176 results match your criteria Advances in bioinformatics[Journal]


Structural Prediction and Mutational Analysis of Rv3906c Gene of HRv to Determine Its Essentiality in Survival.

Adv Bioinformatics 2018 15;2018:6152014. Epub 2018 Aug 15.

CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.

The emergence of tuberculosis is at the peak; therefore to station it at its lower level we hereby try bioinformatics approach against [] pathogenesis. Rv3906c is a conserved hypothetical gene of 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 which is a polymerase and localized in the extracellular region and found to be a soluble protein. Read More

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https://www.hindawi.com/journals/abi/2018/6152014/
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http://dx.doi.org/10.1155/2018/6152014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114228PMC
August 2018
18 Reads

Gaussian Fuzzy Number for STR-DNA Similarity Calculation Involving Familial and Tribal Relationships.

Adv Bioinformatics 2018 29;2018:8602513. Epub 2018 Jul 29.

Faculty of Dentistry, Universitas Indonesia, Salemba Campus, Jakarta 10430, Indonesia.

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. Read More

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https://www.hindawi.com/journals/abi/2018/8602513/
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http://dx.doi.org/10.1155/2018/8602513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6087604PMC
July 2018
18 Reads

Creation of Individual Scientific Concept-Centered Semantic Maps Based on Automated Text-Mining Analysis of PubMed.

Adv Bioinformatics 2018 26;2018:4625394. Epub 2018 Jul 26.

Institute of Biomedical Chemistry, RAS, Moscow, Russia.

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. Read More

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http://dx.doi.org/10.1155/2018/4625394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6083525PMC
July 2018
18 Reads

Big Data Management for Healthcare Systems: Architecture, Requirements, and Implementation.

Adv Bioinformatics 2018 21;2018:4059018. Epub 2018 Jun 21.

Department of computer sciencne, Mohammadia School of Engineering, Mohammed V University, Rabat, Morocco.

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. Read More

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http://dx.doi.org/10.1155/2018/4059018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6032968PMC
June 2018
1 Read

A Novel Framework for Coarse Protein Structure Prediction.

Adv Bioinformatics 2018 20;2018:7607384. Epub 2018 Jun 20.

Department of ECE, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.

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. Read More

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http://dx.doi.org/10.1155/2018/7607384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031167PMC
June 2018
2 Reads

In Silico Characterization and Structural Modeling of p36 Immunosuppressive Protein.

Adv Bioinformatics 2018 8;2018:7963401. Epub 2018 Apr 8.

Animal and Human Health Program, International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya.

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. Read More

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http://dx.doi.org/10.1155/2018/7963401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5911333PMC
April 2018
9 Reads

Framework for Parallel Preprocessing of Microarray Data Using Hadoop.

Adv Bioinformatics 2018 29;2018:9391635. Epub 2018 Mar 29.

Faculty of Creative Multimedia, Multimedia University, 63100 Cyberjaya, Selangor, Malaysia.

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. Read More

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http://dx.doi.org/10.1155/2018/9391635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896349PMC

Computational Analysis of Bioactive Compounds as Dipeptidyl Peptidase-IV Inhibitor.

Adv Bioinformatics 2017 8;2017:5124165. Epub 2017 Aug 8.

Director-General's Office, Malaysian Agricultural Research and Development Institute, 43400 Selangor, Malaysia.

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 in treating diabetes had been reported in various in vitro experiments. Read More

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http://dx.doi.org/10.1155/2017/5124165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591938PMC
August 2017
12 Reads

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.

Adv Bioinformatics 2017 18;2017:1278932. Epub 2017 Jul 18.

Division of Basic Sciences, University of Crete Medical School, Andrea Kalokerinou Street, Heraklion, Greece.

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. Read More

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http://dx.doi.org/10.1155/2017/1278932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540468PMC
July 2017
29 Reads

An Efficient Approach in Analysis of DNA Base Calling Using Neural Fuzzy Model.

Adv Bioinformatics 2017 31;2017:3686025. Epub 2017 Jan 31.

College of Science and Technology, University of Human Development, Sulaymaniyah, Iraq.

