Modeling Economic Activities and Random Catastrophic Failures of Financial Networks via Gibbs Random Fields
Onural, Levent, Pınar, Mustafa Çelebi, Fırtına, Can
Published in Computational economics (01.08.2021)
Published in Computational economics (01.08.2021)
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Journal Article
RUBICON: a framework for designing efficient deep learning-based genomic basecallers
Singh, Gagandeep, Alser, Mohammed, Denolf, Kristof, Firtina, Can, Khodamoradi, Alireza, Cavlak, Meryem Banu, Corporaal, Henk, Mutlu, Onur
Published in Genome Biology (16.02.2024)
Published in Genome Biology (16.02.2024)
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Journal Article
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
Alser, Mohammed, Lindegger, Joel, Firtina, Can, Almadhoun, Nour, Mao, Haiyu, Singh, Gagandeep, Gomez-Luna, Juan, Mutlu, Onur
Published in Computational and structural biotechnology journal (01.01.2022)
Published in Computational and structural biotechnology journal (01.01.2022)
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Journal Article
Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design
Mutlu, Onur, Firtina, Can
Published in 2023 60th ACM/IEEE Design Automation Conference (DAC) (09.07.2023)
Published in 2023 60th ACM/IEEE Design Automation Conference (DAC) (09.07.2023)
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Conference Proceeding
RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization
Firtina, Can, Soysal, Melina, Lindegger, Joël, Mutlu, Onur
Published in Bioinformatics (Oxford, England) (02.08.2024)
Published in Bioinformatics (Oxford, England) (02.08.2024)
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Journal Article
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Firtina, Can, Bar-Joseph, Ziv, Alkan, Can, Cicek, A Ercument
Published in Nucleic acids research (30.11.2018)
Published in Nucleic acids research (30.11.2018)
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Journal Article
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes
Firtina, Can, Mansouri Ghiasi, Nika, Lindegger, Joel, Singh, Gagandeep, Cavlak, Meryem Banu, Mao, Haiyu, Mutlu, Onur
Published in Bioinformatics (Oxford, England) (30.06.2023)
Published in Bioinformatics (Oxford, England) (30.06.2023)
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Journal Article
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
Firtina, Can, Kim, Jeremie S, Alser, Mohammed, Senol Cali, Damla, Cicek, A Ercument, Alkan, Can, Mutlu, Onur
Published in Bioinformatics (01.06.2020)
Published in Bioinformatics (01.06.2020)
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Journal Article
FastRemap: a tool for quickly remapping reads between genome assemblies
Kim, Jeremie S, Firtina, Can, Cavlak, Meryem Banu, Senol Cali, Damla, Alkan, Can, Mutlu, Onur
Published in Bioinformatics (Oxford, England) (30.09.2022)
Published in Bioinformatics (Oxford, England) (30.09.2022)
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Journal Article
GLANET: genomic loci annotation and enrichment tool
Otlu, Burçak, Firtina, Can, Keles, Sündüz, Tastan, Oznur
Published in Bioinformatics (Oxford, England) (15.09.2017)
Published in Bioinformatics (Oxford, England) (15.09.2017)
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Journal Article
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Cali, Damla Senol, Kalsi, Gurpreet S., Bingol, Zulal, Firtina, Can, Subramanian, Lavanya, Kim, Jeremie S., Ausavarungnirun, Rachata, Alser, Mohammed, Gomez-Luna, Juan, Boroumand, Amirali, Nori, Anant, Scibisz, Allison, Subramoney, Sreenivas, Alkan, Can, Ghose, Saugata, Mutlu, Onur
Published in 2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture (MICRO) (01.10.2020)
Published in 2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture (MICRO) (01.10.2020)
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Conference Proceeding
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Kim, Jeremie S., Firtina, Can, Cavlak, Meryem Banu, Cali, Damla Senol, Hajinazar, Nastaran, Alser, Mohammed, Alkan, Can, Mutlu, Onur
Published in IEEE/ACM transactions on computational biology and bioinformatics (19.08.2024)
Published in IEEE/ACM transactions on computational biology and bioinformatics (19.08.2024)
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Journal Article
Packaging and containerization of computational methods
Alser, Mohammed, Lawlor, Brendan, Abdill, Richard J, Waymost, Sharon, Ayyala, Ram, Rajkumar, Neha, LaPierre, Nathan, Brito, Jaqueline, Ribeiro-Dos-Santos, André M, Almadhoun, Nour, Sarwal, Varuni, Firtina, Can, Osinski, Tomasz, Eskin, Eleazar, Hu, Qiyang, Strong, Derek, Kim, Byoung-Do B D, Abedalthagafi, Malak S, Mutlu, Onur, Mangul, Serghei
Published in Nature protocols (01.09.2024)
Published in Nature protocols (01.09.2024)
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Journal Article
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping
Mao, Haiyu, Alser, Mohammed, Sadrosadati, Mohammad, Firtina, Can, Baranwal, Akanksha, Cali, Damla Senol, Manglik, Aditya, Alserr, Nour Almadhoun, Mutlu, Onur
Published in 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO) (01.10.2022)
Published in 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO) (01.10.2022)
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Conference Proceeding
BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
Firtina, Can, Park, Jisung, Alser, Mohammed, Kim, Jeremie S, Cali, Damla Senol, Shahroodi, Taha, Ghiasi, Nika Mansouri, Singh, Gagandeep, Kanellopoulos, Konstantinos, Alkan, Can, Mutlu, Onur
Published in NAR genomics and bioinformatics (01.03.2023)
Published in NAR genomics and bioinformatics (01.03.2023)
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Journal Article