Jana Hertel - Academia.edu (original) (raw)

Papers by Jana Hertel

PWMs to identify snoRNA boxes. Position-specific weight matrices (PWMs) used to identify boxes of... more PWMs to identify snoRNA boxes. Position-specific weight matrices (PWMs) used to identify boxes of both classes of snoRNAs. (PDF 64 kb)

Copyright information:Taken from "Computational RNomics of Drosophilids&q... more Copyright information:Taken from "Computational RNomics of Drosophilids"http://www.biomedcentral.com/1471-2164/8/406BMC Genomics 2007;8():406-406.Published online 8 Nov 2007PMCID:PMC2216035.Az hits in for two different classification thresholds with the corresponding distribution of the input alignments (relative to the current FlyBase gene track from the UCSC Table Browser, April 2004). In addition, the corresponding distribution for the human ENCODE regions [22] is shown. The numbers differ slightly from ref. [22] since here we have normalized them to 100%. Percentages for the 5'-UTRs are not given due to the very small bar areas; the values are (from left to right): 1.24%, 1.69%, 1.70% and 0.6%. In general, the distribution of structured RNAs closely follows that of conserved sequence, i.e., there is no strong enrichment of RNAz hits in a particular annotation class. The most striking difference between human and fly is the much larger fraction of intronic RNAz hits in the ENCODE data.

Copyright information:Taken from "The expansion of the metazoan microRNA ... more Copyright information:Taken from "The expansion of the metazoan microRNA repertoire"BMC Genomics 2006;7():25-25.Published online 15 Feb 2006PMCID:PMC1388199.Copyright © 2006 Hertel et al; licensee BioMed Central Ltd. (a) Gene tree and most plausible reconstructed history of the cluster. The fourth member of the cluster, , evolves rapidly in flies. Its homology with /is likely but this hairpin might also have evolved . (b) The two most plausible reconstructions for the history of the cluster. Scenario (1) postulates four paralogs in the ancestral vertebrate, where, presumably after the first duplication, one lineage either lost or gained in the middle position of the cluster. Subsequently, in this scenario one copy of the three-membered cluster was lost in actinopterygians, while the two-membered clusters were lost in tetrapoda. Scenario (2) postulates three paralogs in the ancestral vertebrate and the independent loss of the in two distinct clusters in the teleosts. (c) Duplication history of the cluster reconstructed from genomic position information and the gene tree.

Copyright information:Taken from "The expansion of the metazoan microRNA ... more Copyright information:Taken from "The expansion of the metazoan microRNA repertoire"BMC Genomics 2006;7():25-25.Published online 15 Feb 2006PMCID:PMC1388199.Copyright © 2006 Hertel et al; licensee BioMed Central Ltd. Despite the short sequences, the major clades are well separated in this phylogenetic network: there are two vertebrate groups, and , both of which show a tetrapod and a teleost branch; arthropoda and nematoda are also clearly separated; only the basal deuterostomes do not fit very well due to their diverged sequences. (b) Phylogenetic network of sequences, which occur in three clusters each consisting of two miRNAs genes (see inset). A tandem duplication of the ancestral sequence gave rise to a single cluster which was duplicated subsequently. Not all details of the duplication history can be resolved due to the short sequence length. It is clear, however, that the duplication events pre-dated the last common ancestor of tetrapoda and teleosts. It is plausible to associate these cluster duplications with the genome duplications at the origin of the vertebrate lineage. Networks were reconstructed using the neighbor net method.

Relevant to box C/D snoRNAs heatmap. The.csv files contain the box C/D snoRNA families of the pla... more Relevant to box C/D snoRNAs heatmap. The.csv files contain the box C/D snoRNA families of the plant species that are represented in the heatmaps. (CSV 601 kb)

Targets. Complete archive of the rRNA and snRNA targets is provided. These are.txt files, which i... more Targets. Complete archive of the rRNA and snRNA targets is provided. These are.txt files, which include RNAsnoop and Plexy output. (ZIP 139 kb)

List of Genomes and Accession Numbers. The list of all genomes with the accession numbers are add... more List of Genomes and Accession Numbers. The list of all genomes with the accession numbers are added here for all the plants including red algae (.csv format). (CSV 284 kb)