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. This is achieving effective results with high performance in employment. Read More

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http://dx.doi.org/10.1155/2017/3686025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316432PMC
January 2017

Multiple Linear Regression for Reconstruction of Gene Regulatory Networks in Solving Cascade Error Problems.

Adv Bioinformatics 2017 29;2017:4827171. Epub 2017 Jan 29.

Department of Information Technology, Faculty of Computing and Information Technology in Rabigh, King Abdulaziz University, Rabigh, Saudi Arabia.

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. Read More

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http://dx.doi.org/10.1155/2017/4827171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303608PMC
January 2017

Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.

Adv Bioinformatics 2017 16;2017:7167691. Epub 2017 Jan 16.

Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia; Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia.

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. Read More

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http://dx.doi.org/10.1155/2017/7167691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5278191PMC
January 2017
1 Read

In Silico Analysis of SNPs in and Genes That Potentially Cause Autosomal Recessive Parkinson Disease.

Adv Bioinformatics 2016 29;2016:9313746. Epub 2016 Dec 29.

Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.

. Parkinson's disease (PD) is a common neurodegenerative disorder. Mutations in are the second most common agents causing autosomal recessive, early onset PD. Read More

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https://www.hindawi.com/journals/abi/2016/9313746/
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http://dx.doi.org/10.1155/2016/9313746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227114PMC
December 2016
38 Reads

Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites.

Adv Bioinformatics 2016 6;2016:1286510. Epub 2016 Sep 6.

College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA.

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. Read More

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http://dx.doi.org/10.1155/2016/1286510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5028829PMC
September 2016

Systematic Bioinformatic Approach for Prediction of Linear B-Cell Epitopes on Dengue E and prM Protein.

Adv Bioinformatics 2016 1;2016:1373157. Epub 2016 Sep 1.

Faculty of Medicine, General Sir John Kotelawala Defence University, 10390 Ratmalana, Sri Lanka.

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. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5023840PMC
http://dx.doi.org/10.1155/2016/1373157DOI Listing
September 2016
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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.

Adv Bioinformatics 2016 7;2016:5484972. Epub 2016 Sep 7.

Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia; Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia.

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. Read More

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http://dx.doi.org/10.1155/2016/5484972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030393PMC
September 2016
62 Reads

An Optimal Seed Based Compression Algorithm for DNA Sequences.

Adv Bioinformatics 2016 31;2016:3528406. Epub 2016 Jul 31.

Department of Computer Science and Engineering, National Institute of Technology Calicut, Kerala 673601, India.

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. Read More

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http://dx.doi.org/10.1155/2016/3528406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983397PMC
August 2016
6 Reads

Bioinformatics Approach for Prediction of Functional Coding/Noncoding Simple Polymorphisms (SNPs/Indels) in Human BRAF Gene.

Adv Bioinformatics 2016 10;2016:2632917. Epub 2016 Jul 10.

Tropical Medicine Research Institute, Khartoum, Sudan.

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. Read More

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http://dx.doi.org/10.1155/2016/2632917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958420PMC
August 2016
7 Reads

Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem.

Adv Bioinformatics 2016 20;2016:7357123. Epub 2016 Jun 20.

Instituto Tecnológico de Ciudad Madero, Tecnológico Nacional de México, Avenida Sor Juana Inés de la Cruz s/n, Colonia los Mangos, 89440 Ciudad Madero, TAMPS, Mexico.

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). Read More

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http://dx.doi.org/10.1155/2016/7357123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931103PMC
July 2016
2 Reads

FullSSR: Microsatellite Finder and Primer Designer.

Adv Bioinformatics 2016 6;2016:6040124. Epub 2016 Jun 6.

Laboratorio de Genética, CONICET, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.

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. Read More

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http://dx.doi.org/10.1155/2016/6040124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913048PMC
July 2016
31 Reads

Agent-Based Deterministic Modeling of the Bone Marrow Homeostasis.

Adv Bioinformatics 2016 2;2016:8054219. Epub 2016 Jun 2.

Department of Computer Science and Engineering, VNIT Nagpur, Nagpur 440010, India.

