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    1 OF 30

    Meta-analysis study to evaluate the association of MTHFR C677T polymorphism with risk of ischemic stroke.
    Bioinformation 2017 30;13(6):214-219. Epub 2017 Jun 30.
    Department of Bioinformatics, Sri Ramachandra University, Porur, Chennai-600 116, India.
    Ischemic stroke is a condition characterized by reduced blood supply to part of the brain, initiating the ischemic cascade, leading to dysfunction of the brain tissue in that area. It is one of the leading causes of death and disability and is estimated to cause around 5.7 million deaths worldwide. Read More

    Deciphering the Role of microRNAs in BRD4-NUT Fusion Gene Induced NUT Midline Carcinoma.
    Bioinformation 2017 30;13(6):209-213. Epub 2017 Jun 30.
    Bioinformatics Department, MMV, Banaras Hindu University, India.
    NUT midline carcinoma (NMC) is a very aggressive and lethal type of squamous epithelial cell cancer caused due to fusion of BRD4 and NUT genes. The gene fusion results into a new fusion protein that promotes oncogenesis. The detailed molecular mechanisms underlying the NMC are still not clear and new findings are urgently required to complement the current efforts. Read More

    Serum and Plasma Metabolomic Biomarkers for Lung Cancer.
    Bioinformation 2017 30;13(6):202-208. Epub 2017 Jun 30.
    Bioinformatics Lab, Department of Statistics, Rajshahi University, Rajshahi, Bangladesh.
    In drug invention and early disease prediction of lung cancer, metabolomic biomarker detection is very important. Mortality rate can be decreased, if cancer is predicted at the earlier stage. Recent diagnostic techniques for lung cancer are not prognosis diagnostic techniques. Read More

    Combination of bone marrow mesenchymal stem cells and cartilage fragments contribute to enhanced repair of osteochondral defects.
    Bioinformation 2017 30;13(6):196-201. Epub 2017 Jun 30.
    Department of Orthopaedic Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.
    Cartilage tissue engineering using stem cells and biomaterials is considered a promising approach despite poor outcomes. We hypothesise that articular cartilage fragments provides native environmental cues to enhance stem cell differentiation. As such we evaluated the chondrogenic differentiation and repair of critical size defect in a human explant osteochondral model (OD) using bone marrow derived mesenchymal stem cells (BM-MSCs) and homogenised cartilage. Read More

    Designing of a penta-peptide against drug resistant E. coli.
    Bioinformation 2017 30;13(6):192-195. Epub 2017 Jun 30.
    Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala, haryana 133207.
    Drug resistant pathogens are vibrant global problem. Penicillin binding protein 5 (PBP5) plays important role in bacterial cell wall biosynthesis. Mutation in PBP5 is a well-known mechanism for development of drug resistant strain of bacteria. Read More

    Structural insight into the binding of C60-derivatives with enoyl-pyruvate transferase from Helicobacter pylori.
    Bioinformation 2017 30;13(6):185-191. Epub 2017 Jun 30.
    Department of Biochemistry, Huazhong University of science and Technology, China.
    Helicobacter pylori (H. pylori) is a human pathogen associated with acute gastritis and peptic ulcer. The MurA enzyme is an important drug target for the identification of ligands with improved efficacy and acceptable pharmaco-kinetic properties. Read More

    Transcriptome wide identification and characterization of starch branching enzyme in finger millet.
    Bioinformation 2017 30;13(6):179-184. Epub 2017 Jun 30.
    Uttarakhand Technical University, Dehradun, Uttarakhand, 248007, India.
    Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and play an important role in determining the structure and physical properties of starch granules. Multiple SBEs are involved in starch biosynthesis in plants. Finger millet is calcium rich important serial crop belongs to grass family and the transcriptome data of developing spikes is available on NCBI. Read More

