Corrigendum to “A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer”
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): M.Q. Yang, D. Li, W. Yang, Y. Zhang, J. Liu, W. Tong (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

DNA Methylation in Stroke. Update of Latest Advances
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Jerzy Krupinski, Caty Carrera, Elena Muiño, Nuria Torres, Raid Al-Baradie, Natalia Cullell, Israel Fernandez-CadenasAbstractEpigenetic modifications are hereditable and modifiable factors that do not alter the DNA sequence. These epigenetic factors include DNA methylation, acetylation of histones and non-coding RNAs. Epigenetic factors have mainly been associated with cancer but also with other diseases and conditions such as diabetes or obesity. In addition, epigenetic modifications could play an important role in ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

FoldX as Protein Engineering Tool: Better Than Random Based Approaches?
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Oliver Buß, Jens Rudat, Katrin OchsenreitherAbstractImproving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the prediction of bene...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Machine Learning Methods for Histopathological Image Analysis
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Daisuke Komura, Shumpei IshikawaAbstractAbundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions. (Source: Comput...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Computational Methods for Assessing Chromatin Hierarchy
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Pearl Chang, Moloya Gohain, Ming-Ren Yen, Pao-Yang ChenAbstractThe hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling “higher-order” and “primary-order” chro...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Discovery of Novel Functional Centers With Rationally Designed Amino Acid Motifs
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Aloysius Wong, Xuechen Tian, Chris Gehring, Claudius MarondedzeAbstractPlants are constantly exposed to environmental stresses and in part due to their sessile nature, they have evolved signal perception and adaptive strategies that are distinct from those of other eukaryotes. This is reflected at the cellular level where receptors and signalling molecules cannot be identified using standard homology-based searches querying with proteins from prokaryotes and other eukaryotes. One of the reasons for this is the complex doma...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Dimitrios Zafeiris, Sergio Rutella, Graham Roy BallAbstractThe field of machine learning has allowed researchers to generate and analyse vast amounts of data using a wide variety of methodologies. Artificial Neural Networks (ANN) are some of the most commonly used statistical models and have been successful in biomarker discovery studies in multiple disease types. This review seeks to explore and evaluate an integrated ANN pipeline for biomarker discovery and validation in Alzheimer's disease, the most common form of demen...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Current Perspectives of the Chicken Gastrointestinal Tract and Its Microbiome
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Daniel Borda-Molina, Jana Seifert, Amélia Camarinha-SilvaAbstractThe microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system.Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era – Past, present and future
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Chi-Ching Tsang, James Y.M. Tang, Susanna K.P. Lau, Patrick C.Y. WooAbstractAspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical and compu...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Chang XuAbstractDetection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Emilio Siena, Margherita Bodini, Duccio Medini (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

