Detection of structural variants and indels within exome data. Emre Karakoc,
Can Alkan, Brian J. O'Roak, Megan Y. Dennis, Laura Vives, Kenneth Mark, Mark J. Rieder, Deborah A. Nickerson, Evan E. Eichler.
Nature Methods, [Epub Dec 18], 2011.
Identification
and validation of a novel mature microRNA encoded by the Merkel cell
polyomavirus in human Merkel cell carcinomas. Lee S, Paulson KG, Murchison EP, Afanasiev OK,
Alkan C, Leonard JH, Byrd DR, Hannon GJ, Nghiem P.
J Clin Virol. [Epub Sep 8], Nov; 52(3):272-275, 2011.
A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD.
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, Scholz SW, Duckworth J,
Ding J, Harmer DW, Hernandez DG, Johnson JO, Mok K, Ryten M, Trabzuni
D, Guerreiro RJ, Orrell RW, Neal J, Murray A, Pearson J, Jansen IE,
Sondervan D, Seelaar H, Blake D, Young K, Halliwell N, Callister JB,
Toulson G, Richardson A, Gerhard A, Snowden J, Mann D, Neary D, Nalls
MA, Peuralinna T, Jansson L, Isoviita VM, Kaivorinne AL, Hölttä-Vuori
M, Ikonen E, Sulkava R, Benatar M, Wuu J, Chiò A, Restagno G, Borghero
G, Sabatelli M; The ITALSGEN Consortium, Heckerman D, Rogaeva E, Zinman
L, Rothstein JD, Sendtner M, Drepper C, Eichler EE,
Alkan C,
Abdullaev Z, Pack SD, Dutra A, Pak E, Hardy J, Singleton A, Williams
NM, Heutink P, Pickering-Brown S, Morris HR, Tienari PJ, Traynor BJ.
Neuron, [Epub Sep 21], Oct 20; 72(2):257-268, 2011.
Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Mario Ventura Claudia R. Catacchio,
Can Alkan, Tomas Marques-Bonet, Saba Sajjadian,
Tina A. Graves, Fereydoun Hormozdiari, Arcadi Navarro, Maika Malig, Carl Baker, Choli Lee, Emily H. Turner,
Lin Chen, Jeffrey M. Kidd, Nicoletta Archidiacono, Jay Shendure, Richard K. Wilson, Evan E. Eichler.
Genome Research, [Epub Jun 21], Oct;21(10):1640-9, 2011.
Sensitive and fast mapping of di-base encoded reads. Farhad Hormozdiari*, Faraz Hach*, S. Cenk Sahinalp, Evan E. Eichler,
Can Alkan.
Bioinformatics, [Epub May 17], Jul 15;27(14):1915-21, 2011.
Alu repeat discovery and characterization within human genomes. Fereydoun Hormozdiari*, Can Alkan*, Mario
Ventura*, Iman Hajirasouliha, Maika Malig, Faraz Hach, Deniz Yorukoglu,
Phuong Dao, Marzieh Bakshi, S. Cenk Sahinalp, Evan E. Eichler. Genome Research, [Epub Dec 3, 2010], Jun;21(6):840-9, 2011
.
Genome structural variation discovery and genotyping. Can Alkan, Bradley P. Coe, Evan E. Eichler.
Nature Reviews Genetics, [Epub Mar 1], May;12(5):363-76, 2011.
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. Di Kim Nguyen, Fan Yang, Rajinder Kaul, Can Alkan, Anthony Antonellis, Karen F. Friery, Baoli Zhu, Pieter J. de Jong, Christine M. Disteche. Genome Research, [Epub Jan 31], 21(3):402-409, 2011.
