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Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs.
Bioinformatics. 2023 May 4;39(5):btad151. doi: 10.1093/bioinformatics/btad151.
Bioinformatics. 2023.
PMID: 36961334
Free PMC article.
FastRemap: a tool for quickly remapping reads between genome assemblies.
Kim JS, Firtina C, Cavlak MB, Senol Cali D, Alkan C, Mutlu O.
Kim JS, et al. Among authors: senol cali d.
Bioinformatics. 2022 Sep 30;38(19):4633-4635. doi: 10.1093/bioinformatics/btac554.
Bioinformatics. 2022.
PMID: 35976109
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Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.
Firtina C, Kim JS, Alser M, Senol Cali D, Cicek AE, Alkan C, Mutlu O.
Firtina C, et al. Among authors: senol cali d.
Bioinformatics. 2020 Jun 1;36(12):3669-3679. doi: 10.1093/bioinformatics/btaa179.
Bioinformatics. 2020.
PMID: 32167530
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GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.
Kim JS, Senol Cali D, Xin H, Lee D, Ghose S, Alser M, Hassan H, Ergin O, Alkan C, Mutlu O.
Kim JS, et al. Among authors: senol cali d.
BMC Genomics. 2018 May 9;19(Suppl 2):89. doi: 10.1186/s12864-018-4460-0.
BMC Genomics. 2018.
PMID: 29764378
Free PMC article.
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Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.
Senol Cali D, Kim JS, Ghose S, Alkan C, Mutlu O.
Senol Cali D, et al.
Brief Bioinform. 2019 Jul 19;20(4):1542-1559. doi: 10.1093/bib/bby017.
Brief Bioinform. 2019.
PMID: 29617724
Free PMC article.
Review.
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