Nutrient use efficiency in bioenergy cropping systems: Critical research questions (2009)
Brouder, Sylvie, Volenec, Jeffrey J, Turco, Ronald, Smith, Douglas R, Ejeta, Gebisa
Current U.S. plans for energy security rely on converting large areas of cropland from food to biofuel production. Additionally, lands currently considered too marginal for intensive food production...
DOI: 10.1093/bioinformatics/btg152 (2008)
Genome visualization made fast and simple
Generating Programs plus Proofs by Refinement 1 Technical Approach (2008)
We advocate an automated refinement approach to developing programs and their proofs. The approach is partially embodied in the Specware system [6] which has found industrial and government...
REASONING BY CASES AND THE FORMATION OF CONDITIONAL PROGRAMS 1 (2008)
ABSTRACT (1) Reasoning by cases, a natural feature of human reasoning, has been difficult to formulate so that it can be performed naturally when needed. Several difficulties arise: (1) how to...
A DESIGN FOR AN AUTOMATIC PROGRAMMING SYSTEM* (2008)
The algorithm design process proceeds in a top down manner with the production of higher level algorithms resulting in the generation of specifications for lower level algorithms. The workings of...
Assembly reconciliation (2008)
Zimin, Aleksey V., Smith, Douglas R., Sutton, Granger, Yorke, James A.
Motivation: Many genomes are sequenced by a collaboration of several centers, and then each center produces an assembly using their own assembly software. The collaborators then pick the draft...
Rapid whole-genome mutational profiling using next-generation sequencing technologies (2008)
Smith, Douglas R., Quinlan, Aaron R., Peckham, Heather E., Makowsky, Kathryn, Tao, Wei, Woolf, Betty, ...
Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the...
in Knowledge Engineering Reviews, 2001 Synthesis of Ecient Constraint Satisfaction Programs (2007)
Stephen J. Westfold, Douglas R. Smith
In this paper we describe the framework wehavedeveloped in KIDS (Kestrel Interactive Development System) for generating ecient Constraint Satisfaction Programs. WehaveusedKIDS to synthesize global...
Abstract Designware: Software Development by Re nement (2007)
This paper presents a mechanizable framework for software development by re nement. The framework is based on a category of higher-order speci cations. The key idea is representing knowledge about...
The Kestrel Interactive Development System (KIDS) provides automated sup-port for the development of correct and efficient programs from formal specifications. The system has components for...
Abstract. This paper presents a mechanizable framework for software development by refinement. The framework is based on a category of specifications. The key idea is representing knowledge about...
Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome (2007)
Douglas R. Smith, Peter Richterich, Marc Rubenfield, Philip W. Rice, Kathleen Falls, Joan Imrich, ...
The nucleotide sequence of 1.5 Mb of genomic DNA from Mycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to...
Initial sequence and comparative analysis of the cat genome (2007)
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
Roadmap for Enhanced Languages and Methods to Aid Verification (2006)
Leavens, Gary T., Abrial, Jean-Raymond, Batory, Don, Butler, Michael, Coglio, Alessandro, Fisler, Kathi, ...
This roadmap describes ways that researchers in four areas — speci- fication languages, program generation, correctness by construction, and programming languages — might help further the goal of...
Roadmap for Enhanced Languages and Methods to Aid Verification (2006)
Leavens, Gary T., Abrial, Jean-Raymond, Batory, Don, Butler, Michael, Coglio, Alessandro, Fisler, Kathi, ...
This roadmap describes ways that researchers in four areas — speci- fication languages, program generation, correctness by construction, and programming languages — might help further the goal of...
Roadmap for Enhanced Languages and Methods to Aid Verification (2006)
Leavens, Gary T., Abrial, Jean-Raymond, Batory, Don, Butler, Michael, Coglio, Alessandro, Fisler, Kathi, ...
This roadmap describes ways that researchers in four areas — speci- fication languages, program generation, correctness by construction, and programming languages — might help further the goal of...
ACES: Aspect-Oriented Composition of Embedded Systems (2006)
Becker, Marcel, Smith, Douglas R.
Resource management is the key component of any real-time application. Traditional approaches to the development of embedded applications usually restrict their resource management capabilities to...
Correction: Serendipitous discovery of Wolbachiagenomes in multiple Drosophilaspecies (2005)
Salzberg, Steven L, Dunning Hotopp, Julie, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
No abstract available.
