journal
MENU ▼
Read by QxMD icon Read
search

Advances in Bioinformatics

journal
https://www.readbyqxmd.com/read/30186322/structural-prediction-and-mutational-analysis-of-rv3906c-gene-of-mycobacterium-tuberculosis-h-37-rv-to-determine-its-essentiality-in-survival
#1
Md Amjad Beg, Shivangi, Sonu Chand Thakur, Laxman S Meena
The emergence of tuberculosis is at the peak; therefore to station it at its lower level we hereby try bioinformatics approach against Mycobacterium tuberculosis [ M. tuberculosis ] pathogenesis. Rv3906c is a conserved hypothetical gene of M. tuberculosis and contains many GTP binding protein motif DXXG which demonstrate that this gene might be processed in a GTP binding or in GTP hydrolyzing manner. This gene shows interaction with its adjacent genes as well as pcnA which is a polymerase and localized in the extracellular region and found to be a soluble protein...
2018: Advances in Bioinformatics
https://www.readbyqxmd.com/read/30151007/gaussian-fuzzy-number-for-str-dna-similarity-calculation-involving-familial-and-tribal-relationships
#2
Maria Susan Anggreainy, M Rahmat Widyanto, Belawati H Widjaja, Nurtami Soedarsono
We performed locus similarity calculation by measuring fuzzy intersection between individual locus and reference locus and then performed CODIS STR-DNA similarity calculation. The fuzzy intersection calculation enables a more robust CODIS STR-DNA similarity calculation due to imprecision caused by noise produced by PCR machine. We also proposed shifted convoluted Gaussian fuzzy number (SCGFN) and Gaussian fuzzy number (GFN) to represent each locus value as improvement of triangular fuzzy number (TFN) as used in previous research...
2018: Advances in Bioinformatics
https://www.readbyqxmd.com/read/30147721/creation-of-individual-scientific-concept-centered-semantic-maps-based-on-automated-text-mining-analysis-of-pubmed
#3
Ekaterina Ilgisonis, Andrey Lisitsa, Valerya Kudryavtseva, Elena Ponomarenko
Concept-centered semantic maps were created based on a text-mining analysis of PubMed using the BiblioEngine_v2018 software. The objects ("concepts") of a semantic map can be MeSH-terms or other terms (names of proteins, diseases, chemical compounds, etc.) structured in the form of controlled vocabularies. The edges between the two objects were automatically calculated based on the index of semantic similarity, which is proportional to the number of publications related to both objects simultaneously...
2018: Advances in Bioinformatics
https://www.readbyqxmd.com/read/30034468/big-data-management-for-healthcare-systems-architecture-requirements-and-implementation
#4
REVIEW
Naoual El Aboudi, Laila Benhlima
The growing amount of data in healthcare industry has made inevitable the adoption of big data techniques in order to improve the quality of healthcare delivery. Despite the integration of big data processing approaches and platforms in existing data management architectures for healthcare systems, these architectures face difficulties in preventing emergency cases. The main contribution of this paper is proposing an extensible big data architecture based on both stream computing and batch computing in order to enhance further the reliability of healthcare systems by generating real-time alerts and making accurate predictions on patient health condition...
2018: Advances in Bioinformatics
https://www.readbyqxmd.com/read/30026759/a-novel-framework-for-ab-initio-coarse-protein-structure-prediction
#5
Sandhya Parasnath Dubey, S Balaji, N Gopalakrishna Kini, M Sathish Kumar
Hydrophobic-Polar model is a simplified representation of Protein Structure Prediction (PSP) problem. However, even with the HP model, the PSP problem remains NP-complete. This work proposes a systematic and problem specific design for operators of the evolutionary program which hybrids with local search hill climbing, to efficiently explore the search space of PSP and thereby obtain an optimum conformation. The proposed algorithm achieves this by incorporating the following novel features: (i) new initialization method which generates only valid individuals with (rather than random) better fitness values; (ii) use of probability-based selection operators that limit the local convergence; (iii) use of secondary structure based mutation operator that makes the structure more closely to the laboratory determined structure; and (iv) incorporating all the above-mentioned features developed a complete two-tier framework...
