_CR1","doi-asserted-by":"publisher","first-page":"378","DOI":"10.3390\/biology2010378","volume":"2","author":"KS Frese","year":"2013","unstructured":"Frese, K.S., Katus, H.A., Meder, B. (2013). Next-generation sequencing: from understanding biology to personalized medicine. Biology, 2(4), 378\u2013398.","journal-title":"Biology"},{"key":"1452_CR2","first-page":"198","volume":"470","author":"ER Mardis","year":"2011","unstructured":"Mardis, E.R. (2011). A decade\u2019s perspective on dna sequencing technology. Nature Perspective, 470, 198\u2013203.","journal-title":"Nature Perspective"},{"key":"1452_CR3","doi-asserted-by":"crossref","unstructured":"Stephens, Z.D., Lee, S.Y., Faghri, F., Campbell, R.H., Zhai, C., Efron, M.J., et al. (2015). Big data: Astronomical or genomical? PLOS Biology, 13(7).","DOI":"10.1371\/journal.pbio.1002195"},{"issue":"1","key":"1452_CR4","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1145\/375360.375365","volume":"33","author":"G Navarro","year":"2001","unstructured":"Navarro, G. (2001). A guided tour to approximate string matching. ACM Computing Surveys, 33(1), 31\u201388.","journal-title":"ACM Computing Surveys"},{"issue":"4","key":"1452_CR5","first-page":"19","volume":"24","author":"AV Aho","year":"2000","unstructured":"Aho, A.V., & Corasick, M.J. (2000). Efficient string matching: an aid to bibliographic search. IEEE Data Engineering Bulletin, 24(4), 19\u201327.","journal-title":"IEEE Data Engineering Bulletin"},{"issue":"12","key":"1452_CR6","first-page":"2","volume":"11","author":"FF Costa","year":"2012","unstructured":"Costa, F.F. (2012). Big data in genomics: Challenges and solutions. G.I.T Laboratory Journal, 11(12), 2\u20134.","journal-title":"G.I.T Laboratory Journal"},{"key":"1452_CR7","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1038\/498255a","volume":"498","author":"V Marx","year":"2013","unstructured":"Marx, V. (2013). The big challenges of big data. Nature, 498, 255\u2013260.","journal-title":"Nature"},{"key":"1452_CR8","doi-asserted-by":"crossref","unstructured":"Reinert, K., Langmead, B., Weese, D., Evers, D.J. (2015). Alignment of Next-Generation Sequencing Reads Annu. Rev Genomics Hum. Genet., 133\u2013151.","DOI":"10.1146\/annurev-genom-090413-025358"},{"key":"1452_CR9","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nmeth0710-495","volume":"7","author":"M Baker","year":"2010","unstructured":"Baker, M. (2010). Next-generation sequencing: adjusting to data overload. Nature Methods, 7, 495\u2013499.","journal-title":"Nature Methods"},{"key":"1452_CR10","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/nrg3117","volume":"13","author":"TJ Treangen","year":"2012","unstructured":"Treangen, T.J., & Salzberg, S.L. (2012). Repetitive dna and next-generation sequencing: computational challenges and solutions. Nature Reviews, 13, 36\u201346.","journal-title":"Nature Reviews"},{"key":"1452_CR11","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1038\/nmeth.1376","volume":"6","author":"P Flicek","year":"2009","unstructured":"Flicek, P., & Birney, E. (2009). Sense from sequence reads: methods for alignment and assembly. Nature Methods, 6, S6\u2013S12.","journal-title":"Nature Methods"},{"key":"1452_CR12","unstructured":"Yamaguchi, Y., Maruyama, T., Konagaya, A. (2002). High speed homology search with FPGAs. In Proceedings of the Pacific Symposium on Biocomputing (pp. 271\u2013282)."