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@article{DBLP:journals/taco/FirtinaPKSCKSCLAGSM24,
author = {Can Firtina and
Kamlesh R. Pillai and
Gurpreet S. Kalsi and
Bharathwaj Suresh and
Damla Senol Cali and
Jeremie S. Kim and
Taha Shahroodi and
Meryem Banu Cavlak and
Jo{\"{e}}l Lindegger and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Sreenivas Subramoney and
Onur Mutlu},
title = {ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient
Genome Analysis},
journal = {{ACM} Trans. Archit. Code Optim.},
volume = {21},
number = {1},
pages = {19:1--19:29},
year = {2024},
url = {https://doi.org/10.1145/3632950},
doi = {10.1145/3632950},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/taco/FirtinaPKSCKSCLAGSM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LindeggerCAGMM23,
author = {Jo{\"{e}}l Lindegger and
Damla Senol Cali and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Nika Mansouri{-}Ghiasi and
Onur Mutlu},
title = {Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs,
GPUs, and ASICs},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad151},
doi = {10.1093/BIOINFORMATICS/BTAD151},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LindeggerCAGMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/aisy/MutluAS22,
author = {Senol Mutlu and
Amirreza Aghakhani and
Metin Sitti},
title = {Piezo Capsule: Ultrasonic Way of Wireless Pressure Measurement},
journal = {Adv. Intell. Syst.},
volume = {4},
number = {10},
year = {2022},
url = {https://doi.org/10.1002/aisy.202200125},
doi = {10.1002/AISY.202200125},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/aisy/MutluAS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KimFCCAM22,
author = {Jeremie S. Kim and
Can Firtina and
Meryem Banu Cavlak and
Damla Senol Cali and
Can Alkan and
Onur Mutlu},
title = {FastRemap: a tool for quickly remapping reads between genome assemblies},
journal = {Bioinform.},
volume = {38},
number = {19},
pages = {4633--4635},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac554},
doi = {10.1093/BIOINFORMATICS/BTAC554},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KimFCCAM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/asplos/Mansouri-Ghiasi22,
author = {Nika Mansouri{-}Ghiasi and
Jisung Park and
Harun Mustafa and
Jeremie S. Kim and
Ataberk Olgun and
Arvid Gollwitzer and
Damla Senol Cali and
Can Firtina and
Haiyu Mao and
Nour Almadhoun Alserr and
Rachata Ausavarungnirun and
Nandita Vijaykumar and
Mohammed Alser and
Onur Mutlu},
editor = {Babak Falsafi and
Michael Ferdman and
Shan Lu and
Thomas F. Wenisch},
title = {GenStore: a high-performance in-storage processing system for genome
sequence analysis},
booktitle = {{ASPLOS} '22: 27th {ACM} International Conference on Architectural
Support for Programming Languages and Operating Systems, Lausanne,
Switzerland, 28 February 2022 - 4 March 2022},
pages = {635--654},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3503222.3507702},
doi = {10.1145/3503222.3507702},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/asplos/Mansouri-Ghiasi22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LindeggerCAGM22,
author = {Jo{\"{e}}l Lindegger and
Damla Senol Cali and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Onur Mutlu},
title = {Algorithmic Improvement and {GPU} Acceleration of the GenASM Algorithm},
booktitle = {{IEEE} International Parallel and Distributed Processing Symposium,
{IPDPS} Workshops 2022, Lyon, France, May 30 - June 3, 2022},
pages = {162},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/IPDPSW55747.2022.00038},
doi = {10.1109/IPDPSW55747.2022.00038},
timestamp = {Mon, 08 Aug 2022 16:44:20 +0200},
biburl = {https://dblp.org/rec/conf/ipps/LindeggerCAGM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isca/CaliKLBKZFCKM0G22,
