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An Integrated Database to Support Research on Escherichia Coli

Description: We have used logic programming to design and implement a prototype database of genomic information for the model bacterial organism Escherichia coli. This report presents the fundamental database primitives that can be used to access and manipulate data relating to the E. coli genome. The present system, combined with a tutorial manual, provides immediate access to the integrated knowledge base for E. coli chromosome data. It also serves as the foundation for development of more user-friendly i… more
Date: January 1992
Creator: Baehr, Alezandra; Dunham, George; Ginsburg, Adam; Hagstrom, Ray; Joerg, David; Kazic, Toni et al.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Users Guide and Tutorial for PC-GenoGraphics: Version 1

Description: PC-GenoGraphics is a visual database/query facility designed for reasoning with genomic data. Data are represented to reflect variously accurate notions of the location of their sites, etc., along the length of the genome. Sequence data are efficiently stored and queried via a rather versatile language so that entire sequences of organisms will be treatable as they emerge. Other classes of information, such as function descriptions, are stored in a relational form, and joint queries relating th… more
Date: December 1992
Creator: Hagstrom, Ray; Overbeek, Ross & Price, Morgan
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

The technology roadmap for plant/crop-based renewable resources 2020

Description: The long-term well-being of the nation and maintenance of a sustainable leadership position in agriculture, forestry, and manufacturing, clearly depend on current and near-term support of multidisciplinary research for the development of a reliable renewable resource base. This document sets a roadmap and priorities for that research. America needs leadership that will continue to recognize, support, and move rapidly to meet the need to expand the use of sustainable renewable resources. This ro… more
Date: February 22, 1999
Creator: McLaren, J.
Item Type: Refine your search to only Book
Partner: UNT Libraries Government Documents Department
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Interfacing microbiology and biotechnology. Conference abstracts

Description: The Interfacing Microbiology and Biotechnology Conference was attended by over 100 faculty, post-docs, students, and research scientists from the US, Europe, and Latin America. The conference successfully stimulated communication and the dissemination of knowledge among scientists involved in basic and applied research. The focus of the conference was on microbial physiology and genetics and included sessions on C1 metabolism, archaeal metabolism, proteases and chaperones, gene arrays, and meta… more
Date: May 19, 2001
Creator: Maupin, Julia A.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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National Plant Genome Initiative

Description: This report is an update on progress of federal plant genome research. The focus in this report is on plants that are economically important to agribusiness.
Date: December 2001
Creator: National Science and Technology Council (U.S.). Committee on Science. Interagency Working Group on Plant Genomes.
Item Type: Refine your search to only Text
Partner: UNT Libraries
open access

Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis

Description: We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR a… more
Date: February 26, 2002
Creator: Simon, M. I. & Kim, U.-J.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Microbial Forensics: A Scientific Assessment

Description: Microorganisms have been used as weapons in criminal acts, most recently highlighted by the terrorist attack using anthrax in the fall of 2001. Although such ''biocrimes'' are few compared with other crimes, these acts raise questions about the ability to provide forensic evidence for criminal prosecution that can be used to identify the source of the microorganisms used as a weapon and, more importantly, the perpetrator of the crime. Microbiologists traditionally investigate the sources of mic… more
Date: February 17, 2003
Creator: Keim, Paul
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Phylo-VISTA: An interactive visualization tool for multiple DNAsequence alignments

Description: Motivation. The power of multi-sequence comparison forbiological discovery is well established and sequence data from a growinglist of organisms is becoming available. Thus, a need exists forcomputational strategies to visually compare multiple aligned sequencesto support conservation analysis across various species. To be efficientthese visualization algorithms require the ability to universally handlea wide range of evolutionary distances while taking into accountphylogeny Results. We have de… more
Date: April 25, 2003
Creator: Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.; Brudno, Michael; Batzoglou, Serafim; Bethel, E. Wes et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Frontiers of Plant Cell Biology: Signals and Pathways, System-Based Approaches 22nd Symposium in Plant Biology (University of California-Riverside)

Description: The symposium ''Frontiers of Plant Cell Biology: Signals and Pathways, Systems-Based Approaches'' was held January 15-18, 2003 at the Riverside Convention Center in Riverside, California. The host organization for the symposium was the Center for Plant Cell Biology (CEPCEB) at the University of California, Riverside (UCR). The meeting, focusing on systems-based approaches to plant cell biology research, was the first of this kind in the field of plant biology. The speakers and nearly 100 poster… more
Date: June 1, 2003
Creator: Minorsky, Peter V.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing.

