Journal of Integrative Bioinformatics Volume 3 Issue 1

Journal of Integrative Bioinformatics

Volume 3 Issue 1

Contents
Journal Overview

Identification of embryo specific human isoforms using a database of predicted alternative splice forms

Heike Pospisil October 18, 2016 Page range: 1-10

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Abstract

Alternative splicing is one of the most important mechanisms to generate a large number of mRNA and protein isoforms from a small number of genes. Its study became one of the hot topics in computational genome analysis. The repository EASED (Extended Alternatively Spliced EST Database, http://eased.bioinf.mdc-berlin.de/) stores a large collection of splice variants predicted from comparing the human genome against EST databases. It enables finding new unpublished splice forms that could be interesting candidate genes for stage specific, diseases specific or tissue specific splicing. The main idea behind selecting specific splice forms is to compare the number and the origin of ESTs confirming one isoform with the number and the origin of ESTs confirming the opposite isoform. A measure asDcs is introduced to take into account the unequal distribution of ESTs per splice site on one hand, and the possible uncertainties due to the relatively low quality of EST data on the other hand. First, the number of ESTs per splice site is scaled with a modified Hill function. The measure asDcs computes in the second step the distance of each pair of ESTs from equipartition. Equipartition exists if for every number of adult ESTs the same number of embryonic ESTs. The effect of several input parameters for the scaling of true EST values is analysed and can be reproduced on http://cardigan.zbh.uni-hamburg.de/asDcs. Some of the obtained best scoring hits for selected parameters (transcription factor P65, drebrin, and fetuin) have been already described in literature as been involved in embryonic development. This result shows the plausibility of this approach and looks promising for the identification of unplublished embryo specific alternative splice sites in human.

Kinetic Modelling with the Systems Biology Modelling Environment SyBME

Björn H. Junker, Dirk Koschützki, Falk Schreiber October 18, 2016 Page range: 11-20

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Abstract

Kinetic modelling and simulation is an important approach in systems biology. While the focus of current modelling tools is on simulation, model development is a highly iterative process which is currently only partly supported. To support the development of biochemical models, their simulation, and graphical understanding, we designed and implemented SyBME, the Systems Biology Modelling Environment. Here we present the architecture and the main components of SyBME and show its use by modelling sucrose breakdown in developing potato tubers.

A structural keystone for drug design

Kristian Rother, Mathias Dunkel, Elke Michalsky, Silke Trissl, Andrean Goede, Ulf Leser, Robert Preissner October 18, 2016 Page range: 21-31

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3D-structures of proteins and potential ligands are the cornerstones of rational drug design. The first brick to build upon is selecting a protein target and finding out whether biologically active compounds are known. Both tasks require more information than the structures themselves provide. For this purpose we have built a web resource bridging protein and ligand databases. It consists of three parts: i) A data warehouse on annotation of protein structures that integrates many well-known databases such as Swiss-Prot, SCOP, ENZYME and others. ii) A conformational library of structures of approved drugs. iii) A conformational library of ligands from the PDB, linking the realms of proteins and small molecules. The data collection contains structures of 30,000 proteins, 5,000 different ligands from 70,000 ligand-protein complexes, and 2,500 known drugs. Sets of protein structures can be refined by criteria like protein fold, family, metabolic pathway, resolution and textual annotation. The structures of organic compounds (drugs and ligands) can be searched considering chemical formula, trivial and trade names as well as medical classification codes for drugs (ATC). Retrieving structures by 2D-similarity has been implemented for all small molecules using Tanimoto coefficients. For the drug structures, 110,000 structural conformers have been calculated to account for structural flexibility. Two substances can be compared online by 3D-superimposition, where the pair of conformers that fits best is detected. Together, these web-accessible resources can be used to identify promising drug candidates. They have been used in-house to find alternatives to substances with a known binding activity but adverse side effects.

Functional classification of transcription factor binding sites: Information content as a metric

D. Ashok Reddy, B. V. L. S. Prasad, Chanchal K. Mitra October 18, 2016 Page range: 32-44

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Abstract

The information content (relative entropy) of transcription factor binding sites (TFBS) is used to classify the transcription factors (TFs). The TF classes are clustered based on the TFBS clustering using information content. Any TF belonging to the TF class cluster has a chance of binding to any TFBS of the clustered group. Thus, out of the 41 TFBS (in humans), perhaps only 5 -10 TFs may be actually needed and in case of mouse instead of 13 TFs, we may have actually 5 or so TFs. The JASPAR database of TFBS are used in this study. The experimental data on TFs of specific gene expression from TRRD database is also coinciding with our computational results. This gives us a new way to look at the protein classification- not based on their structure or function but by the nature of their TFBS.

Network integration of data and analysis of oncology interest

P. Romano, G. Bertolini, F. De Paoli, M. Fattore, D. Marra, G. Mauri, E. Merelli, I. Porro, S. Scaglione, L. Milanesi October 18, 2016 Page range: 45-55

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The Human Genome Project has deeply transformed biology and the field has since then expanded to the management, processing, analysis and visualization of large quantities of data from genomics, proteomics, medicinal chemistry and drug screening. This huge amount of data and the heterogeneity of software tools that are used implies the adoption on a very large scale of new, flexible tools that can enable researchers to integrate data and analysis on the network. ICT technology standards and tools, like Web Services and related languages, and workflow management systems, can support the creation and deployment of such systems. While a number of Web Services are appearing and personal workflow management systems are also being more and more offered to researchers, a reference portal enabling the vast majority of unskilled researchers to take profit from these new technologies is still lacking. In this paper, we introduce the rationale for the creation of such a portal and present the architecture and some preliminary results for the development of a portal for the enactment of workflows of interest in oncology.

3D image and graph based Computation of Protein Surface

Aruna Ranganath, K.C. Shet, N. Vidyavathi October 18, 2016 Page range: 56-62

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The accessible surface of a macromolecule is a significant determinant of its action. The interaction between biomolecules or protein-ligand is dependent on their surfaces rather than their bulk properties. Identifying these local properties of bimolecular surfaces plays a vital role in the area of biomedicine. For example, identifying binding sites, docking etc. In this paper we describe an algorithm for computing the molecular surface of protein. The algorithm considers the 3D structure of the protein as a 3D image. The algorithm constructs a 3D graph corresponding to the size of 3D image data volume; the graph nodes correspond to image voxels.The idea is drawn from the cost minimization in a graph developed by Thedens and Fleagle[1]. The algorithm uses a Dynamic Programming Technique to avoid combinatorial explosion of the legal local surface.

Noise in Genetic Toggle Switch Models

M. Andrecut, S. A. Kauffman October 18, 2016 Page range: 63-77

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In this paper we study the intrinsic noise effect on the switching behavior of a simple genetic circuit corresponding to the genetic toggle switch model. The numerical results obtained from a noisy mean-field model are compared to those obtained from the stochastic Gillespie simulation of the corresponding system of chemical reactions. Our results show that by using a two step reaction approach for modeling the transcription and translation processes one can make the system to lock in one of the steady states for exponentially long times.

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).

> Information on submission process