mrFAST & mrsFAST Publications:

• Personalized copy number and segmental duplication maps using next-generation sequencing.  C. Alkan, J.M. Kidd, T. Marques-Bonet, G. Aksay, F. Antonacci, F. Hormozdiari, J.O. Kitzman, C. Baker, M. Malig, O. Mutlu, S.C. Sahinalp, R.A. Gibbs, E.E. Eichler, Nature Genetics,  Oct, 41(10):1061-1067, 2009.
• mrsFAST: a cache-oblivious algorithm for short-read mapping.  F. Hach, F. Hormozdiari, C. Alkan, F. Hormozdiari, I. Birol, E.E. Eichler, S.C.Sahinalp, Nature Methods, Aug;7(8):576-7, 2010.
• Accelerating read mapping with FastHASH. H. Xin, D. Lee, F. Hormozdiari, S. Yedkar, O. Mutlu, C. Alkan. BMC Genomics, 14(Suppl 1):S13, 2013.
• mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. F. Hach, I. Sarrafi, F. Hormozdiari, C. Alkan, E.E. Eichler, S.C. Sahinalp. Nucleic Acids Research, Jul;42(Web Server issue):W494-500, 2014.

List of papers citing mrFAST

List of papers citing mrsFAST

• 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
• 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.
  
• 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.
  
• 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.
• 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
• 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.
  
• 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.
• 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.
• A map of human genome variation from population-scale sequencing.  1000 Genomes Project Consortium. Nature, Oct 28;467(7319):1061-73, 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.
• 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.
• 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.
  
• 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.
  
• 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 analysis of algorithms for next-generation sequencing read alignment. Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk. Bioinformatics, Oct 15;27(20):2790-6, 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.
• 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], 9(2): 176-178, 2012.
• Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp. Genome Research, Dec;21(12):2203-12, 2011.
  
• 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.
• 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.
• 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.
  
• 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.
• An integrated map of genetic variation from 1,092 human genomes. 1000 Genomes Project Consortium. Nature, Nov 1;491(7422):56-65, 2012.