Serendipitous discovery of Wolbachiagenomes in multiple Drosophilaspecies (2005)
Salzberg, Steven L, Hotopp, Julie, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
Abstract Background The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005)
Salzberg, Steven L., Dunning Hotopp, Julie C., Delcher, Arthur L., Pop, Mihai, Smith, Douglas R, Eisen, Michael B., ...
Background: The Trace Archive is a repository for the raw, unanalyzed data generated by largescale genome sequencing projects. The existence of this data offers scientists the possibility of...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005)
Salzberg, Steven L., Dunning Hotopp, Julie C., Delcher, Arthur L., Pop, Mihai, Smith, Douglas R, Eisen, Michael B., ...
Background: The Trace Archive is a repository for the raw, unanalyzed data generated by largescale genome sequencing projects. The existence of this data offers scientists the possibility of...
Design improvements for low flow electrospray mass spectrometry of biomolecules / (2004)
Thesis (Ph. D.)--State University of New York at Buffalo, 2004.
Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica (2004)
Malek, Joel A., Wierzbowski, Jamey M., Tao, Wei, Bosak, Stephanie A., Saranga, David J., Doucette-Stamm, Lynn, ...
Protein interaction maps can reveal novel pathways and functional complexes, allowing ‘guilt by association’ annotation of uncharacterized proteins. To address the need for large‐scale...
Real-Time Asset Rescheduling With Execution Monitoring and Accurate Asset Tracking (2003)
Smith, Douglas R., Fitzpatrick, Stephen, Westfold, Stephen J.
Through the use of software transformational synthesis technology, synthesize rescheduling algorithms that reschedule transportation assets using data from automatic identification technology and...
Exo-Proofreading, A Versatile SNP Scoring Technology (2003)
Cahill, Patrick, Bakis, Michele, Hurley, James, Kamath, Veena, Nielsen, William, Weymouth, Dina, ...
We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3′-to-5′ exonuclease proofreading activity of many DNA polymerases. The assay...
Exo-Proofreading, A Versatile SNP Scoring Technology (2003)
Cahill, Patrick, Bakis, Michele, Hurley, James, Kamath, Veena, Nielsen, William, Weymouth, Dina, ...
Genome visualization made fast and simple (2003)
Gibson, René, Smith, Douglas R.
Summary: The easiest way to gain a quick overall understanding of genomic data is with a visual display that allows the user to view information about an entire genome or chromosome at once. We have...
Guarded transitions in evolving specifications (2002)
Dusko Pavlovic, Douglas R. Smith
Abstract. We represent state machines in the category of specifications, where assignment statements correspond exactly to interpretations be-tween theories [7, 8]. However, the guards on an...
Composition and refinement of evolving specifications (2002)
Viatthias Anlauff, Dusko Pavlovic, Douglas R. Smith
Abstract. We represent state machines in the category of specifications, where assignment statements correspond exactly to in terpretations be-tween theories [6, 9]. However, the guards on an...
AND ACCURATE ASSET TRACKING (2002)
Michael L. Talbert, Douglas R. Smith, Stephen Fitzpatrick, Stephen J. Westfold
The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the
Jörk Nölling, Gary Breton, Marina V. Omelchenko, Kira S. Makarova, Qiandong Zeng, Rene Gibson, ...
The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and a 192-kb...
Composition and refinement of behavioral specifications (2001)
Dusko Pavlovic, Douglas R. Smith
This paper presents a mechanizable framework for specifying, developing, and reasoning about complex systems. The framework combines features from algebraic specifications, abstract state machines,...
Composition and Refinement of Behavioral Specifications (2001)
Dusko Pavlovic, Douglas R. Smith
This paper presents a mechanizable framework for specifying, developing, and reasoning about complex systems. The framework combines features from algebraic specifications, abstract state machines,...
Derivation of glue code for agent interoperation (2000)
Mark Burstein, Drew Mcdermott, Douglas R. Smith, Stephen J. Westfold
{smith, westf old}kestrel. edu Getting agents to communicate requires translating the data structures of the sender (the source representation) to the format required by the receiver (the target...
Derivation of glue code for agent interoperation (2000)
Mark Burstein, Drew Mcdermott, Douglas R. Smith, Stephen J. Westfold
Getting agents to communicate requires translating the data structures of the sender (the source representation) to the format required by the receiver (the target representation). Assuming that...
