The HuRef Browser: a web resource for individual human genomics (2009)
Axelrod, Nelson, Lin, Yuan, Ng, Pauline C., Stockwell, Timothy B., Crabtree, Jonathan, Huang, Jiaqi, ...
The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between...
Comparative genomics of mutualistic viruses of Glyptapantelesparasitic wasps (2008)
Desjardins, Christopher A, Gundersen-Rindal, Dawn E, Hostetler, Jessica B, Tallon, Luke J, Fadrosh, Douglas W, Fuester, Roger W, ...
Abstract Background Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and...
IDEA: Interactive Display for Evolutionary Analyses (2008)
Egan, Amy, Mahurkar, Anup, Crabtree, Jonathan, Badger, Jonathan H, Carlton, Jane M, Silva, Joana C
Abstract Background The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other...
1 Production and Playback of Human Figure Motion for Visual Simulation (2008)
John P. Granieri, Jonathan Crabtree, Norman I. Badler
We describe a system for o-line production and real-time playback of motion for articulated human gures in 3D virtual environments. The key notions are (1) the logical storage of full-body motion in...
BioMed Central Software IDEA: Interactive Display for Evolutionary Analyses (2008)
Bmc Bioinformatics, Amy Egan, Anup Mahurkar, Jonathan Crabtree, Jonathan H Badger, Jane M Carlton, ...
© 2008 Egan et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Presented to the Faculties of the University of Pennsylvania (2007)
Lucian Popa, Val Tannen, Val Tannen, Jonathan Crabtree, Susan Davidson, Alin Deutsch, ...
I am indebted to Val Tannen, my advisor. This dissertation would not have been possible without his invaluable ideas, support, and advice. His deep insight into both fields of databases and...
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...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan A. Eisen, ...
Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan Eisen, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites (2004)
Li Li, Jonathan Crabtree, Steve Fischer, Deborah Pinney, Christian J. Stoeckert, L. David Sibley, ...
ApiEST-DB
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites (2004)
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...
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...
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...
K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources (2001)
Davidson, Susan B, Crabtree, Jonathan, Brunk, Brian P., Schug, Jonathan, Tannen, Val, Overton, Chris, ...
The integration of heterogeneous data sources and software systems is a major issue in the biomed ical community and several approaches have been explored: linking databases, "on-the- fly"...
K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources (2001)
Susan B. Davidson, Jonathan Crabtree, Brian Brunk, Jonathan Schug, Val Tannen, Chris Overton, ...
The integration of heterogeneous data sources and software systems is a major issue in the biomedical community and several approaches have been explored: linking databases, \on-the- y "...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5 (2001)
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The GAIA software framework for genome annotation (1998)
G. Christian Overton, Charles Bailey, Jonathan Crabtree, Mark Gibson, Stephen Fischer, Jonathan Schug
We describe a software framework, GAIA, that supports semiautomated annotation of uncharacterized sequence data. The annotation framework incorporates annotation by data source integration, data...
GAIA: Framework Annotation of Genomic Sequence (1998)
Bailey, L. Charles, Fischer, Stephen, Schug, Jonathan, Crabtree, Jonathan, Gibson, Mark, Overton, G. Christian
Behavioral Control for Real-Time Simulated Human Agents (1995)
Granieri, John P, Becket, Welton, Reich, Barry D, Crabtree, Jonathan, Badler, Norman I
A system for controlling the behaviors of an interactive human-like agent and executing them in real-time, is presented. It relies on an underlying model of continuous behavior, as well as a discrete...
Production and Playback of Human Figure Motion 3D Virtual Environments (1995)
Granieri, John P., Crabtree, Jonathan, Badler, Norman I
We describe a system for off-line production and real-time playback of motion for articulated human figures in 3D virtual environments. The key notions are (1) the logical storage of full body motion...
Behavioral Control for Real-Time Simulated Human Agents (1995)
John Granieri, Welton Becket, Barry Reich, Jonathan Crabtree, Norman Badler
A system for controlling the behaviors of an interactive human-like agent, and executing them in real-time, is presented. It relies on an underlying model of continuous behavior, as well as a...
Weakly wandering sets / (1993)
Thesis (B.A.)--Williams College, Dept. of Mathematics, 1993.
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...
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...
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...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The current strategy for sequencing the mouse genome involves the combination of a whole-genome shotgun approach with clone-based sequencing. High-resolution physical maps will provide a foundation...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., ...
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single...
Joardar, Vinita, Lindeberg, Magdalen, Jackson, Robert W., Selengut, Jeremy, Dodson, Robert, Brinkac, Lauren M., ...
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv....
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
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...
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...
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...
High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5
Crabtree, Jonathan, Wiltshire, Tim, Brunk, Brian, Zhao, Shaying, Schug, Jonathan, Stoeckert, Christian J., ...
The current strategy for sequencing the mouse genome involves the combination of a whole-genome shotgun approach with clone-based sequencing. High-resolution physical maps will provide a foundation...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., ...
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single...
Joardar, Vinita, Lindeberg, Magdalen, Jackson, Robert W., Selengut, Jeremy, Dodson, Robert, Brinkac, Lauren M., ...
Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv....
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan A, ...
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...
Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis
McDonagh, Andrew, Fedorova, Natalie D., Crabtree, Jonathan, Yu, Yan, Kim, Stanley, Chen, Dan, ...
Aspergillus fumigatus is a common mould whose spores are a component of the normal airborne flora. Immune dysfunction permits developmental growth of inhaled spores in the human lung causing...
Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps
Desjardins, Christopher A, Gundersen-Rindal, Dawn E, Hostetler, Jessica B, Tallon, Luke J, Fadrosh, Douglas W, Fuester, Roger W, ...
Comparative genome analysis of two endosymbiotic polydnaviruses from Glyptapanteles parasitic wasps reveals new insights into the evolutionary arms race between host and parasite.
IDEA: Interactive Display for Evolutionary Analyses
Egan, Amy, Mahurkar, Anup, Crabtree, Jonathan, Badger, Jonathan H, Carlton, Jane M, Silva, Joana C
Rasko, David A., Rosovitz, M. J., Myers, Garry S. A., Mongodin, Emmanuel F., Fricke, W. Florian, Gajer, Pawel, ...
Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately...
The HuRef Browser: a web resource for individual human genomics
Axelrod, Nelson, Lin, Yuan, Ng, Pauline C., Stockwell, Timothy B., Crabtree, Jonathan, Huang, Jiaqi, ...
The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between...