Description: OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY a… more
Date: June 1, 2003
Creator: Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Final Report for Grant No. DE-FG02-98ER62583 ''Functional Analysis of the Genome Sequence of Deinococcus radiodurans''

Description: Extremophiles are nearly always defined with singular characteristics that allow existence within a singular extreme environment. The bacterium Deinococcus radiodurans qualifies as a polyextremeophile, showing remarkable resistance to a range of damage caused by ionizing radiation, dessication, ultraviolet radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is most famous for its extreme resistance to ionizing radiation; it not only can grow continuously in the presence of c… more
Date: October 15, 2003
Creator: Daly, Michael J.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Final Technical Report

Description: The results of the DOE-funded Mouse Genome Sequence (MGS) project include a significant enhancement in the capacity of the community to connect biological knowledge with the mouse genome sequence in a comparative context. The resources developed as the result of the activities of the MGS project staff are used extensively by both individual researchers and other informatics groups.
Date: November 24, 2003
Creator: J., Bult Carol
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Robust indexing for automatic data collection

Description: We present improved methods for indexing diffraction patterns from macromolecular crystals. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice. These methods help to correct failures commonly experienced during indexing, and increase the overall success rate of the proc… more
Date: December 9, 2003
Creator: Sauter, Nicholas K.; Grosse-Kunstleve, Ralf W. & Adams, Paul D.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

VISTA - computational tools for comparative genomics

Description: Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/VISTA/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics to… more
Date: January 1, 2004
Creator: Frazer, Kelly A.; Pachter, Lior; Poliakov, Alexander; Rubin,Edward M. & Dubchak, Inna
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Data Standards for the Genomes to Life Program

Description: Existing GTL Projects already have produced volumes of dataand, over the course of the next five years, will produce an estimatedhundreds, or possibly thousands, of terabytes of data from hundreds ofexperiments conducted at dozens of laboratories in National Labs anduniversities across the nation. These data will be the basis forpublications by individual researchers, research groups, andmulti-institutional collaborations, and the basis for future DOEdecisions on funding further research in bio… more
Date: January 31, 2004
Creator: Arkin, Adam; Ambrosiano, John; Babnigg, Gyorgy; Frank, Ed; Geist,Al; Giometti, Carol et al.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Coordination of Programs on Domestic Animal Genomics: The Federal Framework

Description: This report discusses progress by Federal agencies dealing with domestic animal genomics. The work represents an increase in the understanding of domestic animals such as sheep, cattle, swine, bees, and others. Knowledge in this area is crucial for better understanding animal diseases such at bovine spongiform encephalopathy (BSE, or "mad cow disease")
Date: June 2004
Creator: National Science and Technology Council (U.S.). Interagency Working Group on Domestic Animal Genomics.
Item Type: Refine your search to only Text
Partner: UNT Libraries
open access

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

Description: The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy which is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the Pfam5000 strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5… more
Date: July 14, 2004
Creator: Chandonia, John-Marc & Brenner, Steven E.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Genomic Sequence Comparisons, 1987-2003 Final Report

Description: This project was to develop new DNA sequencing and RNA and protein quantitation methods and related genome annotation tools. The project began in 1987 with the development of multiplex sequencing (published in Science in 1988), and one of the first automated sequencing methods. This lead to the first commercial genome sequence in 1994 and to the establishment of the main commercial participants (GTC then Agencourt) in the public DOE/NIH genome project. In collaboration with GTC we contributed t… more
Date: July 29, 2004
Creator: Church, George M.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer

Description: Genomic sequence comparisons between human, mouse and pufferfish (Takifugu rubripes (Fugu))have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change in order to retain in vivo functionality, such elements have been minimally explored experimentally. In this study, we describe the in-depth characterization of an ancient conserved enhancer, Dc2 located near the … more
Date: October 1, 2004
Creator: Poulin, Francis; Nobrega, Marcelo A.; Plajzer-Frick, Ingrid; Holt, Amy; Afzal, Veena; Rubin, Edward M. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

Description: We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized … more
Date: December 1, 2004
Creator: Price, Morgan N.; Huang, Katherine H.; Alm, Eric J. & Arkin, Adam P.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Functional Analysis and Discovery of Microbial Genes Transforming Metallic and Organic Pollutants: Database and Experimental Tools

Description: Microbial functional genomics is faced with a burgeoning list of genes which are denoted as unknown or hypothetical for lack of any knowledge about their function. The majority of microbial genes encode enzymes. Enzymes are the catalysts of metabolism; catabolism, anabolism, stress responses, and many other cell functions. A major problem facing microbial functional genomics is proposed here to derive from the breadth of microbial metabolism, much of which remains undiscovered. The breadth of m… more
Date: December 9, 2004
Creator: Wackett, Lawrence P. & Ellis, Lynda B.M.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
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