keyword
MENU ▼
Read by QxMD icon Read
search

Structural bioinformatics

keyword
https://www.readbyqxmd.com/read/28930970/screening-of-critical-genes-and-micrornas-in-blood-samples-of-patients-with-ruptured-intracranial-aneurysms-by-bioinformatic-analysis-of-gene-expression-data
#1
Lijuan Bo, Bo Wei, Zhanfeng Wang, Daliang Kong, Zheng Gao, Zhuang Miao
BACKGROUND This study aimed to identify more potential genes and miRNAs associated with the pathogenesis of intracranial aneurysms (IAs). MATERIAL AND METHODS The dataset of GSE36791 (accession number) was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened for in the blood samples from patients with ruptured IAs and controls, followed by functional and pathway enrichment analyses. In addition, gene co-expression network was constructed and significant modules were extracted from the network by WGCNA R package...
September 20, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28930581/biophysical-mechanisms-complementing-classical-cell-biology
#2
Richard H W Funk
This overview addresses phenomena in cell- and molecular biology which are puzzling by their fast and highly coordinated way of organization. Generally, it appears that informative processes probably involved are more on the biophysical than on the classical biochemical side. The coordination problem is explained within the first part of the review by the topic of endogenous electrical phenomena. These are found e.g. in fast tissue organization and reorganization processes like development, wound healing and regeneration...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28929030/genomic-analysis-of-p-elements-in-natural-populations-of-drosophila-melanogaster
#3
Casey M Bergman, Shunhua Han, Michael G Nelson, Vladyslav Bondarenko, Iryna Kozeretska
The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations...
2017: PeerJ
https://www.readbyqxmd.com/read/28928938/the-elixir-excelerate-train-the-trainer-pilot-programme-empower-researchers-to-deliver-high-quality-training
#4
Sarah L Morgan, Patricia M Palagi, Pedro L Fernandes, Eija Koperlainen, Jure Dimec, Diana Marek, Lee Larcombe, Gabriella Rustici, Teresa K Attwood, Allegra Via
One of the main goals of the ELIXIR-EXCELERATE project from the European Union's Horizon 2020 programme is to support a pan-European training programme to increase bioinformatics capacity and competency across ELIXIR Nodes. To this end, a Train-the-Trainer (TtT) programme has been developed by the TtT subtask of EXCELERATE's Training Platform, to try to expose bioinformatics instructors to aspects of pedagogy and evidence-based learning principles, to help them better design, develop and deliver high-quality training in future...
2017: F1000Research
https://www.readbyqxmd.com/read/28927873/genome-sequence-of-streptomyces-mangrovisoli-musc-149-t-isolated-from-intertidal-sediments
#5
Hooi-Leng Ser, Wen-Si Tan, Nurul-Syakima Ab Mutalib, Wai-Fong Yin, Kok-Gan Chan, Bey-Hing Goh, Learn-Han Lee
As the largest genus in Actinobacteria family, Streptomyces species have the ability to synthesize numerous compounds of diverse structures with bioactivities. Streptomyces mangrovisoli MUSC 149(T) was previously isolated as a novel streptomycete from mangrove forest in east coast of Peninsular Malaysia. The high quality draft genome of MUSC 149(T) comprises 9,165,825bp with G+C content of 72.5%. Through bioinformatics analysis, 21 gene clusters identified in the genome were associated with the production of bioactive secondary metabolites...
September 6, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28927812/bi-pssm-position-specific-scoring-matrix-based-intelligent-computational-model-for-identification-of-mycobacterial-membrane-proteins
#6
Muslim Khan, Maqsood Hayat, Sher Afzal Khan, Saeed Ahmad, Nadeem Iqbal
Mycobacterium is a pathogenic bacterium, which is a causative agent of tuberculosis (TB) and leprosy. These diseases are very crucial and become the cause of death of millions of people every year in the world. So, the characterize structure of membrane proteins of the protozoan play a vital role in the field of drug discovery because, without any knowledge about this Mycobacterium's membrane protein and their types, the scientists are unable to treat this pathogenic protozoan. So, an accurate and competitive computational model is needed to characterize this uncharacterized structure of mycobacterium...
