Comparative Genomics in C. elegans, C. briggsae, and Other Caenorhabditis Species (2008)
C. C. Elegans, Kevin Strange, Avril Coghlan, Jason E. Stajich, Todd W. Harris
The genome of the nematode Caenorhabditis elegans was the first animal genome sequenced. Subsequent sequencing of the Caenorhabditis briggsae genome enabled a comparison of the genomes of two...
evolution from comparative genomic (2008)
Matthew W. Hahn, Tijl De Bie, Jason E. Stajich, Chi Nguyen, Nello Cristianini
Estimating the tempo and mode of gene family
Hu, Guanggan, Liu, Iris, Sham, Anita, Stajich, Jason E, Dietrich, Fred S, Kronstad, James W
Abstract Background Genome variability can have a profound influence on the virulence of pathogenic microbes. The availability of genome sequences for two strains of the AIDS-associated fungal...
Regier, Jerome C., Shultz, Jeffrey W., Ganley, Austen R. D., Hussey, April, Shi, Diane, Ball, Bernard, ...
This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that...
Resource The Bioperl Toolkit: Perl Modules for the Life Sciences (2007)
Jason E. Stajich, David Block, Kris Boulez, Steven E. Brenner, Lincoln D. Stein, Elia Stupka, ...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive libraryof...
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors (2007)
Stajich, Jason E, Dietrich, Fred S, Roy, Scott W
Abstract Background Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from transcripts before protein translation. Many facets of spliceosomal intron...
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors (2007)
Stajich, Jason E, Dietrich, Fred S, Roy, Scott W
Background: Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from transcripts before protein translation. Many facets of spliceosomal intron evolution,...
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...
BASC: an integrated bioinformatics system for Brassica research (2007)
Erwin, Timothy A., Jewell, Erica G., Love, Christopher G., Lim, Geraldine A. C., Chapman, Ross, Batley, Jacqueline, ...
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational...
BASC: an integrated bioinformatics system for Brassica research (2007)
Erwin, Timothy A., Jewell, Erica G., Love, Christopher G., Lim, Geraldine A. C., Chapman, Ross, Batley, Jacqueline, ...
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational...
Coccidioides Immitis, Coccidioides Posadasii, James A. Fraser, Jason E. Stajich, Eric J. Tarcha, Garry T. Cole, ...
Sexual reproduction of fungi is governed by the mating type (MAT) locus, a specialized region of the genome encoding key transcriptional regulators that direct regulatory networks to specify cell...
BASC: an integrated bioinformatics system for Brassica research (2007)
Erwin, Timothy A., Jewell, Erica G., Love, Christopher G., Lim, Geraldine A. C., Li, Xi, Chapman, Ross, ...
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational...
Fitzpatrick, David A, Logue, Mary E, Stajich, Jason E, Butler, Geraldine
Abstract Background To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome...
Fitzpatrick, David A., Logue, Mary E., Stajich, Jason E., Butler, Geraldine
Background To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing...
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis (2006)
Kahmann, Regine, Bölker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J, ...
Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence...
Comparative analysis of Saccharomyces cerevisiaeWW domains and their interacting proteins (2006)
Hesselberth, Jay R, Miller, John P, Golob, Anna, Stajich, Jason E, Michaud, Gregory A, Fields, Stanley
Abstract Background The WW domain is found in a large number of eukaryotic proteins implicated in a variety of cellular processes. WW domains bind proline-rich protein and peptide ligands, but the...
Evidence of mRNA-Mediated Intron Loss in the Human-Pathogenic Fungus Cryptococcus neoformans† (2006)
Jason E. Stajich, Fred S. Dietrich
Introns are a defining feature of eukaryotic genomes, though the mechanism of intron gain or loss is not well understood. Reverse transcription of mRNA followed by homologous recombination with the...
The evolution of mammalian gene families (2006)
Stajich, Jason E, Cristianini, Nello, Hahn, Matthew W
03
BASC: an integrated bioinformatics system for Brassica research (2006)
Erwin, Timothy A., Jewell, Erica G., Love, Christopher G., Lim, Geraldine A. C., Li, Xi, Chapman, Ross, ...
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational...
Open source tools and toolkits for bioinformatics: significance, and where are we? (2006)
Stajich, Jason E., Lapp, Hilmar
This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose...
