C. Alkan

发表

Reconstructing complex regions of genomes using long-read sequencing technology

Mark J. P. Chaisson, Lawrence S. Hon, Peter H. Sudmant, 2014, Genome research.

Diversity of Human Copy Number Variation and Multicopy Genes

Peter H. Sudmant, J. Kitzman, J. Shendure, 2010, Science.

Haplotype-resolved genome sequencing of a Gujarati Indian individual

Andrew C. Adey, Joseph B Hiatt, Peter H. Sudmant, 2011, Nature Biotechnology.

MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering

C. Alkan, O. Mutlu, M. Alser, 2017, 1707.01631.

Fast and accurate mapping of Complete Genomics reads.

C. Alkan, O. Mutlu, Donghyuk Lee, 2015, Methods.

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

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

Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing

J. Kitzman, C. Baker, E. Eichler, 2009, Nature Genetics.

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

C. Alkan, F. Hormozdiari, Seunghak Lee, 2009, Nature Methods.

Mapping and sequencing of structural variation from eight human genomes

Joshua M. Korn, Nancy F. Hansen, D. Altshuler, 2008, Nature.

Mapping copy number variation by population scale genome sequencing

Kenny Q. Ye, G. T. Marth, Hugo Y. K. Lam, 2010, Nature.

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

Francisco M. De La Vega, Robert E. Beaudoin, E. Eichler, 2009, Genome research.

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.

E. Eichler, C. Alkan, F. Hormozdiari, 2009, Genome research.

Alu repeat discovery and characterization within human genomes.

Deniz Yorukoglu, E. Eichler, M. Malig, 2011, Genome research.

Detection of structural variants and indels within exome data

M. Rieder, B. O’Roak, E. Eichler, 2011, Nature Methods.

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

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

Genome structural variation discovery and genotyping

Bradley P. Coe, B. Coe, E. Eichler, 2011, Nature Reviews Genetics.

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

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

Comparative and demographic analysis of orang-utan genomes

Albert J. Vilella, Zhengyuan O. Wang, Matthew W. Hahn, 2011, Nature.

An integrated map of structural variation in 2,504 human genomes

Gabor T. Marth, Hugo Y. K. Lam, Miriam K. Konkel, 2015, Nature.

The structure and evolution of centromeric transition regions within the human genome

D. Haussler, E. Eichler, J. Bailey, 2004, Nature.

Complete Khoisan and Bantu genomes from southern Africa

Tom H. Pringle, Robert S. Harris, E. Eichler, 2010, Nature.

Characterization of Missing Human Genome Sequences and Copy-number Polymorphic Insertions

E. Eichler, M. Malig, F. Antonacci, 2010, Nature Methods.

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Adrian W. Briggs, Michael F. Siebauer, Peter H. Sudmant, 2012, Science.

A Draft Sequence of the Neandertal Genome

Philip L. F. Johnson, Nancy F. Hansen, Adrian W. Briggs, 2010, Science.

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Philip L. F. Johnson, Adrian W. Briggs, E. Eichler, 2010, Nature.

Limitations of next-generation genome sequence assembly

E. Eichler, C. Alkan, S. Sajjadian, 2011, Nature Methods.

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

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

Nanopore Sequencing Technology and Tools: Computational Analysis of the Current State, Bottlenecks, and Future Directions

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2017 .

Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.

Bradley P. Coe, Catarina D. Campbell, B. Coe, 2013, American journal of human genetics.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Matthew W. Hahn, Bronwen L. Aken, C. Alkan, 2014, Proceedings of the National Academy of Sciences.

Evaluation of genome scaffolding tools using pooled clone sequencing

C. Alkan, E. Dal, 2018, Turkish journal of biology = Turk biyoloji dergisi.

Insights into hominid evolution from the gorilla genome sequence

Albert J. Vilella, Gregory E. Jordan, Petra C. Schwalie, 2012, Nature.

Discovery of large genomic inversions using long range information

E. Eichler, F. Antonacci, C. Alkan, 2017, BMC Genomics.

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

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

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

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

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

Can Alkan, Kai Fu, Javeed Iqbal, 2022 .

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

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

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.

Great ape genetic diversity and population history

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

Discovery of large genomic inversions using pooled clone sequencing

E. Eichler, F. Antonacci, C. Alkan, 2015, bioRxiv.

Computational studies on evolution and functionality of genomic repeats

C. Alkan, S. C. Sahinalp, 2005 .

An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution.

E. Eichler, J. Bailey, C. Alkan, 2002, Genome informatics. International Conference on Genome Informatics.

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 .

Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools

C. Alkan, Gülfem Demir, 2019, Turkish journal of biology = Turk biyoloji dergisi.

The bonobo genome compared with the chimpanzee and human genomes

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

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

C. Alkan, Z. Bar-Joseph, A. E. Cicek, 2017, bioRxiv.

Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X.

C. Alkan, C. Disteche, R. Kaul, 2011, Genome research.

Individual A High-Coverage Genome Sequence from an Archaic Denisovan

Adrian W. Briggs, Michael F. Siebauer, M. Hammer, 2012 .

Automatic characterization of copy number polymorphism using high throughput sequencing

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

Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer

C. Alkan, Ö. Sahin, S. Wiemann, 2018, Oncogene.

Technology dictates algorithms: recent developments in read alignment

C. Alkan, O. Mutlu, M. Alser, 2020, Genome biology.

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

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2022, ISCA.

Massively Parallel Mapping of Next Generation Sequence Reads Using GPUs

C. Alkan, O. Mutlu, O. Ozturk, 2015 .

Pacific symposium on biocomputing 2011

C. Alkan, F. Hormozdiari, E. Eskin, 2011 .

high-throughput sequenced genomes Combinatorial algorithms for structural variation detection in Material Supplemental

H. Mefford, E. Eichler, C. Alkan, 2009 .

Annotated features of domestic cat – Felis catus genome

C. Alkan, S. O’Brien, T. Marquès-Bonet, 2014, GigaScience.

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

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2019, bioRxiv.

Sequence analysis On genomic repeats and reproducibility

C. Alkan, Can Firtina, 2016 .

Reﬁnement and Discovery of New Hotspots of Copy-Number Variation Associated with Autism Spectrum Disorder

Catarina D. Campbell, B. Coe, C. Baker, 2013 .

SeGraM

Jeremie S. Kim, Damla Senol Cali, Nika Mansouri Ghiasi, 2022, Proceedings of the 49th Annual International Symposium on Computer Architecture.

OP-CBIO140912 1553..1560

C. Alkan, Gennady Pekhimenko, O. Mutlu, 2015 .

Frequent Activating Mutations Of JAK-STAT Pathway Genes In Natural Killer Cell Lymphomas

C. Alkan, L. Staudt, W. Chan, 2013 .

New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset.

E. Eichler, M. Malig, F. Antonacci, 2009, Molecular biology and evolution.

BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis

Jeremie S. Kim, Damla Senol Cali, Nika Mansouri Ghiasi, 2021, bioRxiv.

ÉCOLE: Learning to call copy number variants on whole exome sequencing data

C. Alkan, A. E. Cicek, Fazilet Canset Özden, 2022, bioRxiv.

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

Nika Mansouri Ghiasi, C. Alkan, O. Mutlu, 2022, bioRxiv.

Accelerating read mapping with FastHASH

C. Alkan, O. Mutlu, Donghyuk Lee, 2013, BMC Genomics.

Computational pan-genomics: status, promises and challenges

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

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

O. Gokcumen, C. Alkan, S. C. Sahinalp, 2014, BMC Genomics.

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

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

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).

An integrated map of genetic variation from 1,092 human genomes

Kenny Q. Ye, Mauricio O. Carneiro, Francisco M. De La Vega, 2012, Nature.

