{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T01:43:54Z","timestamp":1787017434342,"version":"build-2736575974"},"publisher-location":"New York, NY, USA","reference-count":72,"publisher":"ACM","license":[{"start":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T00:00:00Z","timestamp":1737331200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2025,1,20]]},"DOI":"10.1145\/3658617.3697545","type":"proceedings-article","created":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T09:23:57Z","timestamp":1741080237000},"page":"1008-1015","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["In-Storage Read-Centric Seed Location Filtering Using 3D-NAND Flash for Genome Sequence Analysis"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-0894-9288","authenticated-orcid":false,"given":"You-Kai","family":"Zheng","sequence":"first","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3970-979X","authenticated-orcid":false,"given":"Ming-Liang","family":"Wei","sequence":"additional","affiliation":[{"name":"Macronix international co., ltd., Hsinchu, Taiwan"},{"name":"Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8983-9835","authenticated-orcid":false,"given":"Hsiang-Yun","family":"Cheng","sequence":"additional","affiliation":[{"name":"Academia Sinica, Taipei, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0091-5027","authenticated-orcid":false,"given":"Chia-Lin","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan"},{"name":"Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6703-3002","authenticated-orcid":false,"given":"Ming-Hsiang","family":"Tsai","sequence":"additional","affiliation":[{"name":"Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-0909-9656","authenticated-orcid":false,"given":"Chia-Chun","family":"Chien","sequence":"additional","affiliation":[{"name":"National Taiwan University, Taipei, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4950-3808","authenticated-orcid":false,"given":"Yuan-Hao","family":"Zhong","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6206-7409","authenticated-orcid":false,"given":"Po-Hao","family":"Tseng","sequence":"additional","affiliation":[{"name":"Macronix international co., ltd., Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6805-4767","authenticated-orcid":false,"given":"Hsiang-Pang","family":"Li","sequence":"additional","affiliation":[{"name":"Macronix international co., ltd., Hsinchu, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"320","published-online":{"date-parts":[[2025,3,4]]},"reference":[{"key":"e_1_3_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1377\/hlthaff.2017.1624"},{"key":"e_1_3_2_1_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.trsl.2009.09.005"},{"key":"e_1_3_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00075-13"},{"key":"e_1_3_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41551-021-00754-5"},{"key":"e_1_3_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_3_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4235"},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(81)90087-5"},{"key":"e_1_3_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02443-7"},{"key":"e_1_3_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_3_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1145\/316542.316550"},{"key":"e_1_3_2_1_11_1","volume-title":"clone sequences and assembly contigs with BWA-MEM\". In: arXiv preprint arXiv:1303.3997","author":"Heng Li.","year":"2013","unstructured":"Heng Li. \"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM\". In: arXiv preprint arXiv:1303.3997 (2013)."},{"key":"e_1_3_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1109\/LCA.2018.2854700"},{"key":"e_1_3_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1109\/TPDS.2016.2515597"},{"key":"e_1_3_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1109\/TPDS.2015.2444376"},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2822687"},{"key":"e_1_3_2_1_16_1","volume-title":"IEEE International Conference on Electronics, Circuits, and Systems (ICECS).","author":"Marcel","year":"2021","unstructured":"Marcel Khalifa et al. \"FiltPIM: In-Memory Filter for DNA Sequencing\". In: IEEE International Conference on Electronics, Circuits, and Systems (ICECS). Nov. 2021."