J3DV: A Java-Based 3D Database Visualization Tool Xiang Fang (2008)
John A. Miller, Jonathan Arnold
SUMMARY Data visualization helps users process, interpret, and act upon data in large data storage. In this paper, we present a Java-based 3D database visualization tool, J3DV. It successfully solved...
Boanerges Aleman-meza, Yihai Yu, Jonathan Arnold, Thiab R. Taha
simulator for computing large ensembles of biochemical and gene
Jorge Cardoso, Amit Sheth, John Miller, Jonathan Arnold, Krys Kochut
Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In workflows or Web processes for e-commerce and Web service...
Massively Parallel Algorithms for Chromosome Reconstruction (2007)
Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnold, David Whitmire
Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is shown to be...
D istrib u ted G enom e (2007)
David Hall, John Miller, Jonathan Arnold, Krys Kochut, Amit Sheth, Michael Weise
U sing W ork ow to B u ild an In fo rm ation M anagem ent System fo r a G eograph ica lly
Genome-wide expression analysis of genetic networks in Neurospora crassa (2007)
David A. Logan, Allison L. Koch, Wubei Dong, James Griffith, Roger Nilsen, Mary E. Case, ...
The products of five structural genes and two regulatory genes of the qa gene cluster of Neurospora crassa control the metabolism of quinic acid (QA) as a carbon source. A detailed genetic network...
GCSDB: an integrated database system for the Georgia Centenarian Study (2006)
Jianliang Dai, Adam Davey, Ilene C. Siegler, Jonathan Arnold, Leonard W. Poon
GCSDB is a web-oriented integrated database system for the Georgia Centenarian Study, a phase III, population-based, multidisciplinary study of centenarians. The Study recruited 244 centenarians and...
Colet, Wolsey and the Politics of Reform: St Paul's Cathedral in 1518 (2006)
Following his entrance into political life as a royal councillor, in 1518 Dean John Colet proposed amendments to the existing St. Paul's Cathedral statutes concerning residence and behaviour of...
ESSENTIAL EUKARYOTIC CORE (2004)
George L. Strobel, Jonathan Arnold
The AIDs-related fungal pathogen Pneumocystis carinii is unusual in having a remarkably compact genome of 7.7 megabase pairs (mbp) whose small size presents the opportunity to identify the essential...
Quality of service for workflows and web service processes (2004)
Jorge Cardoso, John Miller, Amit Sheth, Jonathan Arnold
Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In workflows for e-commerce and Web-services applications, suppliers and...
Quality of service for workflows and web service processes (2004)
Jorge Cardoso, John Miller, Amit Sheth, Jonathan Arnold
Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In workflows for e-commerce and Web-services applications, suppliers and...
Quality of service for workflows and web service processes (2004)
Jorge Cardoso, John Miller, Amit Sheth, Jonathan Arnold
Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In workflows for e-commerce and Web-services applications, suppliers and...
Quality of service for workflows and web service processes (2004)
Jorge Cardoso, John Miller, Amit Sheth, Jonathan Arnold
Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In workflows for e-commerce and Web service applications, suppliers and...
Intelligen: A distributed workflow system for discovering protein-protein interactions (2003)
Krys Kochut, Jonathan Arnold, Amit Sheth, Au Pls
Abstract. A large genomics project involves a significant number of researchers and technicians performing dozens of tasks, either manual (e.g. performing laboratory experiments), computer assisted...
Intelligen: A distributed workflow system for discovering protein-protein interactions (2003)
Krys Kochut, Jonathan Arnold, Amit Sheth
Abstract. A large genomics project involves a significant number of researchers and technicians performing dozens of tasks, either manual (e.g. performing laboratory experiments), computer assisted...
Intelligen: A distributed workflow system for discovering protein-protein interactions (2003)
Krys Kochut, Jonathan Arnold, Amit Sheth
Abstract. A large genomics project involves a significant number of researchers and technicians performing dozens of tasks, either manual (e.g. performing laboratory experiments), computer assisted...
Intelligen: A distributed workflow system for discovering protein-protein interactions (2003)
Krys J. Kochut, Jonathan Arnold, Amit Sheth, John Miller, Eileen Kraemer, Budak Arpinar, ...