Derivation of glue code for agent interoperation (2000)
Mark Burstein, Drew Mcdermott, Douglas R. Smith, Stephen J. Westfold
Getting agents to communicate requires translating the data structures of the sender (the source representation) to the format required by the receiver (the target representation). Assuming that...
Derivation of Glue Code for Agent Interoperation (1999)
Mark Burstein, Drew McDermott, Mark Burstein Gte/bbn, Stephen J. Westfold, Douglas R. Smith
This paper is about getting agents to communicate with each other. By "agent" we mean programs that operate at a high enough semantic level that they can form new connections to other...
Wall pressure fluctuations were measured under the unsteady separation shock/turbulent boundary layer interaction induced by unswept circular cylinders to determine the role of the incoming turbulent...
Toward a Formal Model of the Design and Evolution of Software. (1998)
Green, Cordell, Smith, Douglas R.
This report summarizes recent activities on the development of a formal model of the design and evolution of software. The model is intended to be both descriptive and prescriptive. It is descriptive...
Theory of Algorithm Structure and Design. (1998)
Algorithms and data structures are among the primary constituents of computer software and thus are among basic objects of study in Computer Science. This project is concerned with the structure and...
Theory of Algorithm Structure and Design. (1998)
Algorithms and data structures are among the primary constituents of computer software and thus are among basic objects of study in Computer Science. This project is concerned with the structure and...
Knowledge-Based Software Development Tools, (1998)
Smith, Douglas R., Pressburger, Thomas T.
We describe some of the experimental knowledge-based software development tools under development at Kestrel Institute. In particular, systems for automatically performing algorithm design, deductive...
Automated Support for Software Engineering. (1998)
The key idea of this project is that pararneterized theories and various operations on them provide a uniform conceptual foundation for software engineering. The broad objectives of this project are...
Generic Tools for Transportation Planning and Scheduling. (1998)
Smith, Douglas R., Parra, Eduardo A., Westfold, Stephen J.
This report describes our research on transportation planning and scheduling supported by the ARPA/Rome Lab Planning Initiative (ARPI). The main goal of this project was to develop generic tools to...
Synthesis Approach to Parallel Software Engineering. (1998)
Smith, Douglas R., Emerson, Thomas, Gilham, LiMei, Westfold, Stephen J.
This report describes our research on a synthesis approach to parallel Software Engineering. The main goal of this project was to develop concepts and generic tools to support the synthesis of...
Planware--Domain-Specific Synthesis of High-Performance Schedulers (1998)
Blaine, Lee, Gilham, Limei, Lin, Jumbo, Smith, Douglas R., Westfold, Stephen
The technology aggregated in Planware represents part of a significant long term investment in knowledge based software engineering formulated and guided by AFRL/IFTD. It includes search theories...
Automatic Synthesis of Planners and Schedulers.. (1998)
Smith, Douglas R., Liu, Junbo, Westfold, Stephen J.
This report describes our research on the transformational development of transportation plans and schedules. Our approach to developing scheduling software involves several stages. The first step is...
Agentware: Automated Synthesis of Software Agents (1998)
Smith, Douglas R., Westfold, Stephen J.
This report describes our research on developing and applying synthesis technology to agent-based systems in the DARPA/AFRL COABS program. We summarize our results in the following areas: generic...
Three-Dimensional Particle Image Velocimetry System (1998)
The PIV instrumentation was requested to support two AFOSR-funded research projects. The first project is entitled "Hybrid Control of Turbulent Jets" (Grant No. F49620-00-1-0255). The hybrid approach...
Hybrid Control of Jet Flows (1998)
Naughton, Jonathan W., Smith, Douglas R.
The use of swirl and synthetic jet actuators in a hybrid control scheme is described. The results here are limited to the characterization of (1) swirling jet flows and (2) synthetic jets in a...
Specification-Carrying Software: Evolving Specifications for Dynamic System Composition (1998)
Anlauff, Matthias, Pavlovic, Dusko, Smith, Douglas R.
EPOXI (Evolutionary Programming Over Explicit Interfaces) builds on the advanced mathematical foundation to enable the design and evolution of large-scale, heterogeneous, distributed, time-critical...
A Study of the Formation and Scaling of a Synthetic Jet (1998)
The broad goal of this study was to gain an improved understanding for how synthetic jet actuators perform as flow control devices. This improved understanding is motivated by a need for enhancing...