},{"key":"e_1_3_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1145\/3503222.3507702"},{"key":"e_1_3_2_1_18_1","first-page":"209","volume-title":"IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).","author":"Z\u00fclal","year":"2021","unstructured":"Z\u00fclal Bing\u00f6l et al. \"GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping\". In: IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). June 2021, pp. 209--209."},{"key":"e_1_3_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz234"},{"key":"e_1_3_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4460-0"},{"key":"e_1_3_2_1_21_1","doi-asserted-by":"publisher","DOI":"10.1109\/TETC.2021.3093840"},{"key":"e_1_3_2_1_22_1","first-page":"710","volume-title":"55th IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE.","author":"Haiyu","year":"2022","unstructured":"Haiyu Mao et al. \"Genpip: In-memory acceleration of genome analysis via tight integration of basecalling and read mapping\". In: 55th IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE. 2022, pp. 710--726."},{"key":"e_1_3_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.08.019"},{"key":"e_1_3_2_1_24_1","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2020.3013728"},{"key":"e_1_3_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.210500.116"},{"key":"e_1_3_2_1_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3463"},{"key":"e_1_3_2_1_27_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0064271"},{"key":"e_1_3_2_1_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1583"},{"key":"e_1_3_2_1_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2019.10.004"},{"key":"e_1_3_2_1_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-20282-8"},{"key":"e_1_3_2_1_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mito.2019.10.006"},{"key":"e_1_3_2_1_32_1","volume-title":"Symposium on VLSI Technology. IEEE.","author":"Po-Hao","year":"2021","unstructured":"Po-Hao Tseng et al. \"A Hybrid In-Memory-Searching and In-Memory-Computing Architecture for NVM Based AI Accelerator\". In: Symposium on VLSI Technology. IEEE. 2021."},{"key":"e_1_3_2_1_33_1","first-page":"38","article-title":"Optimal design methods to transform 3D NAND flash into a high-density, high-bandwidth and low-power nonvolatile computing in memory (nvCIM) accelerator for deep-learning neural networks (DNN)","author":"Lue Hang-Ting","year":"2019","unstructured":"Hang-Ting Lue et al. \"Optimal design methods to transform 3D NAND flash into a high-density, high-bandwidth and low-power nonvolatile computing in memory (nvCIM) accelerator for deep-learning neural networks (DNN)\". In: IEEE International Electron Devices Meeting (IEDM). IEEE. 2019, pp. 38--1.","journal-title":"IEEE International Electron Devices Meeting (IEDM). IEEE."},{"key":"e_1_3_2_1_34_1","first-page":"138","volume-title":"IEEE International Solid-State Circuits Conference (ISSCC).","volume":"65","author":"Han-Wen","year":"2022","unstructured":"Han-Wen Hu et al. \"A 512Gb in-memory-computing 3D-NAND flash supporting similar-vector-matching operations on edge-AI devices\". In: IEEE International Solid-State Circuits Conference (ISSCC). Vol. 65. IEEE. 2022, pp. 138--140."},{"key":"e_1_3_2_1_35_1","first-page":"1359","volume-title":"55th IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE.","author":"Hunjun","year":"2022","unstructured":"Hunjun Lee et al. \"3D-FPIM: An Extreme Energy-Efficient DNN Acceleration System Using 3D NAND Flash-Based In-Situ PIM Unit\". In: 55th IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE. 2022, pp. 1359--1376."},{"key":"e_1_3_2_1_36_1","first-page":"270","volume-title":"IEEE Symposium on VLSI Technology and Circuits (VLSI Technology and Circuits).","author":"Po-Hao","year":"2022","unstructured":"Po-Hao Tseng et al. \"In-Memory Approximate Computing Architecture Based on 3D-NAND Flash Memories\". In: IEEE Symposium on VLSI Technology and Circuits (VLSI Technology and Circuits). June 12, 2022, pp. 270--271."