In the new millennium biology has gone through a paradigm shift with the advent of Genomics, the study of the structure, function, and evolution of whole genomes. The term “genomics ” was coined...
An analysis of gene-finding programs for Neurospora crassa (2001)
Kraemer, Eileen, Wang, Jian, Guo, Jinhua, Hopkins, Samuel, Arnold, Jonathan
Motivation: Computational gene identification plays an important role in genome projects. The approaches used in gene identification programs are often tuned to one particular organism, and accuracy...
Physical mapping with automatic capture of hybridization data (2001)
Hall, David, Bhandarkar, Suchendra M., Arnold, Jonathan, Jiang, Tongzhang
Motivation: Contig maps are a type of physical map that show the native order of a set of overlapping genomic clones. Overlaps between clones can be detected by finding common sequences using a...
Reconstructing Distances in Physical Maps of Chromosomes With Nonoverlapping Probes (2000)
John Kececioglu, Sanjay Shete, Jonathan Arnold
We present a new method for reconstructing the distances between probes in physical maps of chromosomes constructed by hybridizing pairs of clones under the so-called sampling-without-replacement...
D istrib u ted G enom e (1999)
David Hall, John Miller, Jonathan Arnold, Krys Kochut, Amit Sheth, Michael Weise
U sing W ork ow to B u ild an In fo rm ation M anagem ent System fo r a G eograph ica lly
Usng Workflow to Build an Information Management System for a. . . (1999)
David Hall, John Miller, Jonathan Arnold, Krys Kochut, Amit Sheth, Michael Weise
Genome projects are very demanding undertakings and are often carried out collaboratively by multiple research centers. There are many different types of tasks that must be performed both by...
Reconstructing Order and Distance in Physical Maps Using Nonoverlapping Probes (1998)
John Kececioglu, Sanjay Shete, Jonathan Arnold
We present a new method for reconstructing both the order and spacing of probes in physical maps of chromosomes constructed by hybridizing pairs of clones under the so-called...
ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling (1994)
Wang, Yuhong, Prade, Rolf A., Griffith, James, Timberlake, William E., Arnold, Jonathan
In the program ODS_BOOTSTRAP we provide a methodology for quickly ordering clones in a genomic library into a physical map and for applying a statistical tool known as the bootstrap to assess the...
Query Driven Simulation As A Tool For Genetic Engineers (1992)
John A. Miller, Jonathan Arnold, Krys J. Kochut, A. Jamie Cuticchia, Walter D. Potter
Simulations/animations of genetic structures and functions, simulations of actual or conceived experiments, and animations of algorithms such as simulated annealing, which is used to reconstruct a...
Chromosome-specific recombinant DNA libraries from the fungus Aspergillus nidulans (1991)
Brody, Howard, Griffith, James, Cuticchia, Anthony J., Arnold, Jonathan, Timberlake, William E.
Development of physical genomic maps is facilitated by identification of overlapping recombinant DNA clones containing long chromosomal DNA inserts. To simplify the analysis required to determine...
Arnold, Jonathan, Cuticchia, A.Jamie, Newsome, David A., Jennings, W.Wesley, Ivarie, Robert
Here we compare several methods for predicting oligonucleotide frequencies in 392 kb of yeast DNA. As in previous work on E. coli, a relatively simple equation based on tetranucleotide frequencies...
Phillips, Gregory J., Arnold, Jonathan, Ivarie, Robert
Several statistical methods were tested for accuracy in predicting observed frequencies of di- through hexanucleotides in 74,444 bp of E. coli DNA. A Markov chain was most accurate overall, whereas...
Phillips, Gregory J., Arnold, Jonathan, Ivarie, Robert
As shown in the accompanying paper (5), the oligonudeotide composition of the E. coli genome is highly asymmetric for sequences up to 6 bp in length when ranked from highest to lowest abundance. We...
A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11 (1986)
Arnold, Jonathan, Eckenrode, Virginia K., Lemke, Klaus, Phillips, Gregory J., Schaeffer, Stephen W.
A computer package written in Fortran-IV for the PDP-11 minicomputer is described. The package's novel features are: (i) software for voice-entry of sequence data; (ii) a less meoory intensive...
2 microfiches in pocket.
