Volume 6, issue 1, December 2011
Beyond the Tree of Life
65 articles in this issue
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Accurate state estimation from uncertain data and models: an application of data assimilation to mathematical models of human brain tumors
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Purine biosynthesis in archaea: variations on a theme
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The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations
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Transcription factor binding sites are highly enriched within microRNA precursor sequences
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On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
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Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins
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Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene
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The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria
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A network-based approach to classify the three domains of life
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Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria
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Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data
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Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome
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Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins
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Biased gene transfer and its implications for the concept of lineage
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A mathematical model for targeting chemicals to tissues by exploiting complex degradation
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Families of transposable elements, population structure and the origin of species
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Expression levels of microRNAs are not associated with their regulatory activities
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Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy
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The public goods hypothesis for the evolution of life on Earth
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Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species
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Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
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Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
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CREST - a large and diverse superfamily of putative transmembrane hydrolases
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Energetics and genetics across the prokaryote-eukaryote divide
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From the scala naturae to the symbiogenetic and dynamic tree of life
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How stands the Tree of Life a century and a half after The Origin?
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Structural influence of gene networks on their inference: analysis of C3NET
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A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis
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Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns
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Interplay of recombination and selection in the genomes of Chlamydia trachomatis
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ConReg-R: Extrapolative recalibration of the empirical distribution of p-values to improve false discovery rate estimates
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A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
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Causal graph-based analysis of genome-wide association data in rheumatoid arthritis
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Why eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity
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MicroRNA expression in multiple myeloma is associated with genetic subtype, isotype and survival
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Evolutionary plasticity determination by orthologous groups distribution
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Statistical methods for detecting periodic fragments in DNA sequence data
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Functional analysis of archaeal MBF1 by complementation studies in yeast
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Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models
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The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon
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