{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,15]],"date-time":"2024-08-15T05:09:04Z","timestamp":1723698544055},"publisher-location":"New York, NY, USA","reference-count":93,"publisher":"ACM","content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2022,6,28]]},"DOI":"10.1145\/3524059.3532367","type":"proceedings-article","created":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T16:13:11Z","timestamp":1655395991000},"update-policy":"http:\/\/dx.doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["KrakenOnMem"],"prefix":"10.1145","author":[{"given":"Taha","family":"Shahroodi","sequence":"first","affiliation":[{"name":"TU Delft, Delft, Netherlands"}]},{"given":"Mahdi","family":"Zahedi","sequence":"additional","affiliation":[{"name":"TU Delft, Delft, Netherlands"}]},{"given":"Abhairaj","family":"Singh","sequence":"additional","affiliation":[{"name":"TU Delft, Delft, Netherlands"}]},{"given":"Stephan","family":"Wong","sequence":"additional","affiliation":[{"name":"TU Delft, Delft, Netherlands"}]},{"given":"Said","family":"Hamdioui","sequence":"additional","affiliation":[{"name":"TU Delft, Delft, Netherlands"}]}],"member":"320","published-online":{"date-parts":[[2022,6,28]]},"reference":[{"key":"e_1_3_2_1_1_1","volume-title":"Compute Caches,\" in HPCA","author":"Aga S.","year":"2017","unstructured":"S. Aga , S. Jeloka , A. Subramaniyan , S. Narayanasamy , D. Blaauw , and R. Das , \" Compute Caches,\" in HPCA , 2017 . S. Aga, S. Jeloka, A. Subramaniyan, S. Narayanasamy, D. Blaauw, and R. Das, \"Compute Caches,\" in HPCA, 2017."},{"key":"e_1_3_2_1_2_1","volume-title":"SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs,\" Bioinformatics","author":"Alser M.","year":"2020","unstructured":"M. Alser , T. Shahroodi , J. Gomez-Luna , C. Alkan , and O. Mutlu , \" SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs,\" Bioinformatics , 2020 . M. Alser, T. Shahroodi, J. Gomez-Luna, C. Alkan, and O. Mutlu, \"SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs,\" Bioinformatics, 2020."},{"key":"e_1_3_2_1_3_1","volume-title":"Roy et al., \"PUMA: A programmable ultra-efficient memristor-based accelerator for machine learning inference,\" in ASPLOS","author":"Ankit A.","year":"2019","unstructured":"A. Ankit , I. E. Hajj , S. R. Chalamalasetti , G. Ndu , M. Foltin , R. S. Williams , P. Faraboschi , W.-m. W. Hwu , J. P. Strachan , K. Roy et al., \"PUMA: A programmable ultra-efficient memristor-based accelerator for machine learning inference,\" in ASPLOS , 2019 . A. Ankit, I. E. Hajj, S. R. Chalamalasetti, G. Ndu, M. Foltin, R. S. Williams, P. Faraboschi, W.-m. W. Hwu, J. P. Strachan, K. Roy et al., \"PUMA: A programmable ultra-efficient memristor-based accelerator for machine learning inference,\" in ASPLOS, 2019."},{"key":"e_1_3_2_1_4_1","author":"Banerjee S. S.","year":"2018","unstructured":"S. S. Banerjee , M. El-Hadedy , J. B. Lim , Z. T. Kalbarczyk , D. Chen , S. S. Lumetta , and R. K. Iyer , \"Asap: Accelerated short-read alignment on programmable hardware\" IEEE Transactions on Computers , 2018 . S. S. Banerjee, M. El-Hadedy, J. B. Lim, Z. T. Kalbarczyk, D. Chen, S. S. Lumetta, and R. K. Iyer, \"Asap: Accelerated short-read alignment on programmable hardware\" IEEE Transactions on Computers, 2018.","journal-title":"\"Asap: Accelerated short-read alignment on programmable hardware\" IEEE Transactions on Computers"},{"key":"e_1_3_2_1_5_1","unstructured":"Barba M Czosnek H and Hadidi A \"Cost in US Dollars per Raw Megabase of DNA Sequence \" https:\/\/www.genome.gov\/about-genomics\/fact-sheets\/DNA-Sequencing-Costs-Data. Barba M Czosnek H and Hadidi A \"Cost in US Dollars per Raw Megabase of DNA Sequence \" https:\/\/www.genome.gov\/about-genomics\/fact-sheets\/DNA-Sequencing-Costs-Data."},{"key":"e_1_3_2_1_6_1","volume-title":"PhymmBL expanded: confidence scores, custom databases, parallelization and more,\" Nature methods","author":"Brady A.","year":"2011","unstructured":"A. Brady and S. Salzberg , \" PhymmBL expanded: confidence scores, custom databases, parallelization and more,\" Nature methods , 2011 . A. Brady and S. Salzberg, \"PhymmBL expanded: confidence scores, custom databases, parallelization and more,\" Nature methods, 2011."},{"key":"e_1_3_2_1_7_1","volume-title":"A Review of Methods and Databases for Metagenomic Classification and Assembly,\" Briefings in bioinformatics","author":"Breitwieser F. P.","year":"2019","unstructured":"F. P. Breitwieser , J. Lu , and S. L. Salzberg , \" A Review of Methods and Databases for Metagenomic Classification and Assembly,\" Briefings in bioinformatics , 2019 . F. P. Breitwieser, J. Lu, and S. L. Salzberg, \"A Review of Methods and Databases for Metagenomic Classification and Assembly,\" Briefings in bioinformatics, 2019."},{"key":"e_1_3_2_1_8_1","volume-title":"Boroumand et al., \"GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis,\" in MICRO","author":"Cali D. S.","year":"2020","unstructured":"D. S. Cali , G. S. Kalsi , Z. Bing\u00f6l , C. Firtina , L. Subramanian , J. S. Kim , R. Ausavarungnirun , M. Alser , J. Gomez-Luna , A. Boroumand et al., \"GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis,\" in MICRO , 2020 . D. S. Cali, G. S. Kalsi, Z. Bing\u00f6l, C. Firtina, L. Subramanian, J. S. Kim, R. Ausavarungnirun, M. Alser, J. Gomez-Luna, A. Boroumand et al., \"GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis,\" in MICRO, 2020."},{"key":"e_1_3_2_1_9_1","volume-title":"Wang et al., \"Advances and future prospects of spin-transfer torque random access memory,\" IEEE Transactions on Magnetics","author":"Chen E.","year":"2010","unstructured":"E. Chen , D. Apalkov , Z. Diao , A. Driskill-Smith , D. Druist , D. Lottis , V. Nikitin , X. Tang , S. Watts , S. Wang et al., \"Advances and future prospects of spin-transfer torque random access memory,\" IEEE Transactions on Magnetics , 2010 . E. Chen, D. Apalkov, Z. Diao, A. Driskill-Smith, D. Druist, D. Lottis, V. Nikitin, X. Tang, S. Watts, S. Wang et al., \"Advances and future prospects of spin-transfer torque random access memory,\" IEEE Transactions on Magnetics, 2010."