author = {Damla Senol Cali and
Konstantinos Kanellopoulos and
Jo{\"{e}}l Lindegger and
Z{\"{u}}lal Bing{\"{o}}l and
Gurpreet S. Kalsi and
Ziyi Zuo and
Can Firtina and
Meryem Banu Cavlak and
Jeremie S. Kim and
Nika Mansouri{-}Ghiasi and
Gagandeep Singh and
Juan G{\'{o}}mez{-}Luna and
Nour Almadhoun Alserr and
Mohammed Alser and
Sreenivas Subramoney and
Can Alkan and
Saugata Ghose and
Onur Mutlu},
editor = {Valentina Salapura and
Mohamed Zahran and
Fred Chong and
Lingjia Tang},
title = {SeGraM: a universal hardware accelerator for genomic sequence-to-graph
and sequence-to-sequence mapping},
booktitle = {{ISCA} '22: The 49th Annual International Symposium on Computer Architecture,
New York, New York, USA, June 18 - 22, 2022},
pages = {638--655},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3470496.3527436},
doi = {10.1145/3470496.3527436},
timestamp = {Tue, 12 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isca/CaliKLBKZFCKM0G22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isvlsi/Mansouri-Ghiasi22,
author = {Nika Mansouri{-}Ghiasi and
Jisung Park and
Harun Mustafa and
Jeremie S. Kim and
Ataberk Olgun and
Arvid Gollwitzer and
Damla Senol Cali and
Can Firtina and
Haiyu Mao and
Nour Almadhoun Alserr and
Rachata Ausavarungnirun and
Nandita Vijaykumar and
Mohammed Alser and
Onur Mutlu},
title = {GenStore: In-Storage Filtering of Genomic Data for High-Performance
and Energy-Efficient Genome Analysis},
booktitle = {{IEEE} Computer Society Annual Symposium on VLSI, {ISVLSI} 2022, Nicosia,
Cyprus, July 4-6, 2022},
pages = {283--287},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/ISVLSI54635.2022.00062},
doi = {10.1109/ISVLSI54635.2022.00062},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isvlsi/Mansouri-Ghiasi22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/micro/MaoASFBCMAM22,
author = {Haiyu Mao and
Mohammed Alser and
Mohammad Sadrosadati and
Can Firtina and
Akanksha Baranwal and
Damla Senol Cali and
Aditya Manglik and
Nour Almadhoun Alserr and
Onur Mutlu},
title = {GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration
of Basecalling and Read Mapping},
booktitle = {55th {IEEE/ACM} International Symposium on Microarchitecture, {MICRO}
2022, Chicago, IL, USA, October 1-5, 2022},
pages = {710--726},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/MICRO56248.2022.00056},
doi = {10.1109/MICRO56248.2022.00056},
timestamp = {Fri, 04 Nov 2022 09:24:05 +0100},
biburl = {https://dblp.org/rec/conf/micro/MaoASFBCMAM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2202-10400,
author = {Nika Mansouri{-}Ghiasi and
Jisung Park and
Harun Mustafa and
Jeremie S. Kim and
Ataberk Olgun and
Arvid Gollwitzer and
Damla Senol Cali and
Can Firtina and
Haiyu Mao and
Nour Almadhoun Alserr and
Rachata Ausavarungnirun and
Nandita Vijaykumar and
Mohammed Alser and
Onur Mutlu},
title = {GenStore: {A} High-Performance and Energy-Efficient In-Storage Computing
System for Genome Sequence Analysis},
journal = {CoRR},
volume = {abs/2202.10400},
year = {2022},
url = {https://arxiv.org/abs/2202.10400},
eprinttype = {arXiv},
eprint = {2202.10400},
timestamp = {Wed, 02 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2202-10400.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-15561,
author = {Jo{\"{e}}l Lindegger and
Damla Senol Cali and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Onur Mutlu},
title = {Algorithmic Improvement and {GPU} Acceleration of the GenASM Algorithm},
journal = {CoRR},
volume = {abs/2203.15561},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.15561},
doi = {10.48550/ARXIV.2203.15561},
eprinttype = {arXiv},
eprint = {2203.15561},
