Open Access Published by De Gruyter

Volume 19 Issue 1 - Tools & Algorithms in Bioinformatics

March 2022

Issue of Journal of Integrative Bioinformatics

Contents
Journal Overview

Publicly Available March 29, 2022

Frontmatter

Page range: i-ii

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Special Section: Tools & Algorithms in Bioinformatics

Open Access December 21, 2021

Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data

Arthur I. Dergilev, Nina G. Orlova, Oxana B. Dobrovolskaya, Yuriy L. Orlov

Article number: 20200036

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Abstract

The development of high-throughput genomic sequencing coupled with chromatin immunoprecipitation technologies allows studying the binding sites of the protein transcription factors (TF) in the genome scale. The growth of data volume on the experimentally determined binding sites raises qualitatively new problems for the analysis of gene expression regulation, prediction of transcription factors target genes, and regulatory gene networks reconstruction. Genome regulation remains an insufficiently studied though plants have complex molecular regulatory mechanisms of gene expression and response to environmental stresses. It is important to develop new software tools for the analysis of the TF binding sites location and their clustering in the plant genomes, visualization, and the following statistical estimates. This study presents application of the analysis of multiple TF binding profiles in three evolutionarily distant model plant organisms. The construction and analysis of non-random ChIP-seq binding clusters of the different TFs in mammalian embryonic stem cells were discussed earlier using similar bioinformatics approaches. Such clusters of TF binding sites may indicate the gene regulatory regions, enhancers and gene transcription regulatory hubs. It can be used for analysis of the gene promoters as well as a background for transcription networks reconstruction. We discuss the statistical estimates of the TF binding sites clusters in the model plant genomes. The distributions of the number of different TFs per binding cluster follow same power law distribution for all the genomes studied. The binding clusters in Arabidopsis thaliana genome were discussed here in detail.

Open Access February 4, 2022

SCARF: a biomedical association rule finding webserver

Balázs Szalkai, Vince Grolmusz

Article number: 20210035

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Abstract

The analysis of enormous datasets with missing data entries is a standard task in biological and medical data processing. Large-scale, multi-institution clinical studies are the typical examples of such datasets. These sets make possible the search for multi-parametric relations since from the plenty of the data one is likely to find a satisfying number of subjects with the required parameter ensembles. Specifically, finding combinatorial biomarkers for some given condition also needs a very large dataset to analyze. For fast and automatic multi-parametric relation discovery association-rule finding tools are used for more than two decades in the data-mining community. Here we present the SCARF webserver for generalized association rule mining. Association rules are of the form: a AND b AND … AND x → y , meaning that the presence of properties a AND b AND … AND x implies property y ; our algorithm finds generalized association rules, since it also finds logical disjunctions (i.e., ORs) at the left-hand side, allowing the discovery of more complex rules in a more compressed form in the database. This feature also helps reducing the typically very large result-tables of such studies, since allowing ORs in the left-hand side of a single rule could include dozens of classical rules. The capabilities of the SCARF algorithm were demonstrated in mining the Alzheimer’s database of the Coalition Against Major Diseases (CAMD) in our recent publication (Archives of Gerontology and Geriatrics Vol. 73, pp. 300–307, 2017). Here we describe the webserver implementation of the algorithm.

Open Access March 7, 2022

`ExceS-A`: an exon-centric split aligner

Franziska Reinhardt, Peter F. Stadler

Article number: 20210040

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Abstract

Spliced alignments are a key step in the construction of high-quality homology-based annotations of protein sequences. The exon/intron structure, which is computed as part of spliced alignment procedures, often conveys important information for the distinguishing paralogous members of gene families. Here we present an exon-centric pipeline for spliced alignment that is intended in particular for applications that involve exon-by-exon comparisons of coding sequences. We show that the simple, blat -based approach has advantages over established tools in particular for genes with very large introns and applications to fragmented genome assemblies.

Open Access February 7, 2022

A systematic study of motif pairs that may facilitate enhancer–promoter interactions

Saidi Wang, Haiyan Hu, Xiaoman Li

Article number: 20210038

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Abstract

Pairs of interacting transcription factors (TFs) have previously been shown to bind to enhancers and promoters and contribute to their physical interactions. However, to date, we have limited knowledge about such TF pairs. To fill this void, we systematically studied the co-occurrence of TF-binding motifs in interacting enhancer–promoter (EP) pairs in seven human cell lines. We discovered 423 motif pairs that significantly co-occur in enhancers and promoters of interacting EP pairs. We demonstrated that these motif pairs are biologically meaningful and significantly enriched with motif pairs of known interacting TF pairs. We also showed that the identified motif pairs facilitated the discovery of the interacting EP pairs. The developed pipeline, EPmotifPair, together with the predicted motifs and motif pairs, is available at https://doi.org/10.6084/m9.figshare.14192000. Our study provides a comprehensive list of motif pairs that may contribute to EP physical interactions, which facilitate generating meaningful hypotheses for experimental validation.

