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(joint first or last authors are marked with * in case of equal contribution)


Toolkit for automated and rapid discovery of structural variants. Arda Soylev, Can Kockan,
Fereydoun Hormozdiari*, Can Alkan*. Methods, Oct 1; 129:3-7, 2017.

Discovery and genotyping of novel sequence insertions in many sequenced individuals.
Pınar Kavak, Yen-Yi Lin, Ibrahim Numanagić, Hossein Asghari, Tunga Güngör, Can Alkan*, Faraz Hach*. Bioinformatics,  33 (14): i161-i169, 2017.
    presented at the 25th Conference on Intelligent Systems for Molecular Biology (ISMB-ECCB 2017), July 21-25, 2017, Prague, Czech Republic.

MAGNET: understanding and improving the accuracy of genome pre-alignment filtering. Mohammed Alser, Onur Mutlu*, Can Alkan*. IPSI Transactions on Internet Research, 13(2), 2017.

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu*, Can Alkan*. Bioinformatics, [epub May 31; doi: 10.1093/bioinformatics/btx342], 2017.

Building and improving reference genome assemblies. Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson. Proceedings of the IEEE, Mar 3, 105(3): 422-435, 2017.

Discovery of large genomic inversions using long range information. Marzieh Eslami Rasekh, Giorgia Chiatante, Mattia Miroballo, Joyce Tang, Mario Ventura, Chris T. Amemiya, Evan E. Eichler, Francesca Antonacci*, Can Alkan*. BMC Genomics, Jan 10;18(1):65, 2017.

Computational pan-genomics: status, promises and challenges. Computational Pan-Genomics Consortium. Briefings in Bioinformatics, [epub Oct 21; doi: 10.1093/bib/bbw089], 2016.

Inter-varietal structural variation in grapevine genomes.
Maria Francesca Cardone, Pietro D'Addabbo, Can Alkan, Carlo Bergamini, Claudia Rita Catacchio, Fabio Anaclerio, Giorgia Chiatante, Annamaria Marra, Giuliana Giannuzzi, Rocco Perniola, Mario Ventura, Donato Antonacci. Plant Journal, 88(4): 648-661, 2016.

On genomic repeats and reproducibility. Can Firtina
and Can Alkan. Bioinformatics, Aug 1;32(15):2243-7, 2016.

Optimal Seed Solver: optimizing seed selection in read mapping.
Hongyi Xin, Sunny Nahar, Richard Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan*, Onur Mutlu*. Bioinformatics, Jun 1;32(11):1632-42, 2016.

Demographically-based evaluation of genomic regions under selection in domestic dogs. 
Adam H. Freedman, Rena M. Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Brian W. Davis, Ilan Gronau, Pedro M. Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi G. Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D. Bustamante, Timothy T. Harkins, Stanley F. Nelson, Tomas Marques-Bonet, Elaine A. Ostrander, Robert K. Wayne, John Novembre. PLoS Genetics, 12(3):e1005851, 2016.

Determining the origin of synchronous multifocal bladder cancer by exome sequencing.
Ömer Acar, Ezgi Özkurt, Gulfem Demir, Hilal Saraç, Can Alkan, Tarık Esen, Mehmet Somel, Nathan A. Lack. BMC Cancer, Nov 9;15:871, 2015.
 
An integrated map of structural variation in 2,504 human genomes. Peter H. Sudmant, Tobias Rausch, Eugene J. Gardner,  Robert E. Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz, Miriam K. Konkel, Ankit Malhotra, Adrian M. Stütz, Xinghua Shi, Francesco Paolo Casale, Jieming Chen, Fereydoun Hormozdiari, Gargi Dayama, Ken Chen, Maika Malig, Mark J. P. Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y. K. Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong, Laura Clarke, Elif Dal, Li Ding, Sarah Emery, Xian Fan, Madhusudan Gujral, Fatma Kahveci, Jeffrey M. Kidd, Yu Kong, Eric-Wubbo Lameijer, Shane McCarthy, Paul Flicek, Richard A. Gibbs, Gabor Marth, Christopher E. Mason, Androniki Menelaou, Donna M. Muzny, Bradley J. Nelson, Amina Noor, Nicholas F. Parrish, Matthew Pendleton, Andrew Quitadamo, Benjamin Raeder, Eric E. Schadt, Mallory Romanovitch, Andreas Schlattl, Robert Sebra, Andrey A. Shabalin, Andreas Untergasser, Jerilyn A. Walker, Min Wang, Fuli Yu, Chengsheng Zhang, Jing Zhang, Xiangqun Zheng-Bradley, Wanding Zhou, Thomas Zichner, Jonathan Sebat, Mark A. Batzer, Steven A. McCarroll, The 1000 Genomes Project Consortium, Ryan E. Mills, Mark B. Gerstein, Ali Bashir, Oliver Stegle, Scott E. Devine, Charles Lee, Evan E. Eichler, Jan O. Korbel. Nature, Oct 1; 526 (7571):75–81, 2015.