},{"issue":"4","key":"1452_CR13","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1109\/TVLSI.2008.2005314","volume":"17","author":"K Benkrid","year":"2009","unstructured":"Benkrid, K., Liu, Y., Benkrid, A. (2009). A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment. IEEE Transactions On Very Large Scale Integration Systems, 17(4), 561\u2013570.","journal-title":"IEEE Transactions On Very Large Scale Integration Systems"},{"key":"1452_CR14","doi-asserted-by":"crossref","unstructured":"Razmyslovich, D., Marcus, G., Gipp, M., Zapatka, M., Szillus, A. (2010). Implementation of Smith-Waterman Algorithm in openCL for GPUs. In IEEE Second International Workshop on High Performance Computational Systems Biology (pp. 48\u201356).","DOI":"10.1109\/PDMC-HiBi.2010.16"},{"key":"1452_CR15","unstructured":"Banerjee, S.S., El-Hadedy, M., Lim, J.B., Kalbarczyk, Z.T., Chen, D., Lumetta, S.S., Iyer, R.K. ASAP: Accelerated Short-Read Alignment on Programmable Hardware."},{"key":"1452_CR16","unstructured":"Ergin, M.A., Hassan, H., Xin, H., Alli, E. (2017). Gatekeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinformatics."},{"key":"1452_CR17","doi-asserted-by":"crossref","unstructured":"Arram, J., Kaplan, T., Luk, W., Jiang, P. (2017). Leveraging FPGAs for accelerating short read alignment. IEEE\/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 14, NO. 3.","DOI":"10.1109\/TCBB.2016.2535385"},{"issue":"1","key":"1452_CR18","first-page":"33","volume":"2","author":"CY Lee","year":"2013","unstructured":"Lee, C.Y., Chiu, Y.C., Wang, L.B., al et. (2013). Common applications of next-generation sequencing technologies in genomic research. Translational Cancer Research, 2(1), 33\u201345.","journal-title":"Translational Cancer Research"},{"key":"1452_CR19","doi-asserted-by":"crossref","unstructured":"Alyass, A., Turcotte, M., Meyre, D. (2015). From big data analysis to personalized medicine for all: challenges and opportunities. BMC Medical Genomics, 8(33).","DOI":"10.1186\/s12920-015-0108-y"},{"key":"1452_CR20","doi-asserted-by":"crossref","unstructured":"Chen, C., & Schmidt, B. (2004). Performance analysis of computational biology applications on hierarchical grid systems. In Proceedings of the IEEE International Symposium on Cluster Computing and the Grid, CCGrid 2004 (pp 426\u2013433). Chicago.","DOI":"10.1109\/CCGrid.2004.1336597"},{"key":"1452_CR21","doi-asserted-by":"crossref","unstructured":"Bader, D.A. (2005). High-performance algorithm engineering for large-scale graph problems and computational biology. In Proceedings of the International Workshop on Experimental and Efficient Algorithms, WEA 2005 (pp. 16\u201321). Springer.","DOI":"10.1007\/11427186_3"},{"key":"1452_CR22","doi-asserted-by":"crossref","unstructured":"Natarajan, S., KrishnaKumar, N., Pal, D., Nandy, S.K. (2018). ReneGENE-GI: empowering precision genomics with FPGAs on HPCs. In Proceedings of the 14th International Symposium on Applied Reconfigurable Computing (ARC).","DOI":"10.1007\/978-3-319-78890-6_15"},{"key":"1452_CR23","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1007\/BF01185432","volume":"12","author":"E Myers","year":"1994","unstructured":"Myers, E. (1994). A sublinear algorithm for approximate keyword searching. Algorithmica, 12, 345\u2013374.","journal-title":"Algorithmica"},{"key":"1452_CR24","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith, T.F., & Waterman, M.S. (1981). Identification of common molecular subsequences. J. Mol Bwl., 147, 195\u2013197.","journal-title":"J. Mol Bwl."},{"key":"1452_CR25","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1093\/nar\/29.2.351","volume":"29","author":"SF Altschul","year":"2001","unstructured":"Altschul, S.F., Bundschuh, R., Olsen, R., Hwa, T. (2001). The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Research, 29, 351\u2013361.","journal-title":"Nucleic Acids Research"},{"key":"1452_CR26","doi-asserted-by":"crossref","unstructured":"Natarajan, S., KrishnaKumar, N., Pavan, M., Pal, D., Nandy, S.K. (2018). ReneGENE-DP: accelerated parallel dynamic programming for genome informatics. In Proceedings of 2018 International Conference on Electronics, Computing and Communication Technologies (IEEE