Regular Contributions

Open Access July 26, 2021

On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection

Kristóf Takács, Vince Grolmusz

Article number: 20200043

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Abstract

The Protein Data Bank (PDB) today contains more than 174,000 entries with the 3-dimensional structures of biological macromolecules. Using the rich resources of this repository, it is possible identifying subsets with specific, interesting properties for different applications. Our research group prepared an automatically updated list of amyloid- and probably amyloidogenic molecules, the PDB_Amyloid collection, which is freely available at the address http://pitgroup.org/amyloid. This resource applies exclusively the geometric properties of the steric structures for identifying amyloids. In the present contribution, we analyze the starting (i.e., prefix) subsequences of the characteristic, parallel beta-sheets of the structures in the PDB_Amyloid collection, and identify further appearances of these length-5 prefix subsequences in the whole PDB data set. We have identified this way numerous proteins, whose normal or irregular functions involve amyloid formation, structural misfolding, or anti-coagulant properties, simply by containing these prefixes: including the T-cell receptor (TCR), bound with the major histocompatibility complexes MHC-1 and MHC-2; the p53 tumor suppressor protein; a mycobacterial RNA polymerase transcription initialization complex; the human bridging integrator protein BIN-1; and the tick anti-coagulant peptide TAP.

Open Access August 18, 2021

Big data in the healthcare system: a synergy with artificial intelligence and blockchain technology

Reyes-González Juan Pablo, Díaz-Peregrino Roberto, Soto-Ulloa Victor, Galvan-Remigio Isabel, Castillo Paul, Ogando-Rivas Elizabeth

Article number: 20200035

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Abstract

In the last decades big data has facilitating and improving our daily duties in the medical research and clinical fields; the strategy to get to this point is understanding how to organize and analyze the data in order to accomplish the final goal that is improving healthcare system, in terms of cost and benefits, quality of life and outcome patient. The main objective of this review is to illustrate the state-of-art of big data in healthcare, its features and architecture. We also would like to demonstrate the different application and principal mechanisms of big data in the latest technologies known as blockchain and artificial intelligence, recognizing their benefits and limitations. Perhaps, medical education and digital anatomy are unexplored fields that might be profitable to investigate as we are proposing. The healthcare system can be revolutionized using these different technologies. Thus, we are explaining the basis of these systems focused to the medical arena in order to encourage medical doctors, nurses, biotechnologies and other healthcare professions to be involved and create a more efficient and efficacy system.

Open Access December 16, 2021

Predicting the possible effect of miR-203a-3p and miR-29a-3p on DNMT3B and GAS7 genes expression

Afgar Ali, Sattarzadeh Bardsiri Mahla, Vahidi Reza, Farsinejad Alireza

Article number: 20210016

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Abstract

Aberrant expression of genes involved in methylation, including DNA methyltransferase 3 Beta ( DNMT3B ), can cause hypermethylation of various tumor suppressor genes. In this regard, various molecular factors such as microRNAs can play a critical role in regulating these methyltransferase enzymes and eventually downstream genes such as growth arrest specific 7 ( GAS7 ). Accordingly, in the present study we aimed to predict regulatory effect of miRNAs on DNMT3B and GAS7 genes expression in melanoma cell line. hsa-miR-203a-3p and hsa-miR-29a-3p were predicted and selected using bioinformatics software. The Real-time PCR technique was performed to investigate the regulatory effect of these molecules on the DNMT3B and GAS7 genes expression. Expression analysis of DNMT3B gene in A375 cell line showed that there was a significant increase compared to control ( p value = 0.0015). Analysis of hsa-miR-203a-3p and hsa-miR-29a-3p indicated the insignificant decreased expression in melanoma cell line compared to control ( p value < 0.05). Compared to control, the expression of GAS7 gene in melanoma cells showed a significant decrease ( p value = 0.0323). Finally, our findings showed that the decreased expression of hsa-miR-203a-3p and hsa-miR-29a-3p can hypothesize that their aberrant expression caused DNMT3B dysfunction, possible methylation of the GAS7 gene, and ultimately decreased its expression. However, complementary studies are necessary to definite comment.

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).

Volume 19 Issue 1 - Tools & Algorithms in Bioinformatics

Issue of Journal of Integrative Bioinformatics

Frontmatter

Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data

Abstract

SCARF: a biomedical association rule finding webserver

Abstract

ExceS-A: an exon-centric split aligner

Abstract

A systematic study of motif pairs that may facilitate enhancer–promoter interactions

Abstract

On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection

Abstract

Big data in the healthcare system: a synergy with artificial intelligence and blockchain technology

Abstract

Predicting the possible effect of miR-203a-3p and miR-29a-3p on DNMT3B and GAS7 genes expression

Abstract

`ExceS-A`: an exon-centric split aligner