CSBJ – Recent Articles
106 views | +0 today
Follow
Your new post is loading...
Your new post is loading...
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Machine Learning Methods for Histopathological Image Analysis - ScienceDirect

Machine Learning Methods for Histopathological Image Analysis - ScienceDirect | CSBJ – Recent Articles | Scoop.it
Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using m…
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

DNA Methylation in Stroke. Update of Latest Advances - ScienceDirect

DNA Methylation in Stroke. Update of Latest Advances - ScienceDirect | CSBJ – Recent Articles | Scoop.it
Epigenetic modifications are hereditable and modifiable factors that do not alter the DNA sequence. These epigenetic factors include DNA methylation, …
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China - ScienceDirect

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China - ScienceDirect | CSBJ – Recent Articles | Scoop.it
In Hong Kong, cattle were traditionally raised by farmers as draft animals to plough rice fields. Due to urbanization in the 20th century, they were g…
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

EMBO Workshop - Microglia 2018 - 18 - 21 March 2018

EMBO Workshop - Microglia 2018 - 18 - 21 March 2018 | CSBJ – Recent Articles | Scoop.it
This workshop will bring together expert and novice researchers studying microglia physiology in health and disease in an interactive meeting format that promotes the latest work in the field.
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Tissue Self-Organisation: Challenging the Systems - 11 - 14 March 2018

Tissue Self-Organisation: Challenging the Systems - 11 - 14 March 2018 | CSBJ – Recent Articles | Scoop.it
This EMBO/EMBL symposium aims at mechanistic understanding of self-organising properties of multi-cellular systems and will bring together researchers working on both the mechanisms and manipulation of tissue morphogenesis.
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

CSBJ journal, partnered with | Drug Safety EU

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Antibody H3 Structure Prediction

Antibody H3 Structure Prediction | CSBJ – Recent Articles | Scoop.it
Abstract: Antibodies are proteins of the immune system that are able to bind to a huge variety of different substances, making them attractive candidates for therapeutic applications. Antibody structures have the potential to be useful during drug development, allowing the implementation of rational design procedures. The most challenging part of the antibody structure to experimentally determine or model is the H3 loop, which in addition is often the most important region in an antibody's binding site. This review summarises the approaches used so far in the pursuit of accurate computational H3 structure prediction. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Chagas disease research and development: Is there light at the end of the tunnel?

Chagas disease research and development: Is there light at the end of the tunnel? | CSBJ – Recent Articles | Scoop.it
Abstract: Chagas disease, or American trypanosomiasis, is the result of infection by the parasite Trypanosoma cruzi. It is endemic in Latin America, and spreading around the globe due to human migration. Although it was first identified more than a century ago, only two old drugs are available for treatment and a lot of questions related to the disease progression, its pathologies, and not to mention the assessment of treatment efficacy, are subject to debate and remain to be answered. Indeed, the current status of evidence and data available does not allow any absolute statement related to treatment needs and outcome for Chagas patients to be made. Although there has been some new impetus in Research and Development for Chagas disease following recent new clinical trials, there is a scientific requirement to review and challenge the current status of evidence and define basic and clinical research priorities and next steps in the field. This should ensure that the best drugs for Chagas disease are developed, but will require a focused and collaborative effort of the entire Chagas disease research community. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Exploring Components of the CO2-Concentrating Mechanism in Alkaliphilic Cyanobacteria Through Genome-Based Analysis

Exploring Components of the CO2-Concentrating Mechanism in Alkaliphilic Cyanobacteria Through Genome-Based Analysis | CSBJ – Recent Articles | Scoop.it
Abstract: In cyanobacteria, the CO2-concentrating mechanism (CCM) is a vital biological process that provides effective photosynthetic CO2 fixation by elevating the CO2 level near the active site of Rubisco. This process enables the adaptation of cyanobacteria to various habitats, particularly in CO2-limited environments. Although CCM of freshwater and marine cyanobacteria are well studied, there is limited information on the CCM of cyanobacteria living under alkaline environments. Here, we aimed to explore the molecular components of CCM in 12 alkaliphilic cyanobacteria through genome-based analysis. These cyanobacteria included 6 moderate alkaliphiles; Pleurocapsa sp. PCC 7327, Synechococcus spp., Cyanobacterium spp., Spirulina subsalsa PCC 9445, and 6 strong alkaliphiles (i.e. Arthrospira spp.). The results showed that both groups belong to β-cyanobacteria based on β-carboxysome shell proteins with form 1B of Rubisco. They also contained standard genes, ccmKLMNO cluster, which is essential for β-carboxysome formation. Most strains did not have the high-affinity Na+/HCO3− symporter SbtA and the medium-affinity ATP-dependent HCO3− transporter BCT1. Specifically, all strong alkaliphiles appeared to lack BCT1. Beside the transport systems, carboxysomal β-CA, CcaA, was absent in all alkaliphiles, except for three moderate alkaliphiles: Pleurocapsa sp. PCC 7327, Cyanobacteriumstranieri PCC 7202, and Spirulina subsalsaPCC 9445. Furthermore, comparative analysis of the CCM components among freshwater, marine, and alkaliphilic β-cyanobacteria revealed that the basic molecular components of the CCM in the alkaliphilic cyanobacteria seemed to share more degrees of similarity with freshwater than marine cyanobacteria. These findings provide a relationship between the CCM components of cyanobacteria and their habitats. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.)