timestamp = {Mon, 04 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-15561.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2205-05883,
author = {Damla Senol Cali and
Konstantinos Kanellopoulos and
Jo{\"{e}}l Lindegger and
Z{\"{u}}lal Bing{\"{o}}l and
Gurpreet S. Kalsi and
Ziyi Zuo and
Can Firtina and
Meryem Banu Cavlak and
Jeremie S. Kim and
Nika Mansouri{-}Ghiasi and
Gagandeep Singh and
Juan G{\'{o}}mez{-}Luna and
Nour Almadhoun Alserr and
Mohammed Alser and
Sreenivas Subramoney and
Can Alkan and
Saugata Ghose and
Onur Mutlu},
title = {SeGraM: {A} Universal Hardware Accelerator for Genomic Sequence-to-Graph
and Sequence-to-Sequence Mapping},
journal = {CoRR},
volume = {abs/2205.05883},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2205.05883},
doi = {10.48550/ARXIV.2205.05883},
eprinttype = {arXiv},
eprint = {2205.05883},
timestamp = {Tue, 17 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2205-05883.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2207-09765,
author = {Can Firtina and
Kamlesh R. Pillai and
Gurpreet S. Kalsi and
Bharathwaj Suresh and
Damla Senol Cali and
Jeremie S. Kim and
Taha Shahroodi and
Meryem Banu Cavlak and
Jo{\"{e}}l Lindegger and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Sreenivas Subramoney and
Onur Mutlu},
title = {ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient
Genome Analysis},
journal = {CoRR},
volume = {abs/2207.09765},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2207.09765},
doi = {10.48550/ARXIV.2207.09765},
eprinttype = {arXiv},
eprint = {2207.09765},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2207-09765.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2208-09985,
author = {Jo{\"{e}}l Lindegger and
Damla Senol Cali and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Nika Mansouri{-}Ghiasi and
Onur Mutlu},
title = {Scrooge: {A} Fast and Memory-Frugal Genomic Sequence Aligner for CPUs,
GPUs, and ASICs},
journal = {CoRR},
volume = {abs/2208.09985},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2208.09985},
doi = {10.48550/ARXIV.2208.09985},
eprinttype = {arXiv},
eprint = {2208.09985},
timestamp = {Mon, 29 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2208-09985.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2209-08600,
author = {Haiyu Mao and
Mohammed Alser and
Mohammad Sadrosadati and
Can Firtina and
Akanksha Baranwal and
Damla Senol Cali and
Aditya Manglik and
Nour Almadhoun Alserr and
Onur Mutlu},
title = {GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration
of Basecalling and Read Mapping},
journal = {CoRR},
volume = {abs/2209.08600},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2209.08600},
doi = {10.48550/ARXIV.2209.08600},
eprinttype = {arXiv},
eprint = {2209.08600},
timestamp = {Wed, 28 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2209-08600.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/micro/SinghACDGCM21,
author = {Gagandeep Singh and
Mohammed Alser and
Damla Senol Cali and
Dionysios Diamantopoulos and
Juan G{\'{o}}mez{-}Luna and
Henk Corporaal and
Onur Mutlu},
title = {FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications},
journal = {{IEEE} Micro},
volume = {41},
number = {4},
pages = {39--48},
year = {2021},
url = {https://doi.org/10.1109/MM.2021.3088396},
doi = {10.1109/MM.2021.3088396},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/micro/SinghACDGCM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcasI/KaraBKADM21,
author = {Ismail Kara and
Mustafa Becermis and
Mohamed Abdel{-}Aal Kamar and
Mustafa Aktan and
Hakan Dogan and
Senol Mutlu},
title = {A 70-to-2 {V} Triboelectric Energy Harvesting System Utilizing Parallel-SSHI
Rectifier and {DC-DC} Converters},
journal = {{IEEE} Trans. Circuits Syst. {I} Regul. Pap.},
volume = {68},
number = {1},