Modeling of stem cells not only describes but also predicts how a stem cell's environment can control its fate. The first stem cell populations discovered were hematopoietic stem cells (HSCs). In this paper, we present a deterministic model of bone marrow (that hosts HSCs) that is consistent with several of the qualitative biological observations. Read More

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http://dx.doi.org/10.1155/2016/8054219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910184PMC

Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions.

Adv Bioinformatics 2016 24;2016:5614058. Epub 2016 May 24.

Diagnostic Genetics, LabPLUS, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand.

The increasing diagnostic use of gene sequencing has led to an expanding dataset of novel variants that lie within consensus splice junctions. The challenge for diagnostic laboratories is the evaluation of these variants in order to determine if they affect splicing or are merely benign. A common evaluation strategy is to use in silico analysis, and it is here that a number of programmes are available online; however, currently, there are no consensus guidelines on the selection of programmes or protocols to interpret the prediction results. Read More

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http://dx.doi.org/10.1155/2016/5614058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894998PMC
June 2016
12 Reads

A Support Vector Machine Classification of Thyroid Bioptic Specimens Using MALDI-MSI Data.

Adv Bioinformatics 2016 17;2016:3791214. Epub 2016 May 17.

Department of Informatics, Systems and Communication, University of Milano-Bicocca, Viale Sarca 336, 20125 Milan, Italy.

Biomarkers able to characterise and predict multifactorial diseases are still one of the most important targets for all the "omics" investigations. In this context, Matrix-Assisted Laser Desorption/Ionisation-Mass Spectrometry Imaging (MALDI-MSI) has gained considerable attention in recent years, but it also led to a huge amount of complex data to be elaborated and interpreted. For this reason, computational and machine learning procedures for biomarker discovery are important tools to consider, both to reduce data dimension and to provide predictive markers for specific diseases. Read More

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http://dx.doi.org/10.1155/2016/3791214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886047PMC
June 2016
1 Read

Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction.

Adv Bioinformatics 2016 4;2016:1276594. Epub 2016 May 4.

Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Room 101, Medical Annex Building, 547 Pedro Gil Street, Ermita, 1000 Manila, Philippines.

Epitope-based design of vaccines, immunotherapeutics, and immunodiagnostics is complicated by structural changes that radically alter immunological outcomes. This is obscured by expressing redundancy among linear-epitope data as fractional sequence-alignment identity, which fails to account for potentially drastic loss of binding affinity due to single-residue substitutions even where these might be considered conservative in the context of classical sequence analysis. From the perspective of immune function based on molecular recognition of epitopes, functional redundancy of epitope data (FRED) thus may be defined in a biologically more meaningful way based on residue-level physicochemical similarity in the context of antigenic cross-reaction, with functional similarity between epitopes expressed as the Shannon information entropy for differential epitope binding. Read More

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http://dx.doi.org/10.1155/2016/1276594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870339PMC

Molecular Docking and In Silico ADMET Study Reveals Acylguanidine 7a as a Potential Inhibitor of β-Secretase.

Adv Bioinformatics 2016 10;2016:9258578. Epub 2016 Apr 10.

Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh 492010, India.

Amyloidogenic pathway in Alzheimer's disease (AD) involves breakdown of APP by β-secretase followed by γ-secretase and results in formation of amyloid beta plaque. β-secretase has been a promising target for developing novel anti-Alzheimer drugs. To test different molecules for this purpose, test ligands like acylguanidine 7a, rosiglitazone, pioglitazone, and tartaric acid were docked against our target protein β-secretase enzyme retrieved from Protein Data Bank, considering MK-8931 (phase III trial, Merck) as the positive control. Read More

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http://dx.doi.org/10.1155/2016/9258578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842033PMC
May 2016
10 Reads

Feature Selection Has a Large Impact on One-Class Classification Accuracy for MicroRNAs in Plants.

Adv Bioinformatics 2016 12;2016:5670851. Epub 2016 Apr 12.

Molecular Biology and Genetics, Izmir Institute of Technology, Urla, 35430 Izmir, Turkey; Bionia Incorporated, IZTEKGEB A8, Urla, 35430 Izmir, Turkey.