Mapping copy number variation by population-scale genome sequencing. Ryan
E. Mills*, Klaudia Walter*, Chip Stewart*, Robert E. Handsaker*, Ken Chen*,
Can Alkan*, Alexej Abyzov*, Seungtai Chris Yoon*, Kai Ye*, R. Keira
Cheetham, Asif Chinwalla, Donald F. Conrad, Yutao Fu, Fabian Grubert,
Iman Hajirasouliha, Fereydoun Hormozdiari, Lilia M. Iakoucheva, Zamin
Iqbal, Shuli Kang, Jeffrey M. Kidd, Miriam K. Konkel, Joshua Korn, Ekta
Khurana, Deniz Kural, Hugo Y. K. Lam, Jing Leng, Ruiqiang Li, Yingrui
Li, Chang-Yun Lin, Ruibang Luo, Xinmeng Jasmine Mu, James Nemesh,
Heather E. Peckham, Tobias Rausch, Aylwyn Scally, Xinghua Shi,
Michael P. Stromberg, Adrian M. Stütz, Alexander Eckehart Urban,
Jerilyn A. Walker, Jiantao Wu, Yujun Zhang, Zhengdong D. Zhang, Mark A.
Batzer, Li Ding, Gabor T. Marth, Gil McVean, Jonathan Sebat, Michael
Snyder, Jun Wang, Kenny Ye, Evan E. Eichler, Mark B. Gerstein, Matthew
E. Hurles, Charles Lee, Steven A. McCarroll, Jan O. Korbel & 1000 Genomes Project. Nature, 470(7332):59-65, 2011.
Comparative and demographic analysis of orang-utan genomes. The International Orangutan Genome Sequencing and Analyis Consortium. Nature, 469(7331):529-533, 2011.
Haplotype-resolved genome sequencing of a Gujarati Indian individual. Jacob O. Kitzman, Alexandra P. McKenzie, Andrew Adey, Joseph B. Hiatt, Rupali P. Patwardhan, Peter H. Sudmant, Sarah B. Ng, Can Alkan, Ruolan Qiu, Evan E. Eichler, Jay Shendure. Nature Biotechnology, [Epub Dec 19, 2010], 29(1):59-63, 2011.
Limitations of next-generation genome sequence assembly. Can Alkan, Saba Sajjadian, Evan E. Eichler. Nature Methods, [Epub Nov 21, 2010], 8(1):61-65, 2011.
* Highlighted in Commentary, "Assemblies: the good, the bad, the ugly", E. Birney, Nature Methods, 8(1):59-60, 2011.
Genome-wide characterization of centromeric satellites from multiple mammalian genomes. Can Alkan*, Maria
Francesca Cardone*, Claudia Rita Catacchio, Francesca Antonacci,
Stephen J. O’Brien, Oliver A. Ryder, Stefania Purgato, Monica Zoli,
Giuliano Della Valle, Evan E. Eichler, and Mario Ventura. Genome Research, [Epub Nov 16, 2010], 21(1): 137-145, 2011.
Genetic history of an archaic hominin group from Denisova Cave in Siberia. David
Reich, Richard E. Green, Martin Kircher, Johannes Krause, Nick
Patterson, Eric Y. Durand, Bence Viola, Adrian W. Briggs, Udo Stenzel,
Philip L. F. Johnson, Tomislav Maricic, Jeffrey M. Good, Tomas
Marques-Bonet, Can Alkan,
Qiaomei Fu, Swapan Mallick, Heng Li, Matthias Meyer, Evan E. Eichler,
Mark Stoneking, Michael Richards, Sahra Talamo, Michael V. Shunkov,
Anatoli P. Derevianko, Jean-Jacques Hublin, Janet Kelso, Montgomery
Slatkin, Svante Pääbo. Nature, Dec; 468(7327):1053-1060, 2010.
Diversity of human copy number variation and multicopy genes. Peter H. Sudmant, Jacob O. Kitzman, Francesca Antonacci,
Can Alkan, Maika Malig, Anya Tsalenko, Nick Sampas, Laurakay Bruhn, Jay Shendure, 1000 Genomes Project, Evan E. Eichler.
Science, Oct 29;330(6004):641-6, 2010.