    Analysis of correlated mutations in Ras G-domain.
    Bioinformation 2017 30;13(6):174-178. Epub 2017 Jun 30.
    Bioinformatics Department, MMV, Banaras Hindu University.
    Ras GTPases are most prevalent proto-oncogenes in human cancer. Mutations in Ras remain untreatable more than three decades after the initial discovery. At the amino acid level, some residues under physical or functional constraints exhibit correlated mutations also known as coevolving/covariant residues. Read More

    Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity.
    Bioinformation 2017 30;13(6):164-173. Epub 2017 Jun 30.
    Biomedical Informatics (P) Ltd, Irulan Sandy Annex, Puducherry 607 402, India.
    Several catalysis, cellular regulation, immune function, cell wall assembly, transport, signaling and inhibition occur through Protein- Protein Interactions (PPI). This is possible with the formation of specific yet stable protein-protein interfaces. Therefore, it is of interest to understand its molecular principles using structural data in relation to known function. Read More

    Molecular docking based screening of Listeriolysin-O for improved inhibitors.
    Bioinformation 2017 31;13(5):160-163. Epub 2017 May 31.
    Vira Vigene research institute, Tehran, Iran.
    Listeriolysine-O (LLO) is a 50KDa protein responsible for Listeria monocytogenes pathogenicity. The structure of LLO (PDB ID: 4CDB) with domains D1 to D4 is known. Therefore, it is of interest to identify conserved regions among LLO variants for destabilizing oligomerization (50 mer complex) of its monomers using appropriate inhibitors. Read More

    QSAR based predictive modeling for anti-malarial molecules.
    Bioinformation 2017 31;13(5):154-159. Epub 2017 May 31.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-67.
    Malaria is a predominant infectious disease, with a global footprint, but especially severe in developing countries in the African subcontinent. In recent years, drug-resistant malaria has become an alarming factor, and hence the requirement of new and improved drugs is more crucial than ever before. One of the promising locations for antimalarial drug target is the apicoplast, as this organelle does not occur in humans. Read More

    Polymorphism of the PAI-1gene (4G/5G) may be linked with Polycystic Ovary Syndrome and associated pregnancy disorders in South Indian Women.
    Bioinformation 2017 31;13(5):149-153. Epub 2017 May 31.
    Genes N Life Healthcare, Hyderabad.
    Polycystic Ovary syndrome (PCOS) is the most common endocrine disorder affecting 5 - 10% of all women of reproductive age group. The present research was carried out to study the impact of Plasminogen Activator Inhibitor (PAI-1) 4G/5G polymorphism (rs1799889) in PCOS, and the risk of developing PCOS in South Indian Population. The study was carried out in 60 subjects of South Indian population (30 PCOS and 30 Non PCOS) recruited from ARC Research and Fertility Centre, Chennai, India. Read More

    Identification of inhibitors against α-Isopropylmalate Synthase of Mycobacterium tuberculosis using docking-MM/PBSA hybrid approach.
    Bioinformation 2017 31;13(5):144-148. Epub 2017 May 31.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067.
    α-Isopropylmalate Synthase (α-IPMS) encoded by leuA in Mycobacterium tuberculosis (M.tb) is involved in the leucine biosynthesis pathway and is extremely critical for the synthesis of branched-chain amino acids (leucine, isoleucine and valine). α-IPMS activity is required not only for the proliferation of M. Read More

    Competitive rational inhibitor design to 4-maleylaceto-acetate isomerase.
    Bioinformation 2017 31;13(5):140-143. Epub 2017 May 31.
    National institute of genetic engineering and biotechnology, Tehran, Iran.
    Tyrosinemia type I is the result of genetic disorder in fomaryl acetoacetase gene that leads to 4-fumaryl acetoacetate accumulation. The current treatment for tyrosinemia type I is nitisinone that inhibits 4-hydroxyphenyl pyruvic dioxygenase in competitive manner. In the present study, we have designed two theoretical chemicals, which could inhibit the direct enzyme responsible for fumarylacetoacetate formation. Read More

