Integrated interdisciplinary workflows for research on historical newspapers: Perspectives from humanities scholars, computer scientists, and librarians.

This article considers the interdisciplinary opportunities and challenges of working with digital cultural heritage, such as digitized historical newspapers, and proposes an integrated digital hermeneutics workflow to combine purely disciplinary research approaches from computer science, humanities, and library work. Common interests and motivations of the above-mentioned disciplines have resulted in interdisciplinary projects and collaborations such as the NewsEye project, which is working on novel solutions on how digital heritage data is (re)searched, accessed, used, and analyzed. We argue that collaborations of different disciplines can benefit from a good understanding of the workflows and traditions of each of the disciplines involved but must find integrated approaches to successfully exploit the full potential of digitized sources.

Interactive exploration of heterogeneous biological networks with Biomine Explorer.

Summary: Biomine Explorer is a web application that enables interactive exploration of large heterogeneous biological networks constructed from selected publicly available biological knowledge sources. It is built on top of Biomine, a system which integrates cross-references from several biological databases into a large heterogeneous probabilistic network. Biomine Explorer offers user-friendly interfaces for search, visualization, exploration and manipulation as well as public and private storage of discovered subnetworks with permanent links suitable for inclusion into scientific publications.

Adaptive Heartbeat Modeling for Beat-to-Beat Heart Rate Measurement in Ballistocardiograms.

We present a method for measuring beat-to-beat heart rate from ballistocardiograms acquired with force sensors. First, a model for the heartbeat shape is adaptively inferred from the signal using hierarchical clustering. Then, beat-to-beat intervals are detected by finding positions where the heartbeat shape best fits the signal.

The use of weighted graphs for large-scale genome analysis.

There is an acute need for better tools to extract knowledge from the growing flood of sequence data. For example, thousands of complete genomes have been sequenced, and their metabolic networks inferred. Such data should enable a better understanding of evolution.

Unobtrusive online monitoring of sleep at home.

We describe an online sleep monitoring service, based on unobtrusive ballistocardiography (BCG) measurement in an ordinary bed. The novelty of the system is that the sleep tracking web application is based on measurements from a fully unobtrusive sensor. The BCG signal is measured with a piezoelectric film sensor under the mattress topper, and sent to the web server for analysis.

Biomine: predicting links between biological entities using network models of heterogeneous databases.

Background: Biological databases contain large amounts of data concerning the functions and associations of genes and proteins. Integration of data from several such databases into a single repository can aid the discovery of previously unknown connections spanning multiple types of relationships and databases.

Results: Biomine is a system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations.

SegMine workflows for semantic microarray data analysis in Orange4WS.

Background: In experimental data analysis, bioinformatics researchers increasingly rely on tools that enable the composition and reuse of scientific workflows. The utility of current bioinformatics workflow environments can be significantly increased by offering advanced data mining services as workflow components. Such services can support, for instance, knowledge discovery from diverse distributed data and knowledge sources (such as GO, KEGG, PubMed, and experimental databases).

Modeling reveals that dynamic regulation of c-FLIP levels determines cell-to-cell distribution of CD95-mediated apoptosis.

The expression levels of caspase-8 inhibitory c-FLIP proteins play an important role in regulating death receptor-mediated apoptosis, as their concentration at the moment when the death-inducing signaling complex (DISC) is formed determines the outcome of the DISC signal. Experimental studies have shown that c-FLIP proteins are subject to dynamic turnover and that their stability and expression levels can be rapidly altered. Even though the influence of c-FLIP on the apoptotic behavior of a single cell has been captured in mathematical simulation studies, the effect of c-FLIP turnover and stability has not been investigated.

Constrained hidden Markov models for population-based haplotyping.

Background: Haplotype Reconstruction is the problem of resolving the hidden phase information in genotype data obtained from laboratory measurements. Solving this problem is an important intermediate step in gene association studies, which seek to uncover the genetic basis of complex diseases. We propose a novel approach for haplotype reconstruction based on constrained hidden Markov models.

HaploRec: efficient and accurate large-scale reconstruction of haplotypes.

Background: Haplotypes extracted from human DNA can be used for gene mapping and other analysis of genetic patterns within and across populations. A fundamental problem is, however, that current practical laboratory methods do not give haplotype information. Estimation of phased haplotypes of unrelated individuals given their unphased genotypes is known as the haplotype reconstruction or phasing problem.

TreeDT: tree pattern mining for gene mapping.

We describe TreeDT, a novel association-based gene mapping method. Given a set of disease-associated haplotypes and a set of control haplotypes, TreeDT predicts likely locations of a disease susceptibility gene. TreeDT extracts, essentially in the form of haplotype trees, information about historical recombinations in the population: A haplotype tree constructed at a given chromosomal location is an estimate of the genealogy of the haplotypes.

A survey of data mining methods for linkage disequilibrium mapping.

Data mining methods are gaining more interest as potential tools in mapping and identification of complex disease loci. The methods are well suited to large numbers of genetic marker loci produced by high-throughput laboratory analyses, but also might be useful for clarifying the phenotype definitions prior to more traditional mapping analyses. Here, the current data mining-based methods for linkage disequilibrium mapping and phenotype analyses are reviewed.

Statistical evaluation of the Predictive Toxicology Challenge 2000-2001.

Motivation: The development of in silico models to predict chemical carcinogenesis from molecular structure would help greatly to prevent environmentally caused cancers. The Predictive Toxicology Challenge (PTC) competition was organized to test the state-of-the-art in applying machine learning to form such predictive models.

Results: Fourteen machine learning groups generated 111 models.