{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T13:30:27Z","timestamp":1742995827278,"version":"3.40.3"},"publisher-location":"Cham","reference-count":23,"publisher":"Springer Nature Switzerland","isbn-type":[{"type":"print","value":"9783031697654"},{"type":"electronic","value":"9783031697661"}],"license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024]]},"DOI":"10.1007\/978-3-031-69766-1_11","type":"book-chapter","created":{"date-parts":[[2024,8,25]],"date-time":"2024-08-25T19:02:05Z","timestamp":1724612525000},"page":"152-166","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["(re)Assessing PiM Effectiveness for\u00a0Sequence Alignment"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-8846-8456","authenticated-orcid":false,"given":"Hamidreza","family":"Ramezanikebrya","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9839-3866","authenticated-orcid":false,"given":"Matei","family":"Ripeanu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,8,26]]},"reference":[{"issue":"21","key":"11_CR1","doi-asserted-by":"publisher","first-page":"4255","DOI":"10.1093\/bioinformatics\/btz234","volume":"35","author":"M Alser","year":"2019","unstructured":"Alser, M., Hassan, H., Kumar, A., Mutlu, O., Alkan, C.: Shouji: a fast and efficient pre-alignment filter for sequence alignment. Bioinformatics 35(21), 4255\u20134263 (2019)","journal-title":"Bioinformatics"},{"issue":"22\u201323","key":"11_CR2","first-page":"5282","volume":"36","author":"M Alser","year":"2020","unstructured":"Alser, M., Shahroodi, T., G\u00f3mez-Luna, J., Alkan, C., Mutlu, O.: SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. Bioinformatics 36(22\u201323), 5282\u20135290 (2020)","journal-title":"Bioinformatics"},{"issue":"7","key":"11_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pbio.1001091","volume":"9","author":"DM Church","year":"2011","unstructured":"Church, D.M., Schneider, V.A., Graves, T., Auger, K., Cunningham, F., Bouk, N., et al.: Modernizing reference genome assemblies. PLOS Biol. 9(7), 1\u20135 (2011)","journal-title":"PLOS Biol."},{"key":"11_CR4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-016-0930-z","volume":"17","author":"J Daily","year":"2016","unstructured":"Daily, J.: Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinform. 17, 1\u201311 (2016)","journal-title":"BMC Bioinform."},{"doi-asserted-by":"crossref","unstructured":"Devaux, F.: The true processing in memory accelerator. In: 2019 IEEE Hot Chips 31 Symposium (HCS), pp. 1\u201324 (2019)","key":"11_CR5","DOI":"10.1109\/HOTCHIPS.2019.8875680"},{"doi-asserted-by":"crossref","unstructured":"Devic, A., Rai, S.B., Sivasubramaniam, A., Akel, A., Eilert, S., Eno, J.: To PIM or not for emerging general purpose processing in DDR memory systems. In: Proceedings of the 49th Annual International Symposium on Computer Architecture, ISCA 2022, pp. 231\u2013244. Association for Computing Machinery, New York (2022)","key":"11_CR6","DOI":"10.1145\/3470496.3527431"},{"doi-asserted-by":"crossref","unstructured":"Diab, S., Nassereldine, A., Alser, M., G\u00f3mez\u00a0Luna, J., Mutlu, O., El\u00a0Hajj, I.: A framework for high-throughput sequence alignment using real processing-in-memory systems. Bioinformatics 39(5), btad155 (2023)","key":"11_CR7","DOI":"10.1093\/bioinformatics\/btad155"},{"key":"11_CR8","series-title":"LNCS","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1007\/978-3-031-48803-0_13","volume-title":"Euro-Par 2023","author":"Y Falevoz","year":"2024","unstructured":"Falevoz, Y., Legriel, J.: Energy efficiency impact of processing in memory: a comprehensive review of workloads on the UPMEM architecture. In: Zeinalipour, D., et al. (eds.) Euro-Par 2023. LNCS, vol. 14352, pp. 155\u2013166. Springer, Cham (2024). https:\/\/doi.org\/10.1007\/978-3-031-48803-0_13"},{"doi-asserted-by":"crossref","unstructured":"Friesel, B., L\u00fctke\u00a0Dreimann, M., Spinczyk, O.: A full-system perspective on UPMEM performance. In: Proceedings of the 1st Workshop on Disruptive Memory Systems, DIMES 2023, pp. 1\u20137. Association for Computing Machinery, New York (2023)","key":"11_CR9","DOI":"10.1145\/3609308.3625266"},{"issue":"3","key":"11_CR10","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1016\/0022-2836(82)90398-9","volume":"162","author":"O Gotoh","year":"1982","unstructured":"Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol. 162(3), 705\u2013708 (1982)","journal-title":"J. Mol. Biol."