MicroRNAs (miRNAs) are short RNA sequences involved in posttranscriptional gene regulation. Their experimental analysis is complicated and, therefore, needs to be supplemented with computational miRNA detection. Currently computational miRNA detection is mainly performed using machine learning and in particular two-class classification. Read More

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http://www.hindawi.com/journals/abi/2016/5670851/
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http://dx.doi.org/10.1155/2016/5670851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844869PMC
May 2016
9 Reads

Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses.

Adv Bioinformatics 2016 14;2016:1673284. Epub 2016 Apr 14.

Laboratory for Structural Biology and Bio-Computing, Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India.

Ebola Virus Disease (EVD) is a life-threatening haemorrhagic fever in humans. Even though there are many reports on EVD, the protein precursor functions and virulent factors of ebolaviruses remain poorly understood. Comparative analyses of Ebolavirus genomes will help in the identification of these important features. Read More

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http://dx.doi.org/10.1155/2016/1673284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848411PMC
May 2016
4 Reads

Robust Feature Selection from Microarray Data Based on Cooperative Game Theory and Qualitative Mutual Information.

Adv Bioinformatics 2016 20;2016:1058305. Epub 2016 Mar 20.

Department of Software Engineering, Islamic Azad University, Mashhad Branch, Mashhad, Iran.

High dimensionality of microarray data sets may lead to low efficiency and overfitting. In this paper, a multiphase cooperative game theoretic feature selection approach is proposed for microarray data classification. In the first phase, due to high dimension of microarray data sets, the features are reduced using one of the two filter-based feature selection methods, namely, mutual information and Fisher ratio. Read More

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http://dx.doi.org/10.1155/2016/1058305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818815PMC

Random versus Deterministic Descent in RNA Energy Landscape Analysis.

Adv Bioinformatics 2016 2;2016:9654921. Epub 2016 Mar 2.

Informatics Department, King's College London, London WC2R 2LS, UK.

Identifying sets of metastable conformations is a major research topic in RNA energy landscape analysis, and recently several methods have been proposed for finding local minima in landscapes spawned by RNA secondary structures. An important and time-critical component of such methods is steepest, or gradient, descent in attraction basins of local minima. We analyse the speed-up achievable by randomised descent in attraction basins in the context of large sample sets where the size has an order of magnitude in the region of ~10(6). Read More

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http://dx.doi.org/10.1155/2016/9654921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4808746PMC

Structural Dynamics of Human Argonaute2 and Its Interaction with siRNAs Designed to Target Mutant tdp43.

Adv Bioinformatics 2016 6;2016:8792814. Epub 2016 Mar 6.

Centre for Bioinformatics, Pondicherry University, Pondicherry 605014, India.

The human Argonaute2 protein (Ago2) is a key player in RNA interference pathway and small RNA recognition by Ago2 is the crucial step in siRNA mediated gene silencing mechanism. The present study highlights the structural and functional dynamics of human Ago2 and the interaction mechanism of Ago2 with a set of seven siRNAs for the first time. The human Ago2 protein adopts two conformations such as "open" and "close" during the simulation of 25 ns. Read More

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http://dx.doi.org/10.1155/2016/8792814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824133PMC
April 2016
2 Reads

Efficacy and Toxicity Assessment of Different Antibody Based Antiangiogenic Drugs by Computational Docking Method.

Adv Bioinformatics 2016 7;2016:7053712. Epub 2016 Mar 7.

Department of Physiology, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata 700 126, India; Society for Systems Biology & Translational Research, No. 103, Block C, Bangur Avenue, Kolkata 700 055, India.

Bevacizumab and trastuzumab are two antibody based antiangiogenic drugs that are in clinical practice for the treatment of different cancers. Presently applications of these drugs are based on the empirical choice of clinical experts that follow towards population based clinical trials and, hence, their molecular efficacies in terms of quantitative estimates are not being explored. Moreover, different clinical trials with these drugs showed different toxicity symptoms in patients. Read More

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http://dx.doi.org/10.1155/2016/7053712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4800073PMC
April 2016
4 Reads

BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins.

Adv Bioinformatics 2016 29;2016:8150784. Epub 2016 Feb 29.