Planware - Domain-Specific Synthesis of High-Performance Schedulers (1998)
Lee Blaine, Limei Gilham, Junbo Liu, Douglas R. Smith, Stephen Westfold
Planware is a domain-specific generator of high-performance scheduling software, currently being developed at Kestrel Institute. Architecturally, Planware is an extension of the Specware system with...
Synthesis of Power Plant Outage Schedules. (1997)
This document provides a report on the creation of domain theories in the power plant outage domain. These were developed in conjunction with the creation of a demonstration system of advanced...
Foundations of Software Development. (1997)
Algorithms and data structures are among the primary constituents of computer software and thus are among basic objects of study in Computer Science. This project is concerned with the structure and...
Complete Genome Sequence of Methanobacterium thermoautotrophicum ΔH: Functional . . . (1997)
Douglas R. Smith, Craig Deloughery, Hongmei Lee, Joann Dubois, ...
the ORF-encoded polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no homology to sequences in public databases. Comparisons with Eucarya-, Bacteria-, and...
Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome (1997)
Smith, Douglas R., Richterich, Peter, Rubenfield, Marc, Rice, Philip W., Butler, Carol, Lee, Hong-Mei, ...
Synthesis of Planning and Scheduling Software (1996)
Douglas R. Smith, Eduardo A. Parra, Stephen J. Westfold
This report describes our research on transportation planning and scheduling supported by the ARPA/Rome Lab Planning Initiative (ARPI). The main goal of this project was to develop generic tools to...
Toward a Classification Approach to Design (1996)
This paper addresses the problem of how to construct refinements of specifications formally and incrementally. The key idea is to use a taxonomy of abstract design concepts, each represented by a...
A High-level Derivation of Global Search Algorithms (with Constraint Propagation) (1996)
Peter Pepper, Douglas R. Smith
In this paper we describe the formal derivation of a transportation scheduling algorithm. The algorithm is based on the concepts of global search and constraint propagation and was originally derived...
Mark H. Burstein, Moulton St, Douglas R. Smith
In a joint project, BBN and Kestrel Institute have developed a prototype of a mixed-initiative scheduling system called ITAS (In-Theater Airlift Scheduler) for the U.S. Air Force, Pacific Command....
Synthesis of High-Performance Transportation Schedulers (1995)
Douglas R. Smith, Eduardo A. Parra, Stephen J. Westfold
This report describes our research on transportation planning and scheduling supported by the ARPA/Rome Lab Planning Initiative (ARPI). The main goal of this project was to develop generic tools to...
Mark H. Burstein, Douglas R. Smith
In a joint project, BBN and Kestrel Institute have developed a prototype of a mixedinitiative scheduling system called ITAS (In-Theater Airlift Scheduler) for the U.S.
Derivation of Parallel Sorting Algorithms (1993)
R. Paige, J. Reif, R. Wachter, Douglas R. Smith
Parallel algorithms can be derived from formal problem specifications by applying a sequence of transformations that embody information about algorithms, data structures, and optimization techniques....
Constructing Specification Morphisms (1993)
This paper is part of a broader research program to explore a mechanizable model of software development based on algebraic specifications and specification morphisms. An algebraic specification (or...
Transformational Approach to Transportation Scheduling (1993)
Douglas R. Smith, Eduardo A. Parra
We have used KIDS (Kestrel Interactive Development System) to derive extremely fast and accurate transportation schedulers from formal specifications. As test data we use strategic transportation...
Reduced occurrence of chimeric YACs in recombinationdeficient hosts (1993)
Ling, Lucy L., Ma, Nancy S.-F., Smith, Douglas R., Miller, David D., Moir, Donald T.
Structure and Design of Problem Reduction Generators (1991)
In this paper we present an axiomatic theory for a class of algorithms, called problem reduction generators, that includes dynamic programming, general branch-and-bound, and game tree search as...
KIDS: A Semi-Automatic Program Development System (1990)
The Kestrel Interactive Development System (KIDS) provides automated support for the development of correct and efficient programs from formal specifications. The system has components for performing...
KIDS - A Knowledge-Based Software Development System (1990)
The Kestrel Interactive Development System (KIDS) provides knowledge-based support for the derivation of correct and efficient programs from formal specifications. We trace the use of KIDS in...
Degree granted by College of Pharmacy.
Ayers, Kevin B., McClung, R. Michael., Smith, Douglas R.
Typescript.
Nucleotide sequence of the E. coli gene coding for dihydrofolate reductase (1980)
Smith, Douglas R., Calvo, Joseph M.
