Open Access Published by De Gruyter

Volume 1 Issue 1

Issue of Journal of Integrative Bioinformatics

Contents
Journal Overview

Open Access September 30, 2016

Ontology-Assisted Database Integration to Support Natural Language Processing and Biomedical Data-mining

Jean-Luc Verschelde, Mariana Casella Dos Santos, Tom Deray, Barry Smith, Werner Ceusters

Page range: 1-10

More Download PDF

Abstract

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language.

Open Access September 30, 2016

Visual Understanding of Metabolic Pathways Across Organisms Using Layout in Two and a Half Dimensions

Ulrik Brandes, Tim Dwyer, Falk Schreiber

Page range: 11-26

More Download PDF

Abstract

We propose a method for visualizing a set of related metabolic pathways across organisms using 2 1/2 dimensional graph visualization. Interdependent, twodimensional layouts of each pathway are stacked on top of each other so that biologists get a full picture of subtle and significant differences among the pathways. The (dis)similarities between pathways are expressed by the Hamming distances of the underlying graphs which are used to compute a stacking order for the pathways. Layouts are determined by a global layout of the union of all pathway graphs using a variant of the proven Sugiyama approach for layered graph drawing. Our variant layout approach allows edges to cross if they appear in different graphs.

Open Access September 30, 2016

Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net

Mika Matsui, Sachie Fujita, Shunichi Suzuki, Hiroshi Matsuno, Satoru Miyano

Page range: 27-37

More Download PDF

Abstract

Matsuno et al.[1] modeled and simulated that multicellular patterning by the Drosophila Delta-Notch signaling pathway by using the software “Genomic Object Net” which was developed based on hybrid functional Petri net (HFPN) architecture. In this model, cellular formation is fixed throughout the simulation. This paper constructs an HFPN model of the Xenopus cell cycle pathway, which includes the mechanism for cell division control as well as checkpoint processes. This model simulates dynamic cell division processes of the early Xenopus embryo, including the changes in cell division cycles from synchronous to asynchronous.

Open Access September 30, 2016

A Multi-Scale Modeling Concept and Computational Tools for the Integrative Analysis of Stationary Metabolic Data

Eric von Lieres, Sören Petersen, Wolfgang Wiechert

Page range: 38-51

More Download PDF

Abstract

Metabolic Engineering aims at the systematic analysis and targeted manipulation of the metabolism in biotechnologically utilized microorganisms [1,2]. Recently, consistent stationary in vivo data sets of intracellular metabolite concentrations, fluxes and specific enzyme activities have become available for this purpose [3,4]. For the integrative analysis of the metabolic data at hand, a novel multi-scale modeling concept, computeralgebraic methods and efficient numerical algorithms are proposed. The available metabolic data are typically afflicted with comparatively large measurement errors. Therefore, reliable comprehensive error estimations are essential for the reasonable interpretation of consecutive outcomes, such as simulation results. The concepts, methods and algorithms are first presented as universal methods and subsequently applied to the anaplerotic regulation in lysine-producing Corynebacterium glutamicum. A multi-scale model is set up, fitted to the available experimental data and validated by the prediction of further experiments. This model is capable of forecasting the quantitative effect of changes in the specific activity of anaplerotic enzymes, namely phosphoenolpyruvate carboxylase, pyruvate carboxylase and phosphoenolpyruvate carboxykinase, on lysine productivity and yield.

Open Access September 30, 2016

Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework

M. Dünßer, R. Lampidis, S. Schmidt, D. Seipel, T. Dandekar

Page range: 52-63

More Download PDF

Abstract

Integration of data in pathogenomics is achieved here considering three different levels of cellular complexity: (i) genome and comparative genomics, (ii) enzyme cascades and pathway analysis, (iii) networks including metabolic network analysis. After direct sequence annotation exploiting tools for protein domain annotation (e.g. AnDOM) and analysis of regulatory elements (e.g. the RNA analyzer tool) the analysis results from extensive comparative genomics are integrated for the first level, pathway alignment adds data for the pathway level, elementary mode analysis and metabolite databanks add to the third level of cellular complexity. For efficient data integration of all data the XML based platform myBSMLStudio2003 is discussed and developed here. It integrates XQuery capabilities, automatic scripting updates for sequence annotation and a JESS expert system shell for functional annotation. In the context of genome annotation platforms in place (GenDB, PEDANT) these different tools and approaches presented here allow improved functional genome annotation as well as data integration in pathogenomics.

Open Access September 30, 2016

Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif

Lesley J. Collins, Thomas J. Macke, David Penny

Page range: 64-79

More Download PDF

Abstract

Non-coding RNAs (ncRNAs) contain both characteristic secondary-structure and short sequence motifs. However, “complex” ncRNAs (RNA bound to proteins in ribonucleoprotein complexes) can be hard to identify in genomic sequence data. Programs able to search for ncRNAs were previously limited to ncRNA molecules that either align very well or have highly conserved secondary-structure. The RNAmotif program uses additional information to find ncRNA gene candidates through the design of an appropriate “descriptor” to model sequence motifs, secondary-structure and protein/RNA binding information. This enables searches of those ncRNAs that contain variable secondary-structure and limited sequence motif information. Applying the biologically-based concept of “positive and negative controls” to the RNAmotif search technique, we can now go beyond the testing phase to successfully search real genomes, complete with their background noise and related molecules. Descriptors are designed for two “complex” ncRNAs, the U5snRNA (from the spliceosome) and RNaseP RNA, which successfully uncover these sequences from some eukaryotic genomes. We include explanations about the construction of the input “descriptors” from known biological information, to allow searches for other ncRNAs. RNAmotif maximizes the input of biological knowledge into a search for an ncRNA gene and now allows the investigation of some of the hardest-to-find, yet important, genes in some very interesting eukaryotic organisms.