pages = {210--223},
year = {2021},
url = {https://doi.org/10.1109/TCSI.2020.3025468},
doi = {10.1109/TCSI.2020.3025468},
timestamp = {Tue, 26 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcasI/KaraBKADM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2106-06433,
author = {Gagandeep Singh and
Mohammed Alser and
Damla Senol Cali and
Dionysios Diamantopoulos and
Juan G{\'{o}}mez{-}Luna and
Henk Corporaal and
Onur Mutlu},
title = {FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications},
journal = {CoRR},
volume = {abs/2106.06433},
year = {2021},
url = {https://arxiv.org/abs/2106.06433},
eprinttype = {arXiv},
eprint = {2106.06433},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2106-06433.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FirtinaKACCAM20,
author = {Can Firtina and
Jeremie S. Kim and
Mohammed Alser and
Damla Senol Cali and
A. Erc{\"{u}}ment {\c{C}}i{\c{c}}ek and
Can Alkan and
Onur Mutlu},
title = {Apollo: a sequencing-technology-independent, scalable and accurate
assembly polishing algorithm},
journal = {Bioinform.},
volume = {36},
number = {12},
pages = {3669--3679},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa179},
doi = {10.1093/BIOINFORMATICS/BTAA179},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FirtinaKACCAM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/micro/AlserBCKGAM20,
author = {Mohammed Alser and
Z{\"{u}}lal Bing{\"{o}}l and
Damla Senol Cali and
Jeremie S. Kim and
Saugata Ghose and
Can Alkan and
Onur Mutlu},
title = {Accelerating Genome Analysis: {A} Primer on an Ongoing Journey},
journal = {{IEEE} Micro},
volume = {40},
number = {5},
pages = {65--75},
year = {2020},
url = {https://doi.org/10.1109/MM.2020.3013728},
doi = {10.1109/MM.2020.3013728},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/micro/AlserBCKGAM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/micro/CaliKBFSKAAGBNS20,
author = {Damla Senol Cali and
Gurpreet S. Kalsi and
Z{\"{u}}lal Bing{\"{o}}l and
Can Firtina and
Lavanya Subramanian and
Jeremie S. Kim and
Rachata Ausavarungnirun and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Amirali Boroumand and
Anant Nori and
Allison Scibisz and
Sreenivas Subramoney and
Can Alkan and
Saugata Ghose and
Onur Mutlu},
title = {GenASM: {A} High-Performance, Low-Power Approximate String Matching
Acceleration Framework for Genome Sequence Analysis},
booktitle = {53rd Annual {IEEE/ACM} International Symposium on Microarchitecture,
{MICRO} 2020, Athens, Greece, October 17-21, 2020},
pages = {951--966},
publisher = {{IEEE}},
year = {2020},
url = {https://doi.org/10.1109/MICRO50266.2020.00081},
doi = {10.1109/MICRO50266.2020.00081},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/micro/CaliKBFSKAAGBNS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2008-00961,
author = {Mohammed Alser and
Z{\"{u}}lal Bing{\"{o}}l and
Damla Senol Cali and
Jeremie S. Kim and
Saugata Ghose and
Can Alkan and
Onur Mutlu},
title = {Accelerating Genome Analysis: {A} Primer on an Ongoing Journey},
journal = {CoRR},
volume = {abs/2008.00961},
year = {2020},
url = {https://arxiv.org/abs/2008.00961},
eprinttype = {arXiv},
eprint = {2008.00961},
timestamp = {Fri, 07 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2008-00961.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-07692,
author = {Damla Senol Cali and
Gurpreet S. Kalsi and
Z{\"{u}}lal Bing{\"{o}}l and
Can Firtina and
Lavanya Subramanian and
Jeremie S. Kim and
Rachata Ausavarungnirun and
Mohammed Alser and
Juan G{\'{o}}mez{-}Luna and
Amirali Boroumand and
Anant Nori and
Allison Scibisz and
Sreenivas Subramoney and
Can Alkan and
Saugata Ghose and
Onur Mutlu},
title = {GenASM: {A} High-Performance, Low-Power Approximate String Matching