    Molecular docking analysis of nitisinone with homogentisate 1,2 dioxygenase.
    Bioinformation 2017 31;13(5):136-139. Epub 2017 May 31.
    National institute of genetic engineering and biotechnology, Tehran, Iran.
    Alkaptonuria is an inherited disease that is caused by homogenticate accumulation. Deficiency or mutation in Homogentisate 1,2 dioxygenase gene (chromosome 3q21-q23) leads to production of incorrectly folded or truncated enzyme. Several studies indicated that competitive inhibitors of Homogentisate 1,2 dioxygenase like Nitisinone could be used for Alkaptonuria treatment. Read More

    Dengue Symptoms Significance in Anti-Dengue Drug Development: Road Less Travelled.
    Bioinformation 2017 31;13(5):131-135. Epub 2017 May 31.
    SRM University, Delhi-NCR, Sonepat, Haryana, Centre for Drug Design Discovery & Development (C-4D), PR Institute of Medical Science & Research, Delhi-NCR, Sonepat, New Delhi, India.
    Dengue outbreak has affected rural areas of Delhi-NCR, Haryana widely but it lacks in surveillance. High cases of dengue symptoms were reported in these regions whereas dengue symptoms have been a neglected issue in the anti-dengue drug development. Therefore, this study aims to analyze the status of the dengue infection, a rural issue of Delhi-NCR, Haryana and to identify the significance of dengue symptoms in anti-dengue drug development. Read More

    Linear epitope prediction in HPV type 16 E7 antigen and their docked interaction with human TMEM 50A structural model.
    Bioinformation 2017 31;13(5):122-130. Epub 2017 May 31.
    Department of Computer Science and Information Technology, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad-211007, India.
    Human Papilloma Virus (HPV) HPV type 16 E7 antigen is a known target in cervical cancer. We report the predicted potential epitopes in the E7 antigen. We further describe the subsequent interaction of these linear epitope peptides with the human TMEM 50 A structural model using molecular docking. Read More

    Nucleotide composition determines the role of translational efficiency in human genes.
    Bioinformation 2017 28;13(2):46-53. Epub 2017 Feb 28.
    Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
    The basic sequence features were analysed that influence gene expression via codon usage bias of the selected forty coding sequences of Homo sapiens in a simple prokaryotic model i.e. E. Read More

    Virtual screening following rational drug design based approach for introducing new anti amyloid beta aggregation agent.
    Bioinformation 2017 28;13(2):42-45. Epub 2017 Feb 28.
    Viravigene research institute, Tehran, Iran.
    Amyloid β (Aβ) sheets aggregations is the main reason of Alzheimer disease. The interacting areas between monomers are residue number 38 to 42. Inhibition of interaction between Aβ molecules prevents plaque formation. Read More

    Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues.
    Bioinformation 2017 28;13(2):31-41. Epub 2017 Feb 28.
    Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
    Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species. Through targeting the signature sequence in MPK4 of papaya using orthologs from Arabidopsis, the predicted sequence of MPK4 was studied using a comparative in silico approach between different plant species and the MAP cascade complex of MEKK1/MKK1/MKK2. Read More

    optCluster: An R Package for Determining the Optimal Clustering Algorithm.
    Bioinformation 2017 31;13(3):101-103. Epub 2017 Mar 31.
    Department of Biostatistics, University of Florida, Gainesville, Florida, 32611, USA.
    There exist numerous programs and packages that perform validation for a given clustering solution; however, clustering algorithms fare differently as judged by different validation measures. If more than one performance measure is used to evaluate multiple clustering partitions, an optimal result is often difficult to determine by visual inspection alone. This paper introduces optCluster, an R package that uses a single function to simultaneously compare numerous clustering partitions (created by different algorithms and/or numbers of clusters) and obtain a "best" option for a given dataset. Read More

    T-cell epitopes predicted from the Nucleocapsid protein of Sin Nombre virus restricted to 30 HLA alleles common to the North American population.
    Bioinformation 2017 31;13(3):94-100. Epub 2017 Mar 31.
    Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu,India.
    Hantavirus cardiopulmonary syndrome in North America is caused by Sin Nombre virus (SNV) and poses a public health problem. We identified T-cell epitopes restricted to HLA alleles commonly seen in the N. American population. Read More