Open Access September 30, 2016

Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization

Guido Dieterich, Dirk W. Heinz, Joachim Reichelt

Page range: 80-89

More Download PDF

Abstract

The 3D structures of biomacromolecules stored in the Protein Data Bank [1] were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT [2] entries as well InterPro [3] domains and function sites with the corresponding 3D-structures. OMIM [4] (Online Mendelian Inheritance in Man) records, containing information of genetic disorders, were extracted and linked to the structures. The exhaustive all-against-all 3D structure comparison of protein structures stored in DALI [5] was condensed into single files for each PDB entry. Results are stored in XML format facilitating its incorporation into related software. The resulting annotation of the protein structures allows functional sites to be identified upon visualization.

Open Access September 30, 2016

Genlight: Interactive high-throughput sequence analysis and comparative genomics

Michael Beckstette, Jens T. Mailänder, Richard J. Marhöfer, Alexander Sczyrba, Enno Ohlebusch, Robert Giegerich, Paul M. Selzer

Page range: 90-107

More Download PDF

Abstract

With rising numbers of fully sequenced genomes the importance of comparative genomics is constantly increasing. Although several software systems for genome comparison analyses do exist, their functionality and flexibility is still limited, compared to the manifold possible applications. Therefore, we developed Genlight(http://piranha.techfak.uni-bielefeld.de.), a Client/Server based program suite for large scale sequence analysis and comparative genomics. Genlight uses the object relational database system PostgreSQL together with a state of the art data representation and a distributed execution approach for large scale analysis tasks. The system includes a wide variety of comparison and sequence manipulation methods and supports the management of nucleotide sequences as well as protein sequences. The comparison methods are complemented by a large variety of visualization methods for the assessment of the generated results. In order to demonstrate the suitability of the system for the treatment of biological questions, Genlight was used to identify potential drug and vaccine targets of the pathogen Helicobacter pylori.

Open Access September 30, 2016

Integrating Genomic and Proteomic Data: The Integr8 Project

Manuela Pruess, Paul Kersey, Rolf Apweiler

Page range: 108-115

More Download PDF

Abstract

Integr8 (http://www.ebi.ac.uk/integr8/) has been developed to provide an integration layer for the exploitation of genomic and proteomic data. High-quality databases from major bioinformatics centres in Europe are included, and some core data and the relationships of biological entities to each other and to entries in other databases are stored. Thus, a framework exists that allows for new kinds of data to be integrated, and an entity-centric view of complete genomes and proteomes is offered. Integr8 is an automatically populated database, providing different entry points to the data, depending on the user’s entity of interest. The Proteome Analysis database for statistical analysis and the Genome Reviews for annotated genome information are the main developments within the Integr8 project. With the BioMart application, an interactive querying tool for performing customisable proteome analysis and data mining is offered. Future developments will especially focus on the Genome Reviews, including mapping not yet annotated protein sequences onto their corresponding genomes, generating new predictions for non-coding RNA genes, and generally extending the scope to lower metazoan organisms.

About this journal

Objective
Journal of Integrative Bioinformatics (JIB) is an international open access journal publishing original peer-reviewed research articles in all aspects of integrative bioinformatics.

Molecular biology produces huge amounts of data in the post-genomic era. This includes data describing metabolic mechanisms and pathways, structural genomic organization, patterns of regulatory regions; proteomics, transcriptomics, and metabolomics. On the one hand, analysis of this data uses essentially the methods and concepts of computer science; on the other hand, the range of biological tasks solved by researchers determines the range and scope of the data. Currently, there are about 1,000 database systems and various analytical tools available via the Internet which are directed at solving various biological tasks.

The challenge we have is to integrate these list-parts and relationships from genomics and proteomics at novel levels of understanding. Integrative Bioinformatics is a new area of research using the tools of computer science and electronic infrastructure applied to Biotechnology. These tools will also represent the backbone of the concept of a virtual cell.

Topics

Software applications/tools and databases covering the following topics:

Molecular Databases, Information Systems and Data Warehouses
Integration of Data, Methods and Tools
Metabolic and Regulatory Network Modeling and Simulation
Signal Pathways and Cell Control
Network Analysis
Medical Informatics, Biomedicine and Biotechnology
Integrative Approaches for Drug Design
Integrative Data and Text Mining Approaches
Integrative, whole cell and molecular modeling
Visualization and animation

Review papers are also welcome with regard to JIB.tools.

Article formats
Research articles, Review papers, Workshop contributions (if peer-reviewed)

Article processing charges (APCs)
Each unsolicited article, which is accepted for publication in the Journal of Integrative Bioinformatics is subject to an Article Processing Charge of 1,000€.
The Open Access publication of invited articles for Special Issues is sponsored by the editors.

Inquiries concerning APCs should be addressed to the Editorial Office at De Gruyter (see contact details below).