Marcus H. Stoiber
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View article: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework Open
Direct nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of modified…
View article: Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework
Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework Open
Direct nanopore-based RNA sequencing can be used to detect post-transcriptional base modifications, such as m6A methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challe…
View article: Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements Open
View article: Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish Open
Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-…
View article: *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments Open
Background Over the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotati…
View article: Age-related gene expression in luminal epithelial cells is driven by a microenvironment made from myoepithelial cells
Age-related gene expression in luminal epithelial cells is driven by a microenvironment made from myoepithelial cells Open
Luminal epithelial cells in the breast gradually alter gene and protein expression with age, appearing to lose lineage-specificity by acquiring myoepithelial-like characteristics. We hypothesize that the luminal lineage is particularly sen…
View article: Early transcriptional response pathways in <i>Daphnia magna</i> are coordinated in networks of crustacean‐specific genes
Early transcriptional response pathways in <i>Daphnia magna</i> are coordinated in networks of crustacean‐specific genes Open
Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor l…
View article: BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal
BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal Open
All current nanopore basecalling applications begin with the segmentation of raw signal into discrete events, which are ultimately processed into called bases. We propose the basecRAWller algorithm, a pair of unidirectional recurrent neura…
View article: <i>De novo</i>Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
<i>De novo</i>Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing Open
Advances in nanopore sequencing technology have enabled investigation of the full catalogue of covalent DNA modifications. We present the first algorithm for the identification of modified nucleotides without the need for prior training da…
View article: Diverse Hormone Response Networks in 41 Independent<i>Drosophila</i>Cell Lines
Diverse Hormone Response Networks in 41 Independent<i>Drosophila</i>Cell Lines Open
Steroid hormones induce cascades of gene activation and repression with transformative effects on cell fate . Steroid transduction plays a major role in the development and physiology of nearly all metazoan species, and in the progression …
View article: Extensive cross-regulation of post-transcriptional regulatory networks in <i>Drosophila</i>
Extensive cross-regulation of post-transcriptional regulatory networks in <i>Drosophila</i> Open
In eukaryotic cells, RNAs exist as ribonucleoprotein particles (RNPs). Despite the importance of these complexes in many biological processes, including splicing, polyadenylation, stability, transportation, localization, and translation, t…
View article: Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility Open
\n\t\t\t\t\tFasting glucose and insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in …
View article: Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility Open
View article: Biological Networks: Dynamics, Mechanisms and Responses
Biological Networks: Dynamics, Mechanisms and Responses Open
The study of biological networks has been central to our understanding of life and its complex, dynamic nature. The elucidation of molecular networks began with the discovery and characterization of key cellular processes including metabol…