},{"key":"e_1_3_2_1_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/mp.2016.24"},{"key":"e_1_3_2_1_38_1","doi-asserted-by":"crossref","first-page":"e0281934","DOI":"10.1371\/journal.pone.0281934","article-title":"Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study","volume":"2","author":"Tsegaselassie Workalemahu","year":"2023","unstructured":"Tsegaselassie Workalemahu et al. \"Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study\". In: Plos one 18.2, e0281934 (2023).","journal-title":"Plos one 18"},{"key":"e_1_3_2_1_39_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2014.06.013"},{"key":"e_1_3_2_1_40_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.coviro.2011.07.008"},{"issue":"79","key":"e_1_3_2_1_41_1","first-page":"389","article-title":"Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome","volume":"14","author":"Falk Marni J","year":"2012","unstructured":"Marni J Falk et al. \"Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome\". In: Discovery medicine 14.79 (2012), p. 389.","journal-title":"Discovery medicine"},{"key":"e_1_3_2_1_42_1","doi-asserted-by":"crossref","first-page":"e0139253","DOI":"10.1371\/journal.pone.0139253","article-title":"PCR-free enrichment of mitochondrial DNA from human blood and cell lines for high quality next-generation DNA sequencing","volume":"10","author":"Gould Meetha P","year":"2015","unstructured":"Meetha P Gould et al. \"PCR-free enrichment of mitochondrial DNA from human blood and cell lines for high quality next-generation DNA sequencing\". In: PLoS One 10.10, e0139253 (2015).","journal-title":"PLoS One 10"},{"key":"e_1_3_2_1_43_1","doi-asserted-by":"publisher","DOI":"10.1002\/humu.24279"},{"key":"e_1_3_2_1_44_1","doi-asserted-by":"crossref","first-page":"e0224847","DOI":"10.1371\/journal.pone.0224847","article-title":"Ion torrent high throughput mitochondrial genome sequencing (HTMGS)","volume":"11","author":"Harvey NR","year":"2019","unstructured":"NR Harvey et al. \"Ion torrent high throughput mitochondrial genome sequencing (HTMGS)\". In: Plos one 14.11, e0224847 (2019).","journal-title":"Plos one 14"},{"key":"e_1_3_2_1_45_1","doi-asserted-by":"crossref","first-page":"e0127280","DOI":"10.1371\/journal.pone.0127280","article-title":"Mitochondrial mutations in subjects with psychiatric disorders","volume":"5","author":"Adolfo Sequeira","year":"2015","unstructured":"Adolfo Sequeira et al. \"Mitochondrial mutations in subjects with psychiatric disorders\". In: PloS one 10.5, e0127280 (2015).","journal-title":"PloS one 10"},{"key":"e_1_3_2_1_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cancergen.2018.04.091"},{"key":"e_1_3_2_1_47_1","first-page":"1","volume-title":"Association of mitochondrial DNA variation with high myopia in a Han Chinese population","author":"Shilai Xing","year":"2023","unstructured":"Shilai Xing et al. \"Association of mitochondrial DNA variation with high myopia in a Han Chinese population\". In: Molecular Genetics and Genomics (2023), pp. 1--13."},{"key":"e_1_3_2_1_48_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsigen.2018.07.015"},{"key":"e_1_3_2_1_49_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-04182-2"},{"key":"e_1_3_2_1_50_1","volume-title":"Synth4bench: a framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms\". In: bioRxiv, 582313","author":"Fragkouli Styliani-Christina","year":"2024","unstructured":"Styliani-Christina Fragkouli et al. \"Synth4bench: a framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms\". In: bioRxiv, 582313 (2024)."},{"key":"e_1_3_2_1_51_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-019-0636-y"},{"key":"e_1_3_2_1_52_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-47135-3"},{"key":"e_1_3_2_1_53_1","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2021.3088396"},{"key":"e_1_3_2_1_54_1","first-page":"S13","article-title":"Accelerating Read Mapping with FastHASH","volume":"1","author":"Hongyi Xin","year":"2013","unstructured":"Hongyi Xin et al. \"Accelerating Read Mapping with FastHASH\". In: BMC Genomics 14.1, S13 (Jan. 21, 2013).","journal-title":"BMC Genomics 14"},{"key":"e_1_3_2_1_55_1","volume-title":"understanding and improving the accuracy of genome pre-alignment filtering\". In: arXiv preprint arXiv:1707.01631 (July 8","author":"Alser Mohammed","year":"2017","unstructured":"Mohammed Alser, Onur Mutlu, and Can Alkan. \"MAGNET: understanding and improving the accuracy of genome pre-alignment filtering\". In: arXiv preprint arXiv:1707.01631 (July 8, 2017)."