},{"key":"e_1_3_2_1_10_1","doi-asserted-by":"crossref","unstructured":"L. Cheng Y. Li K.-S. Yin S.-Y. Hu Y.-T. Su M.-M. Jin Z.-R. Wang T.-C. Chang and X.-S. Miao \"Functional demonstration of a memristive arithmetic logic unit (memalu) for in-memory computing \" Advanced Functional Materials 2019. L. Cheng Y. Li K.-S. Yin S.-Y. Hu Y.-T. Su M.-M. Jin Z.-R. Wang T.-C. Chang and X.-S. Miao \"Functional demonstration of a memristive arithmetic logic unit (memalu) for in-memory computing \" Advanced Functional Materials 2019.","DOI":"10.1002\/adfm.201905660"},{"key":"e_1_3_2_1_11_1","volume-title":"PRIME: A novel processing-in-memory architecture for neural network computation in reram-based main memory,\" ISCA","author":"Chi P.","year":"2016","unstructured":"P. Chi , S. Li , C. Xu , T. Zhang , J. Zhao , Y. Liu , Y. Wang , and Y. Xie , \" PRIME: A novel processing-in-memory architecture for neural network computation in reram-based main memory,\" ISCA , 2016 . P. Chi, S. Li, C. Xu, T. Zhang, J. Zhao, Y. Liu, Y. Wang, and Y. Xie, \"PRIME: A novel processing-in-memory architecture for neural network computation in reram-based main memory,\" ISCA, 2016."},{"key":"e_1_3_2_1_12_1","volume-title":"SIMD C Library for Global, Semi-global, and Local Pairwise Sequence Alignments,\" BMC bioinformatics","author":"Daily J.","year":"2016","unstructured":"J. Daily , \"Parasail : SIMD C Library for Global, Semi-global, and Local Pairwise Sequence Alignments,\" BMC bioinformatics , 2016 . J. Daily, \"Parasail: SIMD C Library for Global, Semi-global, and Local Pairwise Sequence Alignments,\" BMC bioinformatics, 2016."},{"key":"e_1_3_2_1_13_1","volume-title":"precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods,\" Bioinformatics","author":"Dr\u00f6ge J.","year":"2015","unstructured":"J. Dr\u00f6ge , I. Gregor , and A. C. McHardy , \"Taxator-tk : precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods,\" Bioinformatics , 2015 . J. Dr\u00f6ge, I. Gregor, and A. C. McHardy, \"Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods,\" Bioinformatics, 2015."},{"key":"e_1_3_2_1_14_1","volume-title":"Combining edge and cloud computing for low-power, cost-effective metagenomics analysis\" Future Generation Computer Systems","author":"D'Agostino D.","year":"2019","unstructured":"D. D'Agostino , L. Morganti , E. Corni , D. Cesini , and I. Merelli , \" Combining edge and cloud computing for low-power, cost-effective metagenomics analysis\" Future Generation Computer Systems , 2019 . D. D'Agostino, L. Morganti, E. Corni, D. Cesini, and I. Merelli, \"Combining edge and cloud computing for low-power, cost-effective metagenomics analysis\" Future Generation Computer Systems, 2019."},{"key":"e_1_3_2_1_15_1","volume-title":"Neural cache: Bit-serial in-cache acceleration of deep neural networks,\" in ISCA","author":"Eckert C.","year":"2018","unstructured":"C. Eckert , X. Wang , J. Wang , A. Subramaniyan , R. Iyer , D. Sylvester , D. Blaaauw , and R. Das , \" Neural cache: Bit-serial in-cache acceleration of deep neural networks,\" in ISCA , 2018 . C. Eckert, X. Wang, J. Wang, A. Subramaniyan, R. Iyer, D. Sylvester, D. Blaaauw, and R. Das, \"Neural cache: Bit-serial in-cache acceleration of deep neural networks,\" in ISCA, 2018."},{"key":"e_1_3_2_1_16_1","volume-title":"Fpgasw: Accelerating large-scale smith-waterman sequence alignment application with backtracking on fpga linear systolic array,\" Interdisciplinary Sciences: Computational Life Sciences","author":"Fei X.","year":"2018","unstructured":"X. Fei , Z. Dan , L. Lina , M. Xin , and Z. Chunlei , \" Fpgasw: Accelerating large-scale smith-waterman sequence alignment application with backtracking on fpga linear systolic array,\" Interdisciplinary Sciences: Computational Life Sciences , 2018 . X. Fei, Z. Dan, L. Lina, M. Xin, and Z. Chunlei, \"Fpgasw: Accelerating large-scale smith-waterman sequence alignment application with backtracking on fpga linear systolic array,\" Interdisciplinary Sciences: Computational Life Sciences, 2018."},{"key":"e_1_3_2_1_17_1","volume-title":"Nori et al., \"pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation,\" arXiv preprint","author":"Ferreira J. D.","year":"2021","unstructured":"J. D. Ferreira , G. Falcao , J. G\u00f3mez-Luna , M. Alser , L. Orosa , M. Sadrosadati , J. S. Kim , G. F. Oliveira , T. Shahroodi , A. Nori et al., \"pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation,\" arXiv preprint , 2021 . J. D. Ferreira, G. Falcao, J. G\u00f3mez-Luna, M. Alser, L. Orosa, M. Sadrosadati, J. S. Kim, G. F. Oliveira, T. Shahroodi, A. Nori et al., \"pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation,\" arXiv preprint, 2021."},{"key":"e_1_3_2_1_18_1","volume-title":"A review of scalable bioinformatics pipelines,\" Data Science and Engineering","author":"Fjukstad B.","year":"2017","unstructured":"B. Fjukstad and L. A. Bongo , \" A review of scalable bioinformatics pipelines,\" Data Science and Engineering , 2017 . B. Fjukstad and L. A. Bongo, \"A review of scalable bioinformatics pipelines,\" Data Science and Engineering, 2017."},{"key":"e_1_3_2_1_19_1","volume-title":"Duality cache for data parallel acceleration,\" in ISCA","author":"Fujiki D.","year":"2019","unstructured":"D. Fujiki , S. Mahlke , and R. Das , \" Duality cache for data parallel acceleration,\" in ISCA , 2019 . D. Fujiki, S. Mahlke, and R. Das, \"Duality cache for data parallel acceleration,\" in ISCA, 2019."},{"key":"e_1_3_2_1_20_1","unstructured":"G. V. RESEARCH \"Metagenomics market size share and trends analysis report by product (sequencing and data analytics) by technology (sequencing function) by application (environmental) and segment forecasts 2018 - 2025.