Can Alkan

According to our database, Can Alkan authored at least 48 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping.

Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan

IEEE Trans. Computers, May, 2024

An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data.

Mona Shojaei, Navid Mohammadvand, Tunca Dogan, Can Alkan, Rengül Çetin-Atalay, Aybar C. Acar

Comput. Biol. Medicine, February, 2024

2023

Identification of protein-protein interaction bridges for multiple sclerosis.

Gözde Yazici, Burcu Kurt Vatandaslar, Ilknur Aydin Canturk, Fatmagul I Aydinli, Ozge Arici Duz, Emre Karakoç, Bilal Ersen Kerman, Can Alkan

Bioinform., April, 2023

Pairwise sequence alignment with block and character edit operations.

Ahmet Cemal Alicioglu, Mahmud Sami Aydin, Can Alkan

CoRR, 2023

GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping.

Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu

CoRR, 2023

2022

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.

Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel

PLoS Comput. Biol., December, 2022

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering.

Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu

CoRR, 2022

FastRemap: a tool for quickly remapping reads between genome assemblies.

Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu

Bioinform., 2022

Fast characterization of segmental duplication structure in multiple genome assemblies.

Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic

Algorithms Mol. Biol., 2022

SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping.

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

Proceedings of the ISCA '22: The 49th Annual International Symposium on Computer Architecture, New York, New York, USA, June 18, 2022

2021

SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs.

Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu

Bioinform., 2021

BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies.

Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

2020

Accelerating Genome Analysis: A Primer on an Ongoing Journey.

Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu

IEEE Micro, 2020

Automatic characterization of copy number polymorphism using high throughput sequencing.

Can Alkan

Turkish J. Electr. Eng. Comput. Sci., 2020

Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.

Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu

Bioinform., 2020

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis.

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

Proceedings of the 53rd Annual IEEE/ACM International Symposium on Microarchitecture, 2020

2019

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes.

Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu

CoRR, 2019

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing.

Arda Soylev, Thong Minh Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari

Bioinform., 2019

Shouji: a fast and efficient pre-alignment filter for sequence alignment.

Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan

Bioinform., 2019

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu

Briefings Bioinform., 2019

2018

SLIDER: Fast and Efficient Computation of Banded Sequence Alignment.

Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan

CoRR, 2018

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu

BMC Genom., 2018

Fast characterization of segmental duplications in genome assemblies.

Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach

Bioinform., 2018

2017

Building and Improving Reference Genome Assemblies.

Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson

Proc. IEEE, 2017

Discovery and genotyping of novel sequence insertions in many sequenced individuals.

Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör, Can Alkan, Faraz Hach

Bioinform., 2017

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan

Bioinform., 2017

2016

Coinami: A Cryptocurrency with DNA Sequence Alignment as Proof-of-work.

Atalay Mert Ileri, Halil I. Ozercan, Alper Gundogdu, Ahmet K. Senol, M. Yusuf Özkaya, Can Alkan

CoRR, 2016

GateKeeper: Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture.

Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, Can Alkan

CoRR, 2016

Optimal seed solver: optimizing seed selection in read mapping.

Hongyi Xin, Sunny Nahar, Richard L. Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu

Bioinform., 2016

On genomic repeats and reproducibility.

Can Firtina, Can Alkan

Bioinform., 2016

2015

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.

Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu

Bioinform., 2015

Can you Really Anonymize the Donors of Genomic Data in Today's Digital World?

Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan, Erman Ayday

Proceedings of the Data Privacy Management, and Security Assurance, 2015

Improving Genome Assemblies Using Multi-platform Sequence Data.

Pinar Kavak, Bekir Ergüner, Duran Üstek, Bayram Yüksel, Mahmut Samil Sagiroglu, Tunga Güngör, Can Alkan

Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2015

2014

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp

Nucleic Acids Res., 2014

2013

Accelerating read mapping with FastHASH.

Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu, Can Alkan

BMC Genom., 2013

2012

Sensitive and fast mapping of di-base encoded reads.

Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan

Bioinform., 2012

SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp

Bioinform., 2012

2011

Session Introduction.

Can Alkan, Emidio Capriotti, Eleazar Eskin, Fereydoun Hormozdiari, Maricel G. Kann

Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2010

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.

Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp

Bioinform., 2010

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.

Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp

Bioinform., 2010

Session Introduction.

Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes.

Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp

Proceedings of the Research in Computational Molecular Biology, 2009

2007

Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data.

Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler

PLoS Comput. Biol., 2007

taveRNA: a web suite for RNA algorithms and applications.

Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp

Nucleic Acids Res., 2007

2006

RNA-RNA Interaction Prediction and Antisense RNA Target Search.

Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang

J. Comput. Biol., 2006

RNA Secondary Structure Prediction Via Energy Density Minimization.

Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler

Proceedings of the Research in Computational Molecular Biology, 2006

2005

Manipulating multiple sequence alignments via MaM and WebMaM.

Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp

Nucleic Acids Res., 2005

2004

The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis.

Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün

J. Comput. Biol., 2004