Centre for Chemistry and Biotechnology, Deakin University, Geelong, VIC 3217, Australia.

The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL) proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Read More

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http://dx.doi.org/10.1155/2016/8150784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4789356PMC
April 2016
3 Reads

In Silico Approach for SAR Analysis of the Predicted Model of DEPDC1B: A Novel Target for Oral Cancer.

Adv Bioinformatics 2016 29;2016:3136024. Epub 2016 Feb 29.

School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong.

With the incidence rate of oral carcinogenesis increasing in the Southeast-Asian countries, due to increase in the consumption of tobacco and betel quid as well as infection from human papillomavirus, specifically type 16, it becomes crucial to predict the transition of premalignant lesion to cancerous tissue at an initial stage in order to control the process of oncogenesis. DEPDC1B, downregulated in the presence of E2 protein, was recently found to be overexpressed in oral cancer, which can possibly be explained by the disruption of the E2 open reading frame upon the integration of viral genome into the host genome. DEPDC1B mediates its effect by directly interacting with Rac1 protein, which is known to regulate important cell signaling pathways. Read More

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http://dx.doi.org/10.1155/2016/3136024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4789359PMC
April 2016
2 Reads

Large-Scale Recurrent Neural Network Based Modelling of Gene Regulatory Network Using Cuckoo Search-Flower Pollination Algorithm.

Adv Bioinformatics 2016 16;2016:5283937. Epub 2016 Feb 16.

Department of Computer Science and Engineering, University of Calcutta, Kolkata 700 098, India.

The accurate prediction of genetic networks using computational tools is one of the greatest challenges in the postgenomic era. Recurrent Neural Network is one of the most popular but simple approaches to model the network dynamics from time-series microarray data. To date, it has been successfully applied to computationally derive small-scale artificial and real-world genetic networks with high accuracy. Read More

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http://www.hindawi.com/journals/abi/2016/5283937/
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http://dx.doi.org/10.1155/2016/5283937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771889PMC
March 2016
3 Reads

Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking.

Adv Bioinformatics 2016 14;2016:9841250. Epub 2016 Feb 14.

Department of Biochemistry, Sri Krishnadevaraya University, Anantapur 515 003, India.

The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. Read More

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http://dx.doi.org/10.1155/2016/9841250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769735PMC
March 2016
4 Reads
1 Citation

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin.

Adv Bioinformatics 2016 6;2016:8701201. Epub 2016 Jan 6.

School of Life Science, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019, India.

2-Haloalkanoic acid dehalogenase enzymes have broad range of applications, starting from bioremediation to chemical synthesis of useful compounds that are widely distributed in fungi and bacteria. In the present study, a total of 81 full-length protein sequences of 2-haloalkanoic acid dehalogenase from bacteria and fungi were retrieved from NCBI database. Sequence analysis such as multiple sequence alignment (MSA), conserved motif identification, computation of amino acid composition, and phylogenetic tree construction were performed on these primary sequences. Read More

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http://dx.doi.org/10.1155/2016/8701201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736600PMC
February 2016
1 Read

FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing.

Adv Bioinformatics 2015 31;2015:303605. Epub 2015 Dec 31.

Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, ON, Canada M5S 3E1.

Sequencing and restriction analysis of genes like 16S rRNA and HSP60 are intensively used for molecular identification in the microbial communities. With aid of the rapid progress in bioinformatics, genome sequencing became the method of choice for bacterial identification. However, the genome sequencing technology is still out of reach in the developing countries. Read More

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http://dx.doi.org/10.1155/2015/303605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735980PMC
February 2016
1 Read

HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis.

Adv Bioinformatics 2015 20;2015:760423. Epub 2015 Dec 20.

Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA; Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA.

The emerging genome-wide hairpin bisulfite sequencing (hairpin-BS-Seq) technique enables the determination of the methylation pattern for DNA double strands simultaneously. Compared with traditional bisulfite sequencing (BS-Seq) techniques, hairpin-BS-Seq can determine methylation fidelity and increase mapping efficiency. However, no computational tool has been designed for the analysis of hairpin-BS-Seq data yet. Read More

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http://dx.doi.org/10.1155/2015/760423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4698518PMC
January 2016
5 Reads

Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus.