A global reference for human genetic variation.
1000 Genomes Project Consortium. Nature, Oct 1; 526 (7571):68–74, 2015.
     Elif Dal, Fatma Kahveci, and Can Alkan contributed to the structural variation analyses.

Robustness of massively parallel sequencing platforms.
Pınar Kavak
, Bayram Yüksel, Soner Aksu, M. Oğuzhan Külekçi, Tunga Güngör, Faraz Hach, S. Cenk Sahinalp, Turkish Human Genome Project, Can Alkan*, M. Şamil Sağıroğlu*. PLoS ONE, Sep 18;10(9):e0138259, 2015.

Can you really anonymize the donors of genomic data in today’s digital world?
Mohammed Alser
, Nour Almadhoun, Azita Nouri, Can Alkan*, Erman Ayday*. 10th International Workshop on Data Privacy Management (DPM 2015 - LNCS 9481), pp. 237-244, September 21-22, 2015, Vienna, Austria.

Improving genome assemblies using multi-platform sequence data.
Pınar Kavak
, Bekir Erguner, Duran Üstek, Bayram Yuksel, M. Şamil Sağıroğlu, Tunga Gungor, Can Alkan. 12th Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2015), September 10-12, 2015, Naples, Italy.

Fast and accurate mapping of Complete Genomics reads.
Donghyuk Lee*, Farhad Hormozdiari*, Hongyi Xin, Faraz Hach, Onur Mutlu, Can Alkan. Methods, Jun;79-80:3-10, 2015.

Shifted Hamming Distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.
Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan* and Onur Mutlu*. Bioinformatics, May 15;31(10):1553-60, 2015.

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells.
Can Küçük, Bei Jiang, Xiaozhou Hu, Wenyan Zhang, John K. C. Chan, Wenming Xiao, Nathan Lack, Can Alkan, John C. Williams, Kendra N. Avery, Pınar Kavak, Anna Scuto, Emel Sen, Philippe Gaulard, Lou Staudt, Javeed Iqbal, Weiwei Zhang, Adam Cornish, Qiang Gong, Qunpei Yang, Hong Sun, Francesco d’Amore, Sirpa Leppä, Weiping Liu, Kai Fu, Laurence de Leval, Timothy McKeithan and Wing C. Chan. Nature Communications, Jan 14;6:6025, 2015.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.
Michael J. Montague, Gang Li, Barbara Gandolfi, Razib Khan, Bronwen L. Aken, Steven M. J. Searle, Patrick Minx, LaDeana Hillier, Daniel C. Koboldt, Brian W. Davis, Carlos A. Driscoll, Christina S. Barr, Kevin Blackistone, Javier Quilez, Belen Lorente-Galdos, Tomas Marques-Bonet, Can Alkan, Gregg W. C. Thomas, Matthew W. Hahn, Marilyn Menotti-Raymond, Stephen J. O’Brien, Richard Wilson, Leslie A. Lyons, William J. Murphy and Wesley C. Warren. Proc Natl Acad Sci, Dec 2;111(48):17230-17235, 2014.

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.  Can Alkan
, Pınar Kavak, Mehmet Somel, Omer Gokcumen, Serkan Uğurlu, Ceren Saygı, Elif Dal, Kuyaş Buğra, Tunga Güngör, S Cenk Sahinalp, Nesrin Özören and Cemalettin Bekpen. BMC Genomics, 15(1):963, doi:10.1186/1471-2164-15-963, 2014.

Annotated features of domestic cat – Felis catus genome.
Gaik Tamazian, Serguei Simonov, Pavel Dobrynin, Alexey Makunin, Anton Logachev, Aleksey Komissarov, Andrey Shevchenko, Vladimir Brukhin, Nikolay Cherkasov, Anton Svitin, Klaus-Peter Koepfli, Joan Pontius, Carlos A Driscoll, Kevin Blackistone, Cristina Barr, David Goldman, Agostinho Antunes, Javier Quilez, Belen Lorente-Galdos, Can Alkan, Tomas Marques-Bonet, Marylin Menotti-Raymond, Victor A David, Kristina Narfström, and Stephen J O’Brien. GigaScience, Aug 5; 3:(13), 2014.

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Faraz Hach*, Iman Sarrafi*, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp. Nucl Acids Res, Jul;42(Web Server issue):W494-500, 2014.

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair. Gülşah M Dal, Bekir Ergüner, Mahmut S Sağıroğlu, Bayram Yüksel, Onur Emre Onat, Can Alkan, Tayfun Özçelik. J Med Genet, 51(7):455-459, 2014

Genome sequencing highlights the dynamic early history of dogs. Adam H. Freedman, Ilan Gronau, Rena M. Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Pedro M. Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Holly Beale, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi G. Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D. Bustamante, Timothy T. Harkins, Stanley F. Nelson, Elaine A. Ostrander, Tomas Marques-Bonet, Robert K. Wayne, John Novembre. PLoS Genetics, 10(1): e1004016, 2014.

Reconstructing complex regions of genomes using long-read sequencing technology. John Huddleston, Swati Ranade, Maika Malig, Francesca Antonacci, Mark Chaisson, Lawrence Hon, Peter H. Sudmant, Tina A. Graves, Can Alkan, Megan Y. Dennis, Richard K. Wilson, Stephen W. Turner, Jonas Korlach, Evan E. Eichler. Genome Research, 24(4):688-96, 2014.

Rates and patterns of great ape retrotransposition. Fereydoun Hormozdiari, Miriam K. Konkel, Javier Prado-Martinez, Giorgia Chiatante, Irene Hernando Herraez, Jerilyn A. Walker, Ben Nelson, Can Alkan, Peter H. Sudmant, John Huddleston, Claudia R. Catacchio, Arthur Ko, Maika Malig, Carl Baker, Tomas Marques-Bonet, Mario Ventura, Mark A. Batzer, Evan E. Eichler. Proc Natl Acad Sci, Aug 13;110(33):13457-62, 2013.

Great ape genetic diversity and population history. Javier Prado-Martinez, Peter H. Sudmant, Jeffrey M. Kidd, Heng Li, Joanna L. Kelley, Belen Lorente-Galdos, Krishna R. Veeramah, August E. Woerner, Timothy D. O’Connor, Gabriel Santpere, Alexander Cagan, Christoph Theunert, Ferran Casals, Hafid Laayouni, Kasper Munch, Asger Hobolth, Anders E. Halager, Maika Malig, Jessica Hernandez-Rodriguez, Irene Hernando-Herraez, Kay Prüfer, Marc Pybus, Laurel Johnstone, Michael Lachmann, Can Alkan, Dorina Twigg, Natalia Petit , Carl Baker , Fereydoun Hormozdiari, Marcos Fernandez-Callejo, Marc Dabad, Michael L. Wilson, Laurie Stevison, Cristina Camprubí, Tiago Carvalho, Aurora Ruiz-Herrera, Laura Vives, Marta Mele, Teresa Abello , Ivanela Kondova , Ronald E. Bontrop, Anne Pusey, Felix Lankester, John A. Kiyang, Richard A. Bergl, Elizabeth Lonsdorf, Simon Myers, Mario Ventura, Pascal Gagneux, David Comas, Hans Siegismund, Julie Blanc, Lidia Agueda-Calpena, Marta Gut, Lucinda Fulton, Sarah A. Tishkoff, James C. Mullikin, Richard K. Wilson, Ivo G. Gut, Mary Katherine Gonder, Oliver A. Ryder, Beatrice H. Hahn, Arcadi Navarro,, Joshua M. Akey, Jaume Bertranpetit, David Reich, Thomas Mailund, Mikkel H. Schierup, Christina Hvilsom, Aida M. André s, Jeffrey D. Wall, Carlos D. Bustamante, Michael F. Hammer, Evan E. Eichler, Tomas Marques-Bonet. Nature, 499(7459):471-475, 2013.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.
Javier Prado-Martinez, Irene Hernando-Herraez, Belen Lorente-Galdos, Marc Dabad, Oscar Ramirez, Carlos Baeza-Delgado, Carlos Morcillo-Suarez, Can Alkan, Fereydoun Hormozdiari, Emanuele Raineri, Jordi Estellé, Marcos Fernandez-Callejo, Mònica Valles, Lars Ritscher, Torsten Schöneberg, Elisa de la Calle-Mustienes, Sònia Casillas, Raquel Rubio-Acero, Marta Melé, Johannes Engelken, Mario Caceres, Jose L Gomez-Skarmeta, Marta Gut, Jaume Bertranpetit, Ivo G Gut, Teresa Abello, Evan E Eichler, Ismael Mingarro, Carles Lalueza-Fox, Arcadi Navarro, Tomas Marques-Bonet. BMC Genomics, May 31;14(1):363, 2013.
 
