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Can Alkan
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- affiliation: University of Washington, Seattle, USA
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2020 – today
- 2024
- [j33]Mona Shojaei
, Navid Mohammadvand
An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data. Comput. Biol. Medicine 169: 107810 (2024) - [j32]Zülal Bingöl
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. IEEE Trans. Computers 73(5): 1206-1218 (2024) - 2023
- [j31]Gözde Yazici
Identification of protein-protein interaction bridges for multiple sclerosis. Bioinform. 39(4) (2023) - [i16]Julien Eudine, Mohammed Alser, Gagandeep Singh, Can Alkan, Onur Mutlu:
GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping. CoRR abs/2309.17063 (2023) - [i15]Ahmet Cemal Alicioglu, Mahmud Sami Aydin, Can Alkan:
Pairwise sequence alignment with block and character edit operations. CoRR abs/2311.11082 (2023) - 2022
- [j30]Hamza Iseric, Can Alkan, Faraz Hach
Fast characterization of segmental duplication structure in multiple genome assemblies. Algorithms Mol. Biol. 17(1): 4 (2022) - [j29]Jeremie S. Kim
FastRemap: a tool for quickly remapping reads between genome assemblies. Bioinform. 38(19): 4633-4635 (2022) - [j28]Arda Söylev
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. PLoS Comput. Biol. 18(12): 1010788 (2022) - [c11]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: 638-655 - [i14]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 abs/2205.05883 (2022) - [i13]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 abs/2212.04953 (2022) - 2021
- [j27]Mohammed Alser
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. Bioinform. 36(22-23): 5282-5290 (2021) - [c10]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: 209 - [c9]Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic:
BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. WABI 2021: 15:1-15:18 - [i12]Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan:
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. CoRR abs/2103.14978 (2021) - 2020
- [j26]Can Firtina
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. 36(12): 3669-3679 (2020) - [j25]Can Alkan
Automatic characterization of copy number polymorphism using high throughput sequencing. Turkish J. Electr. Eng. Comput. Sci. 28(1): 253-261 (2020) - [j24]Mohammed Alser, Zülal Bingöl, Damla Senol Cali
Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro 40(5): 65-75 (2020) - [c8]Damla Senol Cali
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO 2020: 951-966 - [i11]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 abs/2008.00961 (2020) - [i10]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 abs/2009.07692 (2020)
2010 – 2019
- 2019
- [j23]Damla Senol Cali
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Briefings Bioinform. 20(4): 1542-1559 (2019) - [j22]Arda Soylev
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing. Bioinform. 35(20): 3923-3930 (2019) - [j21]Mohammed Alser, Hasan Hassan, Akash Kumar
Shouji: a fast and efficient pre-alignment filter for sequence alignment. Bioinform. 35(21): 4255-4263 (2019) - [i9]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 abs/1902.04341 (2019) - [i8]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 abs/1910.09020 (2019) - [i7]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 abs/1912.08735 (2019) - 2018
- [j20]Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan
Fast characterization of segmental duplications in genome assemblies. Bioinform. 34(17): i706-i714 (2018) - [j19]Jeremie S. Kim, Damla Senol Cali
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genom. 19(S2) (2018) - [i6]Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach:
Fast Characterization of Segmental Duplications in Genome Assemblies. CoRR abs/1807.00205 (2018) - [i5]Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, Can Alkan:
SLIDER: Fast and Efficient Computation of Banded Sequence Alignment. CoRR abs/1809.07858 (2018) - 2017
- [j18]Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör
Discovery and genotyping of novel sequence insertions in many sequenced individuals. Bioinform. 33(14): i161-i169 (2017) - [j17]Mohammed Alser, Hasan Hassan, Hongyi Xin
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinform. 33(21): 3355-3363 (2017) - [j16]Karyn Meltz Steinberg
Building and Improving Reference Genome Assemblies. Proc. IEEE 105(3): 422-435 (2017) - [i4]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 abs/1711.01177 (2017) - 2016
- [j15]Hongyi Xin
Optimal seed solver: optimizing seed selection in read mapping. Bioinform. 32(11): 1632-1642 (2016) - [j14]Can Firtina
On genomic repeats and reproducibility. Bioinform. 32(15): 2243-2247 (2016) - [i3]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 abs/1602.03031 (2016) - [i2]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 abs/1604.01789 (2016) - 2015
- [j13]Hongyi Xin
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. Bioinform. 31(10): 1553-1560 (2015) - [c7]Pinar Kavak, Bekir Ergüner, Duran Üstek
Improving Genome Assemblies Using Multi-platform Sequence Data. CIBB 2015: 220-232 - [c6]Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan
Can you Really Anonymize the Donors of Genomic Data in Today's Digital World? DPM/QASA@ESORICS 2015: 237-244 - [i1]Hongyi Xin, Richard L. Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu:
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping. CoRR abs/1506.08235 (2015) - 2014
- [j12]Faraz Hach
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res. 42(Webserver-Issue): 494-500 (2014) - 2013
- [j11]Hongyi Xin
Accelerating read mapping with FastHASH. BMC Genom. 14(S-1): S13 (2013) - 2012
- [j10]Farhad Hormozdiari, Faraz Hach
Sensitive and fast mapping of di-base encoded reads. Bioinform. 28(1): 150 (2012) - [j9]Faraz Hach
SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinform. 28(23): 3051-3057 (2012) - 2011
- [j8]Farhad Hormozdiari, Faraz Hach
Sensitive and fast mapping of di-base encoded reads. Bioinform. 27(14): 1915-1921 (2011) - [c5]Can Alkan, Emidio Capriotti, Eleazar Eskin, Fereydoun Hormozdiari, Maricel G. Kann:
Session Introduction. Pacific Symposium on Biocomputing 2011: 229-230 - 2010
- [j7]Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinform. 26(10): 1277-1283 (2010) - [j6]Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinform. 26(12): 350-357 (2010) - [c4]Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp:
Session Introduction. Pacific Symposium on Biocomputing 2010: 302-304
2000 – 2009
- 2009
- [c3]Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. RECOMB 2009: 218-219 - 2007
- [j5]Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan
taveRNA: a web suite for RNA algorithms and applications. Nucleic Acids Res. 35(Web-Server-Issue): 325-329 (2007) - [j4]Can Alkan
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. PLoS Comput. Biol. 3(9) (2007) - 2006
- [j3]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): 267-282 (2006) - [c2]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: 130-142 - 2005
- [j2]Can Alkan
Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Res. 33(Web-Server-Issue): 295-298 (2005) - [c1]Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang:
RNA-RNA Interaction Prediction and Antisense RNA Target Search. RECOMB 2005: 152-171 - 2004
- [j1]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): 933-944 (2004)
Coauthor Index
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last updated on 2024-05-19 00:57 CEST by the dblp team
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