Adv Bioinformatics 2015 20;2015:678587. Epub 2015 Dec 20.

Laboratory of Cellular Technologies, Institute of Physiology of the National Academy of Sciences of Belarus, Academicheskaya 28, 220072 Minsk, Belarus.

Heterogeneities in nucleotide content distribution along the length of Zaire ebolavirus and Marburg virus genomes have been analyzed. Results showed that there is asymmetric mutational A-pressure in the majority of Zaire ebolavirus genes; there is mutational AC-pressure in the coding region of the matrix protein VP40, probably, caused by its high expression at the end of the infection process; there is also AC-pressure in the 3'-part of the nucleoprotein (NP) coding gene associated with low amount of secondary structure formed by the 3'-part of its mRNA; in the middle of the glycoprotein (GP) coding gene that kind of mutational bias is linked with the high amount of secondary structure formed by the corresponding fragment of RNA negative (-) strand; there is relatively symmetric mutational AU-pressure in the polymerase (Pol) coding gene caused by its low expression level. In Marburg virus all genes, including C-rich fragment of GP coding region, demonstrate asymmetric mutational A-bias, while the last gene (Pol) demonstrates more symmetric mutational AU-pressure. Read More

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http://dx.doi.org/10.1155/2015/678587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4698526PMC
January 2016
8 Reads

Developing of the Computer Method for Annotation of Bacterial Genes.

Adv Bioinformatics 2015 6;2015:635437. Epub 2015 Dec 6.

Bioinformatics Laboratory, Centre of Bioengineering, Russian Academy of Sciences, Prospekt 60-letiya Oktyabrya 7/1, Moscow 117312, Russia; Cybernetics Department, National Research Nuclear University "MEPhI", Kashirskoe shosse 31, Moscow 115409, Russia.

Over the last years a great number of bacterial genomes were sequenced. Now one of the most important challenges of computational genomics is the functional annotation of nucleic acid sequences. In this study we presented the computational method and the annotation system for predicting biological functions using phylogenetic profiles. Read More

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http://dx.doi.org/10.1155/2015/635437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684837PMC
January 2016
1 Read

Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima.

Adv Bioinformatics 2015 26;2015:126858. Epub 2015 Nov 26.

Dimonta, Ltd., Nagornaya Street 15, Building 8, Moscow 117186, Russia ; Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow 119992, Russia.

The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Read More

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http://dx.doi.org/10.1155/2015/126858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674582PMC
December 2015
2 Reads

In Silico Investigation of Flavonoids as Potential Trypanosomal Nucleoside Hydrolase Inhibitors.

Adv Bioinformatics 2015 12;2015:826047. Epub 2015 Nov 12.

Faculty of Pharmaceutical Sciences, UCSI University, 1 Jalan Menara Gading, Taman Connaught, Cheras, 56000 Kuala Lumpur, Malaysia.

Human African Trypanosomiasis is endemic to 37 countries of sub-Saharan Africa. It is caused by two related species of Trypanosoma brucei. Current therapies suffer from resistance and public accessibility of expensive medicines. Read More

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http://dx.doi.org/10.1155/2015/826047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4660014PMC
December 2015
3 Reads

High-Throughput Quantification of Phenotype Heterogeneity Using Statistical Features.

Adv Bioinformatics 2015 20;2015:728164. Epub 2015 Oct 20.

Laboratory of Conception, Optimization and Modelling of Systems, University of Lorraine, 7 rue Marconie, Metz, 57070 Lorraine, France.

Statistical features are widely used in radiology for tumor heterogeneity assessment using magnetic resonance (MR) imaging technique. In this paper, feature selection based on decision tree is examined to determine the relevant subset of glioblastoma (GBM) phenotypes in the statistical domain. To discriminate between active tumor (vAT) and edema/invasion (vE) phenotype, we selected the significant features using analysis of variance (ANOVA) with p value < 0. Read More

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http://dx.doi.org/10.1155/2015/728164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4660016PMC
December 2015
6 Reads

Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants.