\" 2017. G. V. RESEARCH \"Metagenomics market size share and trends analysis report by product (sequencing and data analytics) by technology (sequencing function) by application (environmental) and segment forecasts 2018 - 2025.\" 2017."},{"key":"e_1_3_2_1_21_1","volume-title":"meraligner: A fully parallel sequence aligner,\" in IPDPS","author":"Georganas E.","year":"2015","unstructured":"E. Georganas , A. Bulu\u00e7 , J. Chapman , L. Oliker , D. Rokhsar , and K. Yelick , \" meraligner: A fully parallel sequence aligner,\" in IPDPS , 2015 . E. Georganas, A. Bulu\u00e7, J. Chapman, L. Oliker, D. Rokhsar, and K. Yelick, \"meraligner: A fully parallel sequence aligner,\" in IPDPS, 2015."},{"key":"e_1_3_2_1_22_1","volume-title":"a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes,\" PeerJ","author":"Gregor I.","year":"2016","unstructured":"I. Gregor , J. Dr\u00f6ge , M. Schirmer , C. Quince , and A. C. McHardy , \"PhyloPythiaS+ : a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes,\" PeerJ , 2016 . I. Gregor, J. Dr\u00f6ge, M. Schirmer, C. Quince, and A. C. McHardy, \"PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes,\" PeerJ, 2016."},{"key":"e_1_3_2_1_23_1","volume-title":"Eike et al., \"Memristor based computation-in-memory architecture for data-intensive applications,\" in DATE","author":"Hamdioui S.","year":"2015","unstructured":"S. Hamdioui , L. Xie , H. A. Du Nguyen , M. Taouil , K. Bertels , H. Corp oraal, H. Jiao , F. Catthoor , D. Wouters , L. Eike et al., \"Memristor based computation-in-memory architecture for data-intensive applications,\" in DATE , 2015 . S. Hamdioui, L. Xie, H. A. Du Nguyen, M. Taouil, K. Bertels, H. Corporaal, H. Jiao, F. Catthoor, D. Wouters, L. Eike et al., \"Memristor based computation-in-memory architecture for data-intensive applications,\" in DATE, 2015."},{"key":"e_1_3_2_1_24_1","volume-title":"Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products,\" Chemistry & biology","author":"Handelsman J.","year":"1998","unstructured":"J. Handelsman , M. R. Rondon , S. F. Brady , J. Clardy , and R. M. Goodman , \" Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products,\" Chemistry & biology , 1998 . J. Handelsman, M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman, \"Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products,\" Chemistry & biology, 1998."},{"key":"e_1_3_2_1_25_1","volume-title":"An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm,\" in SAMOS","author":"Houtgast E. J.","year":"2015","unstructured":"E. J. Houtgast , V.-M. Sima , K. Bertels , and Z. Al-Ars , \" An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm,\" in SAMOS , 2015 . E. J. Houtgast, V.-M. Sima, K. Bertels, and Z. Al-Ars, \"An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm,\" in SAMOS, 2015."},{"key":"e_1_3_2_1_26_1","doi-asserted-by":"publisher","DOI":"10.1145\/3352460.3358329"},{"key":"e_1_3_2_1_27_1","doi-asserted-by":"publisher","DOI":"10.1145\/3400302.3415724"},{"key":"e_1_3_2_1_28_1","volume-title":"MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data,\" PLoS computational biology","author":"Huson D. H.","year":"2016","unstructured":"D. H. Huson , S. Beier , I. Flade , A. G\u00f3rska , M. El-Hadidi , S. Mitra , H.-J. Ruscheweyh , and R. Tappu , \" MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data,\" PLoS computational biology , 2016 . D. H. Huson, S. Beier, I. Flade, A. G\u00f3rska, M. El-Hadidi, S. Mitra, H.-J. Ruscheweyh, and R. Tappu, \"MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data,\" PLoS computational biology, 2016."},{"key":"e_1_3_2_1_29_1","volume-title":"Core i9 7900X, i7 7820X and i7 7800X Tested: Die Size Estimates and Arrangements.\" https:\/\/www.anandtech.com\/show\/11550\/the-intel-skylakex-review-core-i9-7900x-i7-7820x-and-i7-7800x-tested\/6","author":"Curtis Ian","year":"2017","unstructured":"Ian Curtis ., \" The Intel Skylake-X Review : Core i9 7900X, i7 7820X and i7 7800X Tested: Die Size Estimates and Arrangements.\" https:\/\/www.anandtech.com\/show\/11550\/the-intel-skylakex-review-core-i9-7900x-i7-7820x-and-i7-7800x-tested\/6 , 2017 . Ian Curtis., \"The Intel Skylake-X Review: Core i9 7900X, i7 7820X and i7 7800X Tested: Die Size Estimates and Arrangements.\" https:\/\/www.anandtech.com\/show\/11550\/the-intel-skylakex-review-core-i9-7900x-i7-7820x-and-i7-7800x-tested\/6, 2017."},{"key":"e_1_3_2_1_30_1","unstructured":"Intel Corp. \"Intel\u00ae Performance Counter Monitor.\" https:\/\/www.intel.com\/software\/pcm 2017. Intel Corp. \"Intel\u00ae Performance Counter Monitor.\" https:\/\/www.intel.com\/software\/pcm 2017."},{"key":"e_1_3_2_1_31_1","volume-title":"RASSA: resistive prealignment accelerator for approximate DNA long read mapping,\" IEEE Micro","author":"Kaplan R.","year":"2018","unstructured":"R. Kaplan , L. Yavits , and R. Ginosar , \" RASSA: resistive prealignment accelerator for approximate DNA long read mapping,\" IEEE Micro , 2018 . R. Kaplan, L. Yavits, and R. Ginosar, \"RASSA: resistive prealignment accelerator for approximate DNA long read mapping,\" IEEE Micro, 2018."},{"key":"e_1_3_2_1_32_1","volume-title":"In-memory hyperdimensional computing,\" Nature Electronics","author":"Karunaratne G.","year":"2020","unstructured":"G. Karunaratne , M. Le Gallo , G. Cherubini , L. Benini , A. Rahimi , and A. Sebastian , \" In-memory hyperdimensional computing,\" Nature Electronics , 2020 . G. Karunaratne, M. Le Gallo, G. Cherubini, L. Benini, A. Rahimi, and A. Sebastian, \"In-memory hyperdimensional computing,\" Nature Electronics, 2020."},{"key":"e_1_3_2_1_33_1","volume-title":"A big data approach to metagenomics for all-food-sequencing,\" BMC bioinformatics","author":"Kobus R.","year":"2020","unstructured":"R. Kobus , J. M. Abu\u00edn , A. M\u00fcller , S. L. Hellmann , J. C. Pichel , T. F. Pena , A. Hildebrandt , T. Hankeln , and B. Schmidt , \" A big data approach to metagenomics for all-food-sequencing,\" BMC bioinformatics , 2020 . R. Kobus, J. M. Abu\u00edn, A. M\u00fcller, S. L. Hellmann, J. C. Pichel, T. F. Pena, A. Hildebrandt, T. Hankeln, and B. Schmidt, \"A big data approach to metagenomics for all-food-sequencing,\" BMC bioinformatics, 2020."