Can Alkan

Can Alkan

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Can Alkan

Publications by authors named "Can Alkan"

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

Turk J Biol 2019 5;43(4):264-273. Epub 2019 Aug 5.

Department of Computer Engineering, Faculty of Engineering, Bilkent University, Bilkent, Ankara Turkey.

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http://dx.doi.org/10.3906/biy-1903-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6710001PMC
August 2019

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

Bioinformatics 2019 Apr 1. Epub 2019 Apr 1.

UC-Davis Genome Center, University of California, Davis, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz237DOI Listing
April 2019

Whole-Genome Shotgun Sequence CNV Detection Using Read Depth.

Methods Mol Biol 2018 ;1833:61-72

Department of Computer Engineering, Bilkent University, Ankara, Turkey.

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http://dx.doi.org/10.1007/978-1-4939-8666-8_4DOI Listing
March 2019

Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment.

Bioinformatics 2019 Mar 28. Epub 2019 Mar 28.

Computer Engineering Department, Bilkent University, Bilkent, Ankara, Turkey.

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http://dx.doi.org/10.1093/bioinformatics/btz234DOI Listing
March 2019

Evaluation of genome scaffolding tools using pooled clone sequencing.

Authors:
Elif Dal Can Alkan

Turk J Biol 2018 10;42(6):471-476. Epub 2018 Dec 10.

Department of Computer Engineering, Faculty of Engineering, Bilkent University , Ankara , Turkey.

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http://dx.doi.org/10.3906/biy-1805-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451843PMC
December 2018

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

Nucleic Acids Res 2018 11;46(21):e125

Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1093/nar/gky724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265270PMC
November 2018

Realizing the potential of blockchain technologies in genomics.

Genome Res 2018 09 3;28(9):1255-1263. Epub 2018 Aug 3.

Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1101/gr.207464.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120626PMC
September 2018

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

BMC Genomics 2018 May 9;19(Suppl 2):89. Epub 2018 May 9.

Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1186/s12864-018-4460-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954284PMC
May 2018

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

Oncogene 2018 04 2;37(17):2251-2269. Epub 2018 Feb 2.

Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800, Ankara, Turkey.

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http://dx.doi.org/10.1038/s41388-017-0108-9DOI Listing
April 2018

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

Brief Bioinform 2018 Apr 2. Epub 2018 Apr 2.

Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.

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https://academic.oup.com/bib/advance-article/doi/10.1093/bib
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http://dx.doi.org/10.1093/bib/bby017DOI Listing
April 2018

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

Bioinformatics 2017 Nov;33(21):3355-3363

Department of Computer Engineering, Bilkent University, Bilkent, Ankara 06800, Turkey.

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http://dx.doi.org/10.1093/bioinformatics/btx342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860160PMC
November 2017

Toolkit for automated and rapid discovery of structural variants.

Methods 2017 10 2;129:3-7. Epub 2017 Jun 2.

Department of Computer Engineering, Bilkent University, Ankara, Turkey. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2017.05.030DOI Listing
October 2017

Discovery of large genomic inversions using long range information.

BMC Genomics 2017 01 10;18(1):65. Epub 2017 Jan 10.

Department of Computer Engineering, Bilkent University, Bilkent, 06800, Ankara, Turkey.

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http://dx.doi.org/10.1186/s12864-016-3444-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223412PMC
January 2017

Inter-varietal structural variation in grapevine genomes.

Plant J 2016 11 16;88(4):648-661. Epub 2016 Sep 16.

Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy.

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http://dx.doi.org/10.1111/tpj.13274DOI Listing
November 2016

On genomic repeats and reproducibility.

Bioinformatics 2016 08 11;32(15):2243-7. Epub 2016 Mar 11.

Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1093/bioinformatics/btw139DOI Listing
August 2016

Optimal seed solver: optimizing seed selection in read mapping.

Bioinformatics 2016 06 14;32(11):1632-42. Epub 2015 Nov 14.

Computer Science Department, Department of Electrical and Computer Engineering.

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http://dx.doi.org/10.1093/bioinformatics/btv670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6363230PMC
June 2016

Robustness of Massively Parallel Sequencing Platforms.

PLoS One 2015 18;10(9):e0138259. Epub 2015 Sep 18.

Advanced Genomics and Bioinformatics Research Group (İGBAM), BİLGEM, The Scientific and Technological Research Council of Turkey (TÜBİTAK), Gebze, Kocaeli, Turkey.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138259PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575192PMC
May 2016

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

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

Fast and accurate mapping of Complete Genomics reads.

Methods 2015 Jun 22;79-80:3-10. Epub 2014 Oct 22.

Department of Computer Engineering, Bilkent University, Ankara, Turkey. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406782PMC
June 2015

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

Bioinformatics 2015 May 10;31(10):1553-60. Epub 2015 Jan 10.

Computer Science Department, Department of Electrical and Computer Engineering, Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA and Department of Computer Engineering, Bilkent University, Bilkent, Ankara 06800, Turkey.

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http://dx.doi.org/10.1093/bioinformatics/btu856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426831PMC
May 2015

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

J Med Genet 2014 Jul 24;51(7):455-9. Epub 2014 Apr 24.

Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey Institute of Materials Science and Nanotechnology (UNAM), Bilkent University, Ankara, Turkey.

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http://dx.doi.org/10.1136/jmedgenet-2013-102197DOI Listing
July 2014

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

Nucleic Acids Res 2014 Jul 8;42(Web Server issue):W494-500. Epub 2014 May 8.

