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...
Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum (2008)
Albang, Richard, Albermann, Kaj, Badger, Jonathan H., Daran, Jean-Marc, Driessen, Arnold J.M., ...
Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin...
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
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...
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...
Derrick E. Fouts, Emmanuel F. Mongodin, Robert E. Mandrell, William G. Miller, David A. Rasko, Jacques Ravel, ...
Although the single genome sequence of the human Campylobacter jejuni yielded some insight, comparison of multiple species of the same genus elucidated greater understanding of virulence mechanisms.
Derrick E. Fouts, Emmanuel F. Mongodin, Robert E. Mandrell, William G. Miller, David A. Rasko, Jacques Ravel, ...
Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are...
Picking fruit from the tree of life: Comments on taxanomic sampling and the quartet method (2001)
A topic of recent interest and controversy in the field of systematic biology is the value of “taxonomic sampling”, the practice of adding additional sequences (taxa) to an analysis to improve...
Li, Ming, Badger, Jonathan H., Chen, Xin, Kwong, Sam, Kearney, Paul, Zhang, Haoyong
Motivation: Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length...
Haney, Paul J., Badger, Jonathan H., Buldak, Gerald L., Reich, Claudia I., Woese, Carl R., Olsen, Gary J.
The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M....
Fouts, Derrick E, Mongodin, Emmanuel F, Mandrell, Robert E, Miller, William G, Rasko, David A, Ravel, Jacques, ...
Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are...
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...
Haney, Paul J., Badger, Jonathan H., Buldak, Gerald L., Reich, Claudia I., Woese, Carl R., Olsen, Gary J.
The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M....
Fouts, Derrick E, Mongodin, Emmanuel F, Mandrell, Robert E, Miller, William G, Rasko, David A, Ravel, Jacques, ...
Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are...
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...
Badger, Jonathan H., Hoover, Timothy R., Brun, Yves V., Weiner, Ronald M., Laub, Michael T., Alexandre, Gladys, ...
The dimorphic prosthecate bacteria (DPB) are α-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this...
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment
Palenik, Brian, Ren, Qinghu, Dupont, Chris L., Myers, Garry S., Heidelberg, John F., Badger, Jonathan H., ...
Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary...
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...
Fouts, Derrick E., Tyler, Heather L., DeBoy, Robert T., Daugherty, Sean, Ren, Qinghu, Badger, Jonathan H., ...
We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a...
Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum
Wu, Dongying, Raymond, Jason, Wu, Martin, Chatterji, Sourav, Ren, Qinghu, Graham, Joel E., ...
In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence...
IDEA: Interactive Display for Evolutionary Analyses
Egan, Amy, Mahurkar, Anup, Crabtree, Jonathan, Badger, Jonathan H, Carlton, Jane M, Silva, Joana C
Yang, Joyce C., Madupu, Ramana, Durkin, A. Scott, Ekborg, Nathan A., Pedamallu, Chandra S., Hostetler, Jessica B., ...
Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring...