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Can Alkan

Research Profile

Genes & Molecular Sequences

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TOP 3
Santhosh Girirajan; Maika Malig; Kenneth Mark; Tiffany H Vu; Can Alkan; Carl Baker; Raphael Bernier; Leslie G Biesecker; Catarina D Campbell; Ze Cheng; Bradley P Coe; Megan Y Dennis; Evan E Eichler
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
Hongyi Xin; Samihan Yedkar; Farhad Hormozdiari; Donghyuk Lee; Onur Mutlu; Can Alkan
Accelerating read mapping with FastHASH.
Faraz Hach; Ibrahim Numanagic; Can Alkan; S Cenk Sahinalp
SCALCE: boosting sequence compression algorithms using locally consistent encoding.

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All Publications

2013: Santhosh Girirajan; Maika Malig; Kenneth Mark; Tiffany H Vu; Can Alkan; Carl Baker; Raphael Bernier; Leslie G Biesecker; Catarina D Campbell; Ze Cheng; Bradley P Coe; Megan Y Dennis; Evan E Eichler
Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.
American journal of human genetics 2013;92(2):221-37.
2013: Hongyi Xin; Samihan Yedkar; Farhad Hormozdiari; Donghyuk Lee; Onur Mutlu; Can Alkan
Accelerating read mapping with FastHASH.
BMC genomics 2013;14 Suppl 1():S13.
2012: Faraz Hach; Ibrahim Numanagic; Can Alkan; S Cenk Sahinalp
SCALCE: boosting sequence compression algorithms using locally consistent encoding.
Bioinformatics (Oxford, England) 2012;28(23):3051-7.
2012: Derek M Bickhart; Maria Francesca Cardone; Evan E Eichler; Jose Fernando Garcia; Yali Hou; Can Alkan; Lakshmi Kumar Matukumalli; Robert D Schnabel; Steven G Schroeder; Jiuzhou Song; Tad S Sonstegard; Jeremy F Taylor; Curtis Van Tassell; Mario Ventura; George E Liu
Copy number variation of individual cattle genomes using next-generation sequencing.
Genome research 2012;22(4):778-90.
2012: Emre Karakoc; Kenneth Mark; Debbie A Nickerson; Brian J O'Roak; Mark J Rieder; Laura Vives; Can Alkan; Megan Y Dennis; Evan E Eichler
Detection of structural variants and indels within exome data.
Nature methods 2012;9(2):176-8.
2011: Sherry Lee; J Helen Leonard; Elizabeth P Murchison; Olga K Afanasiev; Can Alkan; David R Byrd; Gregory J Hannon; Kelly G Paulson; Paul X Nghiem
Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2011;52(3):272-5.
2011: Mario Ventura; Richard K Wilson; Can Alkan; Nicoletta Archidiacono; Carl Baker; Claudia R Catacchio; Lin Chen; Tina Graves; Fereydoun Hormozdiari; Jeffrey M Kidd; Choli Lee; Maika Malig; Tomas Marques-Bonet; Arcadi Navarro; Saba Sajjadian; Jay Shendure; Emily H Turner; Evan E Eichler
Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee.
Genome research 2011;21(10):1640-9.
2011: Farhad Hormozdiari; S Cenk Sahinalp; Evan E Eichler; Faraz Hach; Can Alkan
Sensitive and fast mapping of di-base encoded reads.
Bioinformatics (Oxford, England) 2011;27(14):1915-21.
2011: Fereydoun Hormozdiari; Can Alkan; Mario Ventura; IMAN HAJIRASOULIHA; Maika Malig; Faraz Hach; Deniz Yorukoglu; Phuong Dao; Marzieh Bakhshi; S Cenk Sahinalp; Evan E Eichler
Alu repeat discovery and characterization within human genomes.
Genome research 2011;21(6):840-9.
2011: Jacob O Kitzman; Alexandra P Mackenzie; Andrew Adey; Joseph B Hiatt; Rupali P Patwardhan; Peter H Sudmant; Sarah B Ng; Can Alkan; Ruolan Qiu; Evan E Eichler; Jay Shendure
Haplotype-resolved genome sequencing of a Gujarati Indian individual.
Nature biotechnology 2011;29(1):59-63.
2011: Can Alkan; Saba Sajjadian; Evan E Eichler
Limitations of next-generation genome sequence assembly.
Nature methods 2011;8(1):61-5.
2010: Peter H Sudmant; Jacob O Kitzman; Francesca Antonacci; Can Alkan; Maika Malig; Anya Tsalenko; Nick Sampas; Laurakay Bruhn; Jay Shendure; Evan E Eichler
Diversity of human copy number variation and multicopy genes.
Science (New York, N.Y.) 2010;330(6004):641-6.
2010: Francesca Antonacci; Jeffrey M Kidd; Tomas Marques-Bonet; Brian Teague; Mario Ventura; Santhosh Girirajan; Can Alkan; Catarina D Campbell; Laura Vives; Maika Malig; Jill A Rosenfeld; Blake C Ballif; Lisa Shaffer; Tina A Graves; Richard K Wilson; David C Schwartz; Evan E Eichler
A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk.
Nature genetics 2010;42(9):745-50.