    Epitope design of L1 protein for vaccine production against Human Papilloma Virus types 16 and 18.
    Bioinformation 2017 31;13(3):86-93. Epub 2017 Mar 31.
    Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Chittagong 4202, Bangladesh.
    Cervical cancer accounts for about two-thirds of all cancer cases linked etiologically to Human Papilloma Virus (HPV). 15 oncogenic HPV types can cause cervical cancer, of which HPV16 and HPV18 combinedly account for about 70% of it. So, effective epitope design for the clinically relevant HPV types 16 and 18 would be of major medical benefit. Read More

    Identification and characterization of a cyclosporin binding cyclophilin from Staphylococcus aureus Newman.
    Bioinformation 2017 31;13(3):78-85. Epub 2017 Mar 31.
    Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India.
    Cyclophilins, a class of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes, are inhibited by cyclosporin A (CsA), an immunosuppressive drug. Staphylococcus aureus Newman, a pathogenic bacterium, carries a gene for encoding a putative cyclophilin (SaCyp). SaCyp shows significant homology with other cyclophilins at the sequence level. Read More

    Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes.
    Bioinformation 2017 31;13(3):73-77. Epub 2017 Mar 31.
    Department of Microbiology, Sri Sankara Arts and Science College, Enathur - 631 561.
    Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. Read More

    Antimicrobial activity of various ethanolic plant extracts against pathogenic multi drug resistant Candida spp.
    Bioinformation 2017 31;13(3):67-72. Epub 2017 Mar 31.
    Department of Biosciences, Integral University, Lucknow U.P. India.
    A total of 50 Candida isolates were isolated and identified from clinical specimens and these were tested for resistance to various antifungal drugs. It was observed multi-drug resistance in all candida isolates by 84%, 62%, 60%, 76%, 46, 30%, and 22% against fluconazole, clotrimazole, Amphotericin B, itraconazole, ketoconazole, miconazole and nystatin tested respectively. The isolates, which were found to be resistant to antifungal drugs were selected and subjected to antifungal testing against six ethanolic plants, extract namely Azadiracta indica, Allium sativum, Cordia dichotoma Ocimum sanctum, Syzygium cumini and Trigonella foenum grecum. Read More

    A comparative molecular docking study of curcumin and methotrexate to dihydrofolate reductase.
    Bioinformation 2017 31;13(3):63-66. Epub 2017 Mar 31.
    College of Applied Medical Sciences Jazan University, Jazan, Kingdom of Saudi Arabia.
    Interaction of curcumin (CUR) with the enzyme dihydrofolate reductase (DHFR) was studied by molecular docking using AutoDock 4.2 as the docking software application. AutoDock 4. Read More

    Quantitative Structure Activity Relationship study of the Anti-Hepatitis Peptides employing Random Forests and Extra-trees regressors.
    Bioinformation 2017 31;13(3):60-62. Epub 2017 Mar 31.
    Shiv Nadar University, Gautam Budha Nagar, Uttar Pradesh 201314, India.
    Antimicrobial peptides are host defense peptides being viewed as replacement to broad-spectrum antibiotics due to varied advantages. Hepatitis is the commonest infectious disease of liver, affecting 500 million globally with reported adverse side effects in treatment therapy. Antimicrobial peptides active against hepatitis are called as anti-hepatitis peptides (AHP). Read More

    Annotation of gene sequence and protein structure of brinjal EDS1.
    Bioinformation 2017 2;13(3):54-59. Epub 2017 Mar 2.
    Division of Genomic Resources, IACR-NBPGR, Pusa Campus, New Delhi, India.
    Enhanced Disease Susceptibility1 (EDS1) is a nucleo-cytoplasmic protein, known to be a key regulator of plant basal defense and effector-triggered immunity. Sequence of a single copy brinjal EDS1 gene (SmEDS1) was mined from draft brinjal genome assembly. The extracted sequence was found to be incomplete and polished with the help of transcriptome sequence data. Read More

    Molecular Docking of Phytoligands to the viral protein receptor P. monodon Rab7.
    Bioinformation 2017 30;13(4):116-121. Epub 2017 Apr 30.
    Centre for Drug Discovery and Development, Sathyabama University, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai-600 119, Tamil Nadu, INDIA.
    The development of shrimp aquaculture has been severely affected by viral diseases resulting in a huge economic burden to the industry. White spot disease (WSD) has caused severe mortality in farmed shrimp in many countries. Globally aquaculture industries face huge economic losses due to rapid spread of White Spot Syndrome Virus (WSSV) disease that can cause 100% mortality in a short period of 3-10 days. Read More

    Influence of PCOS in Obese vs. Non-Obese women from Mesenchymal Progenitors Stem Cells and Other Endometrial Cells: An in silico biomarker discovery.
    Bioinformation 2017 30;13(4):111-115. Epub 2017 Apr 30.
    Faculty of Computing and Information Technology, King Abdul-Aziz University, Rabigh-21911, Saudi Arabia.
    Polycystic ovary syndrome (PCOS) is endocrine system disease which affect women ages 18 to 44 where the women's hormones are imbalance. Recently it has been reported to occur in early age. Alteration of normal gene expression in PCOS has shown negative effects on long-term health issues. Read More

    Improved Annotations of 23 Differentially Expressed Hypothetical Proteins in Methicillin Resistant S.aureus.
    Bioinformation 2017 30;13(4):104-110. Epub 2017 Apr 30.
    Department of Science, Davenport University, Lansing, Michigan, United States of America.
    Antibiotic resistant Staphylococcus aureus is a major public health concern effecting millions of people annually. Medical science has documented completely untreatable S. aureus infections. Read More

    Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data.
    Bioinformation 2017 31;13(1):25-30. Epub 2017 Jan 31.
    Biotechnology Research Institute for Drug Discovery, National Institute of AIST, Tokyo, Japan.
    Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. Here, we present a new method to augment regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity. Read More

    Cloning and over expression of non-coding RNA rprA in E.coli and its resistance to Kanamycin without osmotic shock.
    Bioinformation 2017 31;13(1):21-24. Epub 2017 Jan 31.
    Nour Danesh Institute of Higher Education, Department of Biology, Isfahan, Iran.
    Recent reports have indicated that small RNAs have key roles in the response of the E.coli to stress and also in the regulating of virulence factors. It seems that some small non-coding RNAs are involved in multidrug resistance. Read More

    Computational study of 'HUB' microRNA in human cardiac diseases.
    Bioinformation 2017 24;13(1):17-20. Epub 2017 Jan 24.
    Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala - 695 581.
    MicroRNAs (miRNAs) are small non-coding RNAs ~22 nucleotides long that do not encode for proteins but have been reported to influence gene expression in normal and abnormal health conditions. Though a large body of scientific literature on miRNAs exists, their network level profile linking molecules with their corresponding phenotypes, is less explored. Here, we studied a network of 191 human miRNAs reported to play a role in 30 human cardiac diseases. Read More

    High Throughput Virtual Screening to Identify Novel natural product Inhibitors for MethionyltRNA-Synthetase of Brucella melitensis.
    Bioinformation 2017 20;13(1):8-16. Epub 2017 Jan 20.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
    The Brucella melitensis methionyl-tRNA-synthetase (MetRSBm) is a promising target for brucellosis drug development. The virtual screening of large libraries of a drug like molecules against a protein target is a common strategy used to identify novel inhibitors. A High throughput virtual screening was performed to identify hits to the potential antibrucellosis drug target, MetRSBm. Read More

