David S. Roos

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation (2008)

Xia, Dong, Sanderson, Sanya J, Jones, Andrew R, Prieto, Judith H, Yates, John R, Bromley, Elizabeth, ...

Abstract Background Although the genomes of many of the most important human and animal pathogens have now been sequenced, our understanding of the actual proteins expressed by these genomes and how...

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...

Cytoskeletal Components of an Invasion Machine—The Apical Complex of Toxoplasma gondii (2006)

Ke Hu, Jeff Johnson, Laurence Florens, Martin Fraunholz, Sapna Suravajjala, Camille DiLullo, ...

The apical complex of Toxoplasma gondii is widely believed to serve essential functions in both invasion of its host cells (including human cells), and in replication of the parasite. The...

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...

Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum

Waller, Ross F., Keeling, Patrick J., Donald, Robert G. K., Striepen, Boris, Handman, Emanuela, Lang-Unnasch, Naomi, ...

A vestigial, nonphotosynthetic plastid has been identified recently in protozoan parasites of the phylum Apicomplexa. The apicomplexan plastid, or “apicoplast,” is indispensable, but the complete...

Daughter Cell Assembly in the Protozoan Parasite Toxoplasma gondii

Hu, Ke, Mann, Tara, Striepen, Boris, Beckers, Con J. M., Roos, David S., Murray, John M.

The phylum Apicomplexa includes thousands of species of obligate intracellular parasites, many of which are significant human and/or animal pathogens. Parasites in this phylum replicate by assembling...

In Vitro Generation of Novel Pyrimethamine Resistance Mutations in the Toxoplasma gondii Dihydrofolate Reductase

Reynolds, Mary G., Oh, Jung, Roos, David S.

Pyrimethamine is a potent inhibitor of dihydrofolate reductase and is widely used in the treatment of opportunistic infections caused by the protozoan parasite Toxoplasma gondii. In order to assess...

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)

Bahl, Amit, Brunk, Brian, Coppel, Ross L., Crabtree, Jonathan, Diskin, Sharon J., Fraunholz, Martin J., ...

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation...

Measuring tubulin content in Toxoplasma gondii: A comparison of laser-scanning confocal and wide-field fluorescence microscopy

Swedlow, Jason R., Hu, Ke, Andrews, Paul D., Roos, David S., Murray, John M.

Toxoplasma gondii is an intracellular parasite that proliferates within most nucleated cells, an important human pathogen, and a model for the study of human and veterinary parasitic infections. We...

A plastid segregation defect in the protozoan parasite Toxoplasma gondii

He, Cynthia Y., Shaw, Michael K., Pletcher, Charles H., Striepen, Boris, Tilney, Lewis G., Roos, David S.

Apicomplexan parasites—including the causative agents of malaria (Plasmodium sp.) and toxoplasmosis (Toxoplasma gondii)—harbor a secondary endosymbiotic plastid, acquired by lateral genetic...

ToxoDB: accessing the Toxoplasma gondii genome

Kissinger, Jessica C., Gajria, Bindu, Li, Li, Paulsen, Ian T., Roos, David S.

ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST...

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data

Bahl, Amit, Brunk, Brian, Crabtree, Jonathan, Fraunholz, Martin J., Gajria, Bindu, Grant, Gregory R., ...

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and...

RAP1 controls rhoptry targeting of RAP2 in the malaria parasite Plasmodium falciparum

Baldi, Deborah L., Andrews, Katherine T., Waller, Ross F., Roos, David S., Howard, Randall F., Crabb, Brendan S., ...

Rhoptry associated protein 1 (RAP1) and 2 (RAP2), together with a poorly described third protein RAP3, form the low molecular weight complex within the rhoptries of Plasmodium falciparum. These...

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites

Li, Li, Crabtree, Jonathan, Fischer, Steve, Pinney, Deborah, Stoeckert, Christian J., Sibley, L. David, ...

ApiEST-DB (http://www.cbil.upenn.edu/paradbs-servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently...

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

Li, Li, Stoeckert, Christian J., Roos, David S.

The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences....

Multiple Functionally Redundant Signals Mediate Targeting to the Apicoplast in the Apicomplexan Parasite Toxoplasma gondii

Harb, Omar S., Chatterjee, Bithi, Fraunholz, Martin J., Crawford, Michael J., Nishi, Manami, Roos, David S.