},{"key":"e_1_3_2_1_34_1","volume-title":"Accelerating metagenomic read classification on CUDA-enabled GPUs,\" BMC bioinformatics","author":"Kobus R.","year":"2017","unstructured":"R. Kobus , C. Hundt , A. M\u00fcller , and B. Schmidt , \" Accelerating metagenomic read classification on CUDA-enabled GPUs,\" BMC bioinformatics , 2017 . R. Kobus, C. Hundt, A. M\u00fcller, and B. Schmidt, \"Accelerating metagenomic read classification on CUDA-enabled GPUs,\" BMC bioinformatics, 2017."},{"key":"e_1_3_2_1_35_1","volume-title":"KMC 3: counting and manipulating k-mer statistics,\" Bioinformatics","author":"Kokot M.","year":"2017","unstructured":"M. Kokot , M. D\u0142ugosz , and S. Deorowicz , \" KMC 3: counting and manipulating k-mer statistics,\" Bioinformatics , 2017 . M. Kokot, M. D\u0142ugosz, and S. Deorowicz, \"KMC 3: counting and manipulating k-mer statistics,\" Bioinformatics, 2017."},{"key":"e_1_3_2_1_36_1","volume-title":"Cross-layer design and analysis of a low power, high density STT-MRAM for embedded systems,\" in ISCAS","author":"Komalan M.","year":"2017","unstructured":"M. Komalan , S. Sakhare , T. H. Bao , S. Rao , W. Kim , C. Tenllado , J. I. G\u00f3mez , G. S. Kar , A. Furnemont , and F. Catthoor , \" Cross-layer design and analysis of a low power, high density STT-MRAM for embedded systems,\" in ISCAS , 2017 . M. Komalan, S. Sakhare, T. H. Bao, S. Rao, W. Kim, C. Tenllado, J. I. G\u00f3mez, G. S. Kar, A. Furnemont, and F. Catthoor, \"Cross-layer design and analysis of a low power, high density STT-MRAM for embedded systems,\" in ISCAS, 2017."},{"key":"e_1_3_2_1_37_1","volume-title":"MAGIC---Memristor-aided logic\" TCAS II","author":"Kvatinsky S.","year":"2014","unstructured":"S. Kvatinsky , D. Belousov , S. Liman , G. Satat , N. Wald , E. G. Friedman , A. Kolodny , and U. C. Weiser , \" MAGIC---Memristor-aided logic\" TCAS II , 2014 . S. Kvatinsky, D. Belousov, S. Liman, G. Satat, N. Wald, E. G. Friedman, A. Kolodny, and U. C. Weiser, \"MAGIC---Memristor-aided logic\" TCAS II, 2014."},{"key":"e_1_3_2_1_38_1","volume-title":"Seed-and-vote based in-memory accelerator for dna read mapping\" in ICCAD","author":"Laguna A. F.","year":"2020","unstructured":"A. F. Laguna , H. Gamaarachchi , X. Yin , M. Niemier , S. Parameswaran , and X. S. Hu , \" Seed-and-vote based in-memory accelerator for dna read mapping\" in ICCAD , 2020 . A. F. Laguna, H. Gamaarachchi, X. Yin, M. Niemier, S. Parameswaran, and X. S. Hu, \"Seed-and-vote based in-memory accelerator for dna read mapping\" in ICCAD, 2020."},{"key":"e_1_3_2_1_39_1","volume-title":"Scaling read aligners to hundreds of threads on general-purpose processors,\" Bioinformatics","author":"Langmead B.","year":"2019","unstructured":"B. Langmead , C. Wilks , V. Antonescu , and R. Charles , \" Scaling read aligners to hundreds of threads on general-purpose processors,\" Bioinformatics , 2019 . B. Langmead, C. Wilks, V. Antonescu, and R. Charles, \"Scaling read aligners to hundreds of threads on general-purpose processors,\" Bioinformatics, 2019."},{"key":"e_1_3_2_1_40_1","volume-title":"Metalign: Efficient Alignment-Based Metagenomic Profiling via Containment Min Hash,\" BioRxiv","author":"LaPierre N.","year":"2020","unstructured":"N. LaPierre , M. Alser , E. Eskin , D. Koslicki , and S. Mangul , \" Metalign: Efficient Alignment-Based Metagenomic Profiling via Containment Min Hash,\" BioRxiv , 2020 . N. LaPierre, M. Alser, E. Eskin, D. Koslicki, and S. Mangul, \"Metalign: Efficient Alignment-Based Metagenomic Profiling via Containment Min Hash,\" BioRxiv, 2020."},{"key":"e_1_3_2_1_41_1","volume-title":"MiCoP: Microbial Community Profiling Method for Detecting Viral and Fungal Organisms in Metagenomic Samples,\" BMC genomics","author":"LaPierre N.","year":"2019","unstructured":"N. LaPierre , S. Mangul , M. Alser , I. Mandric , N. C. Wu , D. Koslicki , and E. Eskin , \" MiCoP: Microbial Community Profiling Method for Detecting Viral and Fungal Organisms in Metagenomic Samples,\" BMC genomics , 2019 . N. LaPierre, S. Mangul, M. Alser, I. Mandric, N. C. Wu, D. Koslicki, and E. Eskin, \"MiCoP: Microbial Community Profiling Method for Detecting Viral and Fungal Organisms in Metagenomic Samples,\" BMC genomics, 2019."},{"key":"e_1_3_2_1_42_1","volume-title":"Phase change memory architecture and the quest for scalability,\" Communications of the ACM","author":"Lee B. C.","year":"2010","unstructured":"B. C. Lee , E. Ipek , O. Mutlu , and D. Burger , \" Phase change memory architecture and the quest for scalability,\" Communications of the ACM , 2010 . B. C. Lee, E. Ipek, O. Mutlu, and D. Burger, \"Phase change memory architecture and the quest for scalability,\" Communications of the ACM, 2010."},{"key":"e_1_3_2_1_43_1","doi-asserted-by":"crossref","unstructured":"J. Leipzig \"A review of bioinformatic pipeline frameworks \" Briefings in bioinformatics 2017. J. Leipzig \"A review of bioinformatic pipeline frameworks \" Briefings in bioinformatics 2017.","DOI":"10.1093\/bib\/bbw020"},{"key":"e_1_3_2_1_44_1","doi-asserted-by":"publisher","DOI":"10.1145\/3123939.3123977"},{"key":"e_1_3_2_1_45_1","doi-asserted-by":"publisher","DOI":"10.1145\/2897937.2898064"},{"key":"e_1_3_2_1_46_1","volume-title":"Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences,\" Genome biology","author":"Liu B.","year":"2011","unstructured":"B. Liu , T. Gibbons , M. Ghodsi , T. Treangen , and M. Pop , \" Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences,\" Genome biology , 2011 . B. Liu, T. Gibbons, M. Ghodsi, T. Treangen, and M. Pop, \"Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences,\" Genome biology, 2011."},{"key":"e_1_3_2_1_47_1","volume-title":"GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences,\" Concurrency and Computation: Practice and Experience","author":"Liu Y.","year":"2015","unstructured":"Y. Liu and B. Schmidt , \" GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences,\" Concurrency and Computation: Practice and Experience , 2015 . Y. Liu and B. Schmidt, \"GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences,\" Concurrency and Computation: Practice and Experience, 2015."},{"key":"e_1_3_2_1_48_1","volume-title":"CUDASW++ 3.0: Accelerating Smith-Waterman Protein Database Search by Coupling CPU and GPU SIMD Instructions,\" BMC bioinformatics","author":"Liu Y.","year":"2013","unstructured":"Y. Liu , A. Wirawan , and B. Schmidt , \" CUDASW++ 3.0: Accelerating Smith-Waterman Protein Database Search by Coupling CPU and GPU SIMD Instructions,\" BMC bioinformatics , 2013 . Y. Liu, A. Wirawan, and B. Schmidt, \"CUDASW++ 3.0: Accelerating Smith-Waterman Protein Database Search by Coupling CPU and GPU SIMD Instructions,\" BMC bioinformatics, 2013."},{"key":"e_1_3_2_1_49_1","doi-asserted-by":"publisher","DOI":"10.1145\/3410463.3414626"},{"key":"e_1_3_2_1_50_1","author":"Lou Q.","year":"2018","unstructured":"Q. Lou and L. Jiang , \"BRAWL: A Spintronics-Based Portable Basecalling-in-Memory Architecture for Nanopore Genome Sequencing\" IEEE Computer Architecture Letters 2018 . Q. Lou and L. Jiang, \"BRAWL: A Spintronics-Based Portable Basecalling-in-Memory Architecture for Nanopore Genome Sequencing\" IEEE Computer Architecture Letters 2018.","journal-title":"\"BRAWL: A Spintronics-Based Portable Basecalling-in-Memory Architecture for Nanopore Genome Sequencing\" IEEE Computer Architecture Letters"},{"key":"e_1_3_2_1_51_1","volume-title":"Estimating Species Abundance in Metagenomics Data \" PeerJ Computer Science","author":"Thielen J. Lu F. P.","year":"2017","unstructured":"J. Lu F. P. Breitwieser P. Thielen and S. L. Salzberg \" Bracken : Estimating Species Abundance in Metagenomics Data \" PeerJ Computer Science , 2017 . J. Lu F. P. Breitwieser P. Thielen and S. L. Salzberg \"Bracken: Estimating Species Abundance in Metagenomics Data \" PeerJ Computer Science, 2017."},{"key":"e_1_3_2_1_52_1","volume-title":"Evolutionary path to building next generation interconnects,\" in 11th Symposium on High Performance Interconnects","author":"Mayhew D.","year":"2003","unstructured":"D. Mayhew and V. Krishnan \"PCI Express and Advanced Switching : Evolutionary path to building next generation interconnects,\" in 11th Symposium on High Performance Interconnects , 2003 . D. Mayhew and V. Krishnan \"PCI Express and Advanced Switching: Evolutionary path to building next generation interconnects,\" in 11th Symposium on High Performance Interconnects, 2003."},{"key":"e_1_3_2_1_53_1","volume-title":"Pci express and advanced switching: Evolutionary path to building next generation interconnects,\" in HOTI","author":"Mayhew D.","year":"2003","unstructured":"D. Mayhew and V. Krishnan , \" Pci express and advanced switching: Evolutionary path to building next generation interconnects,\" in HOTI , 2003 . D. Mayhew and V. Krishnan, \"Pci express and advanced switching: Evolutionary path to building next generation interconnects,\" in HOTI, 2003."},{"key":"e_1_3_2_1_54_1","volume-title":"Ahsanuddin et al., \"Comprehensive benchmarking and ensemble approaches for metagenomic classifiers,\" Genome biology","author":"McIntyre A. B.","year":"2017","unstructured":"A. B. McIntyre , R. Ounit , E. Afshinnekoo , R. J. Prill , E. H\u00e9naff , N. Alexander , S. S. Minot , D. Danko , J. Foox , S. Ahsanuddin et al., \"Comprehensive benchmarking and ensemble approaches for metagenomic classifiers,\" Genome biology , 2017 . A. B. McIntyre, R. Ounit, E. Afshinnekoo, R. J. Prill, E. H\u00e9naff, N. Alexander, S. S. Minot, D. Danko, J. Foox, S. Ahsanuddin et al., \"Comprehensive benchmarking and ensemble approaches for metagenomic classifiers,\" Genome biology, 2017."},{"key":"e_1_3_2_1_55_1","volume-title":"Fog computing makes bioinformatics ready for the Internet of Things,\" Future Generation Computer Systems","author":"Merelli I.","year":"2018","unstructured":"I. Merelli , L. Morganti , E. Corni , C. Pellegrino , D. Cesini , L. Roverelli , G. Zereik , and D. D'Agostino , \"Low-power portable devices for metagenomics analysis : Fog computing makes bioinformatics ready for the Internet of Things,\" Future Generation Computer Systems , 2018 . I. Merelli, L. Morganti, E. Corni, C. Pellegrino, D. Cesini, L. Roverelli, G. Zereik, and D. D'Agostino, \"Low-power portable devices for metagenomics analysis: Fog computing makes bioinformatics ready for the Internet of Things,\" Future Generation Computer Systems, 2018."},{"key":"e_1_3_2_1_56_1","volume-title":"Bertrand et al., \"Critical Assessment of Metagenome Interpretation-the second round of challenges,\" bioRxiv","author":"Meyer F.","year":"2021","unstructured":"F. Meyer , A. Fritz , Z.-L. Deng , D. Koslicki , A. Gurevich , G. Robertson , M. Alser , D. Antipov , F. Beghini , D. Bertrand et al., \"Critical Assessment of Metagenome Interpretation-the second round of challenges,\" bioRxiv , 2021 . F. Meyer, A. Fritz, Z.-L. Deng, D. Koslicki, A. Gurevich, G. Robertson, M. Alser, D. Antipov, F. Beghini, D. Bertrand et al., \"Critical Assessment of Metagenome Interpretation-the second round of challenges,\" bioRxiv, 2021."},{"key":"e_1_3_2_1_57_1","volume-title":"MG-RAST version 4---lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis,\" Briefings in bioinformatics","author":"Meyer F.","year":"2019","unstructured":"F. Meyer , S. Bagchi , S. Chaterji , W. Gerlach , A. Grama , T. Harrison , T. Paczian , W. L. Trimble , and A. Wilke , \" MG-RAST version 4---lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis,\" Briefings in bioinformatics , 2019 . F. Meyer, S. Bagchi, S. Chaterji, W. Gerlach, A. Grama, T. Harrison, T. Paczian, W. L. Trimble, and A. Wilke, \"MG-RAST version 4---lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis,\" Briefings in bioinformatics, 2019."