    Substitutional Analysis of Orthologous Protein Families Using BLOCKS.
    Bioinformation 2017 19;13(1):1-7. Epub 2017 Jan 19.
    Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India.
    Orthologous proteins, form due to divergence of parental sequence, perform similar function under different environmental and biological conditions. Amino acid changes at locus specific positions form hetero-pairs whose role in BLOCK evolution is yet to be understood. We involve eight protein BLOCKs of known divergence rate to gain insight into the role of hetero-pairs in evolution. Read More

    Molecular docking analysis of UniProtKB nitrate reductase enzyme with known natural flavonoids.
    Bioinformation 2016 27;12(12):425-429. Epub 2016 Dec 27.
    Bioinformatics Division, Osmania University, Hyderabad,Telangana, India.
    The functional inference of UniProtKB nitrate reductase enzyme (UniProtKB - P0AF33) through structural modeling is of interest in plant biology. Therefore, a homology model for UniProtKB variant of the enzyme was constructed using available data with the MODELER software tool. The model was further docked with five natural flavonoid structures such as hesperetin, naringenin, leucocyanidin, quercetin and hesperetin triacetate using the AUTODOCK (version 4. Read More

    Nutritional, Medicinal and Toxicological Attributes of Star-Fruits (Averrhoa carambola L.): A Review.
    Bioinformation 2016 22;12(12):420-424. Epub 2016 Dec 22.
    Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Semeling 08100, Kedah,Malaysia.
    Plants are very complex organisms that produce medicinally important natural products. The Star-fruit producing plant (Averrhoa carambola L.) is a species of woody plant in the family Oxalidaceae native to the Philippines, Indonesia, Malaysia, Vietnam, India, Bangladesh and Sri Lanka; but, cultivated in many parts of the world. Read More

    Structural modelling and phylogenetic analyses of PgeIF4A2 (Eukaryotic translation initiation factor) from Pennisetum glaucum reveal signature motifs with a role in stress tolerance and development.
    Bioinformation 2016 19;12(12):416-419. Epub 2016 Dec 19.
    Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
    Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9. Read More

    Identification and analysis of insulin like peptides in nematode secretomes provide targets for parasite control.
    Bioinformation 2016 14;12(12):412-415. Epub 2016 Dec 14.
    Department of Computational Biology and Bioinformatics, Sam Higginbottom Institute of Agriculture Technology & Sciences,Allahabad, 211007, India.
    Insulin-like (ins) peptides play an important role in development and metabolism across the metazoa. In nematodes, these are also required for dauer formation and longevity and are expressed in different types of neurons across various life stages which demonstrate their role in parasites and could become possible targets for parasite control. To date, many nematode genomes are publically available. Read More

    Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks.
    Bioinformation 2016 4;12(12):408-411. Epub 2016 Dec 4.
    Amity Institute of Biotechnology, Amity University Uttar Pradesh, U.P., India.
    The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. Read More

    A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets.
    Bioinformation 2016 12;12(6):340-346. Epub 2016 Oct 12.
    Plant Breeding Department, Sari Agricultural Sciences and Natural Resources, Iran.
    A Gene Regulatory Network (GRN) is a collection of interactions between molecular regulators and their targets in cells governing gene expression level. Omics data explosion generated from high-throughput genomic assays such as microarray and RNA-Seq technologies and the emergence of a number of pre-processing methods demands suitable guidelines to determine the impact of transcript data platforms and normalization procedures on describing associations in GRNs. In this study exploiting publically available microarray and RNA-Seq datasets and a gold standard of transcriptional interactions in Arabidopsis, we performed a comparison between six GRNs derived by RNA-Seq and microarray data and different normalization procedures. Read More

    Microarray Integrated Analysis of a Gene Network for the CD36 Myocardial Phenotype.
    Bioinformation 2016 11;12(6):332-339. Epub 2016 Oct 11.
    Medical Biotechnology Lab (MedBiotech), Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco.
    CD36 is a multifunctional membrane-type receptor glycoprotein that reacts with oxidized low-density lipoprotein and long-chain fatty acid (LCFA). However, much remains to be understood about the molecular mechanism of the cardio-myopathy observed in CD36-KO mice. In this study, we identify different genes pathways involved in response to CD36 cardio-myopathy phenotype by identifying the differences among biological processes, molecular pathways and networks of interactions that emerge from knocking CD3 and using different bioinformatics tools such as STRING, GeneMANIA and Cytoscape. Read More