Acceleration Framework for Genome Sequence Analysis},
journal = {CoRR},
volume = {abs/2009.07692},
year = {2020},
url = {https://arxiv.org/abs/2009.07692},
eprinttype = {arXiv},
eprint = {2009.07692},
timestamp = {Wed, 23 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-07692.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CaliKGAM19,
author = {Damla Senol Cali and
Jeremie S. Kim and
Saugata Ghose and
Can Alkan and
Onur Mutlu},
title = {Nanopore sequencing technology and tools for genome assembly: computational
analysis of the current state, bottlenecks and future directions},
journal = {Briefings Bioinform.},
volume = {20},
number = {4},
pages = {1542--1559},
year = {2019},
url = {https://doi.org/10.1093/bib/bby017},
doi = {10.1093/BIB/BBY017},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/CaliKGAM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pomacs/GhoseLHCM19,
author = {Saugata Ghose and
Tianshi Li and
Nastaran Hajinazar and
Damla Senol Cali and
Onur Mutlu},
title = {Demystifying Complex Workload-DRAM Interactions: An Experimental Study},
journal = {Proc. {ACM} Meas. Anal. Comput. Syst.},
volume = {3},
number = {3},
pages = {60:1--60:50},
year = {2019},
url = {https://doi.org/10.1145/3366708},
doi = {10.1145/3366708},
timestamp = {Thu, 02 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pomacs/GhoseLHCM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sigmetrics/GhoseLHCM19,
author = {Saugata Ghose and
Tianshi Li and
Nastaran Hajinazar and
Damla Senol Cali and
Onur Mutlu},
editor = {Erich M. Nahum and
Thomas Bonald and
Nick Duffield},
title = {Demystifying Complex Workload-DRAM Interactions: An Experimental Study},
booktitle = {Abstracts of the 2019 SIGMETRICS/Performance Joint International Conference
on Measurement and Modeling of Computer Systems, Phoenix, AZ, USA,
June 24-28, 2019},
pages = {93},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3309697.3331482},
doi = {10.1145/3309697.3331482},
timestamp = {Thu, 02 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sigmetrics/GhoseLHCM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1902-04341,
author = {Can Firtina and
Jeremie S. Kim and
Mohammed Alser and
Damla Senol Cali and
A. Erc{\"{u}}ment {\c{C}}i{\c{c}}ek and
Can Alkan and
Onur Mutlu},
title = {Apollo: {A} Sequencing-Technology-Independent, Scalable, and Accurate
Assembly Polishing Algorithm},
journal = {CoRR},
volume = {abs/1902.04341},
year = {2019},
url = {http://arxiv.org/abs/1902.04341},
eprinttype = {arXiv},
eprint = {1902.04341},
timestamp = {Fri, 11 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1902-04341.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1902-07609,
author = {Saugata Ghose and
Tianshi Li and
Nastaran Hajinazar and
Damla Senol Cali and
Onur Mutlu},
title = {Understanding the Interactions of Workloads and {DRAM} Types: {A}
Comprehensive Experimental Study},
journal = {CoRR},
volume = {abs/1902.07609},
year = {2019},
url = {http://arxiv.org/abs/1902.07609},
eprinttype = {arXiv},
eprint = {1902.07609},
timestamp = {Thu, 02 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1902-07609.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1912-08735,
author = {Jeremie S. Kim and
Can Firtina and
Meryem Banu Cavlak and
Damla Senol Cali and
Mohammed Alser and
Nastaran Hajinazar and
Can Alkan and
Onur Mutlu},
title = {AirLift: {A} Fast and Comprehensive Technique for Remapping Alignments
between Reference Genomes},
journal = {CoRR},
volume = {abs/1912.08735},
year = {2019},
url = {https://arxiv.org/abs/1912.08735},
eprinttype = {arXiv},
eprint = {1912.08735},
timestamp = {Mon, 01 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1912-08735.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcgenomics/KimCXLGAHEAM18,
