Showing papers on "Genomics published in 1994"

Molecular Biotechnology : Principles and Applications of Recombinant DNA

Abstract: Preface Preface to the First Edition PART I FUNDAMENTALS OF MOLECULAR BIOTECHNOLOGY 1. The Development of Molecular Biotechnology 2. DNA, RNA, and Protein Synthesis 3. Recombinant DNA Technology 4. Chemical Synthesis, Amplification, and Sequencing of DNA 5. Bioinformatics, Genomics, and Proteomics 6. Manipulation of Gene Expression in Prokaryotes 7. Heterologous Protein Production in Eukaryotic Cells 8. Directed Mutagenesis and Protein Engineering PART II MOLECULAR BIOTECHNOLOGY OF MICROBIAL SYSTEMS 9. Molecular Diagnostics 10. Protein Therapeutics 11. Nucleic Acids as Therapeutic Agents 12. Vaccines 13 Synthesis of Commercial Products by Recombinant Microorganisms 14. Bioremediation and Biomass Utilization 15. Plant Growth-Promoting Bacteria 16. Microbial Insecticides 17. Large-Scale Production of Proteins from Recombinant Microorganisms PART III MOLECULAR BIOTECHNOLOGY OF EUKARYOTIC SYSTEMS 18. Genetic Engineering of Plants: Methodology 19. Engineering Plants To Overcome Biotic and Abiotic Stress 20. Engineering Plant Quality and Proteins 21. Transgenic Animals PART IV MOLECULAR BIOTECHNOLOGY AND SOCIETY 22. Regulating the Use of Biotechnology 23. Societal Issues in Biotechnology Amino Acids of Proteins and Their Designations Glossary Index

Automated DNA sequencing and analysis.

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

Origins of the Human Genome Project

Abstract: The human genome project was borne of technology, grew into a science bureaucracy in the US and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

The human genome project: deciphering the blueprint of heredity.

Abstract: Understanding Inheritance: An Introduction to Classical and Molecular Genetics Mapping the Genome: The Vision, the Science, the Implementation The Mapping of Chromosome 16 DNA Libraries: Recombinant Clones for Mapping and Sequencing Computation and the Genome Project Rapid DNA Sequencing Based on Single-Molecule Detection Ethical, Legal and Social Implications An Invitation to Genetics in the 21st Century Glossary Index

Two-Dimensional DNA Typing : A Parallel Approach To Genome Analysis

Abstract: Background and technology genome analysis - general consideration general methodology applications future developments

The Human Genome Project

Abstract: The Human Genome Project (HGP) is a coordinated worldwide effort to precisely map the human genome and the genomes of selected model organisms. The first explicit proposal for this project dates from 1985 although its foundations (both conceptual and technological) can be traced back many years in genetics, molecular biology, and biotechnology The HGP has matured rapidly and is producing results of great significance.

Engineering in genomics/spl minus/automating the Genome Center

Abstract: Engineering enters genomics principally through the development of hardware and software tools or processes (operations research) to aid the biologist/geneticist to take different, more, or higher quality data. The Human Genome Project, in order to meet its goals for mapping and sequencing, is pushing to advance the state of the art in instrumentation, automation and computational biology. The focus of the project was to develop the necessary strategies, hardware, and software to complete the identification of all the genes, and obtain the sequence for the entire genome for humans and a select set of relevant organisms (mouse, fruit fly, yeast, E.coli, etc.) by the year 2006. The project has already produced a significant amount of data, is contributing to medicine and is ahead of schedule. But to keep on track, laboratories conducting research in genomics must move into a period where production data gathering is performed in a factory-like setting. The author focuses on some of the research activities of his group, which is developing automation and informatics systems for the Human Genome Project, specifically human genome centers where the production mapping and sequencing will be done. A multidisciplinary group has been assembled from personnel from the Salk Institute (a biological research organization) and General Atomics (an energy and basic sciences research company). The center is conducting research to map and sequence chromosome 11 and Giardia, for starters, and becoming more highly automated daily. >

Requirements for automated sample handling in genome analysis

Abstract: Automated sample handling is one of the critical steps that must be developed as part of an automated genome factory for sequencing the human genome The requirements are stated for a sample handling system that is capable of processing 50,000 samples per day This system is currently under development

Design and implementation of parallel algorithms for gene-finding

Abstract: Finding genes unequivocally in DNA sequences is one of the key goals of the Human Genome project. The human genome is a 3 billion character long DNA sequence and is estimated to contain about 100000 genes. It has been shown by several biologists that genes in a DNA sequence satisfy certain special properties. We use a combination of these properties to design a serial algorithm for gene-finding. To speed up the process of finding genes in long DNA sequences (of the order of /spl ges/100000 characters), we design a parallel algorithm for gene-finding. We have implemented the parallel gene-finding algorithm on the CM-5 multicomputer as well as on a network of HP Apollo workstations under Parallel Virtual Machine software package. Experimental results indicate that our algorithms predict genes with reasonable accuracy. >

The human genome project: genetic and physical mapping.

Abstract: The modern tools of molecular biology, recombinant DNA techniques, have given scientists the ability to isolate and study individual genes from even complex eukaryotic genomes. The availability of genes enables the study o f their structure and biologic function, and their role in normal and abnormal physiologic processes. A worldwide effort to study and understand the entire human genome is under way, which will result in information on the location of all genes, their sequences, and their complex regulation and interactions. As this knowledge becomes available, it will be rapidly applied to the practice of medicine through use in the development of diagnostic tests for genetic-based diseases and in the development of therapeutics.