2010: Faraz Hach; Fereydoun Hormozdiari; Can Alkan; Farhad Hormozdiari; Inanc Birol; Evan E Eichler; S Cenk Sahinalp
mrsFAST: a cache-oblivious algorithm for short-read mapping.
Nature methods 2010;7(8):576-7.
2010: Fereydoun Hormozdiari; IMAN HAJIRASOULIHA; Phuong Dao; Faraz Hach; Deniz Yorukoglu; Can Alkan; Evan E Eichler; S Cenk Sahinalp
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Bioinformatics (Oxford, England) 2010;26(12):i350-7.
2010: Jeffrey M Kidd; Nick Sampas; Francesca Antonacci; Tina Graves; Robert Fulton; Hillary S Hayden; Can Alkan; Maika Malig; Mario Ventura; Giuliana Giannuzzi; Joelle Kallicki; Paige Anderson; Anya Tsalenko; N Alice Yamada; Peter Tsang; Rajinder Kaul; Richard K Wilson; Laurakay Bruhn; Evan E Eichler
Characterization of missing human genome sequences and copy-number polymorphic insertions.
Nature methods 2010;7(5):365-71.
2009: Can Alkan; Jeffrey M Kidd; Tomas Marques-Bonet; Gozde Aksay; Francesca Antonacci; Fereydoun Hormozdiari; Jacob O Kitzman; Carl Baker; Maika Malig; Onur Mutlu; S Cenk Sahinalp; Richard A Gibbs; Evan E Eichler
Personalized copy number and segmental duplication maps using next-generation sequencing.
Nature genetics 2009;41(10):1061-7.
2009: Cemalettin Bekpen; Tomas Marques-Bonet; Can Alkan; Francesca Antonacci; Maria Bruna Leogrande; ventura Mario; Jeffrey M Kidd; Priscillia Siswara; Jonathan C Howard; Evan E Eichler
Death and resurrection of the human IRGM gene.
PLoS genetics 2009;5(3):e1000403.
2009: Tomas Marques-Bonet; Jeffrey M Kidd; ventura Mario; Tina Graves; Ze Cheng; LaDeana W Hillier; Zhaoshi Jiang; Carl Baker; Ray Malfavon-Borja; Lucinda A Fulton; Can Alkan; Gozde Aksay; Santhosh Girirajan; Priscillia Siswara; Lin Chen; Maria Francesca Cardone; Arcadi Navarro; Elaine R Mardis; Richard K Wilson; Evan E Eichler
A burst of segmental duplications in the genome of the African great ape ancestor.
Nature 2009;457(7231):877-81.
2007: andrew sharp; Andy Itsara; Ze Cheng; Can Alkan; Stuart Schwartz; Evan E Eichler
Optimal design of oligonucleotide microarrays for measurement of DNA copy-number.
Human molecular genetics 2007;16(22):2770-9.
2007: Can Alkan; ventura Mario; Nicoletta Archidiacono; Mariano Rocchi; S Cenk Sahinalp; Evan E Eichler
Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.
PLoS computational biology 2007;3(9):1807-18.
2007: Cagri Aksay; Raheleh Salari; Emre Karakoc; Can Alkan; S Cenk Sahinalp
taveRNA: a web suite for RNA algorithms and applications.
Nucleic acids research 2007;35(Web Server issue):W325-9.
2006: Can Alkan; Emre Karakoç; Joseph H Nadeau; S Cenk Sahinalp; Kaizhong Zhang
RNA-RNA interaction prediction and antisense RNA target search.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(2):267-82.
2005: Can Alkan; Eray Tüzün; Jerome Buard; Franck Lethiec; Evan E Eichler; Jeffrey A Bailey; S Cenk Sahinalp
Manipulating multiple sequence alignments via MaM and WebMaM.
Nucleic acids research 2005;33(Web Server issue):W295-8.
2004: Xinwei She; Julie E Horvath; Zhaoshi Jiang; Ge Liu; Terrence S Furey; Laurie A Christ; Royden Clark; Tina Graves; Cassy L Gulden; Can Alkan; Jeffrey A Bailey; Cenk Sahinalp; Mariano Rocchi; David Haussler; Richard K Wilson; Webb Miller; Stuart Schwartz; Evan E Eichler
The structure and evolution of centromeric transition regions within the human genome.
Nature 2004;430(7002):857-64.
2004: Can Alkan; Evan E Eichler; Jeffrey A Bailey; S Cenk Sahinalp; Eray Tüzün
The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(5):933-44.
2003: Ge Liu; Shaying Zhao; Jeffrey A Bailey; S Cenk Sahinalp; Can Alkan; Eray Tuzun; Eric Green; Evan E Eichler
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome.
Genome research 2003;13(3):358-68.
2002: Can Alkan; Jeffrey A Bailey; Evan E Eichler; S Cenk Sahinalp; Eray Tuzun
An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution.
Genome informatics. International Conference on Genome Informatics 2002;13():93-102.
2001: Evan E Eichler; Matthew E Johnson; Can Alkan; Eray Tuzun; C Sahinalp; Doriana Misceo; Nicoletta Archidiacono; Mariano Rocchi
Divergent origins and concerted expansion of two segmental duplications on chromosome 16.
The Journal of heredity 2001;92(6):462-8.