Can Alkan

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 43

Top Topics

Hardware Architecture

Multiple Sclerosis

High Throughput Sequencing

Top Venues

Briefings Bioinform.

Publications

Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IEEE Trans. Computers 73 (5) (2024)
Mona Shojaei, Navid Mohammadvand, Tunca Dogan, Can Alkan, Rengül Çetin-Atalay, Aybar C. Acar
An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data. Comput. Biol. Medicine 169 (2024)
Gözde Yazici, Burcu Kurt Vatandaslar, Ilknur Aydin Canturk, Fatmagul I Aydinli, Ozge Arici Duz, Emre Karakoç, Bilal Ersen Kerman, Can Alkan
Identification of protein-protein interaction bridges for multiple sclerosis. Bioinform. 39 (4) (2023)
Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu
GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping. CoRR (2023)
Ahmet Cemal Alicioglu, Mahmud Sami Aydin, Can Alkan
Pairwise sequence alignment with block and character edit operations. CoRR (2023)
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
FastRemap: a tool for quickly remapping reads between genome assemblies. Bioinform. 38 (19) (2022)
Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic
Fast characterization of segmental duplication structure in multiple genome assemblies. Algorithms Mol. Biol. 17 (1) (2022)
Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. PLoS Comput. Biol. 18 (12) (2022)
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
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. CoRR (2022)
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. CoRR (2022)
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
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. ISCA (2022)
Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. Bioinform. 36 (22-23) (2021)
Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic
BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. WABI (2021)
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IPDPS Workshops (2021)
Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. CoRR (2021)
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
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. CoRR (2020)
Can Alkan
Automatic characterization of copy number polymorphism using high throughput sequencing. Turkish J. Electr. Eng. Comput. Sci. 28 (1) (2020)
Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
Accelerating Genome Analysis: A Primer on an Ongoing Journey. CoRR (2020)
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
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO (2020)
Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro 40 (5) (2020)
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. 36 (12) (2020)
Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Briefings Bioinform. 20 (4) (2019)
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. CoRR (2019)
Arda Soylev, Thong Minh Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing. Bioinform. 35 (20) (2019)
Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
Shouji: a fast and efficient pre-alignment filter for sequence alignment. Bioinform. 35 (21) (2019)
Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs. CoRR (2019)
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. CoRR (2019)
Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan
SLIDER: Fast and Efficient Computation of Banded Sequence Alignment. CoRR (2018)
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
Fast Characterization of Segmental Duplications in Genome Assemblies. CoRR (2018)
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genom. 19 (S2) (2018)
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
Fast characterization of segmental duplications in genome assemblies. Bioinform. 34 (17) (2018)
Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson
Building and Improving Reference Genome Assemblies. Proc. IEEE 105 (3) (2017)
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies. CoRR (2017)
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinform. 33 (21) (2017)
Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör, Can Alkan, Faraz Hach
Discovery and genotyping of novel sequence insertions in many sequenced individuals. Bioinform. 33 (14) (2017)
Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan
GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture. CoRR (2016)
Can Firtina, Can Alkan
On genomic repeats and reproducibility. Bioinform. 32 (15) (2016)
Hongyi Xin, Sunny Nahar, Richard Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
Optimal seed solver: optimizing seed selection in read mapping. Bioinform. 32 (11) (2016)
Atalay Mert Ileri, Halil I. Ozercan, Alper Gundogdu, Ahmet K. Senol, M. Yusuf Özkaya, Can Alkan
Coinami: A Cryptocurrency with DNA Sequence Alignment as Proof-of-work. CoRR (2016)
Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan, Erman Ayday
Can you Really Anonymize the Donors of Genomic Data in Today's Digital World? DPM/QASA@ESORICS (2015)
Pinar Kavak, Bekir Ergüner, Duran Üstek, Bayram Yüksel, Mahmut Samil Sagiroglu, Tunga Güngör, Can Alkan
Improving Genome Assemblies Using Multi-platform Sequence Data. CIBB (2015)
Hongyi Xin, Richard Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping. CoRR (2015)
Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. Bioinform. 31 (10) (2015)
Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu, Can Alkan
Accelerating read mapping with FastHASH. BMC Genom. 14 (S-1) (2013)
Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp
SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinform. 28 (23) (2012)
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
Sensitive and fast mapping of di-base encoded reads. Bioinform. 28 (1) (2012)
Can Alkan, Emidio Capriotti, Eleazar Eskin, Fereydoun Hormozdiari, Maricel G. Kann
Session Introduction. Pacific Symposium on Biocomputing (2011)
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
Sensitive and fast mapping of di-base encoded reads. Bioinform. 27 (14) (2011)
Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp
Session Introduction. Pacific Symposium on Biocomputing (2010)
Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinform. 26 (10) (2010)
Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinform. 26 (12) (2010)
Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. RECOMB (2009)
Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp
taveRNA: a web suite for RNA algorithms and applications. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. PLoS Comput. Biol. 3 (9) (2007)
Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler
RNA Secondary Structure Prediction Via Energy Density Minimization. RECOMB (2006)
Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
RNA-RNA Interaction Prediction and Antisense RNA Target Search. J. Comput. Biol. 13 (2) (2006)
Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp
Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
RNA-RNA Interaction Prediction and Antisense RNA Target Search. RECOMB (2005)
Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün
The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. J. Comput. Biol. 11 (5) (2004)