},{"key":"e_1_3_2_1_58_1","unstructured":"MNEMOSENE partners \"The MNEMOSENE project.\" http:\/\/www.mnemosene.eu\/ 2020. MNEMOSENE partners \"The MNEMOSENE project.\" http:\/\/www.mnemosene.eu\/ 2020."},{"key":"e_1_3_2_1_59_1","volume-title":"A classification of memory-centric computing\" JETC","author":"Nguyen H. A. D.","year":"2020","unstructured":"H. A. D. Nguyen , J. Yu , M. A. Lebdeh , M. Taouil , S. Hamdioui , and F. Catthoor , \" A classification of memory-centric computing\" JETC , 2020 . H. A. D. Nguyen, J. Yu, M. A. Lebdeh, M. Taouil, S. Hamdioui, and F. Catthoor, \"A classification of memory-centric computing\" JETC, 2020."},{"key":"e_1_3_2_1_60_1","volume-title":"CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers,\" BMC genomics","author":"Ounit R.","year":"2015","unstructured":"R. Ounit , S. Wanamaker , T.J. Close , and S. Lonardi , \" CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers,\" BMC genomics , 2015 . R. Ounit, S. Wanamaker, T.J. Close, and S. Lonardi, \"CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers,\" BMC genomics, 2015."},{"key":"e_1_3_2_1_61_1","unstructured":"PCI-SIG \"PCI-E Specification.\" https:\/\/pcisig.com\/specifications. PCI-SIG \"PCI-E Specification.\" https:\/\/pcisig.com\/specifications."},{"key":"e_1_3_2_1_62_1","volume-title":"NVMExplorer: A Framework for Cross-Stack Comparisons of Embedded NonVolatile Memories\" HPCA","author":"Pentecost L.","year":"2021","unstructured":"L. Pentecost , A. Hankin , M. Donato , M. Hempstead , G.-Y. Wei , and D. Brooks , \" NVMExplorer: A Framework for Cross-Stack Comparisons of Embedded NonVolatile Memories\" HPCA , 2021 . L. Pentecost, A. Hankin, M. Donato, M. Hempstead, G.-Y. Wei, and D. Brooks, \"NVMExplorer: A Framework for Cross-Stack Comparisons of Embedded NonVolatile Memories\" HPCA, 2021."},{"key":"e_1_3_2_1_63_1","volume-title":"Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses\" Microbial Genomics","author":"P\u00e9rez-Cobas A. E.","year":"2020","unstructured":"A. E. P\u00e9rez-Cobas , L. Gomez-Valero , and C. Buchrieser , \" Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses\" Microbial Genomics , 2020 . A. E. P\u00e9rez-Cobas, L. Gomez-Valero, and C. Buchrieser, \"Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses\" Microbial Genomics, 2020."},{"key":"e_1_3_2_1_64_1","volume-title":"O'Sullivan et al., \"STT-MRAM array performance improvement through optimization of Ion Beam Etch and MTJ for Last-Level Cache application\" in IMW","author":"Rao S.","year":"2021","unstructured":"S. Rao , W. Kim , S. van Beek , S. Kundu , M. Perumkunnil , S. Cosemans , F. Yasin , S. Couet , R. Carpenter , B. O'Sullivan et al., \"STT-MRAM array performance improvement through optimization of Ion Beam Etch and MTJ for Last-Level Cache application\" in IMW , 2021 . S. Rao, W. Kim, S. van Beek, S. Kundu, M. Perumkunnil, S. Cosemans, F. Yasin, S. Couet, R. Carpenter, B. O'Sullivan et al., \"STT-MRAM array performance improvement through optimization of Ion Beam Etch and MTJ for Last-Level Cache application\" in IMW, 2021."},{"key":"e_1_3_2_1_65_1","volume-title":"GASSST: global alignment short sequence search tool\" Bioinformatics","author":"Rizk G.","year":"2010","unstructured":"G. Rizk and D. Lavenier , \" GASSST: global alignment short sequence search tool\" Bioinformatics , 2010 . G. Rizk and D. Lavenier, \"GASSST: global alignment short sequence search tool\" Bioinformatics, 2010."},{"key":"e_1_3_2_1_66_1","volume-title":"Reducing storage requirements for biological sequence comparison\" Bioinformatics","author":"Roberts M.","year":"2004","unstructured":"M. Roberts , W. Hayes , B. R. Hunt , S. M. Mount , and J. A. Yorke , \" Reducing storage requirements for biological sequence comparison\" Bioinformatics , 2004 . M. Roberts, W. Hayes, B. R. Hunt, S. M. Mount, and J. A. Yorke, \"Reducing storage requirements for biological sequence comparison\" Bioinformatics, 2004."},{"key":"e_1_3_2_1_67_1","volume-title":"Environ. Microbiol.","author":"Rondon M. R.","year":"2000","unstructured":"M. R. Rondon , P. R. August , A. D. Bettermann , S. F. Brady , T. H. Grossman , M. R. Liles , K. A. Loiacono , B. A. Lynch , I. A. MacNeil , C. Minor et al., \"Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms\" Appl . Environ. Microbiol. , 2000 . M. R. Rondon, P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, M. R. Liles, K. A. Loiacono, B. A. Lynch, I. A. MacNeil, C. Minor et al., \"Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms\" Appl. Environ. Microbiol., 2000."},{"key":"e_1_3_2_1_68_1","volume-title":"Dahms et al., \"Critical assessment of metagenome interpretation---a benchmark of metagenomics software\" Nature methods","author":"Sczyrba A.","year":"2017","unstructured":"A. Sczyrba , P. Hofmann , P. Belmann , D. Koslicki , S. Janssen , J. Dr\u00f6ge , I. Gregor , S. Majda , J. Fiedler , E. Dahms et al., \"Critical assessment of metagenome interpretation---a benchmark of metagenomics software\" Nature methods , 2017 . A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki, S. Janssen, J. Dr\u00f6ge, I. Gregor, S. Majda, J. Fiedler, E. Dahms et al., \"Critical assessment of metagenome interpretation---a benchmark of metagenomics software\" Nature methods, 2017."},{"key":"e_1_3_2_1_69_1","volume-title":"Metagenomic microbial community profiling using unique clade-specific marker genes\" Nature methods","author":"Segata N.","year":"2012","unstructured":"N. Segata , L. Waldron , A. Ballarini , V. Narasimhan , O. Jousson , and C. Hutten-hower , \" Metagenomic microbial community profiling using unique clade-specific marker genes\" Nature methods , 2012 . N. Segata, L. Waldron, A. Ballarini, V. Narasimhan, O. Jousson, and C. Hutten-hower, \"Metagenomic microbial community profiling using unique clade-specific marker genes\" Nature methods, 2012."