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MITOS: improved de novo metazoan mitochondrial genome annotation.
About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. ThisExpand
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tRNAdb 2009: compilation of tRNA sequences and tRNA genes
One of the first specialized collections of nucleic acid sequences in life sciences was the ‘compilation of tRNA sequences and sequences of tRNA genes’ (http://www.trna.uni-bayreuth.de). Here, anExpand
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metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.
The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs withinExpand
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Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements
Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondaryExpand
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A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.
About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approachesExpand
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Structure of transfer RNAs: similarity and variability
Transfer RNAs (tRNAs) are ancient molecules whose origin goes back to the beginning of life on Earth. Key partners in the ribosome‐translation machinery, tRNAs read genetic information on messengerExpand
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Genomic and transcriptomic heterogeneity of colorectal tumours arising in Lynch syndrome
Colorectal cancer (CRC) arising in Lynch syndrome (LS) comprises tumours with constitutional mutations in DNA mismatch repair genes. There is still a lack of whole‐genome and transcriptome studies ofExpand
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A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus.
Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves as an emerging model in ecotoxicological studies. We report here on a survey sequencing of itsExpand
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DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control
Although Burkitt lymphomas and follicular lymphomas both have features of germinal center B cells, they are biologically and clinically quite distinct. Here we performed whole-genome bisulfite,Expand
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Hepatitis C-related hepatocellular carcinoma in the era of new generation antivirals
Hepatitis C virus infection is a major cause of hepatocellular carcinoma worldwide. Interferon has been the major antiviral treatment, yielding viral clearance in approximately half of patients. NewExpand
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