A map of human genome variation from population-scale sequencing. 1000 Genomes Project Consortium. Nature, Oct 28;467(7319):1061-73, 2010.
A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. 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 G. Shaffer, Tina A. Graves, Richard K. Wilson,
David C. Schwartz, Evan E. Eichler. Nature Genetics, Sep; 42(9):745–750, 2010.
mrsFAST: a cache-oblivious algorithm for short-read mapping. Faraz Hach, Fereydoun Hormozdiari, Can Alkan, Farhad Hormozdiari, Inanc Birol, Evan E. Eichler, S. Cenk Sahinalp. Nature Methods, Aug;7(8):576-7, 2010.
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yorukoglu, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp. Bioinformatics, Jun 15; 26(12):i350-i357, 2010.
also in Proc. 18th Annual International Conference Intelligent Systems for Molecular Biology (ISMB 2010), July 11-13 2010, Boston, MA, USA.
A Draft Sequence of the Neandertal Genome.
Richard E. Green, Johannes Krause, Adrian W. Briggs, Tomislav Maricic,
Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai,
Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo
Malaspinas, Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan,
Kay Prüfer, Matthias Meyer, Hernán A. Burbano, Jeffrey M. Good, Rigo
Schultz, Ayinuer Aximu-Petri, Anne Butthof, Barbara Höber, Barbara
Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S.
Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm,
Christine Verna, Pavao Rudan, Dejana Brajkovic, Zeljko Kucan, Ivan
Gusic, Vladimir B. Doronichev, Liubov V. Golovanova, Carles
Lalueza-Fox, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W.
Schmitz, Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan
Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet
Kelso, Michael Lachmann, David Reich, Svante Pääbo. Science, 7 May, 328 (5979):710-722, 2010.
Characterization of missing human genome sequences and copy-number polymorphic insertions. 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.
Nature Methods, May, 7 (5):365-371, 2010.
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Iman Hajirasouliha*, Fereydoun Hormozdiari*, Can Alkan*, Jeffrey M. Kidd, Inanc Birol, Evan E. Eichler, S. Cenk Sahinalp. Bioinformatics, May 15; 26(10):1277-83, 2010.
also in HiTSeq 2010: Conference on High Throughput
Sequencing Analysis and Algorithms, Special Interest Group of ISMB
2010: July 9-10 2010, Boston, MA, USA
Complete
Khoisan and Bantu genomes from southern Africa. Stephan C. Schuster,
Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay
R. Kasson, Robert S. Harris, Desiree C. Petersen, Fangqing Zhao, Ji Qi,
Can Alkan,
Jeffrey M. Kidd, Yazhou Sun, Daniela I. Drautz, Pascal Bouffard, Donna
M. Muzny, Jeffrey G. Reid, Lynne V. Nazareth, Qingyu Wang, Richard
Burhans, Cathy Riemer, Nicola E. Wittekindt, Priya Moorjani, Elizabeth
A. Tindall, Charles G. Danko, Wee Siang Teo, Anne M. Buboltz, Zhenhai
Zhang, Qianyi Ma, Arno Oosthuysen, Abraham W. Steenkamp, Hermann
Oostuisen, Philippus Venter, John Gajewski, Yu Zhang, B. Franklin Pugh,
Kateryna D. Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson,
Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E.
Eichler, Ross C. Hardison, Richard A. Gibbs, Timothy T. Harkins,
Vanessa M. Hayes. Nature, Feb, 463(7283):943-947, 2010.
Personalized copy number and segmental duplication maps using next-generation sequencing.
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.
Nature Genetics, [Epub: Aug 30], Oct, 41(10):1061-1067
, 2009.
* Highlighted in News and Views, "Mapping duplicated sequences", DY Chiang and SA McCarroll, Nature Biotechnology, Nov; 27(11):1001-2, 2009.
Sequence
and structural variation in a human genome uncovered by short-read,
massively parallel ligation sequencing using two base encoding. K.J. McKernan,
H.E. Peckham, G.L. Costa, S.F. McLaughlin, Y. Fu, E.F. Tsung, C.R. Clouser, C.