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.) | CSBJ – Recent Articles | Scoop.it
Abstract: Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Fourier Analysis of Conservation Patterns in Protein Secondary Structure

Fourier Analysis of Conservation Patterns in Protein Secondary Structure | CSBJ – Recent Articles | Scoop.it
Abstract: Residue conservation is a common observation in alignments of protein families, underscoring positions important in protein structure and function. Though many methods measure the level of conservation of particular residue positions, currently we do not have a way to study spatial oscillations occurring in protein conservation patterns. It is known that hydrophobicity shows spatial oscillations in proteins, which is characterized by computing the hydrophobic moment of the protein domains. Here, we advance the study of moments of conservation of protein families to know whether there might exist spatial asymmetry in the conservation patterns of regular secondary structures. Analogous to the hydrophobic moment, the conservation moment is defined as the modulus of the Fourier transform of the conservation function of an alignment of related protein, where the conservation function is the vector of conservation values at each column of the alignment. The profile of the conservation moment is useful in ascertaining any periodicity of conservation, which might correlate with the period of the secondary structure. To demonstrate the concept, conservation in the family of potassium ion channel proteins was analyzed using moments. It was shown that the pore helix of the potassium channel showed oscillations in the moment of conservation matching the period of the α-helix. This implied that one side of the pore helix was evolutionarily conserved in contrast to its opposite side. In addition, the method of conservation moments correctly identified the disposition of the voltage sensor of voltage-gated potassium channels to form a 310 helix in the membrane.

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

The effects of shared information on semantic calculations in the gene ontology

The effects of shared information on semantic calculations in the gene ontology | CSBJ – Recent Articles | Scoop.it
Abstract: The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures. No thorough investigation has been made into the behavior, complexity, and performance of semantic methods derived from distinct SI approaches. We apply bootstrapping to compare the generalized performance of 57 gene-to-gene semantic measures across six benchmarks. Considering the number of measures, we additionally evaluate whether these methods can be leveraged through ensemble machine learning to improve prediction performance. Results showed that the choice of ontology type most strongly influenced performance across all evaluations. Combining measures into an ensemble classifier reduces cross-validation error beyond any individual measure for protein interaction prediction. This improvement resulted from information gained through the combination of ontology types as ensemble methods within each GO type offered no improvement. These results demonstrate that multiple SI measures can be leveraged for machine learning tasks such as automated gene function prediction by incorporating methods from across the ontologies. To facilitate future research in this area, we developed the GO Graph Tool Kit (GGTK), an open source C++ library with Python interface (github.com/paulbible/ggtk). 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors | CSBJ – Recent Articles | Scoop.it
Abstract: Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7) bound to its ligand CCL21. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

FoldX as Protein Engineering Tool: Better Than Random Based Approaches? - ScienceDirect

FoldX as Protein Engineering Tool: Better Than Random Based Approaches? - ScienceDirect | CSBJ – Recent Articles | Scoop.it
Improving protein stability is an important goal for basic research as well as for clinical and industrial applications but no commonly accepted and w…
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Amplification and bioinformatics analysis of conserved FAD-binding region of L-amino acid oxidase (LAAO) genes in gastropods compared to other organisms

Amplification and bioinformatics analysis of conserved FAD-binding region of L-amino acid oxidase (LAAO) genes in gastropods compared to other organisms | CSBJ – Recent Articles | Scoop.it
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones - ScienceDirect

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones - ScienceDirect | CSBJ – Recent Articles | Scoop.it
The two classical immunophilin families, found essentially in all living cells, are: cyclophilin (CYN) and FK506-binding protein (FKBP). We previously…
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Harnessing the power of Big Data, AI, and Precision Medicine | BioData West 2018

Harnessing the power of Big Data, AI, and Precision Medicine | BioData West 2018 | CSBJ – Recent Articles | Scoop.it
BioData World West is the most comprehensive event in big data, precision medicine, and AI in healthcare.
more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

CSBJ journal, partnered with | BioData EU

BioData World Congress 2017@ Wellcome Genome Campus, Cambridge
http://www.terrapinn.com/conference/biodata/partner-csbj-journal.stm

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Symposium - Systems Biology of Microbial Infection

Symposium - Systems Biology of Microbial Infection | CSBJ – Recent Articles | Scoop.it

4th International Symposium on Systems Biology of Microbial Infection @ Jena (September 21-22, 2017).
http://www.systems-biology-microbial-infection.com/index.html ;

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

What can mathematical modelling say about CHO metabolism and protein glycosylation?