School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6 School of Informatics and Computing, Indiana University, Bloomington, IN, USA, 47405

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http://dx.doi.org/10.1093/nar/gku370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086126PMC
July 2014

Accelerating read mapping with FastHASH.

BMC Genomics 2013 21;14 Suppl 1:S13. Epub 2013 Jan 21.

Depts. of Computer Science and Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1471-2164-14-S1-S13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549798PMC
August 2013

Great ape genetic diversity and population history.

Nature 2013 Jul 3;499(7459):471-5. Epub 2013 Jul 3.

Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.

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http://dx.doi.org/10.1038/nature12228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822165PMC
July 2013

SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Bioinformatics 2012 Dec 9;28(23):3051-7. Epub 2012 Oct 9.

School of Computing Science, Simon Fraser University, Burnaby, Canada, V5A 1S6.

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http://dx.doi.org/10.1093/bioinformatics/bts593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509486PMC
December 2012

Detection of structural variants and indels within exome data.

Nat Methods 2011 Dec 18;9(2):176-8. Epub 2011 Dec 18.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.1810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269549PMC
December 2011

A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD.

Neuron 2011 Oct 21;72(2):257-68. Epub 2011 Sep 21.

Neuromuscular Diseases Research Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.neuron.2011.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3200438PMC
October 2011

Sensitive and fast mapping of di-base encoded reads.

Bioinformatics 2011 Jul 17;27(14):1915-21. Epub 2011 May 17.

Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-5065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129524PMC
July 2011

Alu repeat discovery and characterization within human genomes.

Genome Res 2011 Jun 3;21(6):840-9. Epub 2010 Dec 3.

School of Computing Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.

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http://dx.doi.org/10.1101/gr.115956.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106317PMC
June 2011

Genome structural variation discovery and genotyping.

Nat Rev Genet 2011 May 1;12(5):363-76. Epub 2011 Mar 1.

Department of Genome Sciences, University of Washington School of Medicine, Foege S413C, 3720 15th Ave NE, Seattle, Washington, USA.

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http://www.nature.com/articles/nrg2958
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http://dx.doi.org/10.1038/nrg2958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108431PMC
May 2011

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

Genome Res 2011 Jan 16;21(1):137-45. Epub 2010 Nov 16.

Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1101/gr.111278.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012921PMC
January 2011

Limitations of next-generation genome sequence assembly.

Nat Methods 2011 Jan 21;8(1):61-5. Epub 2010 Nov 21.

Department of Genome Sciences, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, Washington, USA.

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http://www.nature.com/articles/nmeth.1527
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http://dx.doi.org/10.1038/nmeth.1527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115693PMC
January 2011

Haplotype-resolved genome sequencing of a Gujarati Indian individual.

Nat Biotechnol 2011 Jan 19;29(1):59-63. Epub 2010 Dec 19.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nbt.1740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116788PMC
January 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

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

Genome Res 2009 Jul 15;19(7):1270-8. Epub 2009 May 15.

School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6.

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http://dx.doi.org/10.1101/gr.088633.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704429PMC
July 2009

Comparative analysis of Alu repeats in primate genomes.

Genome Res 2009 May;19(5):876-85

USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA.

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http://dx.doi.org/10.1101/gr.083972.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675976PMC
May 2009

Death and resurrection of the human IRGM gene.

PLoS Genet 2009 Mar 6;5(3):e1000403. Epub 2009 Mar 6.

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644816PMC
March 2009

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

Hum Mol Genet 2007 Nov 28;16(22):2770-9. Epub 2007 Aug 28.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.

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http://dx.doi.org/10.1093/hmg/ddm234DOI Listing
November 2007

Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

PLoS Comput Biol 2007 Sep;3(9):1807-18

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0030181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994983PMC
September 2007

taveRNA: a web suite for RNA algorithms and applications.

Nucleic Acids Res 2007 Jul 8;35(Web Server issue):W325-9. Epub 2007 May 8.

Lab for Computational Biology, SFU, Canada.

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http://dx.doi.org/10.1093/nar/gkm303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933159PMC
July 2007

RNA-RNA interaction prediction and antisense RNA target search.

J Comput Biol 2006 Mar;13(2):267-82

Department of Genome Sciences, University of Washington, Seattle, 98195, USA.

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http://www.liebertpub.com/doi/10.1089/cmb.2006.13.267
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http://dx.doi.org/10.1089/cmb.2006.13.267DOI Listing
March 2006

Manipulating multiple sequence alignments via MaM and WebMaM.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W295-8

Department of EECS, Case Western Reserve University, Cleveland, OH, USA.

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http://dx.doi.org/10.1093/nar/gki406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160167PMC
July 2005

The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis.

J Comput Biol 2004 ;11(5):933-44

Department of EECS, Case Western Reserve University, Cleveland, OH 44106, USA.

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http://dx.doi.org/10.1089/cmb.2004.11.933DOI Listing
March 2005

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

Nature 2004 Aug;430(7002):857-64

Department of Genetics, Center for Computational Genomics and the Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.

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http://dx.doi.org/10.1038/nature02806DOI Listing
August 2004

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

Genome Inform 2002 ;13:93-102

Department of EECS, Center for Computational Genomics, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA.

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November 2003

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

Genome Res 2003 Mar;13(3):358-68

Department of Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.

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http://dx.doi.org/10.1101/gr.923303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430288PMC
March 2003