Bibliography
Recent Publications
· Nagarajan N, et al. “Scaffolding and validation of bacterial genome assemblies using optical restriction maps.” Biofinformatics. 2008 Mar24. [Epub - ahead of print]
· Latreille P, et al. “Optical mapping as a routine tool in bacterial genome sequencing.” BMC Genomics. 2007 Sept 14;4(1):321.
· Mussman M, et al. “Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments.” PLoS Biol. 2007 Sep;5(9):e230.
· Zhou S et al. “Validation of rice genome sequence by optical mapping.” BMC Genomics. 2007 Aug 15;8(1):278.
· Kotewicz ML, et al. “Optical maps distinguish individual strains of Escherichia coli O157 : H7.” Microbiology. 2007 Jun;153(Pt 6):1720-33.
· van het Hoog M, et al. “Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes.” Genome Biol. 2007;8(4):R52.
2000-2006
· Chen Q, et al. “Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12.” Microbiology. 2006 Apr;152(Pt 4):1041-54.
· Galagan JE, et al. "Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae." Nature. 2005 Dec; 438:1105-115.
· Cebula TA. “DNA Detection Strategies: Sequences, Signatures and Significance.” Transcript. https://www.ift.org/fooddefense/25-Cebula-Transcript.pdf
· Machida M, et al. "Genome sequencing and analysis of Aspergillus oryzae." Nature. 2005 Dec; 438:1157-1161.
· Nierman WC, et al. "Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus." Nature. 2005 Dec; 438:1151-1156.
· Reslewic S, et al.. "Whole-genome shotgun Optical Mapping of Rhodospirillum rubrum." Appl Environ Microbiol. 2005 Sep; 71 (9):5511-22.
· Anantharaman TS, et al. "Fast and cheap genome wide haplotype construction via Optical Mapping." Pac Symp Biocomput. 2005:385-96.
· Zhou S, et al. "Single-Molecule Approach to Bacterial Genomic Comparisons via Optical Mapping." J Bacteriol. 2004 Nov; 186 (22):7773-82.
· Zhou S, et al. "Shotgun optical mapping of the entire Leishmania major Friedlin genome." Mol Biochem Parasitol. 2004 Nov; 138 (1):97-106.
· Armbrust EV, et al. "The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism." Science. 2004 Oct 1; 306 (5693):79-86.
· Zhou S, et al. "Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly". Genome Res. 13: 2142-2151, 2003.
· Mishra B, "Optical Mapping," Encyclopedia of the Human Genome, 4:448-453, Nature Publishing Group, Macmillan Publishers Limited, London, UK, June, 2003.
· Wei J, et al. “Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.” Infect Immun. 2003 May;71(5):2775-86. Erratum in: Infect Immun. 2003 Jul;71(7):4223.
· Zhou S, et al. "A whole-genome shotgun optical map of Yersinia pestis strain KIM.” Appl Environ Microbiol. 68: 6321-6331, 2002.
· Welch RA, et al. "Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli", Proc. Natl. Acad. Sci. USA 99: 17020-17024, 2002.
· Lim A, et al. "Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome", Genome Res. 11: 1584-1593, 2001.
· Giacalone J, et al. "Optical mapping of BAC clones from the human Y chromosome DAZ locus", Genome Res. 10: 1421-1429, 2000.
· Aston C, et al. "Optical Mapping in Genomic Analysis", Encyclopedia of Analytical Chemistry: Instrumentation and Applications, (Ed., R. A. Meyers), J. Wiley & Sons, pp. 5105-5122, 2000.
1995-1999
· Lai Z, et al. "A shotgun optical map of the entire Plasmodium falciparum genome", Nature Genetics, 23: 309-313, 1999.
· Lin J, et al. "Whole Genome Shotgun Optical Mapping of Deinococcus radiodurans", Science, 285: 1558-1562, 1999.
· Jing J, et al. "Optical Mapping of Plasmodium falciparum chromosome 2", Genome Research 9(2): 175-181, 1999.
· Aston C, et al. "Optical Mapping and its potential for large-scale sequencing projects", Trends in Biotechnology, vol. 17: 297-302, 1999.
· Anantharaman T, et al. “Genomics via optical mapping. III: Contiging genomic DNA.” Proc Int Conf Intell Syst Mol Biol. 1999;:18-27.
· Aston C, et al. "Optical Mapping: An approach for fine mapping" in Methods in Enzymology, Academic Press, New York, vol. 303, chap. 4, 55-73, 1999.
· Jing J, et al. "Automated High Resolution Optical Mapping Using Arrayed, Fluid Fixed, DNA Molecules", Proc. Natl. Acad. Sci.USA, 95: 8046-8051, 1998.
· Cai W, et al. "High resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping", Proc. Natl. Acad. Sci. USA, 95: 3390-3394, 1998.
· Anantharaman TS, et al. "Genomics via Optical Mapping III: Contiging genomic DNA and variations", Courant Technical Report #760, Courant Institute, NY (March 1998).
· Bautsch W, et al. "Long-range restriction mapping of genomic DNA", in Genome Mapping, A Practical Approach, Oxford University Press, New York, Chapter 12, pages 281-313, 1997.
· Ananthraman TS, et al. "Genomics via Optical Mapping II: Restriction Maps", Journal of Computational Biology, 4, No.2: 91-118, 1997.
· Schwartz DC, et al. "Optical mapping approaches to genomic analysis", Curr. Opinion in Biotechnology, 8: 70-74, 1997.
· Samad AH, et al. "Mapping the genome one molecule at a time-optical mapping", Nature, 378: 516-517, 1995.
· Samad AH, et al. "Optical Mapping: A novel, singe-molecule approach to genomic analysis", Genomic Research, 5: 1-4, 1995.
· Cai W, et al. "Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces", Proc. Natl. Acad. Sci. USA, 92: 5164-5168, 1995.
· Meng X, et al. "Optical mapping of lambda bacteriophage clones using restriction endonucleases", Nature Genetics, 9: 432-438, 1995.