Plasmid pLCl437a contains DNA from Escherichia coli K12 including fol, the structural gene for dihydrofolate reductase. The fol gene was mapped on this plasmid relative to several restriction...
Thesis (M.S. in Chemical Engineering)--Graduate School of Arts and Sciences, University of Pennsylvania, 1976.
Text on back: Motel Washington. At Fairfax Circle. U.S. Highway 50-29 & 211. 1207 E. Lee Hwy. Fairfax, Virginia. Crescent 3-2877. Swimming pool & wading pool. Free T.V. in all rooms. Excellent...
Text on front: Motel Washington, air conditioned. 12 miles southwest of Washington, D.C. U.S. Highways 50-29 & 211. At Fairfax Circle. Fairfax, Virginia. Text on back: TV. Motel Washington. TV. U.S....
Text on front: Motel Washington. Air conditioned. TV. 12 miles southwest of Washingon, D.C. U.S. Highways 50-29 & 211. At Fairfax Circle. Fairfax, Virginia. Text on back: TV. Motel Washington. TV....
Text on front: Holly Hill Motor Lodge, Highways 29-50-211, Fairfax, Va. Text on back: Holly Hill Motor Lodge. AAA. Highways 29-50-211. Fairfax, Va. 14 miles south west of Washington, D.C. Look for...
Text on front: 13 miles south west of Washington, D.C. U.S. Highways 29-50 & 211. Fairfax, Virginia. Text on back: AAA. Patton Motor Hotel. Quality Court United, Inc. U.S. Highways 29, 50 & 211....
Text on back: Colonnade Motel. U.S. Highways 29 & 211. Crescent 3-5733. Fairfax, Virginia. Suburban rates & out of the congested area. Free T.V. in all rooms. Air conditioned. Central heating....
Text on back: Gateway Motor Lodge. U.S. Highways 29-50 & 211. Fairfax, Virginia. Phone: Crescent 3-4240 or Crescent 3-1995. 22 Air-conditioned rooms, with T.V., telephones, wall to wall carpeting &...
Text on back: Greenbrier Motor Lodge. 112 miles west of Washington, D.C. U.S. Highways 50-211 & 29, Fairfax, Virginia. AAA.
Text on front: U.S. Highway 29-50 & 211. 1 mile west of Fairfax Circle. Fairfax, Virginia. Text on back: AAA. TV. Greenbrier Motor Lodge. U.S. Highways 29-50 & 211. Fairfax, Virginia. Approved...
Text on front: U.S. Highway 29-50 & 211. 1 mile west of Fairfax Circle. Fairfax, Virginia. Text on back: AAA. Greenbrier Motor Lodge. TV. U.S. Highways 29-50 & 211. Fairfax, Virginia. Approved...
Text on front: U.S. Highways 29 - 50 & 211. One mile west of Fairfax Circle, Fairfax, Va. Text on back: AAA Greenbrier Motor Lodge. AAA. 12 miles west of Washington, D.C. U.S. Highways 29 - 50 & 211....
Text on front: U.S. Highways 29-50 & 211. At Fairfax Circle. Fairfax, Virginia. Text on back: Hi-Way Motel. Air conditioned. U.S. highways 29-50 & 211. At Fairfax Circle. Fairfax, Virginia. 12 miles...
Text on front: U.S. Highways 29-50 & 211. At Fairfax Circle. Fairfax, Virginia. Hi-Way Motel. Air conditioned. U.S. Highways 29-50 & 211. At Fairfax Circle. Fairfax, Virginia. 12 miles west of...
Text on back: AMHA, American Motor Hotel Association. Hy-Way Motel. Air conditioned. U.S. Highways 29-50 & 211. At Fairfax Circle. Fairfax, Virginia. 12 miles west of Washington, D.C. Television in...
Text on back: Hy-way Motel. Fairfax, Va. Located 12 miles west of Washington, D.C. at junction of U.S. 29-50-211. Completely modern. Free radio in every unit. Owned and operated by Bill and Rosalie...
Text on front: U.S. Highways 50 - 29 & 211. 12 miles west of Washington, D.C. Fairfax, Virginia. Text on back: Quality Courts United. Patton Motor Hotel. AAA. U.S. Highways 50 - 29 & 211, Crescent...
Text on back: Westwood Motel. U.S. highways 29 - 50 & 211. Crescent 3-9835. Fairfax, Virginia. 1/2 mile from Fairfax Circle. 12 miles from Washington, D.C. Air conditioned. Ceramic tiled baths, with...