Duncan, J.K. Ichikawa, C.C. Lee, Z. Zhang, S.S. Ranade, E.T. Dimalanta, F.C.
Hyland, T.D. Sokolsky, L. Zhang, J.A. Sheridan, H. Fu, C.L. Hendrickson, B. Li,
L. Kotler, J.R. Stuart, J.A. Malek, J.M. Manning, A.A. Antipova, D.S. Perez, M.P.
Moore, K.C. Hayashibara, M.R. Lyons, R.E. Beaudoin, B.E. Coleman, M.W. Laptewicz,
A.E. Sannicandro, M.D. Rhodes, R.K. Gottimukkala, S. Yang, V. Bafna, A. Bashir,
A. MacBride, C. Alkan, J.M. Kidd, E.E. Eichler, M.G. Reese, F.M. De La Vega, A.P.
Blanchard. Genome Research, Sep, 19(9): 1527-1541, 2009.
New Insights into Centromere Organization and Evolution from White-cheeked Gibbon and Marmoset. A. Cellamare, C.R Catacchio,
C. Alkan, G. Giannuzzi, F. Antonacci, M.F. Cardone, G. Della Valle, M. Malig, M. Rocchi, E.E. Eichler, M. Ventura.
Molecular Biology and Evolution, Aug; 26(8):1889-900, 2009.
MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Seunghak Lee, Fereydoun Hormozdiari, Can Alkan, Michael Brudno. Nature Methods, Jul, 6(7):473-4, 2009.
Combinatorial algorithms for structural variation detection in high throughput sequenced genomes. Fereydoun Hormozdiari*, Can Alkan*, Evan E. Eichler, S. Cenk Sahinalp. Genome Research, Jul, 19(7):1270-8, 2009.
also in Proc. of the Thirteenth
Annual International
Conference on Research in Computational Molecular Biology (RECOMB 2009), May 18-21 2009, Tucson, AZ, USA
Comparative analysis of Alu repeats in primate genomes. George E. Liu,
Can Alkan, Lu Jiang, Shaying Zhao, Evan E. Eichler.
Genome Research, 19(5):876-885, 2009.
Death and resurrection of the human IRGM gene. Cemalettin Bekpen, Tomas Marques-Bonet, Can Alkan, Francesca
Antonacci, Maria Bruna Leogrande, Mario Ventura, Jeffrey M. Kidd,
Priscillia Siswara, Jonathan C. Howard, Evan E. Eichler. PLoS Genetics, 5(3):e1000403, March 2009.
A burst of segmental duplications in the genome of the African great ape ancestor. Tomas
Marques-Bonet, Jeffrey M. Kidd, Mario Ventura, Tina A. Graves, Ze
Cheng, LaDeanna 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. Nature, Feb 12 2009; 457(7231):877-881, 2009.
Mapping and sequencing of structural variation from eight human genomes. Jeffrey M. Kidd,
Gregory M. Cooper,
William F. Donahue,
Hillary S. Hayden,
Nick Sampas,
Tina Graves,
Nancy Hansen,
Brian Teague,
Can Alkan,
Francesca Antonacci,
Eric Haugen,
Troy Zerr,
N. Alice Yamada,
Peter Tsang,
Tera L. Newman,
Eray Tüzün,
Ze Cheng,
Heather M. Ebling,
Nadeem Tusneem,
Robert David,
Will Gillett,
Karen A. Phelps,
Molly Weaver,
David Saranga,
Adrianne Brand,
Wei Tao,
Erik Gustafson,
Kevin McKernan,
Lin Chen,
Maika Malig,
Joshua D. Smith,
Joshua M. Korn,
Steven A. McCarroll,
David A. Altshuler,
Daniel A. Peiffer,
Michael Dorschner,
John Stamatoyannopoulos,
David Schwartz,
Deborah A. Nickerson,
James C. Mullikin,
Richard K. Wilson,
Laurakay Bruhn,
Maynard V. Olson,
Rajinder Kaul,
Douglas R. Smith,
Evan E. Eichler.
