A spin-wave frequency doubler by domain wall oscillation

We present a new mechanism for spin-wave excitation using a pinned domain wall which is forced to oscillate at its eigenfrequency and radiates spin waves. The domain wall acts as a frequency doubler, as the excited spin waves have twice the frequency of the domain wall oscillation. The investigations have been carried out using micromagnetic simulations and enable the determination of the main characteristics of the excited spin-waves such as frequency, wavelength, and velocity. This behavior is understood by the oscillation in the perpendicular magnetization which shows two anti-nodes oscillating out of phase with respect to each other.Comment: 8 pages, 3 figure

Magnetic domain-wall motion by propagating spin waves

We found by micromagnetic simulations that the motion of a transverse wall (TW) type domain wall in magnetic thin-film nanostripes can be manipulated via interaction with spin waves (SWs) propagating through the TW. The velocity of the TW motion can be controlled by changes of the frequency and amplitude of the propagating SWs. Moreover, the TW motion is efficiently driven by specific SW frequencies that coincide with the resonant frequencies of the local modes existing inside the TW structure. The use of propagating SWs, whose frequencies are tuned to those of the intrinsic TW modes, is an alternative approach for controlling TW motion in nanostripes

Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data : From Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011 Vienna, Austria. 15 July 2011

First published by BioMed Central: Schultheiss, Sebastian J.; Jean, Géraldine; Behr, Jonas; Bohnert, Regina; Drewe, Philipp; Görnitz, Nico; Kahles, André; Mudrakarta, Pramod; Sreedharan, Vipin T.; Zeller, Georg; Rätsch, Gunnar: Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data - In: BMC Bioinformatics. - ISSN 1471-2105 (online). - 12 (2011), suppl. 11, art. A7. - doi:10.1186/1471-2105-12-S11-A7

Persistence and Availability of Web Services in Computational Biology

We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences

Motivation: Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules

Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications

To date only a fraction of the genetic footprint of thyroid function has been clarified. We report a genome-wide association study meta-analysis of thyroid function in up to 271,040 individuals of European ancestry, including reference range thyrotropin (TSH), free thyroxine (FT4), free and total triiodothyronine (T3), proxies for metabolism (T3/FT4 ratio) as well as dichotomized high and low TSH levels. We revealed 259 independent significant associations for TSH (61% novel), 85 for FT4 (67% novel), and 62 novel signals for the T3 related traits. The loci explained 14.1%, 6.0%, 9.5% and 1.1% of the total variation in TSH, FT4, total T3 and free T3 concentrations, respectively. Genetic correlations indicate that TSH associated loci reflect the thyroid function determined by free T3, whereas the FT4 associations represent the thyroid hormone metabolism. Polygenic risk score and Mendelian randomization analyses showed the effects of genetically determined variation in thyroid function on various clinical outcomes, including cardiovascular risk factors and diseases, autoimmune diseases, and cancer. In conclusion, our results improve the understanding of thyroid hormone physiology and highlight the pleiotropic effects of thyroid function on various diseases

Mutations with pathogenic potential in proteins located in or at the composite junctions of the intercalated disk connecting mammalian cardiomyocytes: a reference thesaurus for arrhythmogenic cardiomyopathies and for Naxos and Carvajal diseases

In the past decade, an avalanche of findings and reports has correlated arrhythmogenic ventricular cardiomyopathies (ARVC) and Naxos and Carvajal diseases with certain mutations in protein constituents of the special junctions connecting the polar regions (intercalated disks) of mature mammalian cardiomyocytes. These molecules, apparently together with some specific cytoskeletal proteins, are components of (or interact with) composite junctions. Composite junctions contain the amalgamated fusion products of the molecules that, in other cell types and tissues, occur in distinct separate junctions, i.e. desmosomes and adherens junctions. As the pertinent literature is still in an expanding phase and is obviously becoming important for various groups of researchers in basic cell and molecular biology, developmental biology, histology, physiology, cardiology, pathology and genetics, the relevant references so far recognized have been collected and are presented here in the following order: desmocollin-2 (Dsc2, DSC2), desmoglein-2 (Dsg2, DSG2), desmoplakin (DP, DSP), plakoglobin (PG, JUP), plakophilin-2 (Pkp2, PKP2) and some non-desmosomal proteins such as transmembrane protein 43 (TMEM43), ryanodine receptor 2 (RYR2), desmin, lamins A and C, striatin, titin and transforming growth factor-β3 (TGFβ3), followed by a collection of animal models and of reviews, commentaries, collections and comparative studies