Can Alkan

63 papers A* 2B 3C 1Misc 2Journal 52Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
AirLift: A Fast and Comprehensive Technique for Remapping Alignments Between Reference Genomes.
IEEE Trans. Comput. Biol. Bioinform.
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, Onur Mutlu
2026 J jnl
FASTR: Reimagining FASTQ via Compact Image-inspired Representation.
CoRR
Adrian Tkachenko, Sepehr Salem, Ayotomiwa Ezekiel Adeniyi, Zülal Bingöl, Mohammed Nayeem Uddin, Akshat Prasanna, Alexander Zelikovsky, Serghei Mangul, Can Alkan, Mohammed Alser
2025 J jnl
Processing-in-memory for genomics workloads.
CoRR
William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi, Yann Falevoz, Yoshihiro Shibuya, Dominique Lavenier, Irem Boybat, Klea Zambaku, Berkan Sahin, Mohammad Sadrosadati, Onur Mutlu, Abu Sebastian, Rayan Chikhi, The BioPIM Consortium, Can Alkan
2024 J jnl
An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data.
Comput. Biol. Medicine
Mona Shojaei, Navid Mohammadvand, Tunca Dogan, Can Alkan, Rengül Çetin-Atalay, Aybar C. Acar
2024 J jnl
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping.
IEEE Trans. Computers
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
2023 J jnl
GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping.
CoRR
Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
2023 J jnl
Identification of protein-protein interaction bridges for multiple sclerosis.
Bioinform.
Gözde Yazici, Burcu Kurt Vatandaslar, Ilknur Aydin Canturk, Fatmagul I Aydinli, Ozge Arici Duz, Emre Karakoç, Bilal Ersen Kerman, Can Alkan
2023 J jnl
Pairwise sequence alignment with block and character edit operations.
CoRR
Ahmet Cemal Alicioglu, Mahmud Sami Aydin, Can Alkan
2022 J jnl
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.
PLoS Comput. Biol.
Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel
2022 J jnl
Fast characterization of segmental duplication structure in multiple genome assemblies.
Algorithms Mol. Biol.
Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic
2022 J jnl
FastRemap: a tool for quickly remapping reads between genome assemblies.
Bioinform.
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
2022 J jnl
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping.
CoRR
Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri-Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2022 A* conf
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping.
ISCA
Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri-Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2022 J jnl
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering.
CoRR
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu
2021 C conf
BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies.
WABI
Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic
2021 — conf
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping.
IPDPS Workshops
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
2021 J jnl
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping.
CoRR
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
2021 J jnl
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs.
Bioinform.
Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
2020 J jnl
Accelerating Genome Analysis: A Primer on an Ongoing Journey.
CoRR
Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2020 J jnl
Accelerating Genome Analysis: A Primer on an Ongoing Journey.
IEEE Micro
Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2020 J jnl
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.
Bioinform.
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2020 J jnl
Automatic characterization of copy number polymorphism using high throughput sequencing.
Turkish J. Electr. Eng. Comput. Sci.
Can Alkan
2020 A* conf
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis.
MICRO
Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gómez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2020 J jnl
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis.
CoRR
Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gómez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2019 J jnl
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes.
CoRR
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
2019 J jnl
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm.
CoRR
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2019 J jnl
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing.
Bioinform.
Arda Soylev, Thong Minh Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari
2019 J jnl
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.
Briefings Bioinform.
Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2019 J jnl
Shouji: a fast and efficient pre-alignment filter for sequence alignment.
Bioinform.
Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
2019 J jnl
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs.
CoRR
Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
2018 J jnl
Fast Characterization of Segmental Duplications in Genome Assemblies.
CoRR
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
2018 J jnl
Fast characterization of segmental duplications in genome assemblies.
Bioinform.
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
2018 J jnl
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.
BMC Genom.
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
2018 J jnl
SLIDER: Fast and Efficient Computation of Banded Sequence Alignment.
CoRR
Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
2017 J jnl
Building and Improving Reference Genome Assemblies.
Proc. IEEE
Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson
2017 J jnl
Discovery and genotyping of novel sequence insertions in many sequenced individuals.
Bioinform.
Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör, Can Alkan, Faraz Hach
2017 J jnl
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies.
CoRR
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
2017 J jnl
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.
Bioinform.
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
2016 J jnl
Coinami: A Cryptocurrency with DNA Sequence Alignment as Proof-of-work.
CoRR
Atalay Mert Ileri, Halil I. Ozercan, Alper Gundogdu, Ahmet K. Senol, M. Yusuf Özkaya, Can Alkan
2016 J jnl
GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture.
CoRR
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
2016 J jnl
On genomic repeats and reproducibility.
Bioinform.
Can Firtina, Can Alkan
2016 J jnl
Optimal seed solver: optimizing seed selection in read mapping.
Bioinform.
Hongyi Xin, Sunny Nahar, Richard L. Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2015 — conf
Can you Really Anonymize the Donors of Genomic Data in Today's Digital World?
DPM/QASA@ESORICS
Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan, Erman Ayday
2015 — conf
Improving Genome Assemblies Using Multi-platform Sequence Data.
CIBB
Pinar Kavak, Bekir Ergüner, Duran Üstek, Bayram Yüksel, Mahmut Samil Sagiroglu, Tunga Güngör, Can Alkan
2015 J jnl
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping.
CoRR
Hongyi Xin, Richard L. Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2015 J jnl
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.
Bioinform.
Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2014 J jnl
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Nucleic Acids Res.
Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2013 J jnl
Accelerating read mapping with FastHASH.
BMC Genom.
Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu, Can Alkan
2012 J jnl
SCALCE: boosting sequence compression algorithms using locally consistent encoding.
Bioinform.
Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp
2012 J jnl
Sensitive and fast mapping of di-base encoded reads.
Bioinform.
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
2011 J jnl
Sensitive and fast mapping of di-base encoded reads.
Bioinform.
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
2011 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Can Alkan, Emidio Capriotti, Eleazar Eskin, Fereydoun Hormozdiari, Maricel G. Kann
2010 J jnl
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
Bioinform.
Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp
2010 J jnl
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Bioinform.
Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2010 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp
2009 B conf
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes.
RECOMB
Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2007 J jnl
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data.
PLoS Comput. Biol.
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler
2007 J jnl
taveRNA: a web suite for RNA algorithms and applications.
Nucleic Acids Res.
Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp
2006 B conf
RNA Secondary Structure Prediction Via Energy Density Minimization.
RECOMB
Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler
2006 J jnl
RNA-RNA Interaction Prediction and Antisense RNA Target Search.
J. Comput. Biol.
Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
2005 J jnl
Manipulating multiple sequence alignments via MaM and WebMaM.
Nucleic Acids Res.
Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp
2005 B conf
RNA-RNA Interaction Prediction and Antisense RNA Target Search.
RECOMB
Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
2004 J jnl
The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis.
J. Comput. Biol.
Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün