Robert G. Beiko, Robert L. Charlebois
A simulation test bed for hypotheses of genome evolution
A simulation test bed for hypotheses of genome evolution (2008)
Robert G. Beiko, Robert L. Charlebois
Motivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution and lateral genetic transfer....
The Impact of Reticulate Evolution on Genome Phylogeny (2008)
Beiko, Robert G., Doolittle, W. Ford, Charlebois, Robert L.
Genome phylogenies are used to build tree-like representations of evolutionary relationships among genomes. However, in condensing the phylogenetic signals within a set of genomes down to a single...
Corresponding Editor: B. Golding. (2007)
Robert L. Charlebois, Rama K. Singh, Ghislaine Allard, Cynthia Chow, Fabrice Confalonieri, ...
Gene content and organization of a 281-kbp
A simulation test bed for hypotheses of genome evolution (2007)
Beiko, Robert G., Charlebois, Robert L.
Motivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution and lateral genetic transfer....
A simulation test bed for hypotheses of genome evolution (2007)
Beiko, Robert G., Charlebois, Robert L.
Motivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution and lateral genetic transfer....
A simulation test bed for hypotheses of genome evolution (2007)
Beiko, Robert G., Charlebois, Robert L.
Motivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution, and lateral genetic transfer....
Zhaxybayeva, Olga, Gogarten, J. Peter, Charlebois, Robert L., Doolittle, W. Ford, Papke, R. Thane
Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between...
Zhaxybayeva, Olga, Gogarten, J. Peter, Charlebois, Robert L., Doolittle, W. Ford, Papke, R. Thane
Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between...
Bapteste, Eric, Charlebois, Robert L, MacLeod, Dave, Brochier, Céline
Abstract Background The origin of the nuclear compartment has been extensively debated, leading to several alternative views on the evolution of the eukaryotic nucleus. Until recently, too little...
MacLeod, Dave, Charlebois, Robert L, Doolittle, Ford, Bapteste, Eric
Abstract Background When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent...
Beiko, Robert G, Charlebois, Robert L
Abstract Background The multitude of motif detection algorithms developed to date have largely focused on the detection of patterns in primary sequence. Since sequence-dependent DNA structure and...
Computing prokaryotic gene ubiquity: Rescuing the core from extinction (2004)
Charlebois, Robert L., Doolittle, W. Ford
The genomic core concept has found several uses in comparative and evolutionary genomics. Defined as the set of all genes common to (ubiquitous among) all genomes in a phylogenetically coherent...
Albers, Sonja-V., Elferink, Marieke G.L., Charlebois, Robert L., Sensen, Christoph W., Driessen, Arnold J.M., Konings, Wil N.
The archaeon Sulfolobus solfataricus grows optimally at 80°C and pH 2.5 to 3.5 on carbon sources such as yeast extracts, tryptone, and various sugars. Cells rapidly accumulate glucose. This...
Andrew St, Robert L. Charlebois
Anonymous probes from the genome of Halobacterium salinarium GRB and 12 gene probes were hybridized to the cosmid clones representing the chromosome and plasmids of Halobacterium salinarium GRB and...
Jean, Andrew St, Trieselmann, Bruce A., Charlebois, Robert L.
We have constructed a complete, five-enzyme restriction map of the genome of the archaeon Halobacterium sp. GRB, based on a set of 84 overlapping cosmid clones. Fewer than 30 kbp, in three gaps,...
Typescript. Also microfilm. 16 mm.
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Napoli, Alessandra, Van Der Oost, John, Sensen, Christoph W., Charlebois, Robert L., Rossi, Mosé, Ciaramella, Maria
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite...
Albers, Sonja-V., Elferink, Marieke G. L., Charlebois, Robert L., Sensen, Christoph W., Driessen, Arnold J. M., Konings, Wil N.
The archaeon Sulfolobus solfataricus grows optimally at 80°C and pH 2.5 to 3.5 on carbon sources such as yeast extracts, tryptone, and various sugars. Cells rapidly accumulate glucose. This...
Clarke, G. D. Paul, Beiko, Robert G., Ragan, Mark A., Charlebois, Robert L.
Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are...
Computing prokaryotic gene ubiquity: Rescuing the core from extinction
Charlebois, Robert L., Doolittle, W. Ford
The genomic core concept has found several uses in comparative and evolutionary genomics. Defined as the set of all genes common to (ubiquitous among) all genomes in a phylogenetically coherent...
Weighted Genome Trees: Refinements and Applications†
Gophna, Uri, Doolittle, W. Ford, Charlebois, Robert L.
There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear...
Bapteste, Eric, Charlebois, Robert L, MacLeod, Dave, Brochier, Céline
An analysis of the taxonomic distribution, evolutionary rates and phylogenies of 65 proteins related to the nuclear pore complex shows high heterogeneity of evolutionary rates between these proteins.
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
She, Qunxin, Singh, Rama K., Confalonieri, Fabrice, Zivanovic, Yvan, Allard, Ghislaine, Awayez, Mariana J., ...
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable...
Napoli, Alessandra, Van Der Oost, John, Sensen, Christoph W., Charlebois, Robert L., Rossi, Mosé, Ciaramella, Maria
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite...
Albers, Sonja-V., Elferink, Marieke G. L., Charlebois, Robert L., Sensen, Christoph W., Driessen, Arnold J. M., Konings, Wil N.
The archaeon Sulfolobus solfataricus grows optimally at 80°C and pH 2.5 to 3.5 on carbon sources such as yeast extracts, tryptone, and various sugars. Cells rapidly accumulate glucose. This...
Clarke, G. D. Paul, Beiko, Robert G., Ragan, Mark A., Charlebois, Robert L.
Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are...
Computing prokaryotic gene ubiquity: Rescuing the core from extinction
Charlebois, Robert L., Doolittle, W. Ford
The genomic core concept has found several uses in comparative and evolutionary genomics. Defined as the set of all genes common to (ubiquitous among) all genomes in a phylogenetically coherent...
Weighted Genome Trees: Refinements and Applications†
Gophna, Uri, Doolittle, W. Ford, Charlebois, Robert L.
There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear...
Bapteste, Eric, Charlebois, Robert L, MacLeod, Dave, Brochier, Céline
An analysis of the taxonomic distribution, evolutionary rates and phylogenies of 65 proteins related to the nuclear pore complex shows high heterogeneity of evolutionary rates between these proteins.
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
Zhaxybayeva, Olga, Gogarten, J. Peter, Charlebois, Robert L., Doolittle, W. Ford, Papke, R. Thane
Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between...