Search results for "Bioinformatics"
showing 10 items of 1632 documents
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
2020
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species…
Cancer: Clinical Background and Key Challenges
2011
This chapter is aimed at a wide audience ranging from biologists to medical students and cancer specialists. It provides a comprehensive overview of systems approaches to the pathology and treatment of cancer. In particular, it addresses diagnosis and therapy by interconnecting various aspects of cancer at both the molecular and clinical level, and contrasts the unifying features of malignancies with the daunting diversity of cancer types, stages, and evolutionary processes during treatment. The importance is emphasized of both prevention and innovative treatments in reducing the cancer burden, and of early detection as the link between these two major areas. It sets the stage for analysis …
Non-invasive localization of atrial ectopic beats by using simulated body surface P-wave integral maps
2017
Non-invasive localization of continuous atrial ectopic beats remains a cornerstone for the treatment of atrial arrhythmias. The lack of accurate tools to guide electrophysiologists leads to an increase in the recurrence rate of ablation procedures. Existing approaches are based on the analysis of the P-waves main characteristics and the forward body surface potential maps (BSPMs) or on the inverse estimation of the electric activity of the heart from those BSPMs. These methods have not provided an efficient and systematic tool to localize ectopic triggers. In this work, we propose the use of machine learning techniques to spatially cluster and classify ectopic atrial foci into clearly diffe…
Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
2017
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; M…
Expression of the genetic suppressor element 24.2 (GSE24.2) decreases DNA damage and oxidative stress in X-linked dyskeratosis congenita cells.
2014
This is an open-access article distributed under the terms of the Creative Commons Attribution License.-- et al.
snoRNPs Regulate Telomerase Activity in Neuroblastoma and Are Associated with Poor Prognosis
2013
AbstractAmplification of the MYCN oncogene is strongly associated with poor prognosis in neuroblastoma (NB). In addition to MYCN amplification, many studies have focused on identifying patients with a poor prognosis based on gene expression profiling. The majority of prognostic signatures today are comprised of large gene lists limiting their clinical application. In addition, although of prognostic significance,most of these signatures fail to identify cellular processes that can explain their relation to prognosis. Here, we determined prognostically predictive genes in a data set containing 251 NBs. Gene Ontology analysis was performed on significant genes with a positive hazard ratio to …
tert-Butyl N-benzyl-N-[4-(4-fluorobenzoylmethyl)-2-pyridyl]carbamate
2008
In the crystal structure of the title compound, C25H25FN2O3, the pyridine ring makes dihedral angles of 75.1 (3), 39.4 (3) and 74.6 (3)° with the phenyl ring, the carbamate plane and the 4-fluorophenyl ring, respectively. The phenyl ring makes dihedral angles of 77.2 (3) and 23.6 (3)° with the carbamate plane and the 4-fluorophenyl ring, respectively. The 4-fluorophenyl ring is perpendicular to the carbamate plane, the dihedral angle between them being 89.5 (3)°.
tert-ButylN-(4-methyl-2-pyridyl)carbamate
2008
The crystal structure of the title compound, C11H16N2O2, contains two crystallographically independent molecules forming dimers by pairs of intermolecular N—H...N hydrogen bonds. The two molecules are related by a pseudo-twofold axis. The dihedral angle between the pyridine ring and the carbamate plane differs in the two molecules [12.1 (3) and 3.5 (3)°].
tert-Butyl N-benzyl-N-(4-methyl-2-pyridyl)carbamate
2008
In the crystal structure of the title compound, C18H22N2O2, the pyridine ring makes dihedral angles of 83.71 (6) and 9.2 (1)° with the phenyl ring and the carbamate plane, respectively. The phenyl ring and the carbamate plane are nearly perpendicular to one another, with a dihedral angle of 87.17 (7)°.
2,4-Di-tert-butyl-6-({[2-(di-methyl-amino)-eth-yl](2-hy-droxy-benz-yl)amino}-meth-yl)phenol.
2014
The title compound, C26H40N2O2, has both its N atoms in trigonal-pyramidal geometries. The molecular structure is stabilized by O—H...N and C—H...O hydrogen bonds. In the crystal, C—H...π interactions lead to the formation of a supramolecular helical chain along theb-axis direction.