},{"key":"11_CR11","doi-asserted-by":"publisher","first-page":"52565","DOI":"10.1109\/ACCESS.2022.3174101","volume":"10","author":"J G\u00f3mez-Luna","year":"2022","unstructured":"G\u00f3mez-Luna, J., Hajj, I.E., Fernandez, I., Giannoula, C., Oliveira, G.F., Mutlu, O.: Benchmarking a new paradigm: experimental analysis and characterization of a real processing-in-memory system. IEEE Access 10, 52565\u201352608 (2022)","journal-title":"IEEE Access"},{"key":"11_CR12","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.future.2023.07.008","volume":"149","author":"A Haghi","year":"2023","unstructured":"Haghi, A., Marco-Sola, S., Alvarez, L., Diamantopoulos, D., Hagleitner, C., Moreto, M.: WFA-FPGA: an efficient accelerator of the wavefront algorithm for short and long read genomics alignment. Futur. Gener. Comput. Syst. 149, 39\u201358 (2023)","journal-title":"Futur. Gener. Comput. Syst."},{"doi-asserted-by":"crossref","unstructured":"Hyun, B., Kim, T., Lee, D., Rhu, M.: Pathfinding future PIM architectures by demystifying a commercial PIM technology. In: 2024 IEEE International Symposium on High-Performance Computer Architecture (HPCA). IEEE Computer Society (2024)","key":"11_CR13","DOI":"10.1109\/HPCA57654.2024.00029"},{"unstructured":"Intel Corporation: Intel advisor. https:\/\/www.intel.com\/content\/www\/us\/en\/developer\/tools\/oneapi\/advisor.html","key":"11_CR14"},{"doi-asserted-by":"crossref","unstructured":"Lavenier, D., Cimadomo, R., Jodin, R.: Variant calling parallelization on processor-in-memory architecture. In: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 204\u2013207 (2020)","key":"11_CR15","DOI":"10.1109\/BIBM49941.2020.9313351"},{"unstructured":"Li, H.: Ksw2 github repository. https:\/\/github.com\/lh3\/ksw2","key":"11_CR16"},{"issue":"18","key":"11_CR17","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H.: Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18), 3094\u20133100 (2018)","journal-title":"Bioinformatics"},{"key":"11_CR18","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1093\/bioinformatics\/btaa777","volume":"37","author":"S Marco-Sola","year":"2020","unstructured":"Marco-Sola, S., Moure, J., Moreto, M., Espinosa, A.: Fast gap-affine pairwise alignment using the wavefront algorithm. Bioinformatics 37, 456\u2013463 (2020)","journal-title":"Bioinformatics"},{"unstructured":"Moreto, M., Marco-Sola, S.: Accelerating the wavefront alignment algorithm on CPUs, GPUs and FPGAs. In: 4th Workshop on Accelerator Architecture in Computational Biology and Bioinformatics (AACBB), New York, NY, USA (2022)","key":"11_CR19"},{"issue":"3","key":"11_CR20","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48(3), 443\u2013453 (1970)","journal-title":"J. Mol. Biol."},{"unstructured":"Nider, J., et\u00a0al.: A case study of processing-in-memory in off-the-shelf systems. In: 2021 USENIX Annual Technical Conference (USENIX ATC 2021), pp. 117\u2013130. USENIX Association (2021)","key":"11_CR21"},{"doi-asserted-by":"crossref","unstructured":"Turakhia, Y., Bejerano, G., Dally, W.J.: Darwin: a genomics co-processor provides up to 15,000x acceleration on long read assembly. In: Proceedings of the Twenty-Third International Conference on Architectural Support for Programming Languages and Operating Systems, ASPLOS 2018, pp. 199\u2013213. Association for Computing Machinery, New York (2018)","key":"11_CR22","DOI":"10.1145\/3173162.3173193"},{"doi-asserted-by":"crossref","unstructured":"Vasimuddin, M., Misra, S., Li, H., Aluru, S.: Efficient architecture-aware acceleration of bwa-mem for multicore systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), pp. 314\u2013324 (2019)","key":"11_CR23","DOI":"10.1109\/IPDPS.2019.00041"}],"container-title":["Lecture Notes in Computer Science","Euro-Par 2024: Parallel Processing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-69766-1_11","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,25]],"date-time":"2024-08-25T19:09:51Z","timestamp":1724612991000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-69766-1_11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"ISBN":["9783031697654","9783031697661"],"references-count":23,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-69766-1_11","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2024]]},"assertion":[{"value":"26 August 2024","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"Euro-Par","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"European Conference on Parallel Processing","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Madrid","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2024","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"26 August 2024","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"30 August 2024","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"30","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"europar2024","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/2024.euro-par.org\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}