    Novel aromatase inhibitors selection using induced fit docking and extra precision methods: Potential clinical use in ER-alpha-positive breast cancer.
    Bioinformation 2016 10;12(6):324-331. Epub 2016 Oct 10.
    Cancer Science Institute of Singapore, National University of Singapore, Singapore-117599; National University Cancer Institute, National University Health System, Singapore-119074; Department of Biological Sciences, University of North Texas, Denton-762035017, Texas, USA; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore-117600; Faculty of Health Sciences, School of Biomedical Sciences, Curtin University, Bently, Western Australia-6102.
    Aromatase (CYP19A1) the key enzyme of estrogen biosynthesis, is often deregulated in breast cancer patients. It catalyzes the conversion of androgen to estrogen, thus responsible for production of estrogen in human body. However, it causes over-production of estrogen which eventually leads to proliferation of breast cancer cells. Read More

    An analysis of horseradish peroxidase enzyme for effluent treatment.
    Bioinformation 2016 10;12(6):318-323. Epub 2016 Oct 10.
    Department of Microbiology, Osmania University, Hyderabad - 500 007, India.
    The present study explains computational methods to design thermostable horseradish peroxidase enzyme using the crystal structure available from Protein Data Bank (PDB ID: 6ATJ). Multiple mutations were introduced to the original enzyme and developed a model by using Modeler9.14. Read More

    Virtual screening of natural compounds as inhibitors of EGFR 696-1022 T790M associated with non-small cell lung cancer.
    Bioinformation 2016 10;12(6):311-317. Epub 2016 Oct 10.
    Department of Biotechnology, Kumaun University, Bhimtal Campus Bhimtal, Uttarakhand, India.
    Non-small cell lung cancer (NSCLC) is the most dominating and lethal type of lung cancer triggering more than 1.3 million deaths per year. The most effective line of treatment against NSCLC is to target epidermal growth factor receptor (EGFR) activating mutation. Read More

    An Analysis of Adenovirus Genomes Using Whole Genome Software Tools.
    Bioinformation 2016 30;12(6):301-310. Epub 2016 Aug 30.
    Department of Biology, University of Tampa, 401 W. Kennedy Blvd. Box 3F, Tampa, FL 33606.
    The evolution of sequencing technology has lead to an enormous increase in the number of genomes that have been sequenced. This is especially true in the field of virus genomics. In order to extract meaningful biological information from these genomes, whole genome data mining software tools must be utilized. Read More

    Identification of potential leads against 4-hydroxytetrahydrodipicolinate synthase from Mycobacterium tuberculosis.
    Bioinformation 2016 2;12(11):400-407. Epub 2016 Dec 2.
    Department of Bioengineering, Faculty of Engineering, Integral University Lucknow, Uttar Pradesh, India-226026.
    4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) is an important enzyme needed for the biosynthesis of lysine and many more key metabolites in Mycobacterium tuberculosis (Mtb). Inhibition of DHDPS is supposed to a promising therapeutic target due to its specific role in sporulation, cross-linking of the peptidiglycan polymers and biosynthesis of amino acids. In this work, a known inhibitor-based similarity search was carried out against a natural products database (Super Natural II) towards identification of more potent phyto-inhibitors. Read More

    Variation in synonymous codon usage in Paenibacillus sp. 32O-W genome.
    Bioinformation 2016 1;12(11):396-399. Epub 2016 Dec 1.
    Department of Molecular Biology & Bioinformatics, Tripura University, Suryamaninagar, Tripura-799022, India; Bioinformatics Centre, Tripura University, Suryamaninagar, Tripura-799022, India.
    Paenibacillus sp. 32O-W, which is attributed for biodesulfurization of petroleum, has 56.34% genomic G+C content. Read More

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