TY - STD TI - OpGen Inc. 2015. Available from: http://www.opgen.com. Accessed 9 Dec 2015. UR - http://www.opgen.com ID - ref1 ER - TY - STD TI - BioNano Genomics Inc. 2015. Available from: http://www.bionanogenomics.com. Accessed 9 Dec 2015. UR - http://www.bionanogenomics.com ID - ref2 ER - TY - STD TI - Nabsys Inc. 2015. Available from: http://www.nabsys.com. Accessed 9 Dec 2015. UR - http://www.nabsys.com ID - ref3 ER - TY - JOUR AU - Dong, Y. AU - Xie, M. AU - Jiang, Y. AU - Xiao, N. AU - Du, X. AU - Wang, W. PY - 2013 DA - 2013// TI - Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus) JO - Nat Biotechnol VL - 31 UR - https://doi.org/10.1038/nbt.2478 DO - 10.1038/nbt.2478 ID - Dong2013 ER - TY - JOUR AU - Ganapathy, G. AU - Howard, J. AU - Ward, J. AU - Zhang, G. AU - Phillippy, A. AU - Jarvis, E. PY - 2014 DA - 2014// TI - High-coverage sequencing and annotated assemblies of the budgerigar genome JO - GigaScience VL - 3 UR - https://doi.org/10.1186/2047-217X-3-11 DO - 10.1186/2047-217X-3-11 ID - Ganapathy2014 ER - TY - JOUR AU - Lam, E. T. AU - Hastie, A. AU - Lin, C. AU - Ehrlich, D. AU - Nagarajan, N. AU - Kwok, P. Y. PY - 2012 DA - 2012// TI - Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly JO - Nat Biotechnol VL - 30 UR - https://doi.org/10.1038/nbt.2303 DO - 10.1038/nbt.2303 ID - Lam2012 ER - TY - JOUR AU - Ray, M. AU - Goldstein, S. AU - Zhou, S. AU - Potamousis, K. AU - Sarkar, D. AU - Schwartz, D. PY - 2013 DA - 2013// TI - Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-505 DO - 10.1186/1471-2164-14-505 ID - Ray2013 ER - TY - JOUR AU - Waterman, M. S. AU - Smith, T. F. AU - Katcher, H. PY - 1984 DA - 1984// TI - Algorithms for restriction map comparisons JO - Nucleic Acids Res VL - 12 UR - https://doi.org/10.1093/nar/12.1Part1.237 DO - 10.1093/nar/12.1Part1.237 ID - Waterman1984 ER - TY - JOUR AU - Mendelowitz, L. AU - Pop, M. PY - 2014 DA - 2014// TI - Computational methods for optical mapping JO - GigaScience VL - 3 UR - https://doi.org/10.1186/2047-217X-3-33 DO - 10.1186/2047-217X-3-33 ID - Mendelowitz2014 ER - TY - JOUR AU - Nagarajan, N. AU - Read, T. D. AU - Pop, M. PY - 2008 DA - 2008// TI - Scaffolding and validation of bacterial genome assemblies using optical restriction maps JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn102 DO - 10.1093/bioinformatics/btn102 ID - Nagarajan2008 ER - TY - JOUR AU - Lin, H. AU - Goldstein, S. AU - Mendelowitz, L. AU - Zhou, S. AU - Schwartz, D. AU - Pop, M. PY - 2012 DA - 2012// TI - AGORA: assembly guided by optical restriction alignment JO - BMC Bioinforma VL - 13 UR - https://doi.org/10.1186/1471-2105-13-189 DO - 10.1186/1471-2105-13-189 ID - Lin2012 ER - TY - BOOK AU - Antoniotti, M. AU - Anantharaman, T. AU - Paxia, S. AU - Mishra, B. PY - 2001 DA - 2001// TI - Genomics via optical mapping IV: sequence validation via optical map matching PB - New York University CY - New York, NY, USA ID - Antoniotti2001 ER - TY - JOUR AU - Valouev, A. AU - Li, L. AU - Liu, Y. C. AU - Schwartz, D. C. AU - Yang, Y. AU - Waterman, M. S. PY - 2006 DA - 2006// TI - Alignment of optical maps JO - J Comput Biol VL - 13 UR - https://doi.org/10.1089/cmb.2006.13.442 DO - 10.1089/cmb.2006.13.442 ID - Valouev2006 ER - TY - CHAP AU - Anantharaman, T. S. AU - Mishra, B. PY - 2001 DA - 2001// TI - A probabilistic analysis of false positives in optical map alignment and validation BT - First international workshop on algorithms in bioinformatics (WABI) PB - Springer CY - Aarhus, Denmark ID - Anantharaman2001 ER - TY - JOUR AU - Sarkar, D. AU - Goldstein, S. AU - Schwartz, D. C. AU - Newton, M. A. PY - 2012 DA - 2012// TI - Statistical significance of optical map alignments JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2011.0221 DO - 10.1089/cmb.2011.0221 ID - Sarkar2012 ER - TY - JOUR AU - Anantharaman, T. S. AU - Mishra, B. AU - Schwartz, D. C. PY - 1997 DA - 1997// TI - Genomics via optical mapping II: ordered restriction maps JO - J Comput Biol VL - 4 UR - https://doi.org/10.1089/cmb.1997.4.91 DO - 