Text on front: Breezeway Motel. Highways 29-50 and 211, Fairfax, VA. Text on back: Breezeway Motel. New, modern & fireproof. 13 miles west of Washington, D.C. On four lane highway. Rubber foam...
Text on back: Circle Motor Court Motel. U.S. Highways 29 - 50 & 211. At Fairfax Circle, Fairfax, Virginia. 12 miles west of Washington, D.C. Modern steam heated cottages & dining room. Reservations...
Sunset Grove Motor Court (1940)
Text on front: Sunset Grove Motor Court, U.S. highways 29-50 & 211, Fairfax, VA. Text on back: Sunset Grove Motor Court. 14 miles west of Washington, D.C. on U.S. highways 29-50 & 211. Television....
Text on front: Westwood Motel, Highways 29 - 50 & 211, Fairfax, Va. Text on back: Westwood Motel. Television & radios in rooms. One of Virginia's newest motels. Modern tile baths, tubs with showers....
Text on front: U.S. Highway 29--50 & 211...12 1/2 miles west of Washington, D.C....Fairfax, Virginia. Text on back: Boulevard Motel. U.S. Highway 29--50 & 211...near Fairfax Circle, Fairfax,...
Text on front: U.S. Highway 50...Fairfax, Virginia. Text on back: TV. Chilla Villa Motel. U.S. Highway 50. Fairfax, Virginia. 17 miles west of Washington, D.C. Reservations telephone Crescent 3-9885....
Text on front: Chilla-Villa Motel. U.S.(Winchester) highway 50, Fairfax, VA. Text on back: Chilla Villa Motel.
Text on front: AAA. Virginia Inn. Your home tonight. 15 miles southwest of U.S. Highways 29 & 211. Washington, D.C. Fairfax, Virginia. Text on back: AAA. Virginia Inn. Quality Courts United, Inc. On...
Nölling, Jörk, Breton, Gary, Omelchenko, Marina V., Makarova, Kira S., Zeng, Qiandong, Gibson, Rene, ...
The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and a 192-kb...
Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica
Malek, Joel A., Wierzbowski, Jamey M., Tao, Wei, Bosak, Stephanie A., Saranga, David J., Doucette-Stamm, Lynn, ...
Protein interaction maps can reveal novel pathways and functional complexes, allowing ‘guilt by association’ annotation of uncharacterized proteins. To address the need for large-scale protein...
Exo-Proofreading, A Versatile SNP Scoring Technology
Cahill, Patrick, Bakis, Michele, Hurley, James, Kamath, Veena, Nielsen, William, Weymouth, Dina, ...
We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3′-to-5′ exonuclease proofreading activity of many DNA polymerases. The assay...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Hotopp, Julie C Dunning, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly:...
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Dunning Hotopp, Julie C, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology...
Nölling, Jörk, Breton, Gary, Omelchenko, Marina V., Makarova, Kira S., Zeng, Qiandong, Gibson, Rene, ...
The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and a 192-kb...
Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica
Malek, Joel A., Wierzbowski, Jamey M., Tao, Wei, Bosak, Stephanie A., Saranga, David J., Doucette-Stamm, Lynn, ...
Protein interaction maps can reveal novel pathways and functional complexes, allowing ‘guilt by association’ annotation of uncharacterized proteins. To address the need for large-scale protein...
Exo-Proofreading, A Versatile SNP Scoring Technology
Cahill, Patrick, Bakis, Michele, Hurley, James, Kamath, Veena, Nielsen, William, Weymouth, Dina, ...
We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3′-to-5′ exonuclease proofreading activity of many DNA polymerases. The assay...
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Hotopp, Julie C Dunning, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly:...
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
Salzberg, Steven L, Dunning Hotopp, Julie C, Delcher, Arthur L, Pop, Mihai, Smith, Douglas R, Eisen, Michael B, ...
A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology...
Initial sequence and comparative analysis of the cat genome
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, Clamp, Michele, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
Schaeffer, Stephen W., Bhutkar, Arjun, McAllister, Bryant F., Matsuda, Muneo, Matzkin, Luciano M., O'Grady, Patrick M., ...
The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of...
Rapid whole-genome mutational profiling using next-generation sequencing technologies
Smith, Douglas R., Quinlan, Aaron R., Peckham, Heather E., Makowsky, Kathryn, Tao, Wei, Woolf, Betty, ...
Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the...