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E: Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genetics 2011

by Todd J. Treangen, Eduardo P. C. Rocha
"... Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication ..."
Abstract - Cited by 44 (1 self) - Add to MetaCart
outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas

Stochastic mRNA synthesis in mammalian cells

by Arjun Raj, Charles S. Peskin, Daniel Tranchina, Diana Y. Vargas, Sanjay Tyagi - PLOS BIOL , 2006
"... Individual cells in genetically homogeneous populations have been found to express different numbers of molecules of specific proteins. We investigated the origins of these variations in mammalian cells by counting individual molecules of mRNA produced from a reporter gene that was stably integrated ..."
Abstract - Cited by 143 (15 self) - Add to MetaCart
of the bursts. The model showed that increasing the level of transcription factors increases the average size of the bursts rather than their frequency. These results demonstrate that gene expression in mammalian cells is subject to large, intrinsically random fluctuations and raise questions about how cells

A Function Accounting for Training Set Size and Marker Density to Model the Average Accuracy of Genomic Prediction

by Malena Erbe, Birgit Gredler, Franz Reinhold Seefried, Beat Bapst, Henner Simianer , 2013
"... Prediction of genomic breeding values is of major practical relevance in dairy cattle breeding. Deterministic equations have been suggested to predict the accuracy of genomic breeding values in a given design which are based on training set size, reliability of phenotypes, and the number of independ ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
Prediction of genomic breeding values is of major practical relevance in dairy cattle breeding. Deterministic equations have been suggested to predict the accuracy of genomic breeding values in a given design which are based on training set size, reliability of phenotypes, and the number

Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary

by unknown authors
"... Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation ..."
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. Furthermore, we demonstrate that, notwithstanding the remarkable plasticity, there is an upper limit to chromosome-size variation in diploid eukaryotes with linear chromosomes. Strikingly, variation in chromosome size for 886 chromosomes in 68 eukaryotic genomes (including 22 human autosomes) can be viably

Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary

by unknown authors
"... Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation ..."
Abstract - Add to MetaCart
. Furthermore, we demonstrate that, notwithstanding the remarkable plasticity, there is an upper limit to chromosome-size variation in diploid eukaryotes with linear chromosomes. Strikingly, variation in chromosome size for 886 chromosomes in 68 eukaryotic genomes (including 22 human autosomes) can be viably

Boomsma: Genetic determination of telomere size in humans: A twin study of three age groups

by P. Eline Slagboom, Simone Droog, Dorret Boomsma, Am. J. Hum Genet - Am J Hum Genet , 1994
"... Reduction of telomere length has been postulated to be a causal factor in cellular aging. Human telomeres terminate in tandemly arranged repeat arrays consisting of the (TTAGGG) motif. The length of these arrays in cells from human mitotic tissues is inversely related to the age of the donor, indica ..."
Abstract - Cited by 97 (0 self) - Add to MetaCart
fragments (TRFs) in HaeIII-digested genomic DNA from 123 human MZ and DZ twin pairs 2-95 years of age. The average rate of telomere shortening was 31 bp/year, which is similar to that observed by others. Statistical analysis in 115 pairs 2-63 years of age indicates a 78 % heritability for mean TRF length

Of Protein Size and Genomes

by Nereide S. Santos-magalhães, Hélio M. De Oliveira
"... Abstract:- An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized. Genome figures are presented, which support the averag ..."
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the average protein size of a species as a criterion for assessing life complexity. The human gene distribution in the 23 chromosomes is investigated emphasizing the genomic rate, the mean ‘exon ’ length, and the mean ‘exons ’ per gene. It is shown that storing all genes of a single human definitely requires

BIOINFORMATICS GNARE – A Grid-based Server for the Analysis of User Submitted Genomes

by Dinanath Sulakhe, Mustafa Syed, Alexis Rodriguez, Yi Zhang, Elizabeth M. Glass, Margaret F. Romine
"... GNARE (GeNome Analysis Research Environment) is a bioinformatics server that supports both automated and expert-driven (interactive) analysis of user-submitted genomes and metagenomes. These analyses include gene function prediction and development of organism-specific metabolic reconstructions from ..."
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with information from public databases. GNARE uses automated workflows and a Grid-based computational backend, to perform high-throughput analysis of genomes. The use of distributed computing in GNARE allows the analysis of an average-sized prokaryotic genome in less than five hours. Contact:

Genome scan meta-analysis of schizophrenia and bipolar disorder, part II: Schizophrenia

by Douglas F. Levinson, Matthew D. Levinson, Ricardo Segurado, Cathryn M. Lewis - American Journal of Human Genetics , 2003
"... This is the first of three articles on a meta-analysis of genome scans of schizophrenia (SCZ) and bipolar disorder (BPD) that uses the rank-based genome scan meta-analysis (GSMA) method. Here we used simulation to determine the power of GSMA to detect linkage and to identify thresholds of significan ..."
Abstract - Cited by 41 (6 self) - Add to MetaCart
, given the bin’s place in the order of average ranks). GSMA detected linkage with power comparable to or greater than the underlying NPL scores. Weighting for sample size increased power. When no genomewide significant P values were observed, the presence of linkage could be inferred from the number

The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats

by Andrew J. Alverson, Shi Zhuo, Danny W. Rice, Daniel B. Sloan, Jeffrey D. Palmer , 2011
"... The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), an ..."
Abstract - Cited by 1 (1 self) - Add to MetaCart
that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence
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