A Review of Matched-pairs Feature Selection Methods for Gene Expression Data Analysis
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Sen Liang, Anjun Ma, Sen Yang, Yan Wang, Qin MaAbstractWith the rapid accumulation of gene expression data from various technologies, e.g., microarray, RNA-sequencing (RNA-seq), and single-cell RNA-seq, it is necessary to carry out dimensional reduction and feature (signature genes) selection in support of making sense out of such high dimensional data. These computational methods significantly facilitate further data analysis and interpretation, such as gene function enrichment analysis, cancer biomarker detection, and dr...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Jessica D. Forbes, Natalie C. Knox, Christy-Lynn Peterson, Aleisha R. ReimerAbstractClinical metagenomics (CMg) is the discipline that refers to the sequencing of all nucleic acid material present within a clinical specimen with the intent to recover clinically relevant microbial information. From a diagnostic perspective, next-generation sequencing (NGS) offers the ability to rapidly identify putative pathogens and predict their antimicrobial resistance profiles to optimize targeted treatment regimens. Since the introduct...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Following Ribosome Footprints to Understand Translation at a Genome Wide Level
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Guillermo Eastman, Pablo Smircich, José R. Sotelo-SilveiraAbstractProtein translation is a key step in gene expression. The development of Ribosome Profiling has allowed the global analysis of this process at sub-codon resolution. In the last years the method has been applied to several models ranging from bacteria to mammalian cells yielding a surprising amount of insight on the mechanism and the regulation of translation. In this review we describe the key aspects of the experimental protocol and comment on the ma...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Lung Cancer Therapy Targeting Histone Methylation: Opportunities and Challenges
Publication date: 2018Source: Computational and Structural Biotechnology Journal, Volume 16Author(s): Yuchen Chen, Xinran Liu, Yangkai Li, Chuntao Quan, Ling Zheng, Kun HuangAbstractLung cancer is one of the most common malignancies. In spite of the progress made in past decades, further studies to improve current therapy for lung cancer are required. Dynamically controlled by methyltransferases and demethylases, methylation of lysine and arginine residues on histone proteins regulates chromatin organization and thereby gene transcription. Aberrant alterations of histone methylation have been demonstrated to be associated ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Blockchain Technology for Healthcare: Facilitating the Transition to Patient-Driven Interoperability
Publication date: Available online 30 June 2018Source: Computational and Structural Biotechnology JournalAuthor(s): William J. Gordon, Christian CataliniAbstractInteroperability in healthcare has traditionally been focused around data exchange between business entities, for example, different hospital systems. However, there has been a recent push towards patient-driven interoperability, in which health data exchange is patient-mediated and patient-driven. Patient-centered interoperability, however, brings with it new challenges and requirements around security and privacy, technology, incentives, and governance that must ...
Source: Computational and Structural Biotechnology Journal - July 5, 2018 Category: Biotechnology Source Type: research

Blockchain Technology for Healthcare: Facilitating the Transition to Patient-Driven Interoperability
Publication date: Available online 30 June 2018 Source:Computational and Structural Biotechnology Journal Author(s): William J. Gordon, Christian Catalini Interoperability in healthcare has traditionally been focused around data exchange between business entities, for example, different hospital systems. However, there has been a recent push towards patient-driven interoperability, in which health data exchange is patient-mediated and patient-driven. Patient-centered interoperability, however, brings with it new challenges and requirements around security and privacy, technology, incentives, and governance that must be ad...
Source: Computational and Structural Biotechnology Journal - July 1, 2018 Category: Biotechnology Source Type: research

Lung Cancer Therapy Targeting Histone Methylation: Opportunities and Challenges
Publication date: Available online 20 June 2018 Source:Computational and Structural Biotechnology Journal Author(s): Yuchen Chen, Xinran Liu, Yangkai Li, Chuntao Quan, Ling Zheng, Kun Huang Lung cancer is one of the most common malignancies. In spite of the progress made in past decades, further studies to improve current therapy for lung cancer are required. Dynamically controlled by methyltransferases and demethylases, methylation of lysine and arginine residues on histone proteins regulates chromatin organization and thereby gene transcription. Aberrant alterations of histone methylation have been demonstrated to be as...
Source: Computational and Structural Biotechnology Journal - June 21, 2018 Category: Biotechnology Source Type: research

ctDNA and CTCs in Liquid Biopsy – Current Status and where we Need to Progress
Publication date: Available online 1 June 2018 Source:Computational and Structural Biotechnology Journal Author(s): Martin H.D. Neumann, Sebastian Bender, Thomas Krahn, Thomas Schlange We discuss the current status of liquid biopsy and its advantages and challenges with a focus on pre-analytical sample handling, technologies and workflows. The potential of circulating tumor cells and circulating tumor DNA is pointed out and an overview of corresponding technologies is given. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - June 2, 2018 Category: Biotechnology Source Type: research

Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era – past, present and future
Publication date: Available online 31 May 2018 Source:Computational and Structural Biotechnology Journal Author(s): Chi-Ching Tsang, James Y.M. Tang, Susanna K.P. Lau, Patrick C.Y. Woo Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical, ...
Source: Computational and Structural Biotechnology Journal - June 1, 2018 Category: Biotechnology Source Type: research