Alignments (in.aln format) representing co-evolution of conserved snoRNA-rRNA target interactions... more Alignments (in.aln format) representing co-evolution of conserved snoRNA-rRNA target interactions. (ZIP 109 kb)

ePoPE output details of box H/ACA snoRNAs. Detailed analysis of the predicted box H/ACA snoRNAs, ... more ePoPE output details of box H/ACA snoRNAs. Detailed analysis of the predicted box H/ACA snoRNAs, lost genes, and lost families as outputted by ePoPE. (ODT 16.9 kb)

ePoPE output details of box C/D snoRNAs. Detailed analysis of the predicted box C/D snoRNAs, lost... more ePoPE output details of box C/D snoRNAs. Detailed analysis of the predicted box C/D snoRNAs, lost genes, and lost families as outputted by ePoPE. (ODT 176 kb)

Relevant to box H/ACA snoRNAs heatmap. The.csv files contain the box H/ACA snoRNA families of the... more Relevant to box H/ACA snoRNAs heatmap. The.csv files contain the box H/ACA snoRNA families of the plant species that are represented in the heatmaps. (CSV 211 kb)

doi:10.1093/nar/gkp600 Accurate and efficient reconstruction of deep

he increase of bodyplan complexityin early bilaterian evolution is corre-lates with the advent an... more he increase of bodyplan complexityin early bilaterian evolution is corre-lates with the advent and diversificationof microRNAs. These small RNAs guideanimal development by regulating tem-poral transitions in gene expressioninvolved in cell fate choices and transi-tions between pluripotency and differenti-ation. One of the two known microRNAswhose origins date back before the bilate-rian ancestor is mir-100. In Bilateria, itappears stably associated in polycistronictranscripts with let-7 and mir-125, twokey regulators of development. In verte-brates, these three microRNA familieshave expanded to form a complex systemof developmental regulators. In this con-tribution, we disentangle the evolutionaryhistory of the let-7 locus, which wasrestructured independently in nematodes,platyhelminths, and deuterostomes. Thefoundation of a second let-7 locus inthe common ancestor of vertebrates andurochordates predates the vertebrate-specific genome duplications, which thencaused a rapid expansion...

Journal of integrative bioinformatics, Jan 5, 2017

The miRBase currently reports more than 25,000 microRNAs in several hundred genomes that belong t... more The miRBase currently reports more than 25,000 microRNAs in several hundred genomes that belong to more than 1000 families of homologous sequences. Quantitative investigations of miRNA gene evolution requires the construction of data sets that are consistent in their coverage and include those genomes that are of interest in a given study. Given the size and structure of data, this can be achieved only with the help of a fully automatic pipeline that improves the available seed alignments, extends the set of available sequences by homology search, and reliably identifies true positive homology search results. Here we describe the current progress towards such a system, emphasizing the task of improving and completing the initial seed alignment.

Copyright information:Taken from "The expansion of the metazoan microRNA ... more Copyright information:Taken from "The expansion of the metazoan microRNA repertoire"BMC Genomics 2006;7():25-25.Published online 15 Feb 2006PMCID:PMC1388199.Copyright © 2006 Hertel et al; licensee BioMed Central Ltd. Despite the short sequences, the major clades are well separated in this phylogenetic network: there are two vertebrate groups, and , both of which show a tetrapod and a teleost branch; arthropoda and nematoda are also clearly separated; only the basal deuterostomes do not fit very well due to their diverged sequences. (b) Phylogenetic network of sequences, which occur in three clusters each consisting of two miRNAs genes (see inset). A tandem duplication of the ancestral sequence gave rise to a single cluster which was duplicated subsequently. Not all details of the duplication history can be resolved due to the short sequence length. It is clear, however, that the duplication events pre-dated the last common ancestor of tetrapoda and teleosts. It is plausible to associate these cluster duplications with the genome duplications at the origin of the vertebrate lineage. Networks were reconstructed using the neighbor net method.

doi:10.1093/nar/gkp600 Accurate and efficient reconstruction of deep

Journal of integrative bioinformatics, Jan 5, 2017