Refinement and Discovery of New Hotspots of Copy-Number Variation Associated with Autism Spectrum Disorder. Santhosh Girirajan*, Megan Y. Dennis*, Carl Baker, Maika Malig, Bradley P. Coe, Catarina D. Campbell, Kenneth Mark, Tiffany H. Vu, Can Alkan, Ze Cheng, Leslie G. Biesecker, Raphael Bernier, Evan E. Eichler. Am J Hum Genet, Feb 7;92(2):221-37, 2013.

Accelerating read mapping with FastHASH. Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu, Can Alkan. BMC Genomics, 14(Suppl 1):S13, 2013.
  presented at Eleventh Asia Pacific Bioinformatics Conference (APBC 2013), January 21-14 2013, Vancouver, BC, Canada.
 
An integrated map of genetic variation from 1,092 human genomes. 1000 Genomes Project Consortium. Nature, Nov 1; 491(7422):56-65, 2012.
 * Can Alkan contributed to the structural variation analyses.

SCALCE: boosting sequence compression algorithms using locally consistent encoding. Faraz Hach, Ibrahim Numanagić, Can Alkan, S. Cenk Sahinalp. Bioinformatics, Dec
1;28(23):3051-57, 2012.

A high-coverage genome sequence from an archaic Denisovan individual. Matthias Meyer, Martin Kircher, Marie-Theres Gansauge, Heng Li, Fernando Racimo, Swapan Mallick, Joshua G. Schraiber, Flora Jay, Kay Prüfer, Cesare de Filippo, Peter H. Sudmant, Can Alkan, Qiaomei Fu, Ron Do, Nadin Rohland, Arti Tandon, Michael Siebauer, Richard E. Green, Katarzyna Bryc, Adrian W. Briggs, Udo Stenzel, Jesse Dabney, Jay Shendure, Jacob Kitzman, Michael F. Hammer, Michael V. Shunkov, Anatoli P. Derevianko, Nick Patterson, Aida M. Andrés, Evan E. Eichler, Montgomery Slatkin, David Reich, Janet Kelso, Svante Pääbo. Science, 338(6014):222-226, 2012.

The bonobo genome compared with the chimpanzee and human genomes. Kay Prüfer, Kasper Munch, Ines Hellmann, Keiko Akagi, Jason R. Miller, Brian Walenz, Sergey Koren, Granger Sutton, Chinnappa Kodira, Roger Winer, James R. Knight, James C. Mullikin, Stephen J. Meader, Chris P. Ponting, Gerton Lunter, Saneyuki Higashino, Asger Hobolth, Julien Dutheil, Emre Karakoç, Can Alkan, Saba Sajjadian, Claudia Rita Catacchio, Mario Ventura, Tomas Marques-Bonet, Evan E. Eichler, Claudine André, Rebeca Atencia, Lawrence Mugisha, Jörg Junhold, Nick Patterson, Michael Siebauer, Jeffrey M. Good, Anne Fischer, Susan E. Ptak, Michael Lachmann, David E. Symer, Thomas Mailund, Mikkel H. Schierup, Aida M. Andrés, Janet Kelso, Svante Pääbo. Nature, 486(7404):527-531, 2012.