Nature May 1 2008;453(7191):56-64, 2008.
Optimal design of oligonucleotide microarrays for measurement of DNA copy number.
Andrew J. Sharp, Andy Itsara, Ze Cheng,
Can Alkan, Stuart Schwartz, Evan E. Eichler.
Human Molecular Genetics, Nov 15; 16(22):2770-2779, 2007.
Organization and Evolution of Primate Centromeric DNA from Whole Genome Shotgun Sequence Data.
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler.
PLoS Computational Biology
, 3(9): e181, September 2007.
taveRNA: a web suite for RNA algorithms and applications.
Cagri Aksay, Raheleh Salari, Emre Karakoç,
Can Alkan, S. Cenk Sahinalp.
Nucleic Acids Research
, July 1, 2007; Vol. 35 (Web Server Issue): W325-329, 2007.
RNA Secondary Structure
Prediction via Energy Density Minimization.
Can Alkan*, Emre
Karakoç*, S. Cenk Şahinalp, Peter Unrau, H. Alexander Ebhardt, Kaizhong
Zhang,
Jeremy Buhler.
Proc. of the Tenth Annual International
Conference on Research in Computational Molecular Biology (RECOMB 2006
- LNBI 3909), pp. 130-142, April 2-5, 2006 Venice, Italy
RNA-RNA Interaction Prediction and
Antisense RNA Target Search. Can Alkan, Emre Karakoç, Joe
Nadeau, S. Cenk Şahinalp, Kaizhong Zhang.
Journal of
Computational Biology, March 2006, Vol. 13, No. 2: 267-282, 2006.
also in Proc. of the Ninth
Annual International
Conference on Research in Computational Molecular Biology (RECOMB 2005
- LNBI 3500), pp. 152-171, May 14-18 2005, Cambridge, MA, USA
Manipulating Multiple Sequence
Alignments via MaM and WebMaM.
Can Alkan, Eray Tüzün, Jerome
Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, S. Cenk
Şahinalp.
Nucleic Acids Research, July 1; 33 (Web Server issue):
W295–W298, 2005.
The Role of Unequal Crossover in
Alpha-Satellite DNA Evolution: A Computational Analysis.
Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, S. Cenk
Şahinalp, Eray Tüzün.
Journal of
Computational Biology, Oct 2004, Vol. 11, No. 5: 933-944,
2004.
The structure and
evolution of centromeric transition regions within the human
genome. She X, Horvath JE, Jiang Z, Liu G, Furey TS,
Christ L, Clark R, Graves T, Gulden CL,
Alkan C, Bailey JA,
Şahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W,
Schwartz S, Eichler EE.
Nature 2004 Aug
19;430(7002):857-64, 2004.
Analysis of Primate Genomic Variation
Reveals a Repeat-Driven Expansion of the Human Genome. G.
Liu, NISC Comparative Sequencing Program, S. Zhao, J. A. Bailey, S.
C. Şahinalp,
C. Alkan, E. Tüzün, E. D. Green, E. E.
Eichler.
Genome Research, 13(3):358-368,
2003.
An algorithmic analysis of the role of
unequal crossover in alpha-satellite DNA evolution.
Can
Alkan, Jeff Bailey, Evan Eichler, S. Cenk Şahinalp, Eray
Tüzün.
Genome Informatics Workshop, Tokyo,
Japan, vol.18 pp 93-102, 2002.
Divergent Origins and Concerted Expansion
of
Two Segmental Duplications on Chromosome 16. E. E.
Eichler, M. E. Johnson,
C. Alkan, E. Tüzün, C.
Şahinalp, D. Misceo, N. Archidiacono, and M.
Rocchi.
Journal of Heredity 2001 92:
462-468, 2001.