Protein Sequences Recapitulate Genetic Code Evolution
Publication date: Available online 30 May 2018 Source:Computational and Structural Biotechnology Journal Author(s): Hervé Seligmann Several hypotheses predict ranks of amino acid assignments to genetic code's codons. Analyses here show that average positions of amino acid species in proteins correspond to assignment ranks, in particular as predicted by Juke's neutral mutation hypothesis for codon assignments. In all tested protein groups, including co- and post-translationally folding proteins, ‘recent’ amino acids are on average closer to gene 5′ extremities than ‘ancient’ ones. Analy...
Source: Computational and Structural Biotechnology Journal - May 31, 2018 Category: Biotechnology Source Type: research

Corrigendum to “A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer”
Publication date: Available online 1 May 2018 Source:Computational and Structural Biotechnology Journal Author(s): M.Q. Yang, D. Li, W. Yang, Y. Zhang, J. Liu, W. Tong (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - May 5, 2018 Category: Biotechnology Source Type: research

Corrigendum to [a Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer]
Publication date: Available online 1 May 2018 Source:Computational and Structural Biotechnology Journal Author(s): M.Q. Yang, D. Li, W. Yang, Y. Zhang, J. Liu, W. Tong (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - May 2, 2018 Category: Biotechnology Source Type: research

Following ribosome footprints to understand translation at a genome wide level
Publication date: Available online 1 May 2018 Source:Computational and Structural Biotechnology Journal Author(s): G. Eastman, P. Smircich, J.R. Sotelo Silveira Protein translation is a key step in gene expression. The development of Ribosome Profiling has allowed the global analysis of this process at sub-codon resolution. In the last years the method has been applied to several models ranging from bacteria to mammalian cells yielding a surprising amount of insight on the mechanism and the regulation of translation. In this review we describe the key aspects of the experimental protocol and comment on the main conclusion...
Source: Computational and Structural Biotechnology Journal - May 2, 2018 Category: Biotechnology Source Type: research

Functional prediction of hypothetical transcription factors of Escherichia coli K-12 based on expression data
Publication date: Available online 27 March 2018 Source:Computational and Structural Biotechnology Journal Author(s): Emanuel Flores-Bautista, Carenne Ludeña Cronick, Anny Rodriguez Fersaca, Mario Alberto Martinez-Nuñez, Ernesto Perez-Rueda The repertoire of 304 DNA-binding transcription factors (TFs) in Escherichia coli K-12 has been described recently, with 196 TFs experimentally characterized and 108 proteins predicted by sequence comparisons. Based on 303 expression profile patterns retrieved from the Colombos database 12 clusters were identified, including hypothetical and experimentally characterized T...
Source: Computational and Structural Biotechnology Journal - March 28, 2018 Category: Biotechnology Source Type: research

Ordering protein contact matrices
Publication date: Available online 16 March 2018 Source:Computational and Structural Biotechnology Journal Author(s): Chuan Xu, Guillaume Bouvier, Benjamin Bardiaux, Michael Nilges, Thérèse Malliavin, Abdel Lisser Numerous biophysical approaches provide information about residues spatial proximity in proteins. However, correct assignment of the protein fold from this proximity information is not straightforward if the spatially close protein residues are not assigned to residues in the primary sequence. Here, we propose an algorithm to assign such residue numbers by ordering the columns and lines of the raw ...
Source: Computational and Structural Biotechnology Journal - March 17, 2018 Category: Biotechnology Source Type: research

Current perspectives of the chicken gastrointestinal tract and its microbiome
Publication date: Available online 15 March 2018 Source:Computational and Structural Biotechnology Journal Author(s): D. Borda-Molina, J. Seifert, A. Camarinha-Silva The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system. Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different sectio...
Source: Computational and Structural Biotechnology Journal - March 16, 2018 Category: Biotechnology Source Type: research

