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Bioinformatics & Computational Biology

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https://www.readbyqxmd.com/read/28302551/role-of-structural-bioinformatics-in-drug-discovery-by-computational-snp-analysis-a-proposed-protocol-for-analyzing-variation-at-the-protein-level
#1
REVIEW
David K Brown, Özlem Tastan Bishop
With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28301747/single-cell-transcriptional-analysis
#2
Angela R Wu, Jianbin Wang, Aaron M Streets, Yanyi Huang
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented...
March 16, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301675/review-article-bioinformatics-an-overview-and-its-applications
#3
W J S Diniz, F Canduri
Technological advancements in recent years have promoted a marked progress in understanding the genetic basis of phenotypes. In line with these advances, genomics has changed the paradigm of biological questions in full genome-wide scale (genome-wide), revealing an explosion of data and opening up many possibilities. On the other hand, the vast amount of information that has been generated points the challenges that must be overcome for storage (Moore's law) and processing of biological information. In this context, bioinformatics and computational biology have sought to overcome such challenges...
March 15, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28293298/rapid-development-of-entity-based-data-models-for-bioinformatics-with-persistence-object-oriented-design-and-structured-interfaces
#4
Elishai Ezra Tsur
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed...
2017: BioData Mining
https://www.readbyqxmd.com/read/28286470/screening-the-molecular-framework-underlying-local-dendritic-mrna-translation
#5
REVIEW
Sanjeev V Namjoshi, Kimberly F Raab-Graham
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28269042/binding-affinity-prediction-of-s-cerevisiae-14-3-3-and-gyf-peptide-recognition-domains-using-support-vector-regression
#6
Volkan Uslan, Huseyin Seker
Proteins interact with other proteins and bio-molecules to carry out biological processes in a cell. Computational models help understanding complex biochemical processes that happens throughout the life of a cell. Domain-mediated protein interaction to peptides one such complex problem in bioinformatics that requires computational predictive models to identify meaningful bindings. In this study, domain-peptide binding affinity prediction models are proposed based on support vector regression. Proposed models are applied to yeast bmh 14-3-3 and syh GYF peptide-recognition domains...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28266743/the-hair-follicle-enigma
#7
Bruno A Bernard
The hair follicle is a mini organ endowed with a unique structure and cyclic behavior. Despite the intense research efforts which have been devoted at deciphering the hair follicle biology over the past 70 years, one must admit that hair follicle remains an enigma. In this brief review, various aspects of hair follicle biology will be addressed, and more importantly, unsolved questions and new possible research tracks will be highlighted, including hair follicle glycobiology and exosome mediated cell-cell interactions...
March 7, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/28266272/multiscale-molecular-simulations-applied-to-nucleic-acid-dendrimer-interactions-studies
#8
Fernando Danilo González-Nilo, Ingrid Araya-Durán, Valeria Márquez-Miranda
BACKGROUND: Dendrimers are monodisperse, regular, three-dimensional and small-scale macromolecules that can be used to release substances such as drugs, markers, and genetic material into the cells. Among these substances, nucleic acids such as plasmid DNA, antisense oligonucleotides (asODN), and small-interfering RNA (siRNA) are widely used as therapeutic macromolecules for the treatment and prevention of diverse diseases. Several studies were focused on the modification of dendrimers aiming to improve their affinity for nucleic acids and their ability to release nucleic acids inside the cells...
March 5, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28263393/voromqa-assessment-of-protein-structure-quality-using-interatomic-contact-areas
#9
Kliment Olechnovič, Česlovas Venclovas
In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge-based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue-residue or atom-atom interactions collected from experimentally determined structures...
March 6, 2017: Proteins
https://www.readbyqxmd.com/read/28254551/in-silico-identification-of-a-therapeutic-target-for-photo-activated-disinfection-with-indocyanine-green-modeling-and-virtual-screening-analysis-of-arg-gingipain-from-porphyromonas-gingivalis
#10
Maryam Pourhajibagher, Abbas Bahador
BACKGROUND: Porphyromonas gingivalis is a momentous bacterial etiological agent associated with periodontitis, peri-implantitis as well as endodontic infections. The potential advantage of Photo-activated disinfection (PAD) as a promising novel approach is the choice of a suitable target site, specific photosensitizer, and wavelength of light for delivery of the light from source to target. Since Arg-gingipain is a cysteine proteinase that is involved in the virulence of P. gingivalis, it was evaluated as a target site for PAD with indocyanine green (ICG) as a photosensitizer...
February 27, 2017: Photodiagnosis and Photodynamic Therapy
https://www.readbyqxmd.com/read/28251962/-chromatin-and-polycomb-biology-and-bioinformatics
#11
R A Kudrin, A A Mironov, E D Stavrovskaya
All cells of a multicellular eukaryotic organism carry almost the same genome, still they obviously demonstrate phenotypes of very divergent kinds. The most probable explanation of the divergence is that different groups of genes are expressed in cells of different types. Expression is regulated at all steps between DNA and a protein, but transcription regulation is the most common regulatory mechanism. Transcription factors, which bind to specific areas of chromatin, can mediate the regulation. Their binding depends on the chromatin structure, which drastically differs among cell types...