2018: Advances in Bioinformatics
https://www.readbyqxmd.com/read/29849611/in-silico-characterization-and-structural-modeling-of-dermacentor-andersoni-p36-immunosuppressive-protein
#6
Martin Omulindi Oyugi, Johnson Kangethe Kinyua, Esther Nkirote Magiri, Milcah Wagio Kigoni, Evenilton Pessoa Costa, Naftaly Wang'ombe Githaka
Ticks cause approximately $17-19 billion economic losses to the livestock industry globally. Development of recombinant antitick vaccine is greatly hindered by insufficient knowledge and understanding of proteins expressed by ticks. Ticks secrete immunosuppressant proteins that modulate the host's immune system during blood feeding; these molecules could be a target for antivector vaccine development. Recombinant p36, a 36 kDa immunosuppressor from the saliva of female Dermacentor andersoni , suppresses T-lymphocytes proliferation in vitro...
2018: Advances in Bioinformatics
https://www.readbyqxmd.com/read/29796018/framework-for-parallel-preprocessing-of-microarray-data-using-hadoop
#7
Amirhossein Sahlabadi, Ravie Chandren Muniyandi, Mahdi Sahlabadi, Hossein Golshanbafghy
Nowadays, microarray technology has become one of the popular ways to study gene expression and diagnosis of disease. National Center for Biology Information (NCBI) hosts public databases containing large volumes of biological data required to be preprocessed, since they carry high levels of noise and bias. Robust Multiarray Average (RMA) is one of the standard and popular methods that is utilized to preprocess the data and remove the noises. Most of the preprocessing algorithms are time-consuming and not able to handle a large number of datasets with thousands of experiments...
2018: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28932239/computational-analysis-of-gynura-bicolor-bioactive-compounds-as-dipeptidyl-peptidase-iv-inhibitor
#8
Lina Rozano, Muhammad Redha Abdullah Zawawi, Muhamad Aizuddin Ahmad, Indu Bala Jaganath
The inhibition of dipeptidyl peptidase-IV (DPPIV) is a popular route for the treatment of type-2 diabetes. Commercially available gliptin-based drugs such as sitagliptin, anagliptin, linagliptin, saxagliptin, and alogliptin were specifically developed as DPPIV inhibitors for diabetic patients. The use of Gynura bicolor in treating diabetes had been reported in various in vitro experiments. However, an understanding of the inhibitory actions of G. bicolor bioactive compounds on DPPIV is still lacking and this may provide crucial information for the development of more potent and natural sources of DPPIV inhibitors...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28804499/empirical-comparison-of-visualization-tools-for-larger-scale-network-analysis
#9
REVIEW
Georgios A Pavlopoulos, David Paez-Espino, Nikos C Kyrpides, Ioannis Iliopoulos
Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today's indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28261268/an-efficient-approach-in-analysis-of-dna-base-calling-using-neural-fuzzy-model
#10
Safa A Hameed, Raed I Hamed
This paper presented the issues of true representation and a reliable measure for analyzing the DNA base calling is provided. The method implemented dealt with the data set quality in analyzing DNA sequencing, it is investigating solution of the problem of using Neurofuzzy techniques for predicting the confidence value for each base in DNA base calling regarding collecting the data for each base in DNA, and the simulation model of designing the ANFIS contains three subsystems and main system; obtain the three features from the subsystems and in the main system and use the three features to predict the confidence value for each base...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28250767/multiple-linear-regression-for-reconstruction-of-gene-regulatory-networks-in-solving-cascade-error-problems
#11
Faridah Hani Mohamed Salleh, Suhaila Zainudin, Shereena M Arif
Gene regulatory network (GRN) reconstruction is the process of identifying regulatory gene interactions from experimental data through computational analysis. One of the main reasons for the reduced performance of previous GRN methods had been inaccurate prediction of cascade motifs. Cascade error is defined as the wrong prediction of cascade motifs, where an indirect interaction is misinterpreted as a direct interaction. Despite the active research on various GRN prediction methods, the discussion on specific methods to solve problems related to cascade errors is still lacking...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28191015/combined-docking-with-classical-force-field-and-quantum-chemical-semiempirical-method-pm7
#12
A V Sulimov, D C Kutov, E V Katkova, V B Sulimov
Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method...