BASC: an integrated bioinformatics system for Brassica research (2006)
Erwin, Timothy A., Jewell, Erica G., Love, Christopher G., Lim, Geraldine A. C., Li, Xi, Chapman, Ross, ...
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational...
Investigating hookworm genomes by comparative analysis of two Ancylostomaspecies (2005)
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
Abstract Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans . Applying genomics techniques to...
Disentangling the Effects of Demography and Selection in Human History (2005)
Stajich, Jason E., Hahn, Matthew W.
Demographic events affect all genes in a genome, whereas natural selection has only local effects. Using publicly available data from 151 loci sequenced in both European-American and African-American...
Estimating the tempo and mode of gene family evolution from comparative genomic data (2005)
Hahn, Matthew W., De Bie, Tijl, Stajich, Jason E., Nguyen, Chi, Cristianini, Nello
Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible...
Disentangling the Effects of Demography and Selection in Human History (2004)
Stajich, Jason E., Hahn, Matthew W.
Demographic events affect all genes in a genome, while natural selection has only local effects. Using publicly-available data from 151 loci sequenced in both European-American and African-American...
Disentangling the Effects of Demography and Selection in Human History (2004)
Stajich, Jason E., Hahn, Matthew W.
Demographic events affect all genes in a genome, while natural selection has only local effects. Using publicly-available data from 151 loci sequenced in both European-American and African-American...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
With the Caenorhabditis briggsae genome now in hand, C. elegans biologists have a powerful new research tool to refine their knowledge of gene function in C. elegans and to study the path of genome...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
The Effects of Selection against Spurious Transcription Factor Binding Sites (2003)
Hahn, Matthew W., Stajich, Jason E., Wray, Gregory A.
Most genomes contain nucleotide sequences with no known function; such sequences are assumed to be free from constraints, evolving only according to the vagaries of mutation. Here we show that...
The Effects of Selection Against Spurious Transcription Factor Binding Sites (2003)
Hahn, Matthew W., Stajich, Jason E., Wray, Gregory A.
Most genomes contain nucleotide sequences with no known function; such sequences are assumed to be free of constraints, evolving only according to the vagaries of mutation. Here we show that...
The Effects of Selection against Spurious Transcription Factor Binding Sites (2003)
Hahn, Matthew W., Stajich, Jason E., Wray, Gregory A.
Most genomes contain nucleotide sequences with no known function; such sequences are assumed to be free from constraints, evolving only according to the vagaries of mutation. Here we show that...
The Generic Genome Browser: A Building Block for a Model Organism System Database (2002)
Stein, Lincoln D., Mungall, Christopher, Shu, ShengQiang, Caudy, Michael, Mangone, Marco, Day, Allen, ...
The Bioperl Toolkit: Perl Modules for the Life Sciences (2002)
Stajich, Jason E., Block, David, Boulez, Kris, Brenner, Steven E., Chervitz, Stephen A., Dagdigian, Chris, ...
The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein, Lincoln D., Mungall, Christopher, Shu, ShengQiang, Caudy, Michael, Mangone, Marco, Day, Allen, ...
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser...
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, Jason E., Block, David, Boulez, Kris, Brenner, Steven E., Chervitz, Stephen A., Dagdigian, Chris, ...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
Identification of Cryptococcus neoformans Temperature-Regulated Genes with a Genomic-DNA Microarray†
Kraus, Peter R., Boily, Marie-Josée, Giles, Steven S., Stajich, Jason E., Allen, Andria, Cox, Gary M., ...
The ability to survive and proliferate at 37°C is an essential virulence attribute of pathogenic microorganisms. A partial-genome microarray was used to profile gene expression in the...
Investigating hookworm genomes by comparative analysis of two Ancylostoma species
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
Estimating the tempo and mode of gene family evolution from comparative genomic data
Hahn, Matthew W., De Bie, Tijl, Stajich, Jason E., Nguyen, Chi, Cristianini, Nello
Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible...
Evidence of mRNA-Mediated Intron Loss in the Human-Pathogenic Fungus Cryptococcus neoformans†
Stajich, Jason E., Dietrich, Fred S.
Introns are a defining feature of eukaryotic genomes, though the mechanism of intron gain or loss is not well understood. Reverse transcription of mRNA followed by homologous recombination with the...
Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins
Hesselberth, Jay R, Miller, John P, Golob, Anna, Stajich, Jason E, Michaud, Gregory A, Fields, Stanley
A protein interaction map for 12 of the 13 WW domains present in the proteins of S. cerevisiae was generated by using protein microarray data.
