Ulrich Bodenhofer

Fachhochschule Oberösterreich | fh-ooe · School of Informatics, Communications and Media

Understanding the relationship between protein sequence and structure is one of the great challenges in biology. In the case of the ubiquitous coiled-coil motif, structure and occurrence have been described in extensive detail, but there is a lack of insight into the rules that govern oligomerization, i.e. how many α-helices form a given coiled coi...

Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, the so-called exemplars. We provide an R implementation of this promising new clustering technique to account for the ubiquity of R in bioinformatics. This article...

KeBABS provides a powerful, flexible, and easy to use framework for kernel-based analysis of biological sequences in R. It includes efficient implementations of the most important sequence kernels, also including variants that allow for taking sequence annotations and positional information into account. KeBABS seamlessly integrates three common su...

Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega, and MUSCLE. The p...

OBJECTIVES Machine learning methods potentially provide a highly accurate and detailed assessment of expected individual patient risk before elective cardiac surgery. Correct anticipation of this risk allows for the improved counselling of patients and avoidance of possible complications. We therefore investigated the benefit of modern machine lear...

Background and objectives Fainting is a well-known side effect of blood donation. Such adverse experiences can diminish the return rate for further blood donations. Identifying factors associated with fainting could help prevent adverse incidents during blood donation. Materials and methods Data of 85,040 blood donations from whole blood and apher...

Regression is the task of calculating a numerical value based on an object’s set of characteristics. One important sub-branch consists of methods that learn regression functions from example data. The following chapter will provide an overview of the most basic concepts and methods of this type of data-driven regression. While we refer to the previ...

Classification, the task of assigning objects to a given set of categories, is used in almost every field. One important sub-branch of classification consists of methods that learn classification functions from example data. The following chapter will provide an overview of the most basic concepts and methods of this type of data-driven classificat...

Background MicroRNAs are small non-coding RNAs with pivotal regulatory functions in multiple cellular processes. Their significance as molecular predictors for breast cancer was demonstrated in the past 15 years. The aim of this study was to elucidate the role of hsa-miR-3651 for predicting of local control (LC) in early breast cancer. Results By...

Background: In order to characterize the various subtypes of breast cancer more precisely and improve patients selection for breast conserving therapy (BCT), molecular profiling has gained importance over the past two decades. MicroRNAs, which are small non-coding RNAs, can potentially regulate numerous downstream target molecules and thereby inte...

Objectives Juvenile idiopathic arthritis (JIA) is the most common class of childhood rheumatic diseases, with distinct disease subsets that may have diverging pathophysiological origins. Both adaptive and innate immune processes have been proposed as primary drivers, which may account for the observed clinical heterogeneity, but few high-depth stud...

Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease, with a strongly debated pathophysiological origin. Both adaptive and innate immune processes have been proposed as primary drivers, which may account for the observed clinical heterogeneity, but few high-depth studies have been performed. Here we profiled the adapti...

Chromatography is one of the most versatile unit operations in the biotechnological industry. Regulatory initiatives like Process Analytical Technology and Quality by Design led to the implementation of new chromatographic devices. Those represent an almost inexhaustible source of data. However, the analysis of large datasets is complicated, and si...

Rabies is caused by lyssaviruses, and is one of the oldest known zoonoses. In recent years, more than 21,000 nucleotide sequences of rabies viruses (RABV), from the prototype species rabies lyssavirus, have been deposited in public databases. Subsequent phylogenetic analyses in combination with metadata suggest geographic distributions of RABV. How...

We present an approach for convolving single-nucleotide variants (SNVs) with a position kernel in order to augment SNVs with information about close-by SNVs. By means of the Position-Dependent Kernel Association Test (PODKAT), we demonstrate the potential of this approach to leverage the analysis of rare and private SNVs. Finally, we also provide s...