Prediction of dyslipidemia using gene mutations, family history of diseases and anthropometric indicators in children and adolescents: the CASPIAN-III study
Publication date: Available online 2 March 2018 Source:Computational and Structural Biotechnology Journal Author(s): Hamid R. Marateb, Roya Kelishadi, Mohammad Reza Mohebian, Shaghayegh Haghjooy Javanmard, Amir Ali Tavallaei, Mohammad Hasan Tajadini, Motahar Heidari-Beni, Miguel Angel Mañanas, Mohammad Esmaeil Motlagh, Ramin Heshmat, Marjan Mansourian Dyslipidemia, the disorder of lipoprotein metabolism resulting in high lipid profile, is an important modifiable risk factor for coronary heart diseases (CHDs). It is associated with more than four million worldwide deaths per year. Half of the children with dyslipide...
Source: Computational and Structural Biotechnology Journal - March 3, 2018 Category: Biotechnology Source Type: research

Amplification and bioinformatics analysis of conserved FAD-binding region of L-amino acid oxidase (LAAO) genes in gastropods compared to other organisms
This study aimed to investigate the conserved FAD-binding region of the L-amino acid oxidase (LAAO) genes in twelve gastropod genera commonly found in Thailand compared to those in other organisms using molecular cloning, nucleotide sequencing and bioinformatics analysis. Genomic DNA of gastropods and other invertebrates was extracted and screened using primers specific to the conserved FAD-binding region of LAAO. The amplified 143-bp fragments were cloned and sequenced. The obtained nucleotide sequences of 21 samples were aligned and phylogenetically compared to the LAAO-conserved FAD-binding regions of 210 other organism...
Source: Computational and Structural Biotechnology Journal - March 3, 2018 Category: Biotechnology Source Type: research

Highlighting clinical metagenomics for enhanced diagnostic decision-making: A step towards wider implementation
Publication date: Available online 27 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Jessica D. Forbes, Natalie C. Knox, Christy-Lynn Peterson, Aleisha R. Reimer Clinical metagenomics (CMg) is the discipline that refers to the sequencing of all nucleic acid material present within a clinical specimen with the intent to recover clinically relevant microbial information. From a diagnostic perspective, next-generation sequencing (NGS) offers the ability to rapidly identify putative pathogens and predict their antimicrobial resistance profiles to optimize targeted treatment regimens. Since ...
Source: Computational and Structural Biotechnology Journal - February 28, 2018 Category: Biotechnology Source Type: research

Discovery of novel functional centers with rationally designed amino acid motifs
Publication date: Available online 27 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Aloysius Wong, Xuechen Tian, Chris Gehring, Claudius Marondedze Plants are constantly exposed to environmental stresses and in part due to their sessile nature, they have evolved signal perception and adaptive strategies that are distinct from those of other eukaryotes. This is reflected at the cellular level where receptors and signalling molecules can not be identified using standard homology-based searches querying with proteins from prokaryotes and other eukaryotes. One of the reasons for this is th...
Source: Computational and Structural Biotechnology Journal - February 28, 2018 Category: Biotechnology Source Type: research

A Review of Matched-pairs Feature Selection Methods for Gene Expression Data Analysis
Publication date: Available online 25 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Sen Liang, Anjun Ma, Sen Yang, Yan Wang, Qin Ma With the rapid accumulation of gene expression data from various technologies, e.g., microarray, RNA-sequencing (RNA-seq), and single-cell RNA-seq, it is necessary to carry out dimensional reduction and feature (signature genes) selection in support of making sense out of such high dimensional data. These computational methods significantly facilitate further data analysis and interpretation, such as gene function enrichment analysis, cancer biomarker dete...
Source: Computational and Structural Biotechnology Journal - February 26, 2018 Category: Biotechnology Source Type: research

An Artificial Neural Network integrated pipeline for biomarker discovery using Alzheimer's Disease as a case study
Publication date: Available online 21 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Dimitrios Zafeiris, Sergio Rutella, Graham Roy Ball The field of machine learning has allowed researchers to generate and analyse vast amounts of data using a wide variety of methodologies. Artificial Neural Networks (ANN) are some of the most commonly used statistical models and have been successful in biomarker discovery studies in multiple disease types. This review seeks to explore and evaluate an integrated ANN pipeline for biomarker discovery and validation in Alzheimer's disease, the most common ...
Source: Computational and Structural Biotechnology Journal - February 22, 2018 Category: Biotechnology Source Type: research