Most species of the protozoan phylum Apicomplexa harbor an endosymbiotic organelle—the apicoplast—acquired when an ancestral parasite engulfed a eukaryotic plastid-containing alga. Several...

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...

Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...

Dynamics of Toxoplasma gondii Differentiation†

Dzierszinski, Florence, Nishi, Manami, Ouko, Lillian, Roos, David S.

Parasite differentiation is commonly associated with transitions between complex life cycle stages and with long-term persistence in the host, and it is therefore critical for pathogenesis. In the...

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

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...

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...

Cytoskeletal Components of an Invasion Machine—The Apical Complex of Toxoplasma gondii

Hu, Ke, Johnson, Jeff, Florens, Laurence, Fraunholz, Martin, Suravajjala, Sapna, DiLullo, Camille, ...

The apical complex of Toxoplasma gondii is widely believed to serve essential functions in both invasion of its host cells (including human cells), and in replication of the parasite. The...

Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum

Waller, Ross F., Keeling, Patrick J., Donald, Robert G. K., Striepen, Boris, Handman, Emanuela, Lang-Unnasch, Naomi, ...

A vestigial, nonphotosynthetic plastid has been identified recently in protozoan parasites of the phylum Apicomplexa. The apicomplexan plastid, or “apicoplast,” is indispensable, but the complete...

Daughter Cell Assembly in the Protozoan Parasite Toxoplasma gondii

Hu, Ke, Mann, Tara, Striepen, Boris, Beckers, Con J. M., Roos, David S., Murray, John M.

The phylum Apicomplexa includes thousands of species of obligate intracellular parasites, many of which are significant human and/or animal pathogens. Parasites in this phylum replicate by assembling...

In Vitro Generation of Novel Pyrimethamine Resistance Mutations in the Toxoplasma gondii Dihydrofolate Reductase

Reynolds, Mary G., Oh, Jung, Roos, David S.

Pyrimethamine is a potent inhibitor of dihydrofolate reductase and is widely used in the treatment of opportunistic infections caused by the protozoan parasite Toxoplasma gondii. In order to assess...

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)

Bahl, Amit, Brunk, Brian, Coppel, Ross L., Crabtree, Jonathan, Diskin, Sharon J., Fraunholz, Martin J., ...

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates finished and draft genome sequence data and annotation...

Measuring tubulin content in Toxoplasma gondii: A comparison of laser-scanning confocal and wide-field fluorescence microscopy

Swedlow, Jason R., Hu, Ke, Andrews, Paul D., Roos, David S., Murray, John M.

Toxoplasma gondii is an intracellular parasite that proliferates within most nucleated cells, an important human pathogen, and a model for the study of human and veterinary parasitic infections. We...

A plastid segregation defect in the protozoan parasite Toxoplasma gondii

He, Cynthia Y., Shaw, Michael K., Pletcher, Charles H., Striepen, Boris, Tilney, Lewis G., Roos, David S.

Apicomplexan parasites—including the causative agents of malaria (Plasmodium sp.) and toxoplasmosis (Toxoplasma gondii)—harbor a secondary endosymbiotic plastid, acquired by lateral genetic...

ToxoDB: accessing the Toxoplasma gondii genome

Kissinger, Jessica C., Gajria, Bindu, Li, Li, Paulsen, Ian T., Roos, David S.

ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST...

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data

Bahl, Amit, Brunk, Brian, Crabtree, Jonathan, Fraunholz, Martin J., Gajria, Bindu, Grant, Gregory R., ...

PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and...

RAP1 controls rhoptry targeting of RAP2 in the malaria parasite Plasmodium falciparum

Baldi, Deborah L., Andrews, Katherine T., Waller, Ross F., Roos, David S., Howard, Randall F., Crabb, Brendan S., ...

Rhoptry associated protein 1 (RAP1) and 2 (RAP2), together with a poorly described third protein RAP3, form the low molecular weight complex within the rhoptries of Plasmodium falciparum. These...

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites

Li, Li, Crabtree, Jonathan, Fischer, Steve, Pinney, Deborah, Stoeckert, Christian J., Sibley, L. David, ...

ApiEST-DB (http://www.cbil.upenn.edu/paradbs-servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently...