We employ machine learning to predict the 30-days mortality after heart valve surgeries from demographic and preoperative parameters. We achieve AUC values of almost 84%, while the standard EuroSCORE I provides an AUC of only slightly more than 70% for the given cohort. These results indicate (1) that state-of-the-art machine learning is superior t...

Recent studies have revealed that immune repertoires contain a substantial fraction of public clones, which may be defined as Ab or TCR clonal sequences shared across individuals. It has remained unclear whether public clones possess predictable sequence features that differentiate them from private clones, which are believed to be generated largel...

Recent studies have revealed that immune repertoires contain a substantial fraction of public clones, which are defined as antibody or T-cell receptor (TCR) clonal sequences shared across individuals. As of yet, it has remained unclear whether public clones possess predictable sequence features that separate them from private clones, which are beli...

Background: A long-term analysis by the Early Breast Cancer Trialist Group (EBCTG) revealed a strong correlation between local control and cancer-specific mortality. MicroRNAs (miRs), short (20–25 nucleotides) non-coding RNAs, have been described as prognosticators and predictors for breast cancer in recent years. The aim of the current study was t...

Emerging resistance towards antimicrobials and the lack of new antibiotic drug candidates underscore the need for optimization of current diagnostics and therapies to diminish the evolution and spread of multidrug-resistance. As the antibiotic resistance status of a bacterial pathogen is defined by its genome, resistance profiling by applying next-...

Background A long-term analysis by the Early Breast Cancer Trialist Group (EBCTG) revealed a strong correlation between local control and cancer-specific mortality. MicroRNAs (miRs), short (20–25 nucleotides) non-coding RNAs, have been described as prognosticators and predictors for breast cancer in recent years. The aim of the current study was to...

The pharmaceutical industry is faced with steadily declining R&D efficiency which results in fewer drugs reaching the market despite increased investment. A major cause for this low efficiency is the failure of drug candidates in late-stage development owing to safety issues or previously undiscovered side-effects. We analyzed to what extent gene e...

The pharmaceutical industry is faced with steadily declining R&D efficiency which results in fewer drugs reaching the market despite increased investment. A major cause for this low efficiency is the failure of drug candidates in late-stage development owing to safety issues or previously undiscovered side-effects. We analyzed to what extent gene e...

Integrating gene expression profiles with certain proteins can improve our understanding of the fundamental mechanisms in protein–ligand binding. This paper spotlights the integration of gene expression data and target prediction scores, providing insight into mechanism of action (MoA). Compounds are clustered based upon the similarity of their pre...

The glycosylphosphatidylinositol (GPI)-anchored molecule CD59 has been implicated in the modulation of T cell responses, but the underlying molecular mechanism of CD59 influencing T cell signaling remained unclear. Here we analyzed Jurkat T cells stimulated via anti-CD3ε- or anti-CD59-coated surfaces, using time-resolved single-cell Ca(2+) imaging...

Graded properties of binary and unary fuzzy connectives (valued in MTL△MTL△-algebras) are studied, including graded monotony, a generalized Lipschitz property, commutativity, associativity, unit and null elements, and the dominance relation between fuzzy connectives. The apparatus of Fuzzy Class Theory (or higher-order fuzzy logic) is employed as a...

Rank correlation measures are intended to measure to which extent there is a monotonic association between two observables. While they are mainly designed for ordinal data, they are not ideally suited for noisy numerical data. In order to better account for noisy data, a family of rank correlation measures has previously been introduced that replac...

Functional heterogeneity has been considered as a principle mechanism of the adaptive immune response. Here we developed an imaging-based method for studying Ca2+ signaling at the single-cell level as a function of time and stimulus. Jurkat T cells were exposed to stimulatory anti-CD3ε- or anti-CD59-coated surfaces and individual Ca2+ time traces w...

To gain deeper insights into principles of cell biology, it is essential to understand how cells reorganize their genomes by chromatin remodeling. We analyzed chromatin remodeling on next generation sequencing data from resting and activated T cells to determine a whole-genome chromatin remodeling landscape. We consider chromatin remodeling in term...

Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correcti...

Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obt...

*Overview* | Coiled coils are usually described as consisting of two up to seven α-helices that are wrapped around each other. They can associate as either homomeric or heteromeric structures and bind in parallel or antiparallel topologies. Another characteristic of all coiled coils is the periodic recurrence of a sequence [abcdefg]n called heptad...

The implicational interpretation of fuzzy rules has received little attention in real-world applications so far. This is largely due to the fact that ensuring continuity of the resulting function is not a straightforward task. This paper targets this subject. Departing from consistent linguistic descriptions/rule bases, we introduce sufficient cond...

The paper studies graded properties of MTL_Delta-valued binary connectives, focusing on conjunctive connectives such as t-norms, uninorms, aggregation operators, or quasicopulas. The graded properties studied include monotony, a generalized Lipschitz property, unit and null elements, commutativity, associativity, and idempotence. Finally, a graded...

Biclustering of transcriptomic data groups genes and samples simultaneously. It is emerging as a standard tool for extracting knowledge from gene expression measurements. We propose a novel generative approach for biclustering called 'FABIA: Factor Analysis for Bicluster Acquisition'. FABIA is based on a multiplicative model, which accounts for lin...

Elevation of intracellular free Calcium is part of the key signals during T-cell activation by antigens. Following activation a remarkable variety of this signals - ranging from infrequent spikes to sustained oscillations and plateaus - is shaped by the interactions of the different Calcium sources and sinks in the cell.We present an approach to st...

This article presents an approach for finding displacements of print layers from sequences of sample images semi-automatically with the aim to simplify and shorten the setup of inspection systems for printing processes in which the perfect alignment of print layers cannot be guaranteed. The basic idea behind the proposed approach is to identify pix...

This paper demonstrates that several known sequence kernels can be expressed in a unified framework in which the position specificity is modeled by fuzzy equivalence relations. In addition to this interpretation, we address the practical issues of positive semi- definiteness, computational complexity, and the extraction of inter- pretable features...

The present paper introduces an approach to construct lexicographic compositions of similarity-based fuzzy orderings. This construction is demonstrated by means of non-trivial examples. As this is a crucial fea- ture of lexicographic composition, the preservation of linearity is studied in detail. We obtain once again that it is essential for meani...

This paper studies fuzzy relations in the graded framework of Fuzzy Class Theory (FCT). This includes (i) rephrasing existing work on graded properties of binary fuzzy relations in the framework of Fuzzy Class Theory and (ii) generalizing existing crisp results on fuzzy relations to the graded framework. Our particular aim is to demonstrate that Fu...

This paper introduces strict fuzzy orderings in the framework of similarity-based fuzzy orderings, i.e. where a context of similarity/indistinguishability is given by means of a fuzzy equivalence relation. We consider how to construct strict fuzzy orderings from partial fuzzy orderings and vice versa. The appropriateness of the concepts introduced...

The goal of this paper is to demonstrate that established rank correlation measures are not ideally suited for measuring rank correlation for numerical data that are perturbed by noise. We propose to use robust rank correlation measures based on fuzzy orderings. We demonstrate that the new measures overcome the robustness problems of existing rank...

The aim of this paper is to present a general framework for comparing fuzzy sets with respect to a general class of fuzzy orderings. This approach includes known techniques based on generalizing the crisp linear ordering of real numbers by means of the extension principle, however, in its general form, it is applicable to any fuzzy subsets of any k...

In Part I of this series of papers [ibid. 15, No. 2, 201–218 (2008; Zbl 1160.03036)], a general approach for ordering fuzzy sets with respect to fuzzy orderings was presented. Part I also highlighted three limitations of this approach. The present paper addresses these limitations and proposes solutions for overcoming them. We first consider a fuzz...

Graded properties of binary and unary fuzzy connectives (valued in MTL-algebras) are studied, including graded monotony, a generalized Lipschitz property, commutativity, associativity, unit and null elements, and the dominance relation between fuzzy connectives. The apparatus of Fuzzy Class Theory (or higher-order fuzzy logic) is employed as a tool...