10.1089/cmb.1997.4.91 ID - Anantharaman1997 ER - TY - CHAP AU - Anantharaman, T. S. AU - Mishra, B. AU - Schwartz, D. C. PY - 1999 DA - 1999// TI - Genomics via optical mapping III: contiging genomic DNA BT - Proceedings of the 7th international conference on intelligent systems for molecular biology (ISMB 1999) PB - AAAI CY - Heidelberg, Germany ID - Anantharaman1999 ER - TY - JOUR AU - Karp, R. M. AU - Rabin, M. O. PY - 1987 DA - 1987// TI - Efficient randomized pattern-matching algorithms JO - IBM J Res Dev VL - 31 UR - https://doi.org/10.1147/rd.312.0249 DO - 10.1147/rd.312.0249 ID - Karp1987 ER - TY - CHAP AU - Muggli, M. D. AU - Puglisi, S. J. AU - Boucher, C. PY - 2014 DA - 2014// TI - Efficient indexed alignment of contigs to optical maps BT - Algorithms in Bioinformatics (WABI 2014). vol. 8701 of LNCS PB - Springer CY - Wrocław, Poland ID - Muggli2014 ER - TY - CHAP AU - Verzotto, D. AU - Teo, A. S. M. AU - Hillmer, A. M. AU - Nagarajan, N. PY - 2015 DA - 2015// TI - Index-based map-to-sequence alignment in large eukaryotic genomes BT - Proceedings of the fifth RECOMB satellite workshop on massively parallel sequencing (RECOMB-Seq 2015) PB - Cold Spring Harbor Labs Journals CY - Warsaw (Poland) ID - Verzotto2015 ER - TY - CHAP AU - Califano, A. AU - Rigoutsos, I. PY - 1993 DA - 1993// TI - FLASH: a fast look-up algorithm for string homology BT - Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB 1993) PB - AAAI CY - Bethesda, MD, USA ID - Califano1993 ER - TY - JOUR AU - Storey, J. D. AU - Tibshirani, R. PY - 2003 DA - 2003// TI - Statistical significance for genomewide studies JO - Proc Nat Acad Sci VL - 100 UR - https://doi.org/10.1073/pnas.1530509100 DO - 10.1073/pnas.1530509100 ID - Storey2003 ER - TY - JOUR AU - Kawahara, Y. AU - de la Bastide, M. AU - Hamilton, J. AU - Kanamori, H. AU - McCombie, R. AU - Matsumoto, T. PY - 2013 DA - 2013// TI - Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data JO - Rice VL - 6 UR - https://doi.org/10.1186/1939-8433-6-4 DO - 10.1186/1939-8433-6-4 ID - Kawahara2013 ER - TY - CHAP AU - Anantharaman, T. S. AU - Mysore, V. AU - Mishra, B. ED - Altman, R. B. ED - Jung, T. A. ED - Klein, T. E. ED - Dunker, A. K. ED - Hunter, L. PY - 2005 DA - 2005// TI - Fast and cheap genome wide haplotype construction via optical mapping BT - Proceedings of the 10th Pacific Symposium on Biocomputing (PSB 2005) PB - World Scientific CY - Hawaii, USA ID - Anantharaman2005 ER - TY - JOUR AU - Teo, A. S. M. AU - Verzotto, D. AU - Yao, F. AU - Nagarajan, N. AU - Hillmer, A. M. PY - 2015 DA - 2015// TI - Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line JO - GigaScience VL - 4 UR - https://doi.org/10.1186/s13742-015-0106-1 DO - 10.1186/s13742-015-0106-1 ID - Teo2015 ER - TY - JOUR AU - Yao, F. AU - Ariyaratne, P. N. AU - Hillmer, A. M. AU - Liu, E. T. AU - Ruan, Y. PY - 2012 DA - 2012// TI - Long span DNA Paired-End-Tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons JO - PLOS ONE VL - e46152 ID - Yao2012 ER - TY - JOUR AU - Li, R. AU - Zhu, H. AU - Ruan, J. AU - Wang, J. AU - Fang, X. AU - Wang, J. PY - 2010 DA - 2010// TI - De novo assembly of human genomes with massively parallel short read sequencing JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.097261.109 DO - 10.1101/gr.097261.109 ID - Li2010 ER - TY - JOUR AU - Gao, S. AU - Sung, W. K. AU - Nagarajan, N. PY - 2011 DA - 2011// TI - Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences JO - J Comput Biol VL - 18 UR - https://doi.org/10.1089/cmb.2011.0170 DO - 10.1089/cmb.2011.0170 ID - Gao2011 ER - TY - BOOK AU - Verzotto, D. AU - Teo, A. S. M. AU - Hillmer, A. M. AU - Nagarajan, N. PY - 2015 DA - 2015// TI - Supporting software for OPTIMA, a tool for sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis ID - Verzotto2015 ER - TY - BOOK AU - Teo, A. S. M. AU - Verzotto, D. AU - Yao, F. AU - Nagarajan, N. AU - Hillmer, A. M. PY - 2015 DA - 2015// TI - Supporting single-molecule optical genome mapping data from human HapMap and colorectal cancer cell lines ID - Teo2015 ER -