Coyne, Robert S, Thiagarajan, Mathangi, Jones, Kristie M, Wortman, Jennifer R, Tallon, Luke J, Haas, Brian J, ...
Abstract Background Tetrahymena thermophila , a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic...
Haas, Brian J, Salzberg, Steven L, Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E, Orvis, Joshua, ...
Abstract EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM,...
Haas, Brian U., Salzberg, Steven L., Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E., Orvis, Joshua, ...
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when...
Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa (2007)
Kelly A. Brayton, David R. Herndon, Linda Hannick, Lowell S. Kappmeyer, Shawn J. Berens, ...
Babesia bovis is an apicomplexan tick-transmitted pathogen of cattle imposing a global risk and severe constraints to livestock health and economic development. The complete genome sequence was...
Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA (2007)
Robyn M. Perrin, Natalie D. Fedorova, Jin Woo Bok, Robert A. Cramer Jr., Jennifer R. Wortman, H. Stanley Kim, ...
Secondary metabolites, including toxins and melanins, have been implicated as virulence attributes in invasive aspergillosis. Although not definitively proved, this supposition is supported by the...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert P., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the ~160-megabase genome,...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert ., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert ., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase...
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae (2005)
Galagan, James E., Calvo, Sarah E., Cuomo, Christina, Ma, Li-Jun, Wortman, Jennifer R., Batzoglou, Serafim, ...
The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a...
Comparative analysis of programmed cell death pathways in filamentous fungi (2005)
Fedorova, Natalie D, Badger, Jonathan H, Robson, Geoff D, Wortman, Jennifer R, Nierman, William C
Abstract Background Fungi can undergo autophagic- or apoptotic-type programmed cell death (PCD) on exposure to antifungal agents, developmental signals, and stress factors. Filamentous fungi can also...
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Abstract Background Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome...
DAGchainer: a tool for mining segmental genome duplications and synteny (2004)
Brian J. Haas, Arthur L. Delcher, Jennifer R. Wortman, Steven L. Salzberg
Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order...
DAGchainer: a tool for mining segmental genome duplications and synteny (2004)
Haas, Brian J., Delcher, Arthur L., Wortman, Jennifer R., Salzberg, Steven L.
Summary: Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved...
DAGchainer: A tool for mining segmental genome duplications and synteny (2004)
Haas, Brian J., Delcher, Arthur L., Wortman, Jennifer R., Salzberg, Steven L.
Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order...
DAGchainer: A tool for mining segmental genome duplications and synteny (2004)
Haas, Brian J., Delcher, Arthur L., Wortman, Jennifer R., Salzberg, Steven L.
Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies (2003)
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
Identification and characterization of a p53 homologue in Drosophila melanogaster
Jin, Shengkan, Martinek, Sebastian, Joo, Woo S., Wortman, Jennifer R., Mirkovic, Nebojsa, Sali, Andrej, ...
The tumor suppressor gene p53 in mammalian cells plays a critical role in safeguarding the integrity of genome. It functions as a sequence-specific transcription factor. Upon activation by a variety...
Annotation of the Arabidopsis Genome1
Wortman, Jennifer R., Haas, Brian J., Hannick, Linda I., Smith, Roger K., Maiti, Rama, Ronning, Catherine M., ...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
Ayele, Mulu, Haas, Brian J., Kumar, Nikhil, Wu, Hank, Xiao, Yongli, Van Aken, Susan, ...
Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences...
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Comparative analysis of programmed cell death pathways in filamentous fungi
Fedorova, Natalie D, Badger, Jonathan H, Robson, Geoff D, Wortman, Jennifer R, Nierman, William C
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Identification and characterization of a p53 homologue in Drosophila melanogaster
Jin, Shengkan, Martinek, Sebastian, Joo, Woo S., Wortman, Jennifer R., Mirkovic, Nebojsa, Sali, Andrej, ...
The tumor suppressor gene p53 in mammalian cells plays a critical role in safeguarding the integrity of genome. It functions as a sequence-specific transcription factor. Upon activation by a variety...
Annotation of the Arabidopsis Genome1
Wortman, Jennifer R., Haas, Brian J., Hannick, Linda I., Smith, Roger K., Maiti, Rama, Ronning, Catherine M., ...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
Ayele, Mulu, Haas, Brian J., Kumar, Nikhil, Wu, Hank, Xiao, Yongli, Van Aken, Susan, ...
Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences...
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Comparative analysis of programmed cell death pathways in filamentous fungi
Fedorova, Natalie D, Badger, Jonathan H, Robson, Geoff D, Wortman, Jennifer R, Nierman, William C
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA
Perrin, Robyn M, Fedorova, Natalie D, Bok, Jin Woo, Cramer, Robert A, Wortman, Jennifer R, Kim, H. Stanley, ...
Secondary metabolites, including toxins and melanins, have been implicated as virulence attributes in invasive aspergillosis. Although not definitively proved, this supposition is supported by the...
Town, Christopher D., Cheung, Foo, Maiti, Rama, Crabtree, Jonathan, Haas, Brian J., Wortman, Jennifer R., ...
We sequenced 2.2 Mb representing triplicated genome segments of Brassica oleracea, which are each paralogous with one another and homologous with a segmentally duplicated region of the Arabidopsis...
Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa
Brayton, Kelly A, Lau, Audrey O. T, Herndon, David R, Hannick, Linda, Kappmeyer, Lowell S, Berens, Shawn J, ...
Babesia bovis is an apicomplexan tick-transmitted pathogen of cattle imposing a global risk and severe constraints to livestock health and economic development. The complete genome sequence was...
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
Fedorova, Natalie D., Khaldi, Nora, Joardar, Vinita S., Maiti, Rama, Amedeo, Paolo, Anderson, Michael J., ...
We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri...
Haas, Brian J, Salzberg, Steven L, Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E, Orvis, Joshua, ...
EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes.
Coyne, Robert S, Thiagarajan, Mathangi, Jones, Kristie M, Wortman, Jennifer R, Tallon, Luke J, Haas, Brian J, ...
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...