Can Alkan

发表

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

Erman Ayday, Mohammed Alser, Nour Almadhoun, 2015, DPM/QASA@ESORICS.

RNA-RNA Interaction Prediction and Antisense RNA Target Search

Kaizhong Zhang, Süleyman Cenk Sahinalp, Can Alkan, 2005, RECOMB.

Optimal seed solver: optimizing seed selection in read mapping

Onur Mutlu, Gennady Pekhimenko, Carl Kingsford, 2015, Bioinform..

SCALCE: boosting sequence compression algorithms using locally consistent encoding

Faraz Hach, Süleyman Cenk Sahinalp, Can Alkan, 2012, Bioinform..

Accelerating Genome Analysis: A Primer on an Ongoing Journey

Onur Mutlu, Saugata Ghose, Jeremie S. Kim, 2020, IEEE Micro.

Polishing Copy Number Variant Calls on Exome Sequencing Data via Deep Learning

Can Alkan, Furkan Özden, A. Ercüment Çiçek, 2020 .

A robust benchmark for detection of germline large deletions and insertions

Ken Chen, Adam M. Phillippy, Iman Hajirasouliha, 2020, Nature Biotechnology.

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

Can Alkan, Fereydoun Hormozdiari, Arda Soylev, 2018, bioRxiv.

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Onur Mutlu, Juan Gómez-Luna, Mohammed Alser, 2019, Bioinform..

Discovery and genotyping of novel sequence insertions in many sequenced individuals

Faraz Hach, Tunga Güngör, Can Alkan, 2017, Bioinform..

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

Onur Mutlu, Gennady Pekhimenko, Carl Kingsford, 2015, Bioinform..

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

Onur Mutlu, Oguz Ergin, Saugata Ghose, 2017, BMC Genomics.

taveRNA: a web suite for RNA algorithms and applications

Süleyman Cenk Sahinalp, Can Alkan, Emre Karakoç, 2007, Nucleic Acids Res..

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

Can Alkan, Atalay Mert Ileri, M. Yusuf Özkaya, 2016, ArXiv.

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

Can Alkan, Fereydoun Hormozdiari, Arda Soylev, 2019, Bioinform..

RNA Secondary Structure Prediction Via Energy Density Minimization

Kaizhong Zhang, Jeremy Buhler, Süleyman Cenk Sahinalp, 2006, RECOMB.

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

Eray Tüzün, Süleyman Cenk Sahinalp, Can Alkan, 2004, J. Comput. Biol..

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Ziv Bar-Joseph, A. Ercument Cicek, Can Alkan, 2017 .

GRIM-filter: fast seed filtering in read mapping using emerging memory technologies

Onur Mutlu, Oguz Ergin, Saugata Ghose, 2017, 1708.04329.

Improving Genome Assemblies Using Multi-platform Sequence Data

Tunga Güngör, Can Alkan, Bekir Ergüner, 2015, CIBB.

LEAP: A Generalization of the Landau-Vishkin Algorithm with Custom Gap Penalties

Onur Mutlu, Jeremie S. Kim, Can Alkan, 2017 .

PERSONAL GENOMICS – Session Introduction

Can Alkan, Maricel G. Kann, Fereydoun Hormozdiari, 2009 .

A robust benchmark for germline structural variant detection

Sergey Koren, Adam M. Phillippy, Iman Hajirasouliha, 2019, bioRxiv.

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

Süleyman Cenk Sahinalp, Can Alkan, Fereydoun Hormozdiari, 2009, RECOMB.

Computational Pan-Genomics: Status, Promises and Challenges

Jan O. Korbel, Ying Zhang, Eleazar Eskin, 2016 .

Accelerating read mapping with FastHASH

Onur Mutlu, Donghyuk Lee, Can Alkan, 2013, BMC Genomics.

Building and Improving Reference Genome Assemblies

Deanna M. Church, Richard K. Wilson, Can Alkan, 2017, Proceedings of the IEEE.

Sensitive and fast mapping of di-base encoded reads

Faraz Hach, Süleyman Cenk Sahinalp, Can Alkan, 2011, Bioinform..

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

Faraz Hach, Süleyman Cenk Sahinalp, Can Alkan, 2014, Nucleic Acids Res..

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

Onur Mutlu, Oguz Ergin, Hasan Hassan, 2016, ArXiv.

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

Rachata Ausavarungnirun, Onur Mutlu, Saugata Ghose, 2020, 2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture (MICRO).

APPLICATIONS OF NEXT-GENERATI ON SEQUENCING REVIEWS

Can Alkan, Evan E. Eichler, E. Eichler, 2011 .

Whole-Genome Shotgun Sequence CNV Detection Using Read Depth.

Can Alkan, Fatma Kahveci, C. Alkan, 2018, Methods in molecular biology.

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

Onur Mutlu, Akash Kumar, Hasan Hassan, 2018, Bioinform..

Fast characterization of segmental duplications in genome assemblies

Faraz Hach, Bonnie Berger, Can Alkan, 2018, Bioinform..

On genomic repeats and reproducibility

Can Alkan, Can Firtina, C. Alkan, 2016, Bioinform..

RNA-RNA Interaction Prediction and Antisense RNA Target Search

Kaizhong Zhang, Süleyman Cenk Sahinalp, Can Alkan, 2006, J. Comput. Biol..

