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)

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)

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 (RECOMB, 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)

taveRNA: a web suite for RNA algorithms and applications. - Cagri Aksay; Raheleh Salari; Emre Karakoç; Can Alkan; Süleyman Cenk Sahinalp (Nucleic Acids Res., 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)

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. - Fereydoun Hormozdiari; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (RECOMB, 2009)

Session Introduction. - Can Alkan; Michael Brudno; Evan E. Eichler; Maricel G. Kann; Süleyman Cenk Sahinalp (Pacific Symposium on Biocomputing, 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)

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)

Session Introduction. - Can Alkan; Emidio Capriotti; Eleazar Eskin; Fereydoun Hormozdiari; Maricel G. Kann (Pacific Symposium on Biocomputing, 2011)

SCALCE: boosting sequence compression algorithms using locally consistent encoding. - Faraz Hach; Ibrahim Numanagic; Can Alkan; Süleyman Cenk Sahinalp (Bioinform., 2012)

Sensitive and fast mapping of di-base encoded reads. - Farhad Hormozdiari; Faraz Hach; Süleyman Cenk Sahinalp; Evan E. Eichler; Can Alkan (Bioinform., 2012)

Accelerating read mapping with FastHASH. - Hongyi Xin; Donghyuk Lee; Farhad Hormozdiari; Samihan Yedkar; Onur Mutlu; Can Alkan (BMC Genom., 2013)

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)

Improving Genome Assemblies Using Multi-platform Sequence Data. - Pinar Kavak; Bekir Ergüner; Duran Üstek; Bayram Yüksel; Mahmut Samil Sagiroglu; Tunga Güngör; Can Alkan (CIBB, 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 (DPM/QASA@ESORICS, 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)

On genomic repeats and reproducibility. - Can Firtina; Can Alkan (Bioinform., 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)

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)

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: 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)

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)

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)

Fast characterization of segmental duplications in genome assemblies. - Ibrahim Numanagic; Alim S. Gökkaya; Lillian Zhang; Bonnie Berger; Can Alkan; Faraz Hach (Bioinform., 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)

SLIDER: Fast and Efficient Computation of Banded Sequence Alignment. - Mohammed Alser; Hasan Hassan; Akash Kumar 001; Onur Mutlu; Can Alkan (CoRR, 2018)

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)

Shouji: a fast and efficient pre-alignment filter for sequence alignment. - Mohammed Alser; Hasan Hassan; Akash Kumar 001; Onur Mutlu; Can Alkan (Bioinform., 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)

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)

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; et al. (MICRO, 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)

Automatic characterization of copy number polymorphism using high throughput sequencing. - Can Alkan (Turkish J. Electr. Eng. Comput. Sci., 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)

BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. - Hamza Iseric; Can Alkan; Faraz Hach; Ibrahim Numanagic (WABI, 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)

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 002; Juan Gómez-Luna; et al. (ISCA, 2022)

Fast characterization of segmental duplication structure in multiple genome assemblies. - Hamza Iseric; Can Alkan; Faraz Hach; Ibrahim Numanagic (Algorithms Mol. Biol., 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)

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. - Meryem Banu Cavlak; Gagandeep Singh 002; Mohammed Alser; Can Firtina; Joël Lindegger; Mohammad Sadrosadati; Nika Mansouri-Ghiasi; Can Alkan; Onur Mutlu (CoRR, 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., 2022)

GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping. - Julien Eudine; Mohammed Alser; Gagandeep Singh 002; Can Alkan; Onur Mutlu (CoRR, 2023)

Pairwise sequence alignment with block and character edit operations. - Ahmet Cemal Alicioglu; Mahmud Sami Aydin; Can Alkan (CoRR, 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., 2023)

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, 2024)

GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. - Zülal Bingöl; Mohammed Alser; Onur Mutlu; Ozcan Ozturk 001; Can Alkan (IEEE Trans. Computers, 2024)

Processing-in-memory for genomics workloads. - 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; et al. (CoRR, 2025)