TY - JOUR AU - Young, A. L. AU - Abaan, H. O. AU - Zerbino, D. AU - Mullikin, J. C. AU - Birney, E. AU - Margulies, E. H. PY - 2010 DA - 2010// TI - A new strategy for genome assembly using short sequence reads and reduced representation libraries JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.097956.109 DO - 10.1101/gr.097956.109 ID - Young2010 ER - TY - JOUR AU - Van Tassell, C. P. AU - Smith, T. P. L. AU - Matukumalli, L. K. AU - Taylor, J. F. AU - Schnabel, R. D. AU - Lawley, C. T. AU - Haudenschild, C. D. AU - Moore, S. S. AU - Warren, W. C. AU - Sonstegard, T. S. PY - 2008 DA - 2008// TI - SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries JO - Nat Meth VL - 5 UR - https://doi.org/10.1038/nmeth.1185 DO - 10.1038/nmeth.1185 ID - Van Tassell2008 ER - TY - JOUR AU - Buermans, H. AU - Ariyurek, Y. AU - van Ommen, G. AU - den Dunnen, J. AU - ’t Hoen, P. PY - 2010 DA - 2010// TI - New methods for next generation sequencing based microRNA expression profiling JO - BMC Genomics VL - 11 UR - https://doi.org/10.1186/1471-2164-11-716 DO - 10.1186/1471-2164-11-716 ID - Buermans2010 ER - TY - JOUR AU - Bystrykh, L. V. AU - Verovskaya, E. AU - Zwart, E. AU - Broekhuis, M. AU - de Haan, G. PY - 2012 DA - 2012// TI - Counting stem cells: methodological constraints JO - Nat Meth VL - 9 UR - https://doi.org/10.1038/nmeth.2043 DO - 10.1038/nmeth.2043 ID - Bystrykh2012 ER - TY - JOUR AU - An, W. AU - Davis, E. S. AU - Thompson, T. L. AU - O'Donnell, K. A. AU - Lee, C. Y. AU - Boeke, J. D. PY - 2009 DA - 2009// TI - Plug and play modular strategies for synthetic retrotransposons JO - Methods VL - 49 UR - https://doi.org/10.1016/j.ymeth.2009.05.013 DO - 10.1016/j.ymeth.2009.05.013 ID - An2009 ER - TY - JOUR AU - Uren, A. G. AU - Mikkers, H. AU - Kool, J. AU - van der Weyden, L. AU - Lund, A. H. AU - Wilson, C. H. AU - Rance, R. AU - Jonkers, J. AU - van Lohuizen, M. AU - Berns, A. AU - Adams, D. J. PY - 2009 DA - 2009// TI - A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites JO - Nat Protocols VL - 4 UR - https://doi.org/10.1038/nprot.2009.64 DO - 10.1038/nprot.2009.64 ID - Uren2009 ER - TY - JOUR AU - Hamady, M. AU - Walker, J. J. AU - Harris, J. K. AU - Gold, N. J. AU - Knight, R. PY - 2008 DA - 2008// TI - Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex JO - Nat Meth VL - 5 UR - https://doi.org/10.1038/nmeth.1184 DO - 10.1038/nmeth.1184 ID - Hamady2008 ER - TY - JOUR AU - Kircher, M. AU - Kelso, J. PY - 2010 DA - 2010// TI - High-throughput DNA sequencing concepts and limitations JO - BioEssays VL - 32 UR - https://doi.org/10.1002/bies.200900181 DO - 10.1002/bies.200900181 ID - Kircher2010 ER - TY - JOUR AU - Parameswaran, P. AU - Jalili, R. AU - Tao, L. AU - Shokralla, S. AU - Gharizadeh, B. AU - Ronaghi, M. AU - Fire, A. Z. PY - 2007 DA - 2007// TI - A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm760 DO - 10.1093/nar/gkm760 ID - Parameswaran2007 ER - TY - JOUR AU - Nguyen, P. AU - Ma, J. AU - Pei, D. AU - Obert, C. AU - Cheng, C. AU - Geiger, T. PY - 2011 DA - 2011// TI - Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-106 DO - 10.1186/1471-2164-12-106 ID - Nguyen2011 ER - TY - JOUR AU - Gilles, A. AU - Meglecz, E. AU - Pech, N. AU - Ferreira, S. AU - Malausa, T. AU - Martin, J. F. PY - 2011 DA - 2011// TI - Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-245 DO - 10.1186/1471-2164-12-245 ID - Gilles2011 ER - TY - JOUR AU - Carneiro, M. AU - Russ, C. AU - Ross, M. AU - Gabriel, S. AU - Nusbaum, C. AU - DePristo, M. PY - 2012 DA - 2012// TI - Pacific biosciences sequencing technology for genotyping and variation discovery in human data JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-375 DO - 10.1186/1471-2164-13-375 ID - Carneiro2012 ER - TY - JOUR AU - Bystrykh, L. V. PY - 2012 DA - 2012// TI - Generalized DNA barcode design based on hamming codes JO - PLoS ONE VL - 7 UR - https://doi.org/10.1371/journal.pone.0036852 DO - 10.1371/journal.pone.0036852 ID - Bystrykh2012 ER - TY - JOUR AU - Hamming, R. PY - 1950 DA - 1950// TI - Error detecting and error correcting codes JO - Bell Syst Tech J VL - 26 UR - https://doi.org/10.1002/j.1538-7305.1950.tb00463.x DO - 10.1002/j.1538-7305.1950.tb00463.x ID - Hamming1950 ER - TY - BOOK AU - Hamming, R. W. PY - 1986 DA - 1986// TI - Coding and information theory; 2nd ed PB - Prentice-Hall, Inc CY - Upper Saddle River, NJ, USA ID - Hamming1986 ER - TY - JOUR AU - Krishnan, A. AU - Sweeney, M. AU - Vasic, J. AU - Galbraith, D. AU - Vasic, B. PY - 2011 DA - 2011// TI - Barcodes for DNA sequencing with guaranteed errorcorrection capability JO - Electron Lett VL - 47 UR - https://doi.org/10.1049/el.2010.3546 DO - 10.1049/el.2010.3546 ID - Krishnan2011 ER - TY - JOUR AU - Levenshtein, V. PY - 1966 DA - 1966// TI - Binary codes capable of correcting deletions, insertions and reversals JO - Sov Phys Dokl VL - 10 ID - Levenshtein1966 ER - TY - JOUR AU - Faircloth, B. C. AU - Glenn, T. C. PY - 2012 DA - 2012// TI - Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels JO - PLoS ONE VL - 7 UR - https://doi.org/10.1371/journal.pone.0042543 DO - 10.1371/journal.pone.0042543 ID - Faircloth2012 ER - TY - JOUR AU - Reed, I. AU - Solomon, G. PY - 1960 DA - 1960// TI - Polynomial Codes Over Certain Finite Fields JO - J Soc Ind Appl Math VL - 8 UR - https://doi.org/10.1137/0108018 DO - 10.1137/0108018 ID - Reed1960 ER - TY - CHAP AU - Ashlock, D. AU - Guo, L. AU - Qiu, F. PY - 2002 DA - 2002// TI - Greedy closure evolutionary algorithms BT - Proceedings of the 2002 Congress on Evolutionary Computation, CEC’02 PB - IEEE CY - 445 Hoes Lane, Piscataway, NJ 08854, USA ID - Ashlock2002 ER - TY - CHAP AU - Ashlock, D. AU - Houghten, S. K. PY - 2009 DA - 2009// TI - DNA error correcting codes: no crossover BT - Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB’09 PB - IEEE Press CY - 445 Hoes Lane, Piscataway, NJ 08854, USA ID - Ashlock2009 ER - TY - CHAP AU - Houghten, S. AU - Ashlock, D. AU - Lenarz, J. PY - 2006 DA - 2006// TI - Construction of Optimal Edit Metric Codes BT - Information Theory Workshop, 2006. ITW ’06 Chengdu. IEEE UR - https://doi.org/10.1109/ITW2.2006.323799 DO - 10.1109/ITW2.2006.323799 ID - Houghten2006 ER - TY - JOUR AU - Bogdanova, G. AU - Brouwer, A. AU - Kapralov, S. AU - Ostergard, P. PY - 2001 DA - 2001// TI - Error-correcting codes over an alphabet of four elements JO - Designs Codes Cryptography VL - 23 UR - https://doi.org/10.1023/A:1011275112159 DO - 10.1023/A:1011275112159 ID - Bogdanova2001 ER - TY - JOUR AU - Wagner, R. A. AU - Fischer, M. J. PY - 1974 DA - 1974// TI - The string-to-string correction problem JO - J ACM VL - 21 UR - https://doi.org/10.1145/321796.321811 DO - 10.1145/321796.321811 ID - Wagner1974 ER - TY - JOUR AU - Allison, L. PY - 1992 DA - 1992// TI - Lazy dynamic-programming can be eager JO - Inf Process Lett VL - 43 UR - https://doi.org/10.1016/0020-0190(92)90202-7 DO - 10.1016/0020-0190(92)90202-7 ID - Allison1992 ER - TY - CHAP AU - Clarke, W. AU - Ferreira, H. PY - 2004 DA - 2004// TI - Coding for synchronous, fixed length decoding windows in the presence of insertion/deletion errors BT - AFRICON, 2004. 7th AFRICON Conference in Africa PB - IEEE CY - 445 Hoes Lane, Piscataway, NJ 08854, USA UR - https://doi.org/10.1109/AFRICON.2004.1406677 DO - 10.1109/AFRICON.2004.1406677 ID - Clarke2004 ER - TY - JOUR AU - Golay, M. PY - 1949 DA - 1949// TI - Notes on digital coding JO - Proc IRE VL - 37 ID - Golay1949 ER - TY - JOUR AU - Ben-Dor, A. AU - Karp, R. AU - Schwikowski, B. AU - Yakhini, Z. PY - 2000 DA - 2000// TI - Universal DNA tag systems: a combinatorial design scheme JO - J Comput Biol VL - 7 UR - https://doi.org/10.1089/106652700750050916 DO - 10.1089/106652700750050916 ID - Ben-Dor2000 ER - TY - JOUR AU - Liu, W. AU - Wang, S. AU - Gao, L. AU - Zhang, F. AU - Xu, J. PY - 2004 DA - 2004// TI - DNA sequence design based on template strategy JO - ChemInform VL - 35 ID - Liu2004 ER -