Sensitive and fast mapping of di-base encoded reads

Faraz Hach, Süleyman Cenk Sahinalp, Can Alkan, 2011, Bioinform..

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

Onur Mutlu, Jeremie S. Kim, Mohammed Alser, 2019 .

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

Süleyman Cenk Sahinalp, Can Alkan, Evan E. Eichler, 2007, PLoS Comput. Biol..

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

Onur Mutlu, Oguz Ergin, Hasan Hassan, 2016, Bioinform..

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

Onur Mutlu, A. Ercument Cicek, Jeremie S. Kim, 2019, Bioinform..

SLIDER: Fast and Efficient Computation of Banded Sequence Alignment pdf

Onur Mutlu, Hasan Hassan, Akash Kumar, 2018, ArXiv.

Computational pan-genomics: status, promises and challenges

Ying Zhang, Eleazar Eskin, Knut Reinert, 2016, bioRxiv.

Characterization of segmental duplications and large inversions using Linked-Reads

Iman Hajirasouliha, Can Alkan, Camir Ricketts, 2018, bioRxiv.

Manipulating multiple sequence alignments via MaM and WebMaM

Eray Tüzün, Süleyman Cenk Sahinalp, Can Alkan, 2005, Nucleic Acids Res..

Calling inversions from next-generation sequencing paired-end mapping data with GRIAL

Can Alkan, Sònia Casillas, Evan E. Eichler, 2012 .

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

Faraz Hach, Iman Hajirasouliha, Süleyman Cenk Sahinalp, 2010, Bioinform..

mrsFAST: a cache-oblivious algorithm for short-read mapping

Faraz Hach, Inanc Birol, Can Alkan, 2010, Nature Methods.

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

Onur Mutlu, Saugata Ghose, Jeremie S. Kim, 2017, Briefings Bioinform..

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

Inanç Birol, Iman Hajirasouliha, Süleyman Cenk Sahinalp, 2010, Bioinform..

Fast characterization of segmental duplication structure in multiple genome assemblies

Faraz Hach, Can Alkan, Ibrahim Numanagic, 2022, Algorithms for Molecular Biology.

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

Onur Mutlu, Ozcan Ozturk, Mohammed Alser, 2021, 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

A large, complex structural polymorphism at 16p12.1 underlies microdeletion disease risk

David C. Schwartz, Can Alkan, Evan E. Eichler, 2010, Nature Genetics.

Activating mutations of STAT5B and STAT3 in lymphomas derived from gamma delta-T or NK cells

Can Alkan, Kai Fu, Javeed Iqbal, 2022 .

Complete Khoisan and Bantu genomes from southern

Anton Nekrutenko, Kateryna D. Makova, Francesca Chiaromonte, 2010 .

Great ape genetic diversity and population history

Arcadi Navarro, Thomas Mailund, Jaume Bertranpetit, 2013, Nature.

taveRNA: a web suite for RNA algorithms and applications.

Süleyman Cenk Sahinalp, Can Alkan, Emre Karakoç, 2007, Nucleic acids research.

Copy number variation of individual cattle genomes using next-generation sequencing.

Robert D Schnabel, Can Alkan, Tad S Sonstegard, 2012, Genome research.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Can Alkan, Francesca Antonacci, Stephen J O'Brien, 2011, Genome research.

VALOR2: characterization of large-scale structural variants using linked-reads

Iman Hajirasouliha, Can Alkan, Camir Ricketts, 2020, Genome Biology.

A burst of segmental duplications in the genome of the African great ape ancestor

Arcadi Navarro, Zhaoshi Jiang, Elaine R. Mardis, 2009, Nature.

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

Ilan Gronau, John Novembre, Elaine A. Ostrander, 2016, PLoS genetics.

Death and Resurrection of the Human IRGM Gene

Can Alkan, Evan E. Eichler, Francesca Antonacci, 2009, PLoS genetics.

A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD

David Heckerman, Lorne Zinman, Joanne Wuu, 2011, Neuron.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee.

Arcadi Navarro, Jay Shendure, Can Alkan, 2011, Genome research.

The bonobo genome compared with the chimpanzee and human genomes

Sergey Koren, Thomas Mailund, Asger Hobolth, 2012, Nature.

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells

Can Alkan, Kai Fu, Javeed Iqbal, 2015, Nature Communications.

Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073

Ken Chen, Joshua M. Korn, Afidalina Tumian, 2010 .

Inter-varietal structural variation in grapevine genomes.

Can Alkan, Mario Ventura, Donato Antonacci, 2016, The Plant journal : for cell and molecular biology.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

Arcadi Navarro, Jaume Bertranpetit, Can Alkan, 2013, BMC Genomics.

Robustness of Massively Parallel Sequencing Platforms

Faraz Hach, Tunga Güngör, Can Alkan, 2015, PloS one.

Fast and accurate mapping of Complete Genomics

Faraz Hach, Onur Mutlu, Can Alkan, 2015 .

Toolkit for automated and rapid discovery of structural variants.

Can Alkan, Fereydoun Hormozdiari, Arda Soylev, 2017, Methods.

Genome Sequencing Highlights the Dynamic Early History of Dogs

Ilan Gronau, John Novembre, Elaine A. Ostrander, 2014, PLoS genetics.