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

C. Alkan, I. Hajirasouliha, Camir Ricketts, 2020, Genome Biology.

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

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

Divergent origins and concerted expansion of two segmental duplications on chromosome 16.

E. Eichler, C. Alkan, E. Tuzun, 2001, The Journal of heredity.

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair

C. Alkan, B. Yüksel, T. Özçelik, 2014, Journal of Medical Genetics.

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

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

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

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

Polishing copy number variant calls on exome sequencing data via deep learning

C. Alkan, A. E. Cicek, Fazilet Canset Özden, 2020, bioRxiv.

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

C. Alkan, M. Somel, Arda Söylev, 2021, bioRxiv.

A robust benchmark for detection of germline large deletions and insertions

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

Fast characterization of segmental duplications in genome assemblies

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

Accelerating Genome Analysis: A Primer on an Ongoing Journey

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

Comparative analysis of Alu repeats in primate genomes.

E. Eichler, C. Alkan, Shaying Zhao, 2009, Genome research.

Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome.

E. Eichler, J. Bailey, C. Alkan, 2003, Genome research.

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

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

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

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

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

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

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

C. Baker, E. Eichler, T. Graves, 2009, Nature.

Death and Resurrection of the Human IRGM Gene

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

Complete Khoisan and Bantu genomes from southern

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

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee.

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

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

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

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..

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

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

Fast characterization of segmental duplication structure in multiple genome assemblies

C. Alkan, Faraz Hach, Ibrahim Numanagić, 2022, Algorithms Mol. Biol..

Fast characterization of segmental duplication structure in multiple genome assemblies

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

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

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

Technology dictates algorithms: recent developments in read alignment

C. Alkan, O. Mutlu, M. Alser, 2020, Genome Biology.

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

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

Rates and patterns of great ape retrotransposition

Miriam K. Konkel, Peter H. Sudmant, C. Baker, 2013, Proceedings of the National Academy of Sciences.

Supplemental Section S1 – Genome Sequencing and Assembly........................................... 2 Supplemental Section S2 – Indel Assessment with the Neutral Indel Model ................11 Supplemental Section S3 – Great Ape Divergence Estimate via Wgs Read Mapping..11 Supplemental Section S7 –

Albert J. Vilella, Zhengyuan O. Wang, Miriam K. Konkel, 2022 .

Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas.

C. Alkan, G. Hannon, D. Byrd, 2011, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

MaM : Multiple alignment Manipulator

E. Eichler, J. Bailey, C. Alkan, 2022 .

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

E. Eichler, C. Alkan, M. Cardone, 2012 .

Optimal design of oligonucleotide microarrays for measurement of DNA copy-number.

E. Eichler, S. Schwartz, C. Alkan, 2007, Human molecular genetics.

APPLICATIONS OF NEXT-GENERATI ON SEQUENCING REVIEWS

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

A robust benchmark for germline structural variant detection

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

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

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

Discovery and genotyping of novel sequence insertions in many sequenced individuals

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

A robust benchmark for germline large deletion and insertion detection

Nathan D. Olson, Ian T. Fiddes, Ryan E. Mills, 2022 .

Inter-varietal structural variation in grapevine genomes.

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

Realizing the potential of blockchain technologies in genomics

Atalay Mert Ileri, C. Alkan, Erman Ayday, 2018, Genome research.

BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis

Jeremie S. Kim, Damla Senol Cali, Nika Mansouri Ghiasi, 2021, bioRxiv.

Characterization of segmental duplications and large inversions using Linked-Reads

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

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..

Building and Improving Reference Genome Assemblies

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

On genomic repeats and reproducibility

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

Sensitive and fast mapping of di-base encoded reads

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

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

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

Accelerating Approximate Pattern Matching with Processing-In-Memory ( PIM ) and Single-Instruction Multiple-Data ( SIMD ) Programming

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2018 .