author = {Jeremie S. Kim and
Damla Senol Cali and
Hongyi Xin and
Donghyuk Lee and
Saugata Ghose and
Mohammed Alser and
Hasan Hassan and
Oguz Ergin and
Can Alkan and
Onur Mutlu},
title = {GRIM-Filter: Fast seed location filtering in {DNA} read mapping using
processing-in-memory technologies},
journal = {{BMC} Genom.},
volume = {19},
number = {{S2}},
year = {2018},
url = {https://doi.org/10.1186/s12864-018-4460-0},
doi = {10.1186/S12864-018-4460-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcgenomics/KimCXLGAHEAM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcas/HaydarogluOM17,
author = {Iskender Haydaroglu and
Mehmet Tamer Ozgun and
Senol Mutlu},
title = {Optically Powered Optical Transmitter Using a Single Light-Emitting
Diode},
journal = {{IEEE} Trans. Circuits Syst. {I} Regul. Pap.},
volume = {64-I},
number = {8},
pages = {2003--2012},
year = {2017},
url = {https://doi.org/10.1109/TCSI.2017.2684910},
doi = {10.1109/TCSI.2017.2684910},
timestamp = {Tue, 03 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcas/HaydarogluOM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1711-01177,
author = {Jeremie S. Kim and
Damla Senol Cali and
Hongyi Xin and
Donghyuk Lee and
Saugata Ghose and
Mohammed Alser and
Hasan Hassan and
Oguz Ergin and
Can Alkan and
Onur Mutlu},
title = {GRIM-Filter: Fast Seed Location Filtering in {DNA} Read Mapping Using
Processing-in-Memory Technologies},
journal = {CoRR},
volume = {abs/1711.01177},
year = {2017},
url = {https://doi.org/10.48550/arXiv.1711.01177},
doi = {10.48550/ARXIV.1711.01177},
eprinttype = {arXiv},
eprint = {1711.01177},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1711-01177.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mbec/TumerSMUYO14,
author = {Murat T{\"{u}}mer and
Baykal Sarioglu and
Senol Mutlu and
Yekta {\"{U}}lgen and
Arda D. Yalcinkaya and
Cengizhan Ozturk},
title = {Using a low-amplitude {RF} pulse at echo time {(LARFET)} for device
localization in {MRI}},
journal = {Medical Biol. Eng. Comput.},
volume = {52},
number = {10},
pages = {885--894},
year = {2014},
url = {https://doi.org/10.1007/s11517-014-1184-4},
doi = {10.1007/S11517-014-1184-4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mbec/TumerSMUYO14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mie/SenolSTUK14,
author = {Utku Senol and
Mehmet Samur and
Ozgur Tosun and
Ali Unal and
Mutlu Kartal},
editor = {Christian Lovis and
Brigitte S{\'{e}}roussi and
Arie Hasman and
Louise Pape{-}Haugaard and
Osman Saka and
Stig Kj{\ae}r Andersen},
title = {Evaluation of a Decision Support System for Selecting Appropriate
Radiological Test},
booktitle = {e-Health - For Continuity of Care - Proceedings of MIE2014, the 25th
European Medical Informatics Conference, Istanbul, Turkey, August
31 - September 3, 2014},
series = {Studies in Health Technology and Informatics},
volume = {205},
pages = {1264},
publisher = {{IOS} Press},
year = {2014},
timestamp = {Sat, 11 Oct 2014 14:24:23 +0200},
biburl = {https://dblp.org/rec/conf/mie/SenolSTUK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/esticas/SariogluAOMDY12,
author = {Baykal Sarioglu and
Ozan Aktan and
Ahmet {\"{O}}nc{\"{u}} and
Senol Mutlu and
G{\"{u}}nhan D{\"{u}}ndar and
Arda D. Yalcinkaya},
title = {An Optically Powered {CMOS} Receiver System for Intravascular Magnetic
Resonance Applications},
journal = {{IEEE} J. Emerg. Sel. Topics Circuits Syst.},
volume = {2},
number = {4},
pages = {683--691},
year = {2012},
url = {https://doi.org/10.1109/JETCAS.2012.2223555},
doi = {10.1109/JETCAS.2012.2223555},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/esticas/SariogluAOMDY12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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