September 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28926624/molecular-characterization-expression-analysis-and-heterologous-expression-of-two-translationally-controlled-tumor-protein-genes-from-cucumis-sativus
#7
Xiang Nan Meng, Qiu Min Chen, Hai Yan Fan, Tie Feng Song, Na Cui, Ju Yong Zhao, Shu Min Jia, Ke Xin Meng
The translationally controlled tumor protein (TCTP) is a family of abundant and ubiquitous proteins involved in several important primary functions. Cucumbers harbor two TCTP genes, CsTCTP1 and CsTCTP2; however, their functional roles remain unclear. In this study, we isolated CsTCTP1 and CsTCTP2 (XP-004134215 and XP-004135602, respectively) promoters, full-length cDNA and genomic sequences from Cucumis sativus. Bioinformatics analysis, containing cis-acting elements, structural domains, phylogenetic tree and conserved motifs, suggested the conservation and divergence of CsTCTP1 and CsTCTP2, thus providing knowledge regarding their functions...
2017: PloS One
https://www.readbyqxmd.com/read/28924511/barcoded-ns31-aml2-primers-for-sequencing-of-arbuscular-mycorrhizal-communities-in-environmental-samples
#8
Benjamin S T Morgan, Louise M Egerton-Warburton
PREMISE OF THE STUDY: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28923002/deep-learning-methods-for-protein-torsion-angle-prediction
#9
Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng
BACKGROUND: Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a number of areas such as protein residue-residue contact prediction, secondary structure prediction, and fold recognition. In this work, we developed deep learning methods to improve the prediction of torsion (dihedral) angles of proteins...
September 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28922742/glytoucan-an-accessible-glycan-structure-repository
#10
Michael Tiemeyer, Kazuhiro Aoki, James Paulson, Richard D Cummings, William S York, Niclas G Karlsson, Frederique Lisacek, Nicolle H Packer, Matthew P Campbell, Nobuyuki P Aoki, Akihiro Fujita, Masaaki Matsubara, Daisuke Shinmachi, Shinichiro Tsuchiya, Issaku Yamada, Michael Pierce, René Ranzinger, Hisashi Narimatsu, Kiyoko F Aoki-Kinoshita
Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data...
October 1, 2017: Glycobiology
https://www.readbyqxmd.com/read/28918301/mathematical-fundamentals-for-the-noise-immunity-of-the-genetic-code
#11
Elena Fimmel, Lutz Strüngmann
Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept...
September 13, 2017: Bio Systems
https://www.readbyqxmd.com/read/28917033/secisearch3-and-seblastian-in-silico-tools-to-predict-secis-elements-and-selenoproteins
#12
Marco Mariotti
The computational identification of selenoprotein genes is complicated by the dual meaning of the UGA codon as stop and selenocysteine. SECIS elements are RNA structures essential for selenocysteine incorporation, which have been used as markers for selenoprotein genes in many bioinformatics studies. The most widely used tool for eukaryotic SECIS finding has been recently improved to its third generation, SECISearch3. This program is also a component of Seblastian, a pipeline for the identification of selenoprotein genes that employs SECIS finding as the first step...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28915445/exploring-the-association-of-rs10490924-polymorphism-with-age-related-macular-degeneration-an-in-silico-approach
#13
Farhad Jahanfar, Hamed Hamishehkar
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. The ARMS2 gene encodes a putative small (11kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of the A69S mutation, we performed a detailed analysis of the ARMS2 sequence with a broad set of bioinformatics tools...