RNA-RNA Interaction Prediction and Antisense RNA Target Search

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

taveRNA: a web suite for RNA algorithms and applications

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

taveRNA: a web suite for RNA algorithms and applications.

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

RNA Secondary Structure Prediction Via Energy Density Minimization

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

Genomics technologies to study structural variations in the grapevine genome

C. Alkan, M. Cardone, M. Ventura, 2016 .

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

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

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

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

Individual A High-Coverage Genome Sequence from an Archaic Denisovan

Adrian W. Briggs, Michael F. Siebauer, Peter H. Sudmant, 2012 .

Activating mutations of STAT 5 B and STAT 3 in lymphomas derived from gdT or NK cells

C. Alkan, L. Staudt, W. Chan, 2015 .

A robust benchmark for detection of germline large deletions and insertions

Ian T. Fiddes, Jay M. Sage, Michael D. Kaiser, 2020, Nature Biotechnology.

Author Correction: A robust benchmark for detection of germline large deletions and insertions

Ian T. Fiddes, Jay M. Sage, Michael D. Kaiser, 2020, Nature Biotechnology.

ISMB 2010 Organization

Roger L. Chang, S. Batzoglou, L. Cowen, 2010, Bioinformatics.

BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis

Jeremie S. Kim, Damla Senol Cali, Nika Mansouri Ghiasi, 2021, bioRxiv.

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

C. Alkan, O. Mutlu, M. Alser, 2019, Bioinform..

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

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

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

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2019, bioRxiv.

FastRemap: a tool for quickly remapping reads between genome assemblies

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2022, Bioinform..

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

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

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).

Optimal seed solver: optimizing seed selection in read mapping

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

SLIDER: Fast and Efficient Computation of Banded Sequence Alignment pdf

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

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

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

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

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

Determining the origin of synchronous multifocal bladder cancer by exome sequencing

C. Alkan, Ö. Acar, T. Esen, 2015, BMC Cancer.

Mapping copy number variation by population scale genome sequencing

Joshua M. Korn, Kenny Q. Ye, G. T. Marth, 2010, Nature.

SCALCE: boosting sequence compression algorithms using locally consistent encoding

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

Nanopore Sequencing Technology and Tools: Computational Analysis of the Current State, Bottlenecks, and Future Directions

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2017 .

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

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2017, BMC Genomics.

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

O. Gokcumen, C. Alkan, S. C. Sahinalp, 2014, BMC Genomics.

Whole-Genome Shotgun Sequence CNV Detection Using Read Depth.

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

ECOLE: Learning to call copy number variants on whole exome sequencing data

C. Alkan, A. E. Cicek, Fazilet Canset Özden, 2023, bioRxiv.

Targeting PLK 1 overcomes TDM 1 resistance via CDK 1-dependent phosphorylation and inactivation of Bcl-2 / xL in HER 2-positive breast cancer

C. Alkan, Ö. Sahin, S. Wiemann, 2018 .

Accelerating Genome Analysis: A Primer on an Ongoing Journey

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2020, IEEE Micro.

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.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Bronwen L. Aken, C. Alkan, S. Searle, 2014, Proceedings of the National Academy of Sciences.

Accelerating read mapping with FastHASH

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

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

E. Eichler, C. Alkan, F. Hormozdiari, 2009, RECOMB.

Reconstructing complex regions of genomes using long-read sequencing technology

Mark J. P. Chaisson, Lawrence S. Hon, Peter H. Sudmant, 2014, Genome research.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee.

J. Shendure, E. Eichler, M. Malig, 2011, Genome research.

FastRemap: a tool for quickly remapping reads between genome assemblies

Jeremie S. Kim, Damla Senol Cali, C. Alkan, 2022, Bioinform..

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

C. Alkan, O. Mutlu, M. Alser, 2018, Bioinform..

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

E. Eichler, C. Alkan, E. Mardis, 2009, Nature.

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

Nika Mansouri Ghiasi, C. Alkan, O. Mutlu, 2022, bioRxiv.