CONECCT).","DOI":"10.1109\/CONECCT.2018.8482378"},{"key":"1452_CR27","doi-asserted-by":"crossref","unstructured":"Natarajan, S., KrishnaKumar, N, Anuchan, H.V., Pal, D., Nandy, S.K. (2018). ReneGENE-novo: co-designed algorithm-architecture for accelerated preprocessing and assembly of genomic short reads. In Proceedings of the 14th International Symposium on Applied Reconfigurable Computing (ARC).","DOI":"10.1007\/978-3-319-78890-6_45"},{"key":"1452_CR28","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1093\/bib\/bbq015","volume":"2","author":"H Li","year":"2010","unstructured":"Li, H., & Homer, N. (2010). A survey of sequence alignment algorithms for next-generation sequencing. Briefings in Bioinformatics, 2, 473\u2013483.","journal-title":"Briefings in Bioinformatics"},{"key":"1452_CR29","doi-asserted-by":"crossref","unstructured":"Hatem, A., Bozdag, D., Toland, A.E., Catalyurek, U.V. (2013). Benchmarking short sequence mapping tools. BMC Bioinformatics, 14.","DOI":"10.1186\/1471-2105-14-184"},{"key":"1452_CR30","unstructured":"Natarajan, S., KrishnaKumar, N., Pal, D., Nandy, S.K. (2016). AccuRA: accurate alignment of short reads on scalable reconfigurable accelerators. In Proc. IEEE International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation (SAMOS XVI) (pp. 79\u201387)."},{"key":"1452_CR31","unstructured":"Natarajan, S., KrishnaKumar, N., Pal, D., Nandy, S.K. Accurate and accelerated secondary analysis of genomes: Implications for Genomics, NGS\u201917: Structural Variation and Population Genomics."},{"key":"1452_CR32","unstructured":"SERC, Indian Institute of Science, Bangalore. Sahasrat (Cray XC40). \nhttp:\/\/www.serc.iisc.in\/facilities\/cray-xc40-named-as-sahasrat\n\n."},{"issue":"14","key":"1452_CR33","doi-asserted-by":"publisher","first-page":"1830","DOI":"10.1093\/bioinformatics\/bts276","volume":"28","author":"Y Liu","year":"2012","unstructured":"Liu, Y., Schmidt, B., Maskell, D.L. (2012). CUSHAW: A CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics, 28(14), 1830\u20131837.","journal-title":"Bioinformatics"},{"issue":"1","key":"1452_CR34","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1109\/MDAT.2013.2284198","volume":"31","author":"Y Liu","year":"2014","unstructured":"Liu, Y., & Schmidt, B. (2014). CUSHAW2-GPU: Empowering Faster gapped Short-Read alignment using GPU computing. IEEE Design and Test of Computers, 31(1), 31\u201339.","journal-title":"IEEE Design and Test of Computers"},{"key":"1452_CR35","doi-asserted-by":"crossref","unstructured":"Homer, N., Merriman, B., Nelson, S.F. (2009). BFAST: An alignment tool for large scale genome resequencing. PLoS 4.","DOI":"10.1371\/journal.pone.0007767"}],"container-title":["Journal of Signal Processing Systems"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11265-019-01452-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s11265-019-01452-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11265-019-01452-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,5]],"date-time":"2020-09-05T08:12:42Z","timestamp":1599293562000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s11265-019-01452-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4,23]]},"references-count":35,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2020,10]]}},"alternative-id":["1452"],"URL":"https:\/\/doi.org\/10.1007\/s11265-019-01452-x","relation":{},"ISSN":["1939-8018","1939-8115"],"issn-type":[{"value":"1939-8018","type":"print"},{"value":"1939-8115","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,23]]},"assertion":[{"value":"25 September 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 January 2019","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 April 2019","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 April 2019","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}