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

Li, Li, Stoeckert, Christian J., Roos, David S.

The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences....

Multiple Functionally Redundant Signals Mediate Targeting to the Apicoplast in the Apicomplexan Parasite Toxoplasma gondii

Harb, Omar S., Chatterjee, Bithi, Fraunholz, Martin J., Crawford, Michael J., Nishi, Manami, Roos, David S.

Most species of the protozoan phylum Apicomplexa harbor an endosymbiotic organelle—the apicoplast—acquired when an ancestral parasite engulfed a eukaryotic plastid-containing alga. Several...

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...

Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...

Dynamics of Toxoplasma gondii Differentiation†

Dzierszinski, Florence, Nishi, Manami, Ouko, Lillian, Roos, David S.

Parasite differentiation is commonly associated with transitions between complex life cycle stages and with long-term persistence in the host, and it is therefore critical for pathogenesis. In the...

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

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...

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...

Cytoskeletal Components of an Invasion Machine—The Apical Complex of Toxoplasma gondii

Hu, Ke, Johnson, Jeff, Florens, Laurence, Fraunholz, Martin, Suravajjala, Sapna, DiLullo, Camille, ...

The apical complex of Toxoplasma gondii is widely believed to serve essential functions in both invasion of its host cells (including human cells), and in replication of the parasite. The...

Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii

Boyle, Jon P., Rajasekar, Badri, Saeij, Jeroen P. J., Ajioka, James W., Berriman, Matthew, Paulsen, Ian, ...

Toxoplasma gondii, an obligate intracellular protozoan of the phylum Apicomplexa, is estimated to infect over a billion people worldwide as well as a great many other mammalian and avian hosts....

ApiDB: integrated resources for the apicomplexan bioinformatics resource center

Aurrecoechea, Cristina, Heiges, Mark, Wang, Haiming, Wang, Zhiming, Fischer, Steve, Rhodes, Philippa, ...

ApiDB () represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum...

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...

Mining the Plasmodium genome database to define organellar function: what does the apicoplast do?

Roos, David S, Crawford, Michael J, Donald, Robert G K, Fraunholz, Martin, Harb, Omar S, He, Cynthia Y, ...

Apicomplexan species constitute a diverse group of parasitic protozoa, which are responsible for a wide range of diseases in many organisms. Despite differences in the diseases they cause, these...

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...

Toxoplasma gondii scavenges host-derived lipoic acid despite its de novo synthesis in the apicoplast

Crawford, Michael J, Thomsen-Zieger, Nadine, Ray, Manisha, Schachtner, Joachim, Roos, David S, Seeber, Frank

In contrast to other eukaryotes, which manufacture lipoic acid, an essential cofactor for several vital dehydrogenase complexes, within the mitochondrion, we show that the plastid (apicoplast) of the...

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...

Presentation of Toxoplasma gondii Antigens via the Endogenous Major Histocompatibility Complex Class I Pathway in Nonprofessional and Professional Antigen-Presenting Cells▿

Dzierszinski, Florence, Pepper, Marion, Stumhofer, Jason S., LaRosa, David F., Wilson, Emma H., Turka, Laurence A., ...

Challenge with the intracellular protozoan parasite Toxoplasma gondii induces a potent CD8+ T-cell response that is required for resistance to infection, but many questions remain about the factors...

The Plastid of Toxoplasma gondii Is Divided by Association with the Centrosomes

Striepen, Boris, Crawford, Michael J., Shaw, Michael K., Tilney, Lewis G., Seeber, Frank, Roos, David S.

Apicomplexan parasites harbor a single nonphotosynthetic plastid, the apicoplast, which is essential for parasite survival. Exploiting Toxoplasma gondii as an accessible system for cell biological...

A novel polymer of tubulin forms the conoid of Toxoplasma gondii

Hu, Ke, Roos, David S., Murray, John M.

Toxoplasma gondii is an obligatory intracellular parasite, an important human pathogen, and a convenient laboratory model for many other human and veterinary pathogens in the phylum Apicomplexa, such...

Secretory traffic in the eukaryotic parasite Toxoplasma gondii: less is more

Joiner, Keith A., Roos, David S.

Name a single-celled eukaryote that boasts a small genome size, is easily cultivated in haploid form, for which a wide variety of molecular genetic tools are available, and that exhibits a simple,...