Computational Methods for Assessing Chromatin Hierarchy
Publication date: Available online 15 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Pearl Chang, Moloya Gohain, Ming-Ren-Yen, Pao-Yang Chen The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling “higher-order” and “primary-orde...
Source: Computational and Structural Biotechnology Journal - February 15, 2018 Category: Biotechnology Source Type: research

Differential microbial communities of omnivorous and herbivorous cattle in Southern China
In conclusion, a significant change in the gut microbial community was observed in the omnivorous cattle, suggesting that diet may be one of the factors that may signal an adaptation response by the cattle to maintain feed efficiency as a consequence of the change in environment. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - February 15, 2018 Category: Biotechnology Source Type: research

Interplay between virulence and variability factors as a potential driver of invasive meningococcal disease
Publication date: Available online 15 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Emilio Siena, Margherita Bodini, Duccio Medini (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - February 15, 2018 Category: Biotechnology Source Type: research

Machine Learning Methods for Histopathological Image Analysis
Publication date: Available online 9 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Daisuke Komura, Shumpei Ishikawa Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions. (So...
Source: Computational and Structural Biotechnology Journal - February 10, 2018 Category: Biotechnology Source Type: research

FoldX as protein engineering tool: Better than random based approaches?
Publication date: Available online 3 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Oliver Buß, Jens Rudat, Katrin Ochsenreither Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and widely used strategy for efficient engineering is known. Beside random approaches like error prone PCR or physical techniques to stabilize proteins, e.g. by immobilization, in silico approaches are gaining more attention to apply target-oriented mutagenesis. In this review different algorithms for the predic...
Source: Computational and Structural Biotechnology Journal - February 7, 2018 Category: Biotechnology Source Type: research

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Publication date: Available online 6 February 2018 Source:Computational and Structural Biotechnology Journal Author(s): Chang Xu Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practic...
Source: Computational and Structural Biotechnology Journal - February 7, 2018 Category: Biotechnology Source Type: research

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones
This report provides the first molecular foundation for the model that the CFBP linker acts as an unstructured, flexible loop, allowing the two flanking chaperone modules function independently while linked in cis, likely to assist in the folding of multisubunit client complexes. Graphical abstract (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - December 30, 2017 Category: Biotechnology Source Type: research

Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows
Publication date: 2017 Source:Computational and Structural Biotechnology Journal, Volume 15 Author(s): Pranav Kulkarni, Peter Frommolt While Next-Generation Sequencing (NGS) can now be considered an established analysis technology for research applications across the life sciences, the analysis workflows still require substantial bioinformatics expertise. Typical challenges include the appropriate selection of analytical software tools, the speedup of the overall procedure using HPC parallelization and acceleration technology, the development of automation strategies, data storage solutions and finally the development of ...
Source: Computational and Structural Biotechnology Journal - December 15, 2017 Category: Biotechnology Source Type: research

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning
Publication date: 2017 Source:Computational and Structural Biotechnology Journal, Volume 15 Author(s): Ruibang Luo, Fritz J. Sedlazeck, Charlotte A. Darby, Stephen M. Kelly, Michael C. Schatz Linked-read sequencing, using highly-multiplexed genome partitioning and barcoding, can span hundreds of kilobases to improve de novo assembly, haplotype phasing, and other applications. Based on our analysis of 14 datasets, we introduce LRSim that simulates linked-reads by emulating the library preparation and sequencing process with fine control over variants, linked-read characteristics, and the short-read profile. We conclude fro...
Source: Computational and Structural Biotechnology Journal - December 15, 2017 Category: Biotechnology Source Type: research

DNA Methylation in Stroke. Update of Latest Advances
Publication date: Available online 9 December 2017 Source:Computational and Structural Biotechnology Journal Author(s): Jerzy Krupinski, Caty Carrera, Elena Muiño, Nuria Torres, Raid Al-Baradie, Natalia Cullell, Israel Fernandez-Cadenas Epigenetic modifications are hereditable and modifiable factors that do not alter the DNA sequence. These epigenetic factors include DNA methylation, acetylation of histones and non-coding RNAs. Epigenetic factors have mainly been associated with cancer but also with other diseases and conditions such as diabetes or obesity. In addition, epigenetic modifications could play an import...
Source: Computational and Structural Biotechnology Journal - December 15, 2017 Category: Biotechnology Source Type: research

