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drFAST:

mrsFAST:

mrFAST:

Selected Publications:

  • 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.
  • 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.

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Related Projects:

mrsFAST and mrFAST : Illumina read mappers

mrCaNaVaR : Read depth analysis method to characterize segmental duplications and predict absolute copy numbers.

VariationHunter : Structural variation calling algorithm using read pair mapping information including suboptimal alignments.

NovelSeq : Novel sequence insertion discovery framework.

SPLITREAD : Detection of structural variants and indels from genome and exome sequencing data.

SCALCE : Tool for compression of FASTQ files.

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