Can Alkan, Ph.D. - Publications

Genome Sciences University of Washington, Seattle, Seattle, WA 

87 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Alser M, Shahroodi T, Gómez-Luna J, Alkan C, Mutlu O. SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs. Bioinformatics (Oxford, England). PMID 33315064 DOI: 10.1093/bioinformatics/btaa1015  0.44
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Alkan C, et al. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32699374 DOI: 10.1038/S41587-020-0640-Y  0.72
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Alkan C, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.72
2020 Karaoğlanoğlu F, Ricketts C, Ebren E, Rasekh ME, Hajirasouliha I, Alkan C. VALOR2: characterization of large-scale structural variants using linked-reads. Genome Biology. 21: 72. PMID 32192518 DOI: 10.1186/S13059-020-01975-8  0.72
2020 Firtina C, Kim JS, Alser M, Cali DS, Cicek AE, Alkan C, Mutlu O. Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. Bioinformatics (Oxford, England). PMID 32167530 DOI: 10.1093/Bioinformatics/Btaa179  0.44
2019 Soylev A, Le T, Amini H, Alkan C, Hormozdiari F. Discovery of tandem and interspersed segmental duplications using high throughput sequencing. Bioinformatics (Oxford, England). PMID 30937433 DOI: 10.1093/Bioinformatics/Btz237  0.76
2019 Alser M, Hassan H, Kumar A, Mutlu O, Alkan C. Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment. Bioinformatics (Oxford, England). PMID 30923804 DOI: 10.1093/Bioinformatics/Btz234  0.44
2018 Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics (Oxford, England). 34: i706-i714. PMID 30423092 DOI: 10.1093/Bioinformatics/Bty586  0.76
2018 Kim JS, Senol Cali D, Xin H, Lee D, Ghose S, Alser M, Hassan H, Ergin O, Alkan C, Mutlu O. GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. Bmc Genomics. 19: 89. PMID 29764378 DOI: 10.1186/s12864-018-4460-0  0.44
2018 Senol Cali D, Kim JS, Ghose S, Alkan C, Mutlu O. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Briefings in Bioinformatics. PMID 29617724 DOI: 10.1093/Bib/Bby017  0.44
2017 Kavak P, Lin YY, Numanagic I, Asghari H, Güngör T, Alkan C, Hach F. Discovery and genotyping of novel sequence insertions in many sequenced individuals. Bioinformatics (Oxford, England). 33: i161-i169. PMID 28881988 DOI: 10.1093/Bioinformatics/Btx254  0.76
2017 Soylev A, Kockan C, Hormozdiari F, Alkan C. Toolkit for automated and rapid discovery of structural variants. Methods (San Diego, Calif.). PMID 28583483 DOI: 10.1016/J.Ymeth.2017.05.030  0.76
2017 Alser M, Hassan H, Xin H, Ergin O, Mutlu O, Alkan C. GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping. Bioinformatics (Oxford, England). PMID 28575161 DOI: 10.1093/Bioinformatics/Btx342  0.44
2017 Eslami Rasekh M, Chiatante G, Miroballo M, Tang J, Ventura M, Amemiya CT, Eichler EE, Antonacci F, Alkan C. Discovery of large genomic inversions using long range information. Bmc Genomics. 18: 65. PMID 28073353 DOI: 10.1186/S12864-016-3444-1  0.8
2016 Cardone MF, D'Addabbo P, Alkan C, Bergamini C, Catacchio CR, Anaclerio F, Chiatante G, Marra A, Giannuzzi G, Perniola R, Ventura M, Antonacci D. Inter-varietal structural variation in grapevine genomes. The Plant Journal : For Cell and Molecular Biology. PMID 27419916 DOI: 10.1111/Tpj.13274  0.64
2016 Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, et al. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. Plos Genetics. 12: e1005851. PMID 26943675 DOI: 10.1371/Journal.Pgen.1005851  0.8
2016 Alser M, Almadhoun N, Nouri A, Alkan C, Ayday E. Can you really anonymize the donors of genomic data in today’s digital world? Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9481: 237-244. DOI: 10.1007/978-3-319-29883-2_16  0.8
2015 Xin H, Nahar S, Zhu R, Emmons J, Pekhimenko G, Kingsford C, Alkan C, Mutlu O. Optimal Seed Solver: Optimizing Seed Selection in Read Mapping. Bioinformatics (Oxford, England). PMID 26568624 DOI: 10.1093/Bioinformatics/Btv670  0.44
2015 Acar Ö, Özkurt E, Demir G, Saraç H, Alkan C, Esen T, Somel M, Lack NA. Determining the origin of synchronous multifocal bladder cancer by exome sequencing. Bmc Cancer. 15: 871. PMID 26553077 DOI: 10.1186/S12885-015-1859-8  0.8
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Alkan C, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/Nature15394  0.8
2015 Kavak P, Yüksel B, Aksu S, Kulekci MO, Güngör T, Hach F, Şahinalp SC, Alkan C, Sağıroğlu MŞ. Robustness of Massively Parallel Sequencing Platforms. Plos One. 10: e0138259. PMID 26382624 DOI: 10.1371/Journal.Pone.0138259  0.8
2015 Küçük C, Jiang B, Hu X, Zhang W, Chan JK, Xiao W, Lack N, Alkan C, Williams JC, Avery KN, Kavak P, Scuto A, Sen E, Gaulard P, Staudt L, et al. Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells. Nature Communications. 6: 6025. PMID 25586472 DOI: 10.1038/Ncomms7025  0.8
2015 Xin H, Greth J, Emmons J, Pekhimenko G, Kingsford C, Alkan C, Mutlu O. Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping. Bioinformatics (Oxford, England). 31: 1553-60. PMID 25577434 DOI: 10.1093/Bioinformatics/Btu856  0.8
2015 Lee D, Hormozdiari F, Xin H, Hach F, Mutlu O, Alkan C. Fast and accurate mapping of Complete Genomics reads. Methods (San Diego, Calif.). 79: 3-10. PMID 25461772 DOI: 10.1016/J.Ymeth.2014.10.012  0.8
2014 Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, ... ... Alkan C, et al. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences of the United States of America. 111: 17230-5. PMID 25385592 DOI: 10.1073/Pnas.1410083111  0.8
2014 Alkan C, Kavak P, Somel M, Gokcumen O, Ugurlu S, Saygi C, Dal E, Bugra K, Güngör T, Sahinalp SC, Özören N, Bekpen C. Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa. Bmc Genomics. 15: 963. PMID 25376095 DOI: 10.1186/1471-2164-15-963  0.8
2014 Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, ... ... Alkan C, et al. Annotated features of domestic cat - Felis catus genome. Gigascience. 3: 13. PMID 25143822 DOI: 10.1186/2047-217X-3-13  0.8
2014 Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Research. 42: W494-500. PMID 24810850 DOI: 10.1093/Nar/Gku370  0.8
2014 Dal GM, Ergüner B, Sa??ro?lu MS, Yüksel B, Onat OE, Alkan C, Özçelik T. Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair. Journal of Medical Genetics. 51: 455-9. PMID 24764354 DOI: 10.1136/Jmedgenet-2013-102197  0.8
2014 Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, et al. Genome sequencing highlights the dynamic early history of dogs. Plos Genetics. 10: e1004016. PMID 24453982 DOI: 10.1371/Journal.Pgen.1004016  0.8
2014 Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research. 24: 688-96. PMID 24418700 DOI: 10.1101/Gr.168450.113  0.8
2013 Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C, et al. Rates and patterns of great ape retrotransposition. Proceedings of the National Academy of Sciences of the United States of America. 110: 13457-62. PMID 23884656 DOI: 10.1073/Pnas.1310914110  0.8
2013 Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, ... ... Alkan C, et al. Great ape genetic diversity and population history. Nature. 499: 471-5. PMID 23823723 DOI: 10.1038/Nature12228  0.8
2013 Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, et al. The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild. Bmc Genomics. 14: 363. PMID 23721540 DOI: 10.1186/1471-2164-14-363  0.8
2013 Girirajan S, Dennis MY, Baker C, Malig M, Coe BP, Campbell CD, Mark K, Vu TH, Alkan C, Cheng Z, Biesecker LG, Bernier R, Eichler EE. Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. American Journal of Human Genetics. 92: 221-37. PMID 23375656 DOI: 10.1016/J.Ajhg.2012.12.016  0.8
2013 Xin H, Lee D, Hormozdiari F, Yedkar S, Mutlu O, Alkan C. Accelerating read mapping with FastHASH. Bmc Genomics. 14: S13. PMID 23369189 DOI: 10.1186/1471-2164-14-S1-S13  0.8
2012 Hach F, Numanagic I, Alkan C, Sahinalp SC. SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinformatics (Oxford, England). 28: 3051-7. PMID 23047557 DOI: 10.1093/Bioinformatics/Bts593  0.8
2012 Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, et al. A high-coverage genome sequence from an archaic Denisovan individual. Science (New York, N.Y.). 338: 222-6. PMID 22936568 DOI: 10.1126/Science.1224344  0.8
2012 Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, ... ... Alkan C, et al. The bonobo genome compared with the chimpanzee and human genomes. Nature. 486: 527-31. PMID 22722832 DOI: 10.1038/Nature11128  0.8
2012 Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, ... ... Alkan C, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 483: 169-75. PMID 22398555 DOI: 10.1038/Nature10842  0.8
2012 Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF, Van Tassell CP, Sonstegard TS, Eichler EE, Liu GE. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research. 22: 778-90. PMID 22300768 DOI: 10.1101/Gr.133967.111  0.8