Are Circulating Type 2 Vaccine-Derived Polioviruses (VDPVs) Genetically Distinguishable from Immunodeficiency-Associated VDPVs?
We presented quantitative approaches using genetic information as a surveillance tool for early detection of VDPV outbreaks. This work suggests that genetic variations between cVDPV2 and iVDPV2 may reflect differences in viral micro-environments, host-virus interactions, and selective pressures during person-to-person transmission compared with chronic infections in immunodeficient patients. (Source: Computational and Structural Biotechnology Journal)
Source: Computational and Structural Biotechnology Journal - October 13, 2017 Category: Biotechnology Source Type: research

A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer
Publication date: Available online 10 October 2017 Source:Computational and Structural Biotechnology Journal Author(s): Mary Q. Yang, Dan Li, William Yang, Yifan Zhang, Jun Liu, Weida Tong Clear cell renal cell carcinoma (ccRCC) is the most common and most aggressive form of renal cell cancer (RCC). The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology...
Source: Computational and Structural Biotechnology Journal - October 10, 2017 Category: Biotechnology Source Type: research

Assessing species diversity using metavirome data: methods and challenges
Publication date: Available online 21 September 2017 Source:Computational and Structural Biotechnology Journal Author(s): Damayanthi Herath, Duleepa Jayasundara, David Ackland, Isaam Saeed, Sen-Lin Tang, Saman Halgamuge Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role ...
Source: Computational and Structural Biotechnology Journal - September 22, 2017 Category: Biotechnology Source Type: research

Personalized therapy against preeclampsia by replenishing placental protein 13 (PP13) targeted to patients with impaired PP13 molecule or function
Publication date: Available online 22 September 2017 Source:Computational and Structural Biotechnology Journal Author(s): Hamutal Meiri, George Osol, Irene Cetin, Sveinbjörn Gizurarson, Berthold Huppertz Hypertensive disorders affect about one third of all people aged 20 and above, and are treated with anti-hypertensive drugs. Preeclampsia (PE) is one form of such disorders that only develops during pregnancy. It affects ten million pregnant women globally and additionally causes fetal loss and major newborn disabilities. The syndrome’s origin is multifactorial, and anti-hypertensive drugs are ineffective in tr...
Source: Computational and Structural Biotechnology Journal - September 22, 2017 Category: Biotechnology Source Type: research

Meta-analysis of liver and heart transcriptomic data for functional annotation transfer in mammalian orthologs
Publication date: Available online 26 August 2017 Source:Computational and Structural Biotechnology Journal Author(s): Pía Francesca Loren Reyes, Tom Michoel, Anagha Joshi, Guillaume Devailly Functional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functionally equivalent ones from all predicted orthologs, we collected genome wide expression data in mouse and rat liv...
Source: Computational and Structural Biotechnology Journal - August 27, 2017 Category: Biotechnology Source Type: research

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges
Publication date: Available online 14 August 2017 Source:Computational and Structural Biotechnology Journal Author(s): Zekun Yin, Haidong Lan, Guangming Tan, Mian Lu, Athanasios V. Vasilakos, Weiguo Liu The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the c...
Source: Computational and Structural Biotechnology Journal - August 17, 2017 Category: Biotechnology Source Type: research

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes
Publication date: Available online 12 August 2017 Source:Computational and Structural Biotechnology Journal Author(s): Hervé Seligmann, Ganesh Warthi A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA=0), codons with structures ZXX/XXZ are 5′/3′ asymmetric (CDA=−1/1; CDA=−0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (−/+) signs is an arbitrary convention). Negative/...
Source: Computational and Structural Biotechnology Journal - August 13, 2017 Category: Biotechnology Source Type: research