Ulrich Bodenhofer

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

Professor

About

142
Publications
33,635
Reads
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3,446
Citations
Citations since 2017
16 Research Items
1661 Citations
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2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
Additional affiliations
July 2006 - present
Johannes Kepler University Linz
Position
  • Professor (Associate)
January 2000 - December 2004
Position
  • teaching in machine learning and bioinformatics (see http://www.bioinf.jku.at/teaching/
Education
May 1996 - December 1998
Johannes Kepler University Linz
Field of study
  • Many-valued logic
October 1990 - May 1996
Johannes Kepler University Linz
Field of study
  • Applied Mathematics

Publications

Publications (142)
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Chapter
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...
Chapter
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Preprint
Full-text available
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...
Article
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Article
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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-...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
*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...
Article
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...
Conference Paper
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
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...
Conference Paper
Full-text available
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...
Chapter
Full-text available
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...
Article
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Conference Paper
Full-text available
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...
Article
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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.
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
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...
Conference Paper
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...
Conference Paper
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...
Conference Paper
Full-text available
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
Full-text available
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...
Article
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...
Article
Full-text available
This paper describes the benefits of using fuzzy orderings in flexible query answering systems. We provide a brief overview of those results from the theory of fuzzy orderings that are necessary to couple fuzzy orderings with flexible querying in a meaningful synergistic way. As one case study, we discuss a simple and pragmatic variant of a flexibl...
Article
Full-text available
This article advocates the viewpoint that a close cooperation between the artificial intelli- gence community and researchers studying context-aware mobile and ubiquitous appli- cations will be indispensable for the future success of context-aware applications. The notions of context and context-awareness are introduced. It is shown that typical is...