September 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28913791/enabling-molecular-technologies-for-trait-improvement-in-wheat
#14
Prem L Bhalla, Akanksha Sharma, Mohan B Singh
Wheat is the major staple food crop and a source of calories for humans worldwide. A steady increase in the wheat production is essential to meet the demands of an ever-increasing global population and to achieve food security. The large size and structurally intricate genome of polyploid wheat had hindered the genomic analysis. However, with the advent of new genomic technologies such as next generation sequencing has led to genome drafts for bread wheat and its progenitors and has paved the way to design new strategies for crop improvement...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28912832/unique-organization-and-unprecedented-diversity-of-the-bacteroides-pseudobacteroides-cellulosolvens-cellulosome-system
#15
Olga Zhivin, Bareket Dassa, Sarah Moraïs, Sagar M Utturkar, Steven D Brown, Bernard Henrissat, Raphael Lamed, Edward A Bayer
BACKGROUND: (Pseudo) Bacteroides cellulosolvens is an anaerobic, mesophilic, cellulolytic, cellulosome-producing clostridial bacterium capable of utilizing cellulose and cellobiose as carbon sources. Recently, we sequenced the B. cellulosolvens genome, and subsequent comprehensive bioinformatic analysis, herein reported, revealed an unprecedented number of cellulosome-related components, including 78 cohesin modules scattered among 31 scaffoldins and more than 200 dockerin-bearing ORFs...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28912750/current-and-emerging-technologies-for-probing-molecular-signatures-of-traumatic-brain-injury
#16
REVIEW
Ari Ercole, Sandra Magnoni, Gloria Vegliante, Roberta Pastorelli, Jakub Surmacki, Sarah Elizabeth Bohndiek, Elisa R Zanier
Traumatic brain injury (TBI) is understood as an interplay between the initial injury, subsequent secondary injuries, and a complex host response all of which are highly heterogeneous. An understanding of the underlying biology suggests a number of windows where mechanistically inspired interventions could be targeted. Unfortunately, biologically plausible therapies have to-date failed to translate into clinical practice. While a number of stereotypical pathways are now understood to be involved, current clinical characterization is too crude for it to be possible to characterize the biological phenotype in a truly mechanistically meaningful way...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28903901/genome-wide-analysis-of-the-gst-gene-family-in-gossypium-hirsutum-l
#17
Lei Xu, Wen Chen, Guo-Yang Si, Yi-Yuan Huang, Yi Lin, Yong-Ping Cai, Jun-Shan Gao
Glutathione-S-transferase (GST) is a ubiquitous multi-functional protein superfamily that plays important roles in plant primary and secondary metabolism, stress and intercellular signal transduction. Concomitantly, it also functions as a ligand in the metabolism of plant hormones and substance transport. In order to understand the GST gene family in upland cotton (Gossypium hirsutum L.), herein we analyzed the species, evolutionary relationship, physical location, gene structure, conserved motifs and expression patterns...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28902453/implementing-a-web-based-introductory-bioinformatics-course-for-non-bioinformaticians-that-incorporates-practical-exercises
#18
Antony T Vincent, Yves Bourbonnais, Jean-Simon Brouard, Hélène Deveau, Arnaud Droit, Stéphane M Gagné, Michel Guertin, Claude Lemieux, Louis Rathier, Steve J Charette, Patrick Lagüe
A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become specialized. However, biology students who are not involved in a bioinformatics program also need a solid toolbox of bioinformatics software and skills. Therefore, we have developed a completely online bioinformatics course for non-bioinformaticians, entitled "BIF-1901 Introduction à la bio-informatique et à ses outils (Introduction to bioinformatics and bioinformatics tools)," given by the Department of Biochemistry, Microbiology, and Bioinformatics of Université Laval (Quebec City, Canada)...
September 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28901452/screening-critical-genes-associated-with-malignant-glioma-using-bioinformatics-analysis
#19
Yonggang Xu, Jie Wang, Yanbin Xu, Hong Xiao, Jianhua Li, Zhi Wang
Malignant gliomas are high‑grade gliomas, which are derived from glial cells in the spine or brain. To examine the mechanisms underlying malignant gliomas in the present study, the expression profile of GSE54004, which included 12 grade II astrocytomas, 33 grade III astrocytomas and 98 grade IV astrocytomas, was downloaded from the Gene Expression Omnibus. Using the Limma package in R, the differentially expressed genes (DEGs) in grade III, vs. grade II astrocytoma, grade IV, vs. grade II astrocytoma, and grade IV, vs...
September 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28901420/bioinformatics-analysis-of-genetic-variants-of-endoplasmic-reticulum-aminopeptidase-1-in-ankylosing-spondylitis
#20
Xiaoli Wang, Jie Ma, Jianbing Ma, Yurong Wen, Liesu Meng, Hao Yang, Rui Zhang, Dingjun Hao
According to the results of the first genome-wide association study of ankylosing spondylitis (AS), endoplasmic reticulum aminopeptidase 1 (ERAP1) may serve an important role. However, a number of case-control studies have not been able to replicate this result using the same genetic markers. In the present study, the role of common genetic variants of ERAP1 in AS was investigated using two-stage bioinformatics analysis. In the first stage, a classical meta-analysis was performed to assess AS susceptibility markers in ERAP1 using data from available published case-control association studies...
August 31, 2017: Molecular Medicine Reports
keyword
keyword
13141
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"