CA
Can Alkan
q-bio.GNSoftwarebioinformaticsGenome, HumanAlgorithmsEvolution, MolecularGenetic VariationGenomicscs.ARcs.CE
On Valency
published · living versionsW_92jh5vez·v1 · currentpublished
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping
with Hongyi Xin, Richard Zhu, Sunny Nahar, John Emmons +3
1 version
Preprints & journals
152 papers in the corpus · 2002–2026De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.42632028 · Bingöl, Zülal, Şahin, Berkan, Zambaku, Klea et al.2026 · 0 citationsBriefings in bioinformatics. 2026;27(4)
PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs.42464101 · Solun, Görkem Kadir, Dogrusoz, Ugur, Bingöl, Zülal et al.2026 · 0 citationsBMC bioinformatics. 2026
Rapid adaptive increase of amylase gene copy number in Indigenous Andeans.42086559 · Scheer, Kendra, Landau, Luane J B, Jorgensen, Kelsey et al.2026 · 9 citationsNature communications. 2026;17(1)
GenCore: Genomic distance estimation using Locally Consistent Parsing10.64898/2026.01.10.698768v2 · Ashyralyyev, A., Sirvan, E., Malikic, S. et al.2026 · 1 citationbioRxiv
LCPan: efficient variation graph construction using Locally Consistent Parsing2511.12205v4 · Akmuhammet Ashyralyyev, Zulal Bingol, Begum Filiz Oz et al.2025 · 0 citationsGenome Biology, 27: 197, 2026
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes1912.08735v5 · Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak et al.2019 · 7 citationsIEEE Transactions on Computational Biology and Bioinformatics, 23 (2): 589-597, 2026
Processing-in-memory for genomics workloads2506.00597v2 · William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi et al.2025 · 2 citationsIEEE Micro, 46 (2): 70-80, 2026
LCPan: efficient variation graph construction using Locally Consistent Parsing.41333161 · Ashyralyyev, Akmuhammet, Bingöl, Zülal, Öz, Begüm Filiz et al.2026 · 0 citationsArXiv. 2026
FASTR: Reimagining FASTQ via Compact Image-inspired Representation2601.17184v1 · Adrian Tkachenko, Sepehr Salem, Ayotomiwa Ezekiel Adeniyi et al.2026 · 0 citationsarXiv
FASTR: Reimagining FASTQ via Compact Image-inspired Representation10.64898/2026.01.22.701172v1 · Tkachenko, A., Salem, S., Ezekiel Adeniyi, A. et al.2026 · 0 citationsbioRxiv
Robust software development practices improve citations of RNA-seq tools10.1101/2025.09.05.674580v1 · Sharma, S., Ilgun, E., Okcu, T. et al.2025 · 0 citationsbioRxiv
Rapid Adaptive Increase of Amylase Gene Copy Number in Indigenous Andeans10.1101/2025.03.25.644684v2 · Scheer, K., Landau, L. J. B., Jorgensen, K. et al.2025 · 9 citationsbioRxiv
Population-level gene copy number variations reveal distinct genetic properties of different Malus species.40702434 · Sakina, Aafreen, Alkan, Can, Khan, Awais2025 · 2 citationsBMC genomics. 2025;26(1):687
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering2212.04953v3 · Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser et al.2022 · 16 citationsFrontiers in Genetics, 15: 1429306, 2024
Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.39789608 · Koptekin, Dilek, Yapar, Etka, Vural, Kıvılcım Başak et al.2025 · 19 citationsGenome biology. 2025;26(1):6
Fast characterization of segmental duplication structure in multiple genome assemblies.35303886 · Išerić, Hamza, Alkan, Can, Hach, Faraz et al.2024 · 92 citationsAlgorithms for molecular biology : AMB. 2022;17(1):4
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping2103.14978v3 · Zulal Bingol, Mohammed Alser, Onur Mutlu et al.2021 · 13 citationsIEEE Transactions on Computers, 73 (5): 1206-1218, 2024
Pairwise sequence alignment with block and character edit operations2311.11082v2 · Ahmet Cemal Al\ic\ioglu, Can Alkan2023 · 0 citationsarXiv
An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data.38134749 · Shojaei, Mona, Mohammadvand, Navid, Doğan, Tunca et al.2024 · 0 citationsComputers in biology and medicine. 2024;169:107810
ECOLE: Learning to call copy number variants on whole exome sequencing data.38167256 · Mandiracioglu, Berk, Ozden, Furkan, Kaynar, Gun et al.2024 · 24 citationsNature communications. 2024;15(1):132
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs1910.09020v3 · Mohammed Alser, Taha Shahroodi, Juan Gomez-Luna et al.2019 · 57 citationsBioinformatics, Apr 1;36(22-23):5282-5290, 2021
Technology dictates algorithms: Recent developments in read alignment2003.00110v3 · Mohammed Alser, Jeremy Rotman, Kodi Taraszka et al.2020 · 156 citationsGenome Biol . Aug 26;22(1):249, 2021
FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies2201.06255v3 · Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak et al.2022 · 7 citationsBioinformatics, Sep 30; 38(19):4633-4635, 2022
Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome data10.1101/2023.11.11.566695v1 · Koptekin, D., Yapar, E., Vural, K. B. et al.2023 · 19 citationsbioRxiv
GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping2309.17063v1 · Julien Eudine, Mohammed Alser, Gagandeep Singh et al.2023 · 1 citationarXiv
ECOLE: Learning to call copy number variants on whole exome sequencing data10.1101/2022.11.17.516880v2 · Mandiracioglu, B., Ozden, F., Kaynar, G. et al.2022 · 24 citationsbioRxiv
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis2112.08687v7 · Can Firtina, Jisung Park, Mohammed Alser et al.2021 · 46 citationsNAR Genomics and Bioinformatics, vol. 5, no. 1, p. lqad004, Mar. 2023
Identification of protein-protein interaction bridges for multiple sclerosis.37018152 · Yazıcı, Gözde, Kurt Vatandaslar, Burcu, Aydin Canturk, Ilknur et al.2023 · 2 citationsBioinformatics (Oxford, England). 2023;39(4)
Author Correction: Comparative and demographic analysis of orang-utan genomes.35962045 · Locke, Devin P, Hillier, LaDeana W, Warren, Wesley C et al.2023 · 2 citationsNature. 2022;608(7924):E36
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.36516232 · Söylev, Arda, Çokoglu, Sevim Seda, Koptekin, Dilek et al.2023 · 8 citationsPLoS computational biology. 2022;18(12):e1010788
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering10.1101/2022.12.09.519749v1 · Cavlak, M. B., Singh, G., Alser, M. et al.2022 · 16 citationsbioRxiv
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis10.1101/2022.11.23.517691v1 · Firtina, C., Park, J., Alser, M. et al.2022 · 46 citationsbioRxiv
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes10.1101/2021.02.16.431517v2 · Kim, J. S., Firtina, C., Cavlak, M. B. et al.2021 · 7 citationsbioRxiv
CoViT: Real-time phylogenetics for the SARS-CoV-2 pandemic using Vision Transformers2208.05004v2 · Zuher Jahshan, Can Alkan, Leonid Yavits2022 · 0 citationsarXiv
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data10.1101/2021.12.17.473150v3 · Soylev, A., Cokoglu, S. S., Koptekin, D. et al.2021 · 8 citationsbioRxiv
Polishing copy number variant calls on exome sequencing data via deep learning.35697522 · Özden, Furkan, Alkan, Can, Çiçek, A Ercüment2022 · 16 citationsGenome research. 2022;32(6):1170-1182
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping2205.05883v2 · Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger et al.2022 · 11 citationsarXiv
Polishing Copy Number Variant Calls on Exome Sequencing Data via Deep Learning10.1101/2020.05.09.086082v3 · Ozden, F., Alkan, C., Cicek, A. E.2020 · 16 citationsbioRxiv
VALOR2: characterization of large-scale structural variants using linked-reads.32192518 · Karaoğlanoğlu, Fatih, Ricketts, Camir, Ebren, Ezgi et al.2021 · 23 citationsGenome biology. 2020;21(1):72
A robust benchmark for detection of germline large deletions and insertions.32541955 · Zook, Justin M, Hansen, Nancy F, Olson, Nathan D et al.2020 · 495 citationsNature biotechnology. 2020;38(11):1347-1355
Author Correction: A robust benchmark for detection of germline large deletions and insertions.32699374 · Zook, Justin M, Hansen, Nancy F, Olson, Nathan D et al.2020 · 4 citationsNature biotechnology. 2020;38(11):1357
Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment1809.07858v4 · Mohammed Alser, Hasan Hassan, Akash Kumar et al.2018 · 88 citationsBioinformatics, Nov 1; 35 (21): 4255 - 4263, 2019
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm1902.04341v2 · Can Firtina, Jeremie S. Kim, Mohammed Alser et al.2019 · 67 citationsBioinformatics . 2020 Jun 1;36(12):3669-3679
Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools.31496881 · Demir, Gülfem, Alkan, Can2020 · 1 citationTurkish journal of biology = Turk biyoloji dergisi. 2019;43(4):264-273
GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping1604.01789v3 · Mohammed Alser, Hasan Hassan, Hongyi Xin et al.2016 · 115 citationsBioinformatics. Nov 1;33(21):3355-3363, 2017
Evaluation of genome scaffolding tools using pooled clone sequencing.30983868 · Dal, Elif, Alkan, Can2020 · 0 citationsTurkish journal of biology = Turk biyoloji dergisi. 2018;42(6):471-476
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis2009.07692v1 · Damla Senol Cali, Gurpreet S. Kalsi, Zulal Bingol et al.2020 · 133 citationsarXiv
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing.30937433 · Soylev, Arda, Le, Thong Minh, Amini, Hajar et al.2020 · 61 citationsBioinformatics (Oxford, England). 2019;35(20):3923-3930
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies1711.01177v1 · Jeremie S. Kim, Damla Senol Cali, Hongyi Xin et al.2017 · 130 citationsBMC Genomics, 19 (Suppl 2):89, 2018
Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions1711.08774v4 · Damla Senol Cali, Jeremie S. Kim, Saugata Ghose et al.2017 · 298 citationsBriefings in Bioinformatics. 2019 Jul 19;20(4):1542-1559
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