In vitro reconstruction of the Aspergillus (= Emericella) nidulans genome
Prade, Rolf A., Griffith, James, Kochut, Krys, Arnold, Jonathan, Timberlake, William E.
A physical map of the 31-megabase Aspergillus nidulans genome is reported, in which 94% of 5,134 cosmids are assigned to 49 contiguous segments. The physical map is the result of a two-way ordering...
Arnold, Jonathan, Morrison, Melvin L.
In population studies, adults are frequently difficult or inconvenient to identify for genotype, but a family profile of genotypes can be obtained from an unidentified female crossed with a single...
Asmussen, Marjorie A., Arnold, Jonathan, Avise, John C.
We define and establish the interrelationships of four components of statistical association between a diploid nuclear gene and a uniparentally transmitted, haploid cytoplasmic gene: an allelic...
Fate Mapping Multi-Focus Phenotypes
Arnold, Jonathan, Kankel, Douglas R.
A central assumption used in the genetic fate mapping of anatomical sites responsible for certain mutationally induced abnormalities is that a single pair of bilaterally symmetric sites on the...
Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.
Xu, Zheng, Lance, Britton, Vargas, Claudia, Arpinar, Budak, Bhandarkar, Suchendra, Kraemer, Eileen, ...
A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits...
In vitro reconstruction of the Aspergillus (= Emericella) nidulans genome
Prade, Rolf A., Griffith, James, Kochut, Krys, Arnold, Jonathan, Timberlake, William E.
A physical map of the 31-megabase Aspergillus nidulans genome is reported, in which 94% of 5,134 cosmids are assigned to 49 contiguous segments. The physical map is the result of a two-way ordering...
Arnold, Jonathan, Morrison, Melvin L.
In population studies, adults are frequently difficult or inconvenient to identify for genotype, but a family profile of genotypes can be obtained from an unidentified female crossed with a single...
Asmussen, Marjorie A., Arnold, Jonathan, Avise, John C.
We define and establish the interrelationships of four components of statistical association between a diploid nuclear gene and a uniparentally transmitted, haploid cytoplasmic gene: an allelic...
Fate Mapping Multi-Focus Phenotypes
Arnold, Jonathan, Kankel, Douglas R.
A central assumption used in the genetic fate mapping of anatomical sites responsible for certain mutationally induced abnormalities is that a single pair of bilaterally symmetric sites on the...
Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.
Xu, Zheng, Lance, Britton, Vargas, Claudia, Arpinar, Budak, Bhandarkar, Suchendra, Kraemer, Eileen, ...
A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits...
Cushion, Melanie T., Smulian, A. George, Slaven, Bradley E., Sesterhenn, Tom, Arnold, Jonathan, Staben, Chuck, ...
Members of the genus Pneumocystis are fungal pathogens that cause pneumonia in a wide variety of mammals with debilitated immune systems. Little is known about their basic biological functions,...
GCSDB: an integrated database system for the Georgia Centenarian Study
Dai, Jianliang, Davey, Adam, Siegler, Ilene C, Arnold, Jonathan, Poon, Leonard W
GCSDB is a web-oriented integrated database system for the Georgia Centenarian Study, a phase III, population-based, multidisciplinary study of centenarians. The Study recruited 244 centenarians and...
Genome-wide expression analysis of genetic networks in Neurospora crassa
Logan, David A, Koch, Allison L, Dong, Wubei, Griffith, James, Nilsen, Roger, Case, Mary E, ...
The products of five structural genes and two regulatory genes of the qa gene cluster of Neurospora crassa control the metabolism of quinic acid (QA) as a carbon source. A detailed genetic network...
A genetic network for the clock of Neurospora crassa
Yu, Yihai, Dong, Wubei, Altimus, Cara, Tang, Xiaojia, Griffith, James, Morello, Melissa, ...
A diverse array of organisms from bacteria to humans may have evolved the ability to tell time in the presence or absence of external environmental cues. In the lowly bread mould, Neurospora crassa,...
Systems Biology of the Clock in Neurospora crassa
Dong, Wubei, Tang, Xiaojia, Yu, Yihai, Nilsen, Roger, Kim, Rosemary, Griffith, James, ...
A model-driven discovery process, Computing Life, is used to identify an ensemble of genetic networks that describe the biological clock. A clock mechanism involving the genes white-collar-1 and...