Insights into hominid evolution from the gorilla genome sequence. Aylwyn Scally, Julien Y. Dutheil, LaDeana W. Hillier, Gregory E. Jordan, Ian Goodhead, Javier Herrero, Asger Hobolth, Tuuli Lappalainen, Thomas Mailund, Tomas Marques-Bonet, Shane McCarthy, Stephen H. Montgomery, Petra C. Schwalie, Y. Amy Tang, Michelle C. Ward, Yali Xue, Bryndis Yngvadottir, Can Alkan, Lars N. Andersen, Qasim Ayub, Edward V. Ball, Kathryn Beal, Brenda J. Bradley, Yuan Chen, Chris M. Clee, Stephen Fitzgerald,Tina A. Graves, Yong Gu, Paul Heath, Andreas Heger, Emre Karakoc, Anja Kolb-Kokocinski, Gavin K. Laird, Gerton Lunter, Stephen Meader, Matthew Mort, James C. Mullikin, Kasper Munch, Timothy D. O’Connor, Andrew D. Phillips, Javier Prado-Martinez, Anthony S. Rogers, Saba Sajjadian, Dominic Schmidt, Katy Shaw, Jared T. Simpson, Peter D. Stenson, Daniel J. Turner, Linda Vigilant, Albert J. Vilella, Weldon Whitener, Baoli Zhu, David N. Cooper, Pieter de Jong, Emmanouil T. Dermitzakis, Evan E. Eichler, Paul Flicek, Nick Goldman, Nicholas I. Mundy, Zemin Ning, Duncan T. Odom, Chris P. Ponting, Michael A. Quail, Oliver A. Ryder, Stephen M. Searle, Wesley C. Warren, Richard K. Wilson, Mikkel H. Schierup, Jane Rogers, Chris Tyler-Smith, Richard Durbin. Nature, 483(7388):169-175, 2012.

Copy number variation of individual cattle genomes using next-generation sequencing. Derek M. Bickhart. Yali Hou, Steven G. Schroeder, Can Alkan, Maria Francesca Cardone, Lakshmi K. Matukumalli, Jiuzhou Song, Robert D. Schnabel, Mario Ventura, Jeremy F. Taylor, Jose Fernando Garcia, Curtis P. Van Tassell, Tad S. Sonstegard, Evan E. Eichler, George E. Liu. Genome Research, Apr;22(4):778-90, 2012.

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, 9(2): 176-178, 2012.

Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas. Sherry Lee, Kelly G. Paulson, Elizabeth P. Murchison, Olga K. Afanasiev, Can Alkan, J. Helen Leonard, David R. Byrd, Gregory J. Hannon, Paul Nghiem. J Clin Virol., Nov; 52(3):272-275, 2011.

A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Alan E. Renton, Elisa Majounie, Adrian Waite, Javier Simón-Sánchez, Sara Rollinson, J. Raphael Gibbs, Jennifer C. Schymick, Hannu Laaksovirta, John C. van Swieten, Liisa Myllykangas, Hannu Kalimo, Anders Paetau, Yevgeniya Abramzon, Anne M. Remes, Alice Kaganovich, Sonja W. Scholz, Jamie Duckworth, Jinhui Ding, Daniel W. Harmer, Dena G. Hernandez, Janel O. Johnson, Kin Mok, Mina Ryten, Danyah Trabzuni, Rita J. Guerreiro, Richard W. Orrell, James Neal, Alex Murray, Justin Pearson, Iris E. Jansen, David Sondervan, Harro Seelaar, Derek Blake, Kate Young, Nicola Halliwell, Janis Bennion Callister, Greg Toulson, Anna Richardson, Alex Gerhard, Julie Snowden, David Mann, David Neary, Michael A. Nalls, Terhi Peuralinna, Lilja Jansson, Veli-Matti Isoviita, Anna-Lotta Kaivorinne, Maarit Hölttä-Vuori, Elina Ikonen, Raimo Sulkava, Michael Benatar, Joanne Wuu, Adriano Chiò, Gabriella Restagno, Giuseppe Borghero, Mario Sabatellli and The ITALSGEN Consortium, David Heckerman, Ekaterina Rogaeva, Lorne Zinman, Jeffrey D. Rothstein, Michael Sendtner, Carsten Drepper, Evan E. Eichler, Can Alkan, Ziedulla Abdullaev, Svetlana D. Pack, Amalia Dutra, Evgenia Pak, John Hardy, Andrew Singleton, Nigel M. Williams, Peter Heutink, Stuart Pickering-Brown, Huw R. Morris, Pentti J. Tienari, Bryan J. Traynor. Neuron, 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, 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, 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, Jun;21(6):840-9, 2011.

