Search results for "calling"
showing 10 items of 14 documents
2-methylthiazolidine and 4-ethylguaiacol, male sex pheromone components of the cockroach Nauphoeta cinerea (Dictyoptera, Bladeridae) : A reinvestigat…
1992
49 ref.; International audience; In Nauphoeta cinerea, male calling behavior is associated with sex pheromone release by the sternal glands. The male pheromone that attracts females from a distance is a mixture of 2-methylthiazolidine and 4-ethylguaiacol. It is active at very low concentrations, 0.05 and 0.01 ng, respectively. Two other compounds, 3-hydroxy-2-butanone and 2-methyl-2thiazoline, act at close range, keeping the female in the vicinity of the male. The function of the volatile pheromone and those of previously described contact pheromones are discussed in regard to their possible involvement in the establishment of male dominant-subordinate relationships.
Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
2016
Background: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Results: Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal …
Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data
2017
AbstractThe epigenetics landscape of cells plays a key role in the establishment of cell-type specific gene expression programs characteristic of different cellular phenotypes. Different experimental procedures have been developed to obtain insights into the accessible chromatin landscape including DNase-seq, FAIRE-seq and ATAC-seq. However, current downstream computational tools fail to reliably determine regulatory region accessibility from the analysis of these experimental data. In particular, currently available peak calling algorithms are very sensitive to their parameter settings and show highly heterogeneous results, which hampers a trustworthy identification of accessible chromatin…
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
2016
Various approaches to calling single-nucleotide variants (SNVs) or insertion-or-deletion (indel) mutations have been developed based on next-generation sequencing (NGS). However, most of them are dedicated to a particular type of mutation, e.g. germline SNVs in normal cells, somatic SNVs in cancer/tumor cells, or indels only. In the literature, efficient and integrated callers for both germline and somatic SNVs/indels have not yet been extensively investigated. We present SNVSniffer, an efficient and integrated caller identifying both germline and somatic SNVs/indels from NGS data. In this algorithm, we propose the use of Bayesian probabilistic models to identify SNVs and investigate a mult…
Assessment of computational methods for the analysis of single-cell ATAC-seq data
2019
Abstract Background Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysis presents unique methodological challenges. scATAC-seq experiments sample DNA, which, due to low copy numbers (diploid in humans), lead to inherent data sparsity (1–10% of peaks detected per cell) compared to transcriptomic (scRNA-seq) data (10–45% of expressed genes detected per cell). Such challenges in data generation emphasize the need for informative features to assess cell heterogeneity at the chromatin level. Results We present a benchmarking framework that …
German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing.
2020
We compared the consistency, accuracy and reproducibility of next-generation short read sequencing between ten laboratories involved in food safety (research institutes, state laboratories, universities and companies) from Germany and Austria. Participants were asked to sequence six DNA samples of three bacterial species (Campylobacter jejuni, Listeria monocytogenes and Salmonella enterica) in duplicate, according to their routine in-house sequencing protocol. Four different types of Illumina sequencing platforms (MiSeq, NextSeq, iSeq, NovaSeq) and one Ion Torrent sequencing instrument (S5) were involved in the study. Sequence quality parameters were determined for all data sets and central…
R-Score: A New Parameter to Assess the Quality of Variants’ Calls Assessed by NGS Using Liquid Biopsies
2021
Next-generation sequencing (NGS) has enabled a deeper knowledge of the molecular landscape in non-small cell lung cancer (NSCLC), identifying a growing number of targetable molecular alterations in key genes. However, NGS profiling of liquid biopsies risk for false positive and false negative calls and parameters assessing the quality of NGS calls remains lacking. In this study, we have evaluated the positive percent agreement (PPA) between NGS and digital PCR calls when assessing EGFR mutation status using 85 plasma samples from 82 EGFR-positive NSCLC patients. According to our data, variant allele fraction (VAF) was significantly lower in discordant calls and the median of the absolute va…
Do Unnecessary Tasks Impair Performance Because They Harm Living a Calling? : Testing a Mediation in a Three-Wave Study
2021
This three-wave study explored whether living a calling (at work) mediated the relation between unnecessary tasks (time wasting work tasks) and socio-contextual performance at work (cynicism, organizational citizenship behavior). Participants were 518 Finnish white- and blue-collar employees, who were followed up in 2018, 2019, and 2020. The results of structural equation modeling showed that unnecessary tasks at Time 1 related negatively to living a calling at Time 2, which, in turn, related to cynicism and organizational citizenship behavior at T3. Thus, living a calling mediated the relation between unnecessary tasks and the outcomes. We found no evidence for the moderator role of living…
Genome-wide variant calling in reanalysis of exome sequencing data uncovered a pathogenic TUBB3 variant.
2021
Almost half of all individuals affected by intellectual disability (ID) remain undiagnosed. In the Solve-RD project, exome sequencing (ES) datasets from unresolved individuals with (syndromic) ID (n = 1,472 probands) are systematically reanalyzed, starting from raw sequencing files, followed by genome-wide variant calling and new data interpretation. This strategy led to the identification of a disease-causing de novo missense variant in TUBB3 in a girl with severe developmental delay, secondary microcephaly, brain imaging abnormalities, high hypermetropia, strabismus and short stature. Interestingly, the TUBB3 variant could only be identified through reanalysis of ES data using a genome-wi…
Prefazione al secondo volume dei: Quaderni del Laboratorio Interdisciplinare di ricerca su Corpi, Diritti, Conflitti
2021
Prefazione al secondo volume dei: Quaderni del Laboratorio Interdisciplinare di ricerca su Corpi, Diritti, Conflitti Preface to the second volume of: Papers of the Interdisciplinary Research Laboratory on Bodies, Rights, Conflicts