What can mathematical modelling say about CHO metabolism and protein glycosylation? | CSBJ – Recent Articles | Scoop.it
Abstract: Chinese hamster ovary cells have been in the spotlight for process optimization in recent years, due to being the major, long established cell factory for the production of recombinant proteins. A deep, quantitative understanding of CHO metabolism and mechanisms involved in protein glycosylation has proven to be attainable through the development of high throughput technologies. Here we review the most notable accomplishments in the field of modelling CHO metabolism and protein glycosylation. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Functional Roles for Exosomal MicroRNAs in the Tumour Microenvironment

Functional Roles for Exosomal MicroRNAs in the Tumour Microenvironment | CSBJ – Recent Articles | Scoop.it
Abstract: Extracellular microRNAs are released from cells both passively and actively. The presence of these microRNAs in the tumour microenvironment (TME) can significantly impact on the plasticity of cancer cells leading to the promotion of metastatic and angiogenic processes. These extracellular microRNAs can act not only on other cancer cells, but also cells present in the TME, such as immune cells, endothelial cells, fibroblasts, and others acting to subvert the host immune system and drive tumour progression. In this review we highlight the current understanding of both the mechanisms by which microRNAs are released from tumour cells and the downstream functional effects that extracellular microRNAs have on recipient cells. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Flexible Analog Search with Kernel PCA Embedded Molecule Vectors

Flexible Analog Search with Kernel PCA Embedded Molecule Vectors | CSBJ – Recent Articles | Scoop.it
Abstract: Studying analog series to find structural transformations that enhance the activity and ADME properties of lead compounds is an important part of drug development. Matched molecular pair (MMP) search is a powerful tool for analog analysis that imitates researchers' ability to select pairs of compounds that differ only by small well-defined transformations. Abstraction is a challenge for existing MMP search algorithms, which can result in the omission of relevant, inexact MMPs, and inclusion of irrelevant, contextually dissimilar MMPs. In this work, we present a new method for MMP search that returns approximate results and enables flexible control over abstraction of contextual information. We illustrate the concepts and mechanics of our method with a series of exemplar MMP queries, and then benchmark search accuracy using MMPs found by fragment indexing. We show that we can search for MMPs in a context dependent manner, and accurately approximate context independent fragment index based MMP search over a range of fingerprint and dataset conditions. Our method can be used to search for pairwise correspondences among analog sets and bolster MMP datasets where data is missing or incomplete. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms | CSBJ – Recent Articles | Scoop.it
Abstract: We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions | CSBJ – Recent Articles | Scoop.it
Abstract: Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction. 

more...
No comment yet.
Scooped by Computational and Structural Biotechnology Journal
Scoop.it!

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis | CSBJ – Recent Articles | Scoop.it
Abstract: Cassava is one of the most important food security crops in tropical countries, and a competitive resource for the starch, food, feed and ethanol industries. However, genomics research in this crop is much less developed compared to other economically important crops such as rice or maize. The International Center for Tropical Agriculture (CIAT) maintains the largest cassava germplasm collection in the world. Unfortunately, the genetic potential of this diversity for breeding programs remains underexploited due to the difficulties in phenotypic screening and lack of deep genomic information about the different accessions. A chromosome-level assembly of the cassava reference genome was released this year and only a handful of studies have been made, mainly to find quantitative trait loci (QTL) on breeding populations with limited variability. This work presents the results of pooled targeted resequencing of more than 1500 cassava accessions from the CIAT germplasm collection to obtain a dataset of more than 2000 variants within genes related to starch functional properties and herbicide tolerance. Results of twelve bioinformatic pipelines for variant detection in pooled samples were compared to ensure the quality of the variant calling process. Predictions of functional impact were performed using two separate methods to prioritize interesting variation for genotyping and cultivar selection. Targeted resequencing, either by pooled samples or by similar approaches such as Ecotilling or capture, emerges as a cost effective alternative to whole genome sequencing to identify interesting alleles of genes related to relevant traits within large germplasm collections. 

more...
No comment yet.