Adv Bioinformatics 2015 18;2015:198214. Epub 2015 Oct 18.

Department of Plant Molecular Biology & Bioinformatics, Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamilnadu 641003, India.

Tobacco mosaic virus (TMV) infects several crops of economic importance (e.g., tomato) and remains as one of the major concerns to the farmers. Read More

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http://dx.doi.org/10.1155/2015/198214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4628775PMC
November 2015
4 Reads

Discovering Alzheimer Genetic Biomarkers Using Bayesian Networks.

Adv Bioinformatics 2015 23;2015:639367. Epub 2015 Aug 23.

Systems and Computer Department, Electronics Research Institute (ERI), Giza 12622, Egypt.

Single nucleotide polymorphisms (SNPs) contribute most of the genetic variation to the human genome. SNPs associate with many complex and common diseases like Alzheimer's disease (AD). Discovering SNP biomarkers at different loci can improve early diagnosis and treatment of these diseases. Read More

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http://dx.doi.org/10.1155/2015/639367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561111PMC
September 2015
2 Reads

Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine.

Adv Bioinformatics 2015 11;2015:528097. Epub 2015 Aug 11.

Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Receptor tyrosine kinases are essential proteins involved in cellular differentiation and proliferation in vivo and are heavily involved in allergic diseases, diabetes, and onset/proliferation of cancerous cells. Identifying the interacting partner of this protein, a growth factor ligand, will provide a deeper understanding of cellular proliferation/differentiation and other cell processes. In this study, we developed a method for predicting tyrosine kinase ligand-receptor pairs from their amino acid sequences. Read More

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http://dx.doi.org/10.1155/2015/528097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548105PMC
September 2015
2 Reads

A Review of Feature Selection and Feature Extraction Methods Applied on Microarray Data.

Adv Bioinformatics 2015 11;2015:198363. Epub 2015 Jun 11.

Department of Computing, Imperial College London, London SW7 2AZ, UK.

We summarise various ways of performing dimensionality reduction on high-dimensional microarray data. Many different feature selection and feature extraction methods exist and they are being widely used. All these methods aim to remove redundant and irrelevant features so that classification of new instances will be more accurate. Read More

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http://dx.doi.org/10.1155/2015/198363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480804PMC
July 2015
46 Reads

Development of a machine learning method to predict membrane protein-ligand binding residues using basic sequence information.

Adv Bioinformatics 2015 31;2015:843030. Epub 2015 Jan 31.

Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.

Locating ligand binding sites and finding the functionally important residues from protein sequences as well as structures became one of the challenges in understanding their function. Hence a Naïve Bayes classifier has been trained to predict whether a given amino acid residue in membrane protein sequence is a ligand binding residue or not using only sequence based information. The input to the classifier consists of the features of the target residue and two sequence neighbors on each side of the target residue. Read More

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http://www.hindawi.com/journals/abi/2015/843030/
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http://dx.doi.org/10.1155/2015/843030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329842PMC
March 2015
9 Reads

Semantic annotation for biological information retrieval system.

Adv Bioinformatics 2015 9;2015:597170. Epub 2015 Feb 9.

Computer Science Department, Faculty of Computers and Information, Cairo University, Dr. Ahmed Zewail Street, Orman, Giza 12613, Egypt.

Online literatures are increasing in a tremendous rate. Biological domain is one of the fast growing domains. Biological researchers face a problem finding what they are searching for effectively and efficiently. Read More

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http://dx.doi.org/10.1155/2015/597170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337267PMC
March 2015
2 Reads

A Highly Conserved GEQYQQLR Epitope Has Been Identified in the Nucleoprotein of Ebola Virus by Using an In Silico Approach.

Adv Bioinformatics 2015 1;2015:278197. Epub 2015 Feb 1.

Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh.

Ebola virus (EBOV) is a deadly virus that has caused several fatal outbreaks. Recently it caused another outbreak and resulted in thousands afflicted cases. Effective and approved vaccine or therapeutic treatment against this virus is still absent. Read More

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http://dx.doi.org/10.1155/2015/278197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331325PMC
February 2015
2 Reads