},{"key":"e_1_3_2_1_56_1","doi-asserted-by":"publisher","DOI":"10.1109\/MM.2018.2890253"},{"key":"e_1_3_2_1_57_1","volume-title":"IEEE International Memory Workshop (IMW). IEEE.","author":"Po-Hao","year":"2023","unstructured":"Po-Hao Tseng et al. \"SLC and MLC In-Memory-Approximate-Search Solutions in Commercial 48-layer and 96-layer 3D-NAND Flash Memories\". In: IEEE International Memory Workshop (IMW). IEEE. 2023."},{"key":"e_1_3_2_1_58_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.808"},{"key":"e_1_3_2_1_59_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-3086-9"},{"key":"e_1_3_2_1_60_1","doi-asserted-by":"publisher","DOI":"10.1002\/cpe.3371"},{"key":"e_1_3_2_1_61_1","first-page":"334","volume-title":"IEEE\/ACM International Symposium on Microarchitecture (MICRO).","author":"Anirban","year":"2019","unstructured":"Anirban Nag et al. \"GenCache: Leveraging In-Cache Operators for Efficient Sequence Alignment\". In: IEEE\/ACM International Symposium on Microarchitecture (MICRO). Oct. 12, 2019, pp. 334--346."},{"key":"e_1_3_2_1_62_1","first-page":"1423","volume-title":"Proceedings of the 56th Annual IEEE\/ACM International Symposium on Microarchitecture.","author":"Yi","year":"2023","unstructured":"Yi Huang et al. \"CASA: An Energy-Efficient and High-Speed CAM-based SMEM Seeding Accelerator for Genome Alignment\". In: Proceedings of the 56th Annual IEEE\/ACM International Symposium on Microarchitecture. 2023, pp. 1423--1436."},{"key":"e_1_3_2_1_63_1","doi-asserted-by":"publisher","DOI":"10.1017\/9781108684163"},{"issue":"6","key":"e_1_3_2_1_64_1","article-title":"Dimension Independent Similarity Computation","volume":"14","author":"Zadeh Reza Bosagh","year":"2013","unstructured":"Reza Bosagh Zadeh and Ashish Goel. \"Dimension Independent Similarity Computation.\" In: Journal of Machine Learning Research 14.6 (2013).","journal-title":"Journal of Machine Learning Research"},{"key":"e_1_3_2_1_65_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2023.1094260"},{"key":"e_1_3_2_1_66_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1112"},{"key":"e_1_3_2_1_67_1","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2016.25"},{"key":"e_1_3_2_1_68_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.213611.116"},{"key":"e_1_3_2_1_69_1","doi-asserted-by":"publisher","DOI":"10.1109\/LCA.2020.2973991"},{"key":"e_1_3_2_1_70_1","first-page":"469","volume-title":"51st Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE.","author":"Donghyun","year":"2018","unstructured":"Donghyun Gouk et al. \"Amber: Enabling precise full-system simulation with detailed modeling of all SSD resources\". In: 51st Annual IEEE\/ACM International Symposium on Microarchitecture (MICRO). IEEE. 2018, pp. 469--481."},{"key":"e_1_3_2_1_71_1","doi-asserted-by":"publisher","DOI":"10.1145\/3123939.3124545"},{"key":"e_1_3_2_1_72_1","unstructured":"Macronix International Co. Ltd. MX60LF8G28AD 3V 8Gb Flash Memory. Version 1.1. 2023."}],"event":{"name":"ASPDAC '25: 30th Asia and South Pacific Design Automation Conference","location":"Tokyo Japan","acronym":"ASPDAC '25","sponsor":["SIGDA ACM Special Interest Group on Design Automation","IEICE","IPSJ","IEEE CAS","IEEE CEDA"]},"container-title":["Proceedings of the 30th Asia and South Pacific Design Automation Conference"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3658617.3697545","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3658617.3697545","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T19:44:18Z","timestamp":1750275858000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3658617.3697545"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,20]]},"references-count":72,"alternative-id":["10.1145\/3658617.3697545","10.1145\/3658617"],"URL":"https:\/\/doi.org\/10.1145\/3658617.3697545","relation":{},"subject":[],"published":{"date-parts":[[2025,1,20]]},"assertion":[{"value":"2025-03-04","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}