January 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28227256/binding-affinity-prediction-of-s-cerevisiae-14-3-3-and-gyf-peptide-recognition-domains-using-support-vector-regression
#12
Volkan Uslan, Huseyin Seker, Volkan Uslan, Huseyin Seker, Huseyin Seker, Volkan Uslan
Proteins interact with other proteins and bio-molecules to carry out biological processes in a cell. Computational models help understanding complex biochemical processes that happens throughout the life of a cell. Domain-mediated protein interaction to peptides one such complex problem in bioinformatics that requires computational predictive models to identify meaningful bindings. In this study, domain-peptide binding affinity prediction models are proposed based on support vector regression. Proposed models are applied to yeast bmh 14-3-3 and syh GYF peptide-recognition domains...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28221002/computational-biology-and-chemistry-in-mti-emphasis-on-the-prediction-of-some-admet-properties
#13
REVIEW
Maria A Miteva, Bruno O Villoutreix
Our research and teaching group called MTi (Molécules Thérapeutiques in silico) has developed numerous applications available online, thanks to the RPBS platform (Ressource Parisienne en Bioinformatique Structurale), in the field of chemoinformatics, structural bioinformatics and drug design. Since its opening in 2009, over 200 articles/reviews have been reported and involve virtual screening studies, prediction of druggability, analysis of protein-protein interaction inhibitors, development of databases, data mining and knowledge discovery, as well as combined in silico-in vitro work to search for new hits and chemical probes acting on original targets in several therapeutic areas...
February 21, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28220104/systems-biology-derived-discoveries-of-intrinsic-clocks
#14
REVIEW
Arthur Millius, Hiroki R Ueda
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28209127/repo-an-r-package-for-data-centered-management-of-bioinformatic-pipelines
#15
Francesco Napolitano
BACKGROUND: Reproducibility in Data Analysis research has long been a significant concern, particularly in the areas of Bioinformatics and Computational Biology. Towards the aim of developing reproducible and reusable processes, Data Analysis management tools can help giving structure and coherence to complex data flows. Nonetheless, improved software quality comes at the cost of additional design and planning effort, which may become impractical in rapidly changing development environments...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28205527/an-end-to-end-software-solution-for-the-analysis-of-high-throughput-single-cell-migration-data
#16
Paola Masuzzo, Lynn Huyck, Aleksandra Simiczyjew, Christophe Ampe, Lennart Martens, Marleen Van Troys
The systematic study of single-cell migration requires the availability of software for assisting data inspection, quality control and analysis. This is especially important for high-throughput experiments, where multiple biological conditions are tested in parallel. Although the field of cell migration can count on different computational tools for cell segmentation and tracking, downstream data visualization, parameter extraction and statistical analysis are still left to the user and are currently not possible within a single tool...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28187425/computational-lipidomics-and-lipid-bioinformatics-filling-in-the-blanks
#17
Josch Pauling, Edda Klipp
Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187420/current-progress-of-high-throughput-microrna-differential-expression-analysis-and-random-forest-gene-selection-for-model-and-non-model-systems-an-r-implementation
#18
Jing Zhang, Hanane Hadj-Moussa, Kenneth B Storey
MicroRNAs are short non-coding RNA transcripts that act as master cellular egulators with roles in orchestrating virtually all biological functions. The recent affordability and widespread use of high-throughput microRNA profiling technologies has grown along with the advancement of bioinformatics tools available for analysis of the mounting data flow. While there are many computational resources available for the management of data from genome sequenced animals, researchers are often faced with the challenge of identifying the biological implications of the daunting amount of data generated from these high-throughput technologies...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28185571/hippi-highly-accurate-protein-family-classification-with-ensembles-of-hmms
#19
Nam-Phuong Nguyen, Michael Nute, Siavash Mirarab, Tandy Warnow
BACKGROUND: Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. RESULTS: We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification)...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28182018/genome-wide-base-resolution-mapping-of-dna-methylation-in-single-cells-using-single-cell-bisulfite-sequencing-scbs-seq
#20
Stephen J Clark, Sébastien A Smallwood, Heather J Lee, Felix Krueger, Wolf Reik, Gavin Kelsey
DNA methylation (DNAme) is an important epigenetic mark in diverse species. Our current understanding of DNAme is based on measurements from bulk cell samples, which obscures intercellular differences and prevents analyses of rare cell types. Thus, the ability to measure DNAme in single cells has the potential to make important contributions to the understanding of several key biological processes, such as embryonic development, disease progression and aging. We have recently reported a method for generating genome-wide DNAme maps from single cells, using single-cell bisulfite sequencing (scBS-seq), allowing the quantitative measurement of DNAme at up to 50% of CpG dinucleotides throughout the mouse genome...
March 2017: Nature Protocols
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