This contribution is intended as a position paper that favors the viewpoint that inference based on deductive rules (i.e., the rules are interpreted using fuzzy implication) can indeed be considered as a valuable inference scheme in real-world applications. For this purpose, we highlight the basic concepts behind the most common fuzzy inference sch...

The present paper gives a state-of-the-art overview of representation and construction results for fuzzy weak orders. We do not assume that the underlying domain is finite. Instead, we concentrate on results that hold in the most general case that the underlying domain is possibly infinite. This paper presents three fundamental representation resul...

Without Abstract

Abstract This paper aims to demonstrate that estab- lished rank correlation measures are not ide- ally suited for measuring rank correlation for numerical data that are perturbed by noise. We propose a robust rank correlation mea- sure on the basis of fuzzy orderings. The su- periority of the new measure is demonstrated by means of illustrative exa...

This paper generalizes the well-known representations of fuzzy preorders and similarities according to Valverde to the graded framework of Fuzzy Class Theory (FCT). The results demonstrate that FCT is a powerful tool and that new results and interesting constructions can be obtained by considering fuzzy relations in the graded framework of FCT.

The present paper introduces an approach to construct lexicographic compositions of similarity-based fuzzy orderings. This construc- tion is demonstrated by means of non-trivial examples. As this is a crucial feature of lexicographic composition, the preservation of linearity is studied in detail. We obtain once again that it is essential for meani...

A grammatical framework is presented that augments context-free production rules with semantic production rules that rely on fuzzy relations as representations of fuzzy natural language concepts. It is shown how the well-known technique of syntax-driven semantic analysis can be used to infer from an expression in a language defined in such a semant...

Kernels have proven useful for machine learning, data mining, and computer vision as they provide a means to derive non-linear variants of learning, optimization or classification strategies from linear ones. A central question when applying a kernel-based method is the choice and the design of the kernel function. This paper provides a novel view...

The present paper gives a state-of-the-art overview of general representation results for fuzzy weak orders. We do not assume that the underlying domain of alternatives is finite. Instead, we concentrate on results that hold in the most general case that the underlying domain is possibly infinite. This paper presents three fundamental representatio...

This contribution provides a comprehensive overview on the theoretical framework of aggregating fuzzy relations under the premise of preserving underlying transitivity conditions. As such it discusses the related property of dominance of aggregation operators. After a thorough introduction of all necessary and basic properties of aggregation operat...

This paper addresses the added value that is provided by using distance-based fuzzy relations in flexible query answering. To use distances and/or concepts of gradual similarity in that domain is not new. Within the last ten years, however, results in the theory of fuzzy relations have emerged that permit a smooth and pragmatic, yet ex- pressive an...

This contribution is concerned with the interpretability of fuzzy rule-based systems. While this property is widely considered to be a crucial one in fuzzy rule-based modeling, a more detailed formal investigation of what "interpretability" actually means is not available. So fax, interpretability has most often been associated with rather heuristi...

Abstract A vital problem,for fuzzy classifier systems of the Michigan type is the conflict of competition and co- operation of rules. Whereas the classical approach of a classifier system circumvents this complicacy by the total lack of collaboration of classifiers, the fuzzifica- tion approach has to deal with it. This paper proposes a solution to...

This paper introduces and justifies a similarity- based concept of strict fuzzy orderings and pro- vides constructions how fuzzy orderings can be transformed into strict fuzzy orderings and vice versa. We demonstrate that there is a meaning- ful correspondence between fuzzy orderings and strict fuzzy orderings. Unlike the classical case, however, w...

This contribution is concerned with a detailed investigation of linearity axioms for fuzzy orderings. Different existing concepts are evaluated with respect to three fundamental correspondences from the classical case—linearizability of partial orderings, intersection representation, and one-to-one correspondence between linearity and maximality. A...