Xylophones in Thailand and Java: A Comparative Phenomenology of Musical Instruments (2008)
Asian Music - Volume 39, Number 2, Summer/Fall 2008
Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA
Campbell, Allan, Mrázek, Jan, Karlin, Samuel
Our basic observation is that each genome has a characteristic “signature” defined as the ratios between the observed dinucleotide frequencies and the frequencies expected if neighbors were...
A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes
Karlin, Samuel, Brocchieri, Luciano, Mrázek, Jan, Campbell, Allan M., Spormann, Alfred M.
We provide data and analysis to support the hypothesis that the ancestor of animal mitochondria (Mt) and many primitive amitochondrial (a-Mt) eukaryotes was a fusion microbe composed of a...
Strand compositional asymmetry in bacterial and large viral genomes
Several bacterial genomes exhibit preference for G over C on the DNA leading strand extending from the origin of replication to the ter-region in the genomes of Escherichia coli, Mycoplasma...
Compositional differences within and between eukaryotic genomes
Eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. Comparisons within and between species sample sequences are...
Highly expressed and alien genes of the Synechocystis genome
Mrázek, Jan, Bhaya, Devaki, Grossman, Arthur R., Karlin, Samuel
Comparisons of codon frequencies of genes to several gene classes are used to characterize highly expressed and alien genes on the Synechocystis PCC6803 genome. The primary gene classes include the...
Predicted highly expressed (PHX) and putative alien genes determined by codon usages are characterized in the genome of Deinococcus radiodurans (strain R1). Deinococcus radiodurans (DEIRA) can...
Predicted Highly Expressed Genes of Diverse Prokaryotic Genomes
Our approach in predicting gene expression levels relates to codon usage differences among gene classes. In prokaryotic genomes, genes that deviate strongly in codon usage from the average gene but...
Characterizations of Highly Expressed Genes of Four Fast-Growing Bacteria
Karlin, Samuel, Mrázek, Jan, Campbell, Allan, Kaiser, Dale
Predicted highly expressed (PHX) genes are characterized for the completely sequenced genomes of the four fast-growing bacteria Escherichia coli, Haemophilus influenzae, Vibrio cholerae, and Bacillus...
Amino acid runs in eukaryotic proteomes and disease associations
Karlin, Samuel, Brocchieri, Luciano, Bergman, Aviv, Mrázek, Jan, Gentles, Andrew J.
We present a comparative proteome analysis of the five complete eukaryotic genomes (human, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana), focusing...
Frequent oligonucleotide motifs in genomes of three streptococci
Mrázek, Jan, Gaynon, Lisa H., Karlin, Samuel
Complete genomes of three closely related Gram-positive bacteria Streptococcus pyogenes, Strepto coccus pneumoniae and Lactococcus lactis are analyzed for abundances of short DNA sequence motifs...
Predicting gene expression levels from codon biases in α-proteobacterial genomes
Karlin, Samuel, Barnett, Melanie J., Campbell, Allan M., Fisher, Robert F., Mrázek, Jan
Predicted highly expressed (PHX) genes in five currently available high G+C complete α-proteobacterial genomes are analyzed. These include: the nitrogen-fixing plant symbionts Sinorhizobium meliloti...
Comparative analysis of gene expression among low G+C gram-positive genomes
Karlin, Samuel, Theriot, Julie, Mrázek, Jan
We present a comparative analysis of predicted highly expressed (PHX) genes in the low G+C Gram-positive genomes of Bacillus subtilis, Bacillus halodurans, Listeria monocytogenes, Listeria innocua,...
Predicted highly expressed genes in archaeal genomes
Karlin, Samuel, Mrázek, Jan, Ma, Jiong, Brocchieri, Luciano
Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and...
Karlin, Samuel, Brocchieri, Luciano, Campbell, Allan, Cyert, Martha, Mrázek, Jan
Bacterial, archaeal, yeast, and fly genomes are compared with respect to predicted highly expressed (PHX) genes and several genomic properties. There is a striking difference in the status of PHX...
Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA
Campbell, Allan, Mrázek, Jan, Karlin, Samuel
Our basic observation is that each genome has a characteristic “signature” defined as the ratios between the observed dinucleotide frequencies and the frequencies expected if neighbors were...
A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes
Karlin, Samuel, Brocchieri, Luciano, Mrázek, Jan, Campbell, Allan M., Spormann, Alfred M.