2012 Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA, Eichler EE. Detection of structural variants and indels within exome data. Nature Methods. 9: 176-8. PMID 22179552 DOI: 10.1038/Nmeth.1810  0.8
2011 Renton AE, Majounie E, Waite A, Simón-Sánchez J, Rollinson S, Gibbs JR, Schymick JC, Laaksovirta H, van Swieten JC, Myllykangas L, Kalimo H, Paetau A, Abramzon Y, Remes AM, Kaganovich A, ... ... Alkan C, et al. A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron. 72: 257-68. PMID 21944779 DOI: 10.1016/J.Neuron.2011.09.010  0.8
2011 Lee S, Paulson KG, Murchison EP, Afanasiev OK, Alkan C, Leonard JH, Byrd DR, Hannon GJ, Nghiem P. 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. 52: 272-5. PMID 21907614 DOI: 10.1016/J.Jcv.2011.08.012  0.8
2011 Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, et al. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Research. 21: 1640-9. PMID 21685127 DOI: 10.1101/Gr.124461.111  0.8
2011 Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C. Sensitive and fast mapping of di-base encoded reads. Bioinformatics (Oxford, England). 27: 1915-21. PMID 21586516 DOI: 10.1093/Bioinformatics/Btr303  0.8
2011 Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nature Reviews. Genetics. 12: 363-76. PMID 21358748 DOI: 10.1038/Nrg2958  0.8
2011 Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/Nature09708  0.8
2011 Nguyen DK, Yang F, Kaul R, Alkan C, Antonellis A, Friery KF, Zhu B, de Jong PJ, Disteche CM. 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. Genome Research. 21: 402-9. PMID 21282478 DOI: 10.1101/Gr.108563.110  0.8
2011 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Alkan C, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/Nature09687  0.8
2011 Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnology. 29: 59-63. PMID 21170042 DOI: 10.1038/Nbt.1740  0.8
2011 Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE. Alu repeat discovery and characterization within human genomes. Genome Research. 21: 840-9. PMID 21131385 DOI: 10.1101/Gr.115956.110  0.8
2011 Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nature Methods. 8: 61-5. PMID 21102452 DOI: 10.1038/Nmeth.1527  0.8
2011 Alkan C, Cardone MF, Catacchio CR, Antonacci F, O'Brien SJ, Ryder OA, Purgato S, Zoli M, Della Valle G, Eichler EE, Ventura M. Genome-wide characterization of centromeric satellites from multiple mammalian genomes. Genome Research. 21: 137-45. PMID 21081712 DOI: 10.1101/Gr.111278.110  0.8
2011 Bebek G, Chance M, Koyuturk M, Price ND, De La Vega FM, Bustamante CD, Leal SM, Foster J, Moore J, Bernauer J, Flores S, Huang X, Shin S, Zhou R, Alkan C, et al. Pacific symposium on biocomputing 2011 Pacific Symposium On Biocomputing 2011, Psb 2011. v.  0.76
2010 Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 468: 1053-60. PMID 21179161 DOI: 10.1038/Nature09710  0.8
2010 Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE. Diversity of human copy number variation and multicopy genes. Science (New York, N.Y.). 330: 641-6. PMID 21030649 DOI: 10.1126/Science.1197005  0.8
2010 Antonacci F, Kidd JM, Marques-Bonet T, Teague B, Ventura M, Girirajan S, Alkan C, Campbell CD, Vives L, Malig M, Rosenfeld JA, Ballif BC, Shaffer LG, Graves TA, Wilson RK, et al. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nature Genetics. 42: 745-50. PMID 20729854 DOI: 10.1038/Ng.643  0.8
2010 Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nature Methods. 7: 576-7. PMID 20676076 DOI: 10.1038/Nmeth0810-576  0.8
2010 Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics (Oxford, England). 26: i350-7. PMID 20529927 DOI: 10.1093/Bioinformatics/Btq216  0.8
2010 Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, ... Alkan C, et al. A draft sequence of the Neandertal genome. Science (New York, N.Y.). 328: 710-22. PMID 20448178 DOI: 10.1126/Science.1188021  0.8
2010 Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G, Kallicki J, Anderson P, Tsalenko A, Yamada NA, Tsang P, et al. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nature Methods. 7: 365-71. PMID 20440878 DOI: 10.1038/Nmeth.1451  0.8
2010 Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics (Oxford, England). 26: 1277-83. PMID 20385726 DOI: 10.1093/Bioinformatics/Btq152  0.8
2010 Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/Nature08795  0.8
2010 Alkan C, Brudno M, Eichler EE, Kann MG, Sahinalp SC. Personal genomics Pacific Symposium On Biocomputing 2010, Psb 2010. 302-304.  0.8
2009 Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genetics. 41: 1061-7. PMID 19718026 DOI: 10.1038/Ng.437  0.8
2009 McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, ... ... Alkan C, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research. 19: 1527-41. PMID 19546169 DOI: 10.1101/Gr.091868.109  0.8
2009 Lee S, Hormozdiari F, Alkan C, Brudno M. MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nature Methods. 6: 473-4. PMID 19483690 DOI: 10.1038/Nmeth.F.256  0.8
2009 Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Research. 19: 1270-8. PMID 19447966 DOI: 10.1101/Gr.088633.108  0.8
2009 Cellamare A, Catacchio CR, Alkan C, Giannuzzi G, Antonacci F, Cardone MF, Della Valle G, Malig M, Rocchi M, Eichler EE, Ventura M. New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset. Molecular Biology and Evolution. 26: 1889-900. PMID 19429672 DOI: 10.1093/Molbev/Msp101  0.8
2009 Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. Comparative analysis of Alu repeats in primate genomes. Genome Research. 19: 876-85. PMID 19411604 DOI: 10.1101/Gr.083972.108  0.8
2009 Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE. Death and resurrection of the human IRGM gene. Plos Genetics. 5: e1000403. PMID 19266026 DOI: 10.1371/Journal.Pgen.1000403  0.8
2009 Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, Alkan C, Aksay G, Girirajan S, Siswara P, Chen L, et al. A burst of segmental duplications in the genome of the African great ape ancestor. Nature. 457: 877-81. PMID 19212409 DOI: 10.1038/Nature07744  0.8
2009 Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, Nazareth LV, Muzny DM, Alkan C, Aksay G, Girirajan S, et al. A burst of segmental duplications in the genome of the African great ape ancestor Nature. 458: 238. DOI: 10.1038/nature07881  0.8
2009 Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high throughput sequenced genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 218-219. DOI: 10.1007/978-3-642-02008-7_16  0.8
2008 Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 453: 56-64. PMID 18451855 DOI: 10.1038/Nature06862  0.8
2007 Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler EE. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. Plos Computational Biology. 3: 1807-18. PMID 17907796 DOI: 10.1371/Journal.Pcbi.0030181  0.8
2007 Sharp AJ, Itsara A, Cheng Z, Alkan C, Schwartz S, Eichler EE. Optimal design of oligonucleotide microarrays for measurement of DNA copy-number. Human Molecular Genetics. 16: 2770-9. PMID 17725982 DOI: 10.1093/Hmg/Ddm234  0.8
2007 Aksay C, Salari R, Karakoc E, Alkan C, Sahinalp SC. taveRNA: a web suite for RNA algorithms and applications. Nucleic Acids Research. 35: W325-9. PMID 17488837 DOI: 10.1093/Nar/Gkm303  0.8
2006 Alkan C, Karakoç E, Nadeau JH, Sahinalp SC, Zhang K. RNA-RNA interaction prediction and antisense RNA target search. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 267-82. PMID 16597239 DOI: 10.1089/Cmb.2006.13.267  0.8
2006 Alkan C, Karakoc E, Cenk Sahinalp S, Unrau P, Alexander Ebhardt H, Zhang K, Buhler J. RNA secondary structure prediction via energy density minimization Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 130-142. DOI: 10.1007/11732990_12  0.8
2005 Alkan C, Tüzün E, Buard J, Lethiec F, Eichler EE, Bailey JA, Sahinalp SC. Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Research. 33: W295-8. PMID 15980474 DOI: 10.1093/Nar/Gki406  0.8
2004 Alkan C, Eichler EE, Bailey JA, Sahinalp SC, Tüzün E. The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 933-44. PMID 15700410 DOI: 10.1089/Cmb.2004.11.933  0.8
2004 She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, et al. The structure and evolution of centromeric transition regions within the human genome. Nature. 430: 857-64. PMID 15318213 DOI: 10.1038/Nature02806  0.8
2003 Liu G, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Research. 13: 358-68. PMID 12618366 DOI: 10.1101/Gr.923303  0.8
2002 Alkan C, Bailey JA, Eichler EE, Sahinalp SC, Tuzun E. An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution. Genome Informatics. International Conference On Genome Informatics. 13: 93-102. PMID 14571378 DOI: 10.11234/Gi1990.13.93  0.8
2001 Eichler EE, Johnson ME, Alkan C, Tuzun E, Sahinalp C, Misceo D, Archidiacono N, Rocchi M. Divergent origins and concerted expansion of two segmental duplications on chromosome 16. The Journal of Heredity. 92: 462-8. PMID 11948212 DOI: 10.1093/Jhered/92.6.462  0.8
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