Genome structural variation discovery and genotyping. Can Alkan, Bradley P. Coe, Evan E. Eichler. Nature Reviews Genetics, 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, 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, and 1000 Genomes Project. Nature, 470(7332):59-65, 2011.

Comparative and demographic analysis of orang-utan genomes. The International Orangutan Genome Sequencing and Analysis 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,  29(1):59-63, 2011.

Limitations of next-generation genome sequence assembly. Can Alkan, Saba Sajjadian, Evan E. Eichler. Nature Methods,  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, 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.
 * Can Alkan contributed to the structural variation analyses.

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.
  presented at 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.
  Recipient of the 2010 AAAS Newcomb Cleveland Prize.

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.
  presented at 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, 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. Kevin Judd McKernan, Heather E. Peckham, Gina L. Costa, Stephen F. McLaughlin, Yutao Fu, Eric F. Tsung, Christopher R. Clouser, Cisyla Duncan, Jeffrey K. Ichikawa, Clarence C. Lee, Zheng Zhang, Swati S. Ranade, Eileen T. Dimalanta, Fiona C. Hyland, Tanya D. Sokolsky, Lei Zhang, Andrew Sheridan, Haoning Fu, Cynthia L. Hendrickson, Bin Li, Lev Kotler, Jeremy R. Stuart, Joel A. Malek, Jonathan M. Manning, Alena A. Antipova, Damon S. Perez, Michael P. Moore, Kathleen C. Hayashibara, Michael R. Lyons, Robert E. Beaudoin, Brittany E. Coleman, Michael W. Laptewicz, Adam E. Sannicandro, Michael D. Rhodes, Rajesh K. Gottimukkala, Shan Yang, Vineet Bafna, Ali Bashir, Andrew MacBride, Can Alkan, Jeffrey M. Kidd, Evan E. Eichler, Martin G. Reese, Francisco M. De La Vega, Alan P. Blanchard. Genome Research, Sep, 19(9): 1527-1541, 2009.

New insights into centromere organization and evolution from white-cheeked gibbon and marmoset. Angelo Cellamare, Claudia Rita Catacchio, Can Alkan, Giuliana Giannuzzi, Francesca Antonacci, Maria Francesca Cardone, Giuliano Della Valle, Maika Malig, Mariano Rocchi, Evan 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.
  presented at 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 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 minimizationCan Alkan*, Emre Karakoç, S. Cenk Sahinalp, 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 Sahinalp, Kaizhong Zhang. Journal of Computational Biology, March 2006, Vol. 13, No. 2: 267-282, 2006.
  presented at 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. Xinwei She, Julie E. Horvath, Zhaoshi Jiang, Ge Liu, Terrence S. Furey, Laurie Christ, Royden Clark, Tina Graves, Cassy L. Gulden, Can Alkan, Jeff A. Bailey, Cenk Sahinalp, Mariano Rocchi, David Haussler, Richard K. Wilson, Webb Miller, Stuart Schwartz, Evan E. Eichler. Nature 2004 Aug 19;430(7002):857-64, 2004.

Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Ge Liu, NISC Comparative Sequencing Program, Shaying Zhao, Jeffrey A. Bailey, S. Cenk Şahinalp, Can Alkan, Eray Tüzün, Eric D. Green, Evan 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. Evan E. Eichler, Matthew E. Johnson, Can Alkan, Eray Tüzün, Cenk Şahinalp, D. Misceo, Nicoletta Archidiacono, Mariano Rocchi. Journal of Heredity 2001 92: 462-468, 2001.