Beat Wolf

Beat Wolf
University of Applied Sciences and Arts Western Switzerland · iCoSys — Institut des systèmes complexes

PhD

About

21
Publications
2,105
Reads
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101
Citations
Additional affiliations
October 2012 - present
University of Wuerzburg
Position
  • PhD Student

Publications

Publications (21)
Article
Full-text available
Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze...
Article
Current screening methods for factor VIII gene (F8) mutations can reveal the causative alteration in the vast majority of haemophilia A patients. Yet, standard diagnostic methods fail in about 2 % of cases. This study aimed at analysing the entire intronic sequences of the F8 gene in 15 haemophilia A patients by next generation sequencing. All pati...
Article
Full-text available
Lung cancer is currently the leading cause of cancer related mortality due to late diagnosis and limited treatment intervention. Non-coding RNAs are not translated into proteins and have emerged as fundamental regulators of gene expression. Recent studies reported that microRNAs and long non-coding RNAs are involved in lung cancer development and p...
Conference Paper
Full-text available
Ultrascale computing and bioinformatics are two rapidly growing fields with a big impact right now and even more so in the future. The introduction of next generation sequencing pushes current bioinformatics tools and workflows to their limits in terms of performance. This forces the tools to become increasingly performant to keep up with the growi...
Chapter
Images of Historical Vietnamese stone engravings provide historians with a unique opportunity to study the past of the country. However, due to the large heterogeneity of thousands of images regarding both the text foreground and the stone background, it is difficult to use automatic document analysis methods for supporting manual examination, espe...
Article
Full-text available
The current state of the art for automatic transcription of historical manuscripts is typically limited by the requirement of human-annotated learning samples, which are are necessary to train specific machine learning models for specific languages and scripts. Transcription alignment is a simpler task that aims to find a correspondence between tex...
Article
Full-text available
Camera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian time‐dependent observation model for ca...
Article
Allele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allel...
Chapter
Deep excavations are today mainly designed by manually optimising the wall’s geometry, stiffness and strut or anchor layout. In order to better automate this process for sustained excavations, we are exploring the possibility of approximating key values using a machine learning (ML) model instead of calculating them with time-consuming numerical si...
Preprint
Full-text available
Camera traps are an essential tool to quantify the distribution, abundance and behavior of mobile species. As detection probabilities vary greatly among camera trap locations, they must be accounted for when analyzing such data, which is generally done using occupancy models. We introduces a Bayesian Time-dependent Occupancy Model for Camera Trap d...
Article
Full-text available
Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs with...
Preprint
Full-text available
Allele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allel...
Conference Paper
Full-text available
Analysing next generation sequencing data often involves the use of a sequence aligner to map the sequenced reads against a reference. The output of this process is the basis of many downstream analyses and its quality thus critical. Many different alignment tools exist, each with a multitude of options, creating a vast amount of possibilities to a...
Article
Full-text available
To evaluate the role of constitutive epigenetic changes in normal body cells of BRCA1/BRCA2‐mutation negative patients, we have developed a deep bisulfite sequencing assay targeting the promoter regions of 8 tumor suppressor (TS) genes (BRCA1, BRCA2, RAD51C, ATM, PTEN, TP53, MLH1, RB1) and the estrogene receptor gene (ESR1), which plays a role in t...
Thesis
The field of genetics faces a lot of challenges and opportunities in both research and diagnostics due to the rise of next generation sequencing (NGS), a technology that allows to sequence DNA increasingly fast and cheap. NGS is not only used to analyze DNA, but also RNA, which is a very similar molecule also present in the cell, in both cases prod...
Conference Paper
Full-text available
Next generation sequencing produces an ever increasing amount of data, requiring increasingly fast computing infrastructures to keep up. We present GNATY, a collection of tools for NGS data analysis, aimed at optimizing parts of the sequence analysis process to reduce the hardware requirements. The tools are developed with efficiency in mind, using...
Conference Paper
Full-text available
Building Ultrascale computer systems is a hard problem, not yet solved and fully explored. Combining the computing resources of multiple organizations, often in different administrative domains with heterogeneous hardware and diverse demands on the system, requires new tools and frameworks to be put in place. During previous work we developed POP-J...
Conference Paper
Full-text available
Cost of whole genome sequencing is rapidly approaching 1000 euro, putting it within reach of amateur geneticists, scientifically curious consumers as well as teachers developing hands-on *omics training courses. Current direct-to-consumer offers do not give consumers the possibility to analyze the actual data, try various alignment algorithms and t...
Conference Paper
With the generalization of network-enabled devices such as smart phones, slate computers and tablets, new challenges await the eHealth research community. Indeed, these devices should not only integrate seamlessly into the daily workflow, but their usage must appear as ordinary as possible to the different caregivers. Using RESTful architectures, i...

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Projects

Projects (2)
Project
Offering the best in class NGS data analysis software for desktops and servers.