2017: Advances in Bioinformatics
https://www.readbyqxmd.com/read/28127307/in-silico-analysis-of-snps-in-park2-and-pink1-genes-that-potentially-cause-autosomal-recessive-parkinson-disease
#13
Yousuf Hasan Yousuf Bakhit, Mohamed Osama Mirghani Ibrahim, Mutaz Amin, Yousra Abdelazim Mirghani, Mohamed Ahmed Salih Hassan
Introduction. Parkinson's disease (PD) is a common neurodegenerative disorder. Mutations in PINK1 are the second most common agents causing autosomal recessive, early onset PD. We aimed to identify the pathogenic SNPs in PARK2 and PINK1 using in silico prediction software and their effect on the structure, function, and regulation of the proteins. Materials and Methods. We carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27698666/in-silico-analysis-of-gene-expression-network-components-underlying-pigmentation-phenotypes-in-the-python-identified-evolutionarily-conserved-clusters-of-transcription-factor-binding-sites
#14
Kristopher J L Irizarry, Randall L Bryden
Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27688753/systematic-bioinformatic-approach-for-prediction-of-linear-b-cell-epitopes-on-dengue-e-and-prm-protein
#15
Mahesha N Nadugala, Prasad H Premaratne, Charitha L Goonasekara
B-cell epitopes on the envelope (E) and premembrane (prM) proteins of dengue virus (DENV) were predicted using bioinformatics tools, BepiPred, Ellipro, and SVMTriP. Predicted epitopes, 32 and 17 for E and prM proteins, respectively, were then characterized for their level of conservations. The epitopes, EP4/E (48-55), epitope number 4 of E protein at amino acids 48-55, EP9/E (165-182), EP11/E (218-233), EP20/E (322-349), EP21/E (326-353), EP23/E (356-365), and EP25/E (380-386), showed a high intraserotype conservancy with very low pan-serotype conservancy, demonstrating a potential target as serotype specific diagnostic markers...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27667997/prediction-and-in-silico-identification-of-novel-b-cells-and-t-cells-epitopes-in-the-s1-spike-glycoprotein-of-m41-and-cr88-793-b-infectious-bronchitis-virus-serotypes-for-application-in-peptide-vaccines
#16
Faruku Bande, Siti Suri Arshad, Mohd Hair Bejo, Saeid Kadkhodaei, Abdul Rahman Omar
Bioinformatic analysis was used to predict antigenic B-cell and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. A conserved linear B-cell epitope peptide, YTSNETTDVTS(175-185), was identified in M41 IBV strains while three such epitopes types namely, VSNASPNSGGVD(279-290), HPKCNFRPENI(328-338), and NETNNAGSVSDCTAGT(54-69), were predicted in CR88 IBV strains. Analysis of MHCI binding peptides in M41 IBV strains revealed the presence of 15 antigenic peptides out of which 12 were highly conserved in 96-100% of the total M41 strains analysed...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27555868/an-optimal-seed-based-compression-algorithm-for-dna-sequences
#17
Pamela Vinitha Eric, Gopakumar Gopalakrishnan, Muralikrishnan Karunakaran
This paper proposes a seed based lossless compression algorithm to compress a DNA sequence which uses a substitution method that is similar to the LempelZiv compression scheme. The proposed method exploits the repetition structures that are inherent in DNA sequences by creating an offline dictionary which contains all such repeats along with the details of mismatches. By ensuring that only promising mismatches are allowed, the method achieves a compression ratio that is at par or better than the existing lossless DNA sequence compression algorithms...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27478437/bioinformatics-approach-for-prediction-of-functional-coding-noncoding-simple-polymorphisms-snps-indels-in-human-braf-gene
#18
Mohamed M Hassan, Shaza E Omer, Rahma M Khalf-Allah, Razaz Y Mustafa, Isra S Ali, Sofia B Mohamed
This study was carried out for Homo sapiens single variation (SNPs/Indels) in BRAF gene through coding/non-coding regions. Variants data was obtained from database of SNP even last update of November, 2015. Many bioinformatics tools were used to identify functional SNPs and indels in proteins functions, structures and expressions. Results shown, for coding polymorphisms, 111 SNPs predicted as highly damaging and six other were less. For UTRs, showed five SNPs and one indel were altered in micro RNAs binding sites (3' UTR), furthermore nil SNP or indel have functional altered in transcription factor binding sites (5' UTR)...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27413369/multiphase-simulated-annealing-based-on-boltzmann-and-bose-einstein-distribution-applied-to-protein-folding-problem
#19
Juan Frausto-Solis, Ernesto Liñán-García, Juan Paulo Sánchez-Hernández, J Javier González-Barbosa, Carlos González-Flores, Guadalupe Castilla-Valdez
A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE) is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP) instances. This new approach has four phases: (i) Multiquenching Phase (MQP), (ii) Boltzmann Annealing Phase (BAP), (iii) Bose-Einstein Annealing Phase (BEAP), and (iv) Dynamical Equilibrium Phase (DEP). BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively...
2016: Advances in Bioinformatics
https://www.readbyqxmd.com/read/27366148/fullssr-microsatellite-finder-and-primer-designer
#20
Sebastián Metz, Juan Manuel Cabrera, Eva Rueda, Federico Giri, Patricia Amavet
Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis...
2016: Advances in Bioinformatics
journal
journal
42563
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"