Likelihoods From Summary Statistics: Recent Divergence Between Species
Leman, Scotland C., Chen, Yuguo, Stajich, Jason E., Noor, Mohamed A. F., Uyenoyama, Marcy K.
We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of...
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
Fitzpatrick, David A, Logue, Mary E, Stajich, Jason E, Butler, Geraldine
The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein, Lincoln D., Mungall, Christopher, Shu, ShengQiang, Caudy, Michael, Mangone, Marco, Day, Allen, ...
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser...
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, Jason E., Block, David, Boulez, Kris, Brenner, Steven E., Chervitz, Stephen A., Dagdigian, Chris, ...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
Identification of Cryptococcus neoformans Temperature-Regulated Genes with a Genomic-DNA Microarray†
Kraus, Peter R., Boily, Marie-Josée, Giles, Steven S., Stajich, Jason E., Allen, Andria, Cox, Gary M., ...
The ability to survive and proliferate at 37°C is an essential virulence attribute of pathogenic microorganisms. A partial-genome microarray was used to profile gene expression in the...
Investigating hookworm genomes by comparative analysis of two Ancylostoma species
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
Estimating the tempo and mode of gene family evolution from comparative genomic data
Hahn, Matthew W., De Bie, Tijl, Stajich, Jason E., Nguyen, Chi, Cristianini, Nello
Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible...
Likelihoods From Summary Statistics: Recent Divergence Between Species
Leman, Scotland C., Chen, Yuguo, Stajich, Jason E., Noor, Mohamed A. F., Uyenoyama, Marcy K.
We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of...
Evidence of mRNA-Mediated Intron Loss in the Human-Pathogenic Fungus Cryptococcus neoformans†
Stajich, Jason E., Dietrich, Fred S.
Introns are a defining feature of eukaryotic genomes, though the mechanism of intron gain or loss is not well understood. Reverse transcription of mRNA followed by homologous recombination with the...
Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins
Hesselberth, Jay R, Miller, John P, Golob, Anna, Stajich, Jason E, Michaud, Gregory A, Fields, Stanley
A protein interaction map for 12 of the 13 WW domains present in the proteins of S. cerevisiae was generated by using protein microarray data.
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
Fitzpatrick, David A, Logue, Mary E, Stajich, Jason E, Butler, Geraldine
The Cryptococcus neoformans Catalase Gene Family and Its Role in Antioxidant Defense
Giles, Steven S., Stajich, Jason E., Nichols, Connie, Gerrald, Quincy D., Alspaugh, J. Andrew, Dietrich, Fred, ...
In the present study, we sought to elucidate the contribution of the Cryptococcus neoformans catalase gene family to antioxidant defense. We employed bioinformatics techniques to identify four...
The Evolution of Mammalian Gene Families
Demuth, Jeffery P., Bie, Tijl De, Stajich, Jason E., Cristianini, Nello, Hahn, Matthew W.
Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to...
BASC: an integrated bioinformatics system for Brassica research
Erwin, Timothy A., Jewell, Erica G., Love, Christopher G., Lim, Geraldine A. C., Li, Xi, Chapman, Ross, ...
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational...
Fraser, James A., Stajich, Jason E., Tarcha, Eric J., Cole, Garry T., Inglis, Diane O., Sil, Anita, ...
Sexual reproduction of fungi is governed by the mating type (MAT) locus, a specialized region of the genome encoding key transcriptional regulators that direct regulatory networks to specify cell...
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
Stajich, Jason E, Dietrich, Fred S, Roy, Scott W
Analysis of intron gain and loss in fungal genomes provides support for an intron-rich fungus-animal ancestor.
Hu, Guanggan, Liu, Iris, Sham, Anita, Stajich, Jason E, Dietrich, Fred S, Kronstad, James W
Extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans is revealed through comparative genome hybridization between strains of different mating type, molecular subtype and...
Rosenblum, Erica Bree, Stajich, Jason E., Maddox, Nicole, Eisen, Michael B.
Amphibians around the world are being threatened by an emerging pathogen, the chytrid fungus Batrachochytrium dendrobatidis (Bd). Despite intensive ecological study in the decade since Bd was...
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...
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
Sharpton, Thomas J., Stajich, Jason E., Rounsley, Steven D., Gardner, Malcolm J., Wortman, Jennifer R., Jordar, Vinita S., ...
While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including...