},{"key":"e_1_3_2_1_70_1","volume-title":"Metagenomic microbial community profiling using unique clade-specific marker genes\" Nature methods","author":"Segata N.","year":"2012","unstructured":"N. Segata , L. Waldron , A. Ballarini , V. Narasimhan , O. Jousson , and C. Huttenhower , \" Metagenomic microbial community profiling using unique clade-specific marker genes\" Nature methods , 2012 . N. Segata, L. Waldron, A. Ballarini, V. Narasimhan, O. Jousson, and C. Huttenhower, \"Metagenomic microbial community profiling using unique clade-specific marker genes\" Nature methods, 2012."},{"key":"e_1_3_2_1_71_1","doi-asserted-by":"publisher","DOI":"10.1145\/3123939.3124544"},{"key":"e_1_3_2_1_72_1","volume-title":"ISAAC: A convolutional neural network accelerator with in-situ analog arithmetic in crossbars\" ISCA","author":"Shafiee A.","year":"2016","unstructured":"A. Shafiee , A. Nag , N. Muralimanohar , R. Balasubramonian , J. P. Strachan , M. Hu , R. S. Williams , and V. Srikumar , \" ISAAC: A convolutional neural network accelerator with in-situ analog arithmetic in crossbars\" ISCA , 2016 . A. Shafiee, A. Nag, N. Muralimanohar, R. Balasubramonian, J. P. Strachan, M. Hu, R. S. Williams, and V. Srikumar, \"ISAAC: A convolutional neural network accelerator with in-situ analog arithmetic in crossbars\" ISCA, 2016."},{"key":"e_1_3_2_1_73_1","volume-title":"Scaling equations for the accurate prediction of CMOS device performance from 180 nm to 7 nm\" Integration","author":"Stillmaker A.","year":"2017","unstructured":"A. Stillmaker and B. Baas , \" Scaling equations for the accurate prediction of CMOS device performance from 180 nm to 7 nm\" Integration , 2017 . A. Stillmaker and B. Baas, \"Scaling equations for the accurate prediction of CMOS device performance from 180 nm to 7 nm\" Integration, 2017."},{"key":"e_1_3_2_1_74_1","unstructured":"Synopsys Inc. \"Synopsys Design Compiler\" https:\/\/www.synopsys.com\/support\/training\/rtl-synthesis\/design-compiler-rtl-synthesis.html. Synopsys Inc. \"Synopsys Design Compiler\" https:\/\/www.synopsys.com\/support\/training\/rtl-synthesis\/design-compiler-rtl-synthesis.html."},{"key":"e_1_3_2_1_75_1","volume-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling\" Nature methods","author":"Truong D. T.","year":"2015","unstructured":"D. T. Truong , E. A. Franzosa , T. L. Tickle , M. Scholz , G. Weingart , E. Pasolli , A. Tett , C. Huttenhower , and N. Segata , \" MetaPhlAn2 for enhanced metagenomic taxonomic profiling\" Nature methods , 2015 . D. T. Truong, E. A. Franzosa, T. L. Tickle, M. Scholz, G. Weingart, E. Pasolli, A. Tett, C. Huttenhower, and N. Segata, \"MetaPhlAn2 for enhanced metagenomic taxonomic profiling\" Nature methods, 2015."},{"key":"e_1_3_2_1_76_1","volume-title":"Darwin: A genomics co-processor provides up to 15,000x acceleration on long read assembly\" ACM SIGPLAN Notices","author":"Turakhia Y.","year":"2018","unstructured":"Y. Turakhia , G. Bejerano , and W. J. Dally , \" Darwin: A genomics co-processor provides up to 15,000x acceleration on long read assembly\" ACM SIGPLAN Notices , 2018 . Y. Turakhia, G. Bejerano, and W. J. Dally, \"Darwin: A genomics co-processor provides up to 15,000x acceleration on long read assembly\" ACM SIGPLAN Notices, 2018."},{"key":"e_1_3_2_1_77_1","volume-title":"FPGA-accelerator for DNA sequence alignment based on an efficient data-dependent memory access scheme\" Highly-Efficient Accelerators and Reconfigurable Technologies","author":"Waidyasooriya H. M.","year":"2014","unstructured":"H. M. Waidyasooriya , M. Hariyama , and M. Kameyama , \" FPGA-accelerator for DNA sequence alignment based on an efficient data-dependent memory access scheme\" Highly-Efficient Accelerators and Reconfigurable Technologies , 2014 . H. M. Waidyasooriya, M. Hariyama, and M. Kameyama, \"FPGA-accelerator for DNA sequence alignment based on an efficient data-dependent memory access scheme\" Highly-Efficient Accelerators and Reconfigurable Technologies, 2014."},{"key":"e_1_3_2_1_78_1","author":"Wang K.","year":"2013","unstructured":"K. Wang , J. Alzate , and P. K. Amiri , \"Low-power non-volatile spintronic memory: STT-RAM and beyond,\" Journal of Physics D: Applied Physics , 2013 . K. Wang, J. Alzate, and P. K. Amiri, \"Low-power non-volatile spintronic memory: STT-RAM and beyond,\" Journal of Physics D: Applied Physics, 2013.","journal-title":"\"Low-power non-volatile spintronic memory: STT-RAM and beyond,\" Journal of Physics D: Applied Physics"},{"key":"e_1_3_2_1_79_1","doi-asserted-by":"publisher","DOI":"10.1145\/2744769.2744897"},{"key":"e_1_3_2_1_80_1","volume-title":"Redox-based resistive switching memories-nanoionic mechanisms, prospects, and challenges\" Advanced materials","author":"Waser R.","year":"2009","unstructured":"R. Waser , R. Dittmann , G. Staikov , and K. Szot , \" Redox-based resistive switching memories-nanoionic mechanisms, prospects, and challenges\" Advanced materials , 2009 . R. Waser, R. Dittmann, G. Staikov, and K. Szot, \"Redox-based resistive switching memories-nanoionic mechanisms, prospects, and challenges\" Advanced materials, 2009."},{"key":"e_1_3_2_1_81_1","volume-title":"RazerS 3: faster, fully sensitive read mapping,\" Bioinformatics","author":"Weese D.","year":"2012","unstructured":"D. Weese , M. Holtgrewe , and K. Reinert , \" RazerS 3: faster, fully sensitive read mapping,\" Bioinformatics , 2012 . D. Weese, M. Holtgrewe, and K. Reinert, \"RazerS 3: faster, fully sensitive read mapping,\" Bioinformatics, 2012."},{"key":"e_1_3_2_1_82_1","unstructured":"Wetterstrand KA. \"DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) \" https:\/\/www.genome.gov\/sequencingcostsdata. Wetterstrand KA. \"DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) \" https:\/\/www.genome.gov\/sequencingcostsdata."