A Strategy for the Rapid Identification of Phosphorylation Sites in the Phosphoproteome* (2008)
Justin A. Macdonald, Aaron J. Mackey, William R. Pearson
Edman phosphate ( 32 P) release sequencing provides a high sensitivity means of identifying phosphorylation sites in proteins that complements mass spectrometry techniques. We have developed a...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A, Weinstock, George M, Brown, Susan J, Denell, Robin, Beeman, Richard W, ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A., Weinstock, George M., Brown, Susan J., Denell, Robin, Beeman, Richard W., ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
ToxoDB: an integrated Toxoplasma gondii database resource (2008)
Gajria, Bindu, Bahl, Amit, Brestelli, John, Dommer, Jennifer, Fischer, Steve, Gao, Xin, ...
ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well...
Creating a honey bee consensus gene set (2007)
Elsik, Christine G, Mackey, Aaron J, Reese, Justin T, Milshina, Natalia V, Roos, David S, Weinstock, George M
Abstract Background We wished to produce a single reference gene set for honey bee ( Apis mellifera ). Our motivation was twofold. First, we wished to obtain an improved set of gene models with...
The 2006 NESCent Phyloinformatics Hackathon: A Field Report (2007)
Hilmar Lapp, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, ...
In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a...
The 2006 NESCent Phyloinformatics Hackathon: A Field Report (2007)
Hilmar Lapp, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, ...
In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Robinson, Gene E, Gibbs, Richard A, Worley, Kim C, Evans, Jay D, Maleszka, Ryszard, ...
Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes,...
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups (2006)
Mackey, Aaron J, Stoeckert, Christian J, Roos, David S
The OrthoMCL database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages,...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii (2006)
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
SynView: a GBrowse-compatible approach to visualizing comparative genome data (2006)
Wang, Haiming, Su, Yanqi, Mackey, Aaron J., Kraemer, Eileen T., Kissinger, Jessica C.
Summary: We present SynView, a simple and generic approach to dynamically visualize multi-species comparative genome data. It is a light-weight application based on the popular and configurable...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii (2006)
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups (2006)
Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.
The OrthoMCL database (http://orthomcl.cbil.upenn.edu) houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages,...
The transcriptome of Toxoplasma gondii (2005)
Radke, Jay R, Behnke, Michael S, Mackey, Aaron J, Radke, Josh B, Roos, David S, White, Michael W
Abstract Background Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent...
Khan, Asis, Taylor, Sonya, Su, Chunlei, Mackey, Aaron J., Boyle, Jon, Cole, Robert, ...
Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and...
CRP: Cleavage of Radiolabeled Phosphoproteins (2003)
Aaron J. Mackey, William R. Pearson
The CRP (Cleavage of Radiolabeled Phosphoproteins) program guides the design and interpretation of experiments to identify protein phosphorylation sites by Edman sequencing of unseparated peptides....
CRP: Cleavage of Radiolabeled Phosphoproteins (2003)
Mackey, Aaron J., Haystead, Timothy A.J., Pearson, William R.
The CRP (Cleavage of Radiolabeled Phosphoproteins) program guides the design and interpretation of experiments to identify protein phosphorylation sites by Edman sequencing of unseparated peptides....
Aaron J. Mackey, William R. Pearson
We describe two novel sequence similarity search algorithms, FASTS and FASTF, that use multiple short peptide sequences to identify homologous sequences in protein or DNA databases. FASTS searches...
Aaron J. Mackey, William R. Pearson
We describe two novel sequence similarity search algorithms, FASTS and FASTF, that use multiple short peptide sequences to identify homologous sequences in protein or DNA databases. FASTS searches...
Disperse: a simple and efficient approach to parallel database searching (2000)
Clifford, Raphaël, Mackey, Aaron J.
Summary: A general system for performing multiple independent database searches in parallel is presented. Run-time addition and removal of clients, robust failure and error trapping and near 100%...
CRP: Cleavage of Radiolabeled Phosphoproteins
Mackey, Aaron J., Haystead, Timothy A.J., Pearson, William R.
The CRP (Cleavage of Radiolabeled Phosphoproteins) program guides the design and interpretation of experiments to identify protein phosphorylation sites by Edman sequencing of unseparated peptides....
Khan, Asis, Taylor, Sonya, Su, Chunlei, Mackey, Aaron J., Boyle, Jon, Cole, Robert, ...
Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and...
The transcriptome of Toxoplasma gondii
Radke, Jay R, Behnke, Michael S, Mackey, Aaron J, Radke, Josh B, Roos, David S, White, Michael W
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.
The OrthoMCL database () houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available...
CRP: Cleavage of Radiolabeled Phosphoproteins
Mackey, Aaron J., Haystead, Timothy A.J., Pearson, William R.
The CRP (Cleavage of Radiolabeled Phosphoproteins) program guides the design and interpretation of experiments to identify protein phosphorylation sites by Edman sequencing of unseparated peptides....
Khan, Asis, Taylor, Sonya, Su, Chunlei, Mackey, Aaron J., Boyle, Jon, Cole, Robert, ...
Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and...
The transcriptome of Toxoplasma gondii
Radke, Jay R, Behnke, Michael S, Mackey, Aaron J, Radke, Josh B, Roos, David S, White, Michael W
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Chen, Feng, Mackey, Aaron J., Stoeckert, Christian J., Roos, David S.
The OrthoMCL database () houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
Creating a honey bee consensus gene set
Elsik, Christine G, Mackey, Aaron J, Reese, Justin T, Milshina, Natalia V, Roos, David S, Weinstock, George M
A high-quality consensus gene set for the honey bee (Apis mellifera) created using a new algorithm (GLEAN) is described.
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes
Chen, Feng, Mackey, Aaron J., Vermunt, Jeroen K., Roos, David S.
Orthology detection is critically important for accurate functional annotation, and has been widely used to facilitate studies on comparative and evolutionary genomics. Although various methods are...
ToxoDB: an integrated Toxoplasma gondii database resource
Gajria, Bindu, Bahl, Amit, Brestelli, John, Dommer, Jennifer, Fischer, Steve, Gao, Xin, ...
ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well...
The 2006 NESCent Phyloinformatics Hackathon: A Field Report
Lapp, Hilmar, Bala, Sendu, Balhoff, James P., Bouck, Amy, Goto, Naohisa, Holder, Mark, ...
In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a...