Reconstructing complex regions of genomes using long-read sequencing technology

Adam C. English, Stephen Richards, Yi Han, Min Wang, Vanesa Vee, Jiaxin Qu, Xiang Qin, Donna M. Muzny, Jeffrey G. Reid, Kim C. Worley, Richard A. Gibbs, Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLOS ONE. ,vol. 7, ,(2012) , 10.1371/JOURNAL.PONE.0047768

Chen-Shan Chin, David H Alexander, Patrick Marks, Aaron A Klammer, James Drake, Cheryl Heiner, Alicia Clum, Alex Copeland, John Huddleston, Evan E Eichler, Stephen W Turner, Jonas Korlach, Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Nature Methods. ,vol. 10, pp. 563- 569 ,(2013) , 10.1038/NMETH.2474

Karyn Meltz Steinberg, Francesca Antonacci, Peter H Sudmant, Jeffrey M Kidd, Catarina D Campbell, Laura Vives, Maika Malig, Laura Scheinfeldt, William Beggs, Muntaser Ibrahim, Godfrey Lema, Thomas B Nyambo, Sabah A Omar, Jean-Marie Bodo, Alain Froment, Michael P Donnelly, Kenneth K Kidd, Sarah A Tishkoff, Evan E Eichler, Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nature Genetics. ,vol. 44, pp. 872- 880 ,(2012) , 10.1038/NG.2335

Megan Y. Dennis, Xander Nuttle, Peter H. Sudmant, Francesca Antonacci, Tina A. Graves, Mikhail Nefedov, Jill A. Rosenfeld, Saba Sajjadian, Maika Malig, Holland Kotkiewicz, Cynthia J. Curry, Susan Shafer, Lisa G. Shaffer, Pieter J. de Jong, Richard K. Wilson, Evan E. Eichler, Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication Cell. ,vol. 149, pp. 912- 922 ,(2012) , 10.1016/J.CELL.2012.03.033

Michael C Zody, Zhaoshi Jiang, Hon-Chung Fung, Francesca Antonacci, LaDeana W Hillier, Maria Francesca Cardone, Tina A Graves, Jeffrey M Kidd, Ze Cheng, Amr Abouelleil, Lin Chen, John Wallis, Jarret Glasscock, Richard K Wilson, Amy Denise Reily, Jaime Duckworth, Mario Ventura, John Hardy, Wesley C Warren, Evan E Eichler, Evolutionary toggling of the MAPT 17q21.31 inversion region Nature Genetics. ,vol. 40, pp. 1076- 1083 ,(2008) , 10.1038/NG.193

Kin Fai Au, Jason G. Underwood, Lawrence Lee, Wing Hung Wong, Improving PacBio Long Read Accuracy by Short Read Alignment PLoS ONE. ,vol. 7, pp. e46679- ,(2012) , 10.1371/JOURNAL.PONE.0046679

Can Alkan, Saba Sajjadian, Evan E Eichler, Limitations of next-generation genome sequence assembly Nature Methods. ,vol. 8, pp. 61- 65 ,(2011) , 10.1038/NMETH.1527

Deanna M Church, Valerie A Schneider, Tina Graves, Katherine Auger, Fiona Cunningham, Nathan Bouk, Hsiu-Chuan Chen, Richa Agarwala, William M McLaren, Graham RS Ritchie, Derek Albracht, Milinn Kremitzki, Susan Rock, Holland Kotkiewicz, Colin Kremitzki, Aye Wollam, Lee Trani, Lucinda Fulton, Robert Fulton, Lucy Matthews, Siobhan Whitehead, Will Chow, James Torrance, Matthew Dunn, Glenn Harden, Glen Threadgold, Jonathan Wood, Joanna Collins, Paul Heath, Guy Griffiths, Sarah Pelan, Darren Grafham, Evan E Eichler, George Weinstock, Elaine R Mardis, Richard K Wilson, Kerstin Howe, Paul Flicek, Tim Hubbard, None, Modernizing Reference Genome Assemblies PLoS Biology. ,vol. 9, pp. e1001091- ,(2011) , 10.1371/JOURNAL.PBIO.1001091

P. H. Sudmant, J. Huddleston, C. R. Catacchio, M. Malig, L. W. Hillier, C. Baker, K. Mohajeri, I. Kondova, R. E. Bontrop, S. Persengiev, F. Antonacci, M. Ventura, J. Prado-Martinez, T. Marques-Bonet, E. E. Eichler, , Evolution and diversity of copy number variation in the great ape lineage Genome Research. ,vol. 23, pp. 1373- 1382 ,(2013) , 10.1101/GR.158543.113

Hreinn Stefansson, Agnar Helgason, Gudmar Thorleifsson, Valgerdur Steinthorsdottir, Gisli Masson, John Barnard, Adam Baker, Aslaug Jonasdottir, Andres Ingason, Vala G Gudnadottir, Natasa Desnica, Andrew Hicks, Arnaldur Gylfason, Daniel F Gudbjartsson, Gudrun M Jonsdottir, Jesus Sainz, Kari Agnarsson, Birgitta Birgisdottir, Shyamali Ghosh, Adalheidur Olafsdottir, Jean-Baptiste Cazier, Kristleifur Kristjansson, Michael L Frigge, Thorgeir E Thorgeirsson, Jeffrey R Gulcher, Augustine Kong, Kari Stefansson, A common inversion under selection in Europeans Nature Genetics. ,vol. 37, pp. 129- 137 ,(2005) , 10.1038/NG1508