},{"key":"e_1_3_2_1_83_1","volume-title":"Improved Metagenomic Analysis with Kraken 2,\" Genome biology","author":"Wood D. E.","year":"2019","unstructured":"D. E. Wood , J. Lu , and B. Langmead , \" Improved Metagenomic Analysis with Kraken 2,\" Genome biology , 2019 . D. E. Wood, J. Lu, and B. Langmead, \"Improved Metagenomic Analysis with Kraken 2,\" Genome biology, 2019."},{"key":"e_1_3_2_1_84_1","volume-title":"Kraken 2 Open-Sourced Implementation.\" https:\/\/github.com\/DerrickWood\/kraken2","author":"Wood D. E.","year":"2019","unstructured":"D. E. Wood , J. Lu , and B. Langmead , \" Kraken 2 Open-Sourced Implementation.\" https:\/\/github.com\/DerrickWood\/kraken2 , 2019 . D. E. Wood, J. Lu, and B. Langmead, \"Kraken 2 Open-Sourced Implementation.\" https:\/\/github.com\/DerrickWood\/kraken2, 2019."},{"key":"e_1_3_2_1_85_1","volume-title":"Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments,\" Genome biology","author":"Wood D. E.","year":"2014","unstructured":"D. E. Wood and S. L. Salzberg , \" Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments,\" Genome biology , 2014 . D. E. Wood and S. L. Salzberg, \"Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments,\" Genome biology, 2014."},{"key":"e_1_3_2_1_86_1","volume-title":"A primer on metagenomics,\" PLoS Comput Biol","author":"Wooley J. C.","year":"2010","unstructured":"J. C. Wooley , A. Godzik , and I. Friedberg , \" A primer on metagenomics,\" PLoS Comput Biol , 2010 . J. C. Wooley, A. Godzik, and I. Friedberg, \"A primer on metagenomics,\" PLoS Comput Biol, 2010."},{"key":"e_1_3_2_1_87_1","volume-title":"Sieve: Scalable in-situ dram-based accelerator designs for massively parallel k-mer matching,\" in ISCA","author":"Wu L.","year":"2021","unstructured":"L. Wu , R. Sharifi , M. Lenjani , K. Skadron , and A. Venkat , \" Sieve: Scalable in-situ dram-based accelerator designs for massively parallel k-mer matching,\" in ISCA , 2021 . L. Wu, R. Sharifi, M. Lenjani, K. Skadron, and A. Venkat, \"Sieve: Scalable in-situ dram-based accelerator designs for massively parallel k-mer matching,\" in ISCA, 2021."},{"key":"e_1_3_2_1_88_1","volume-title":"Memristive crossbar arrays for brain-inspired computing\" Nature materials","author":"Xia Q.","year":"2019","unstructured":"Q. Xia and J. J. Yang , \" Memristive crossbar arrays for brain-inspired computing\" Nature materials , 2019 . Q. Xia and J. J. Yang, \"Memristive crossbar arrays for brain-inspired computing\" Nature materials, 2019."},{"key":"e_1_3_2_1_89_1","volume-title":"Scouting logic: A novel memristor-based logic design for resistive computing,\" in ISVLSI","author":"Xie L.","year":"2017","unstructured":"L. Xie , H. A. Du Nguyen , J. Yu , A. Kaichouhi , M. Taouil , M. AlFailakawi , and S. Hamdioui , \" Scouting logic: A novel memristor-based logic design for resistive computing,\" in ISVLSI , 2017 . L. Xie, H. A. Du Nguyen, J. Yu, A. Kaichouhi, M. Taouil, M. AlFailakawi, and S. Hamdioui, \"Scouting logic: A novel memristor-based logic design for resistive computing,\" in ISVLSI, 2017."},{"key":"e_1_3_2_1_90_1","volume-title":"Accelerating read mapping with FastHASH,\" in BMC genomics","author":"Xin H.","year":"2013","unstructured":"H. Xin , D. Lee , F. Hormozdiari , S. Yedkar , O. Mutlu , and C. Alkan , \" Accelerating read mapping with FastHASH,\" in BMC genomics , 2013 . H. Xin, D. Lee, F. Hormozdiari, S. Yedkar, O. Mutlu, and C. Alkan, \"Accelerating read mapping with FastHASH,\" in BMC genomics, 2013."},{"key":"e_1_3_2_1_91_1","volume-title":"Efficient organization of digital periphery to support integer datatype for memristor-based cim,\" in ISVLSI","author":"Zahedi M.","year":"2020","unstructured":"M. Zahedi , M. Mayahinia , M. A. Lebdeh , S. Wong , and S. Hamdioui , \" Efficient organization of digital periphery to support integer datatype for memristor-based cim,\" in ISVLSI , 2020 . M. Zahedi, M. Mayahinia, M. A. Lebdeh, S. Wong, and S. Hamdioui, \"Efficient organization of digital periphery to support integer datatype for memristor-based cim,\" in ISVLSI, 2020."},{"key":"e_1_3_2_1_92_1","volume-title":"Tile Architecture and Hardware Implementation for Computation-in-Memory,\" in ISVLSI","author":"Zahedi M.","year":"2021","unstructured":"M. Zahedi , R. van Duijnen , S. Wong , and S. Hamdioui , \" Tile Architecture and Hardware Implementation for Computation-in-Memory,\" in ISVLSI , 2021 . M. Zahedi, R. van Duijnen, S. Wong, and S. Hamdioui, \"Tile Architecture and Hardware Implementation for Computation-in-Memory,\" in ISVLSI, 2021."},{"key":"e_1_3_2_1_93_1","volume-title":"A process-in-memory architecture for short read alignment in rerams,\" IEEE Computer Architecture Letters","author":"Zokaee F.","year":"2018","unstructured":"F. Zokaee , H. R. Zarandi , and L. Jiang , \"Aligner : A process-in-memory architecture for short read alignment in rerams,\" IEEE Computer Architecture Letters , 2018 . F. Zokaee, H. R. Zarandi, and L.Jiang, \"Aligner: A process-in-memory architecture for short read alignment in rerams,\" IEEE Computer Architecture Letters, 2018."}],"event":{"name":"ICS '22: 2022 International Conference on Supercomputing","location":"Virtual Event","acronym":"ICS '22","sponsor":["SIGARCH ACM Special Interest Group on Computer Architecture"]},"container-title":["Proceedings of the 36th ACM International Conference on Supercomputing"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3524059.3532367","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,22]],"date-time":"2023-08-22T19:13:36Z","timestamp":1692731616000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3524059.3532367"}},"subtitle":["a memristor-augmented HW\/SW framework for taxonomic profiling"],"short-title":[],"issued":{"date-parts":[[2022,6,28]]},"references-count":93,"alternative-id":["10.1145\/3524059.3532367","10.1145\/3524059"],"URL":"https:\/\/doi.org\/10.1145\/3524059.3532367","relation":{},"subject":[],"published":{"date-parts":[[2022,6,28]]},"assertion":[{"value":"2022-06-28","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}