Automated DNA Sequencing and Analysis

Sequencing Instruments and Strategies:<br>E. Chen, The Efficiency of Automated DNA Sequencing.<br>G.M. Church, G. Gryan, N. Lakey, S. Kieffer-Higgins, L. Mintz, M. Temple, M. Rubenfield, L. Jaehn, H. Ghazizadel, K. Robison, and P. Richterick, Automated Multiplex Sequencing.<br>X.C. Huang and R.A. Mathies, Application of Capillary Array Electrophoresis to DNA Sequencing.<br>R. Drmanac, S. Drmanac, J. Jarvis, and I. Labat, Sequencing by Hybridization.<br>A. Martin-Gallardo, J. Lamerdin, and A. Carrano, Shotgun Sequencing.<br>A. Bodenteich, S. Chissoe, Y.-F. Wang, and B. Roe, Shotgun Cloning as the Strategy of Choice to Generate Templates for High Throughput Dideoxynucleotide Sequencing.<br>C.M. Berg, G. Wang, K. Isono, H. Kasai, and D.E. Berg, Transposon-Facilitated Large-Scale DNA Sequencing.<br>C.H. Martin, C.A. Mayeda, C.A. Davis, M.P. Strathmann, and M. Palazzolo, Transposon-Facilitated Sequencing: An Effective Set of Procedures to Sequence DNA Fragments Smaller than 4kb.<br>L. Liu and R.D. Fleischmann, Construction of Exonuclease III Nested Deletion Sets for Rapid DNA Sequencing.<br>M. Adams, Expressed Sequence Tags as Tools for Physiology and Genomics.<br>W.R. McCombie, The Use of Automated DNA Sequencing in the Analysis of cDNAs of Model Organisms.<br>Sample Preparation and Sequencing Methods: Libraries:<br>R.L. Stalligs, N.A. Doggett, A. Ford, J. Longmire, C.E. Hildebrand, L.L. Deaven, and R. Moyzis, Applications of Cosmid Libraries in Genome Mapping and Sequencing Efforts.<br>D.A. Smoller, W.J. Kimmerly, O. Hubbard, C. Ericsson, C.H. Martin, and M.J. Palazzolo, A Role for the P1 Cloning System in Genome Analysis.<br>N.A. Doggett, D.L. Grady, J.L. Longmire, and L.L. Deaven, Generation and Mapping of Chromosome Specific Sequence-Tagged Sites (STS).<br>R. Moreno and R. Fuldner, Construction of cDNA Libraries.<br>M.B. Soares, Construction of Directionally Cloned cDNA Libraries and Phagemid Vectors.<br>A. Swaroop, Construction of Directional cDNA Libraries.<br>J.M. Kwak and J.G. Nam, Preparation of cDNA Libraries from Brassica.<br>J.M. Sikela, T.J. Stevens, J.A. Hopkins, A.S. Wilcox, J. Glod, A.S. Khan, and A.K. Orpana, Abundance Screening of Human cDNA Libraries.<br>G. Lennon, High Density Grid Technologies.<br>Automated Sample Preparation:<br>D.R. Sibson, Solid Phrase Preparation of Sequencing Templates from PCR Products.<br>A. Holmberg, G. Fry, and M. Uhlon, Automatic Preparation of DNA Templatesfor Sequencing on the ABI Catalyst Robotic Workstation.<br>T. Hawkins, Custom Magnetic Particles: Their Use in DNA Purification.<br>Sequencing Methods:<br>W.R. McCombie and A. Martin-Gallardo, Large-Scale Automated Sequencing of Human Chromosomal Regions.<br>L. Rowen and B.F. Koop, Zen and the Art of Large-Scale Genomic Sequencing.<br>J.M. Kelley, Automated Dye Terminator DNA Sequencing.<br>D.M. Muzny, S. Richards, Y. Shen, and R.A. Gibbs, PCR Based Strategies for Gap Closure in Large Scale Sequencing Projects.<br>S. Richards, D.M. Muzny, A.B. Civitello, F. Lu, and R.A. Gibbs, Sequence Map Gaps and Directed Reverse Sequencing for the Completion of Large Sequencing Projects.<br>F. Iris, Optimized Methods for Large-Scale Shotgun DNASequencing in Alu-Rich Genomic Regions.<br>S.G. Burgett and P.R. Rosteck, Jr., Use of Dimethylsulfoxide to Improve Fluorescent, Tag Cycle Sequencing.<br>Informatics: Sequence Assembly Theory and Algorithms:<br>C. Tibbetts, J.M. Bowling, and J.B. Golden, III, Neural Networks for Automated Base Calling of Gel Based DNA Sequencing Ladders.<br>G. Myers, Advances in Sequence Assembly.<br>S. Honda, N.W. Parrott, and C.B. Lawrence, Computer Aided Sequence Reconstruction: Software Support for Multiple Large-Scale Sequencing Strategies.<br>C. Burks, M.L. Engle, S. Forrest, R.J. Parsons, C.A. Soderlund, and P.E. Stolorz, Relaxation and Optimization Methods for Sequence Assembly.<br>Data Analysis Tools:<br>G. Sutton and T. Kerlavage, Software Tools for Protein Similarity Searching.<br>J.M. Claverie, Large-Scale Sequence Analysis.<br>J. Shavlik, Finding Frame Shift Errors in Anonymous DNA.<br>B. Rappaport, J. Gatewood, C. Fields, and N. Doggett, Integrating Repeat Identification withThermal Calculations.<br>J. Jurka, Approaches to Identification and Analysis of Interspersed Repetitive DNA Sequences.<br>O. White and T. Dunning, Compositional Properties of Exons and Introns.<br>E.C. Uberbacher, X. Guan, and R.J. Mural, A Practical Guide to the GRAIL Email Server.<br>S. Henikoff, J. Henikoff, S. Agus, and J.C. Wallace, Searching for Homologies to Protein Blocks by Electronic Mail.<br>C. Fields, Integrating Computational and Experimental Methods.<br>Data Management and Databases:<br>S. Lewis, Design Issues in Developing Laboratory Information Management Systems.<br>J. Cuticchia, A Relational Database Primer for Molecular Biologists.<br>J.M. Cherry and S.W. Cartinhour, ACEDB: A Tool for Biological Information.<br>R. Overbeek and M. Price, The Integration of Curated Biological Databases.