Improving uptake of screening for colorectal cancer: a study on invitation strategies and different test kit use

Objective The aim of this study was to compare the uptake of mail-delivered tests for colorectal cancer screening. We assessed the effect of an advance notification letter and a reminder letter, and analysed the proportion of inappropriately handled tests. Materials and methods Fifteen thousand randomly selected residents of Latvia aged 50–74 years were allocated to receive one of three different test systems: either a guaiac faecal occult blood test (gFOBT) or one of two laboratory-based immunochemical tests (FIT) – FOB Gold or OC-Sensor. Half of the target population received an advance notification letter; all nonresponders were sent a reminder letter. Results The uptake of screening was…

Characteristic Topological Features of Promoter Capture Hi-C Interaction Networks

Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify the biologically significant features, many questions still remain open. In this paper we describe analysis methods of Hi-C (specifically PCHi-C) interaction networks that are strictly focused on topological properties of these networks. The main questions we are trying to answer are: (1) can topological properties of interaction networks for different cell types alone be sufficient to distinguish between these types, and what the most important of such propert…

PASSIM – an open source software system for managing information in biomedical studies

Abstract Background One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweig…

Graph-based network analysis of transcriptional regulation pattern divergence in duplicated yeast gene pairs

The genome and interactome of Saccharomyces cerevisiae have been characterized extensively over the course of the past few decades. However, despite many insights gained over the years, both functional studies and evolutionary analyses continue to reveal many complexities and confounding factors in the construction of reliable transcriptional regulatory network models. We present here a graph-based technique for comparing transcriptional regulatory networks based on network motif similarity for gene pairs. We construct interaction graphs for duplicated transcription factor pairs traceable to the ancestral whole-genome duplication as well as other paralogues in Saccharomyces cerevisiae. We c…

Layout algorithms of graph-like diagrams for GRADE windows graphic editors

We propose a set of layout operations ensuring flexible and convenient interactive editing of communication diagrams and nested entity-relationship models having textual labels on connections. The set includes several procedures for incremental diagram layout. Tools for fully automatic layout and for direct manual painting of graphic primitives are also integrated in a single system. In this way we have filled to some extent the gap between both extremal levels of editing.

Graph-based characterisations of cell types and functionally related modules in promoter capture Hi-C Data

Topological structure analysis of chromatin interaction networks.

Abstract Background Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify biologically significant features, many questions still remain open, in particular regarding potential biological significance of various topological features that are characteristic for chromatin interaction networks. Results It has been previously observed that promoter capture Hi-C (PCHi-C) interaction networks tend to separate easily into well-defined connected components that can be related to certain biological functionality, however, …

Network motif-based analysis of regulatory patterns in paralogous gene pairs

Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focu…