We provide data and analysis to support the hypothesis that the ancestor of animal mitochondria (Mt) and many primitive amitochondrial (a-Mt) eukaryotes was a fusion microbe composed of a...
Strand compositional asymmetry in bacterial and large viral genomes
Several bacterial genomes exhibit preference for G over C on the DNA leading strand extending from the origin of replication to the ter-region in the genomes of Escherichia coli, Mycoplasma...
Compositional differences within and between eukaryotic genomes
Eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. Comparisons within and between species sample sequences are...
Highly expressed and alien genes of the Synechocystis genome
Mrázek, Jan, Bhaya, Devaki, Grossman, Arthur R., Karlin, Samuel
Comparisons of codon frequencies of genes to several gene classes are used to characterize highly expressed and alien genes on the Synechocystis PCC6803 genome. The primary gene classes include the...
Predicted highly expressed (PHX) and putative alien genes determined by codon usages are characterized in the genome of Deinococcus radiodurans (strain R1). Deinococcus radiodurans (DEIRA) can...
Predicted Highly Expressed Genes of Diverse Prokaryotic Genomes
Our approach in predicting gene expression levels relates to codon usage differences among gene classes. In prokaryotic genomes, genes that deviate strongly in codon usage from the average gene but...
Characterizations of Highly Expressed Genes of Four Fast-Growing Bacteria
Karlin, Samuel, Mrázek, Jan, Campbell, Allan, Kaiser, Dale
Predicted highly expressed (PHX) genes are characterized for the completely sequenced genomes of the four fast-growing bacteria Escherichia coli, Haemophilus influenzae, Vibrio cholerae, and Bacillus...
Amino acid runs in eukaryotic proteomes and disease associations
Karlin, Samuel, Brocchieri, Luciano, Bergman, Aviv, Mrázek, Jan, Gentles, Andrew J.
We present a comparative proteome analysis of the five complete eukaryotic genomes (human, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana), focusing...
Frequent oligonucleotide motifs in genomes of three streptococci
Mrázek, Jan, Gaynon, Lisa H., Karlin, Samuel
Complete genomes of three closely related Gram-positive bacteria Streptococcus pyogenes, Strepto coccus pneumoniae and Lactococcus lactis are analyzed for abundances of short DNA sequence motifs...
Predicting gene expression levels from codon biases in α-proteobacterial genomes
Karlin, Samuel, Barnett, Melanie J., Campbell, Allan M., Fisher, Robert F., Mrázek, Jan
Predicted highly expressed (PHX) genes in five currently available high G+C complete α-proteobacterial genomes are analyzed. These include: the nitrogen-fixing plant symbionts Sinorhizobium meliloti...
Comparative analysis of gene expression among low G+C gram-positive genomes
Karlin, Samuel, Theriot, Julie, Mrázek, Jan
We present a comparative analysis of predicted highly expressed (PHX) genes in the low G+C Gram-positive genomes of Bacillus subtilis, Bacillus halodurans, Listeria monocytogenes, Listeria innocua,...
Predicted highly expressed genes in archaeal genomes
Karlin, Samuel, Mrázek, Jan, Ma, Jiong, Brocchieri, Luciano
Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and...
Karlin, Samuel, Brocchieri, Luciano, Campbell, Allan, Cyert, Martha, Mrázek, Jan
Bacterial, archaeal, yeast, and fly genomes are compared with respect to predicted highly expressed (PHX) genes and several genomic properties. There is a striking difference in the status of PHX...
Distinguishing features of δ-proteobacterial genomes
Karlin, Samuel, Brocchieri, Luciano, Mrázek, Jan, Kaiser, Dale
We analyzed several features of five currently available δ-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. The δ...
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...
Mrázek, Jan, Kreutmayer, Simone B., Grässer, Friedrich A., Polacek, Norbert, Hüttenhofer, Alexander
Non-protein-coding RNAs (ncRNAs) fulfill a wide range of cellular functions from protein synthesis to regulation of gene expression. Identification of novel regulatory ncRNAs by experimental...
Distinctive features of large complex virus genomes and proteomes
More than a dozen large DNA viruses exceeding 240-kb genome size were recently discovered, including the “giant” mimivirus with a 1.2-Mb genome size. The detection of mimivirus and other large...
Simple sequence repeats in prokaryotic genomes
Mrázek, Jan, Guo, Xiangxue, Shah, Apurva
Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA...