1,576 results match your criteria Bioinformation[Journal]


Towards Personalized Medicine: An Improved Assembly Procedure for Early Detection of Drug Resistant HIV Minor Quasispecies in Patient Samples.

Bioinformation 2018 18;14(8):449-454. Epub 2018 Sep 18.

Center for Information Technology, National Institutes of Health, Bethesda, Maryland 10891.

The third-generation sequencing technology, PacBio, has shown an ability to sequence the HIV virus amplicons in their full length. The long read of PaBio offers a distinct advantage to comprehensively understand the virus evolution complexity at quasispecies level (i.e. Read More

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September 2018

Bioinformation Informs the Allostasiome: Translational Environmental Restoration (TER) for the Climate Crisis Medical Emergency.

Bioinformation 2018 6;14(8):446-448. Epub 2018 Sep 6.

UCLA Center for the Health Sciences, Part-Time Faculty Biostatistics, CSUN, Department of the Health Sciences, Climate Reality Project Leadership Corps, International Research Consulting.

Health care is optimized when the best evidence base (BEB) is translated into policies whose effectiveness can be verified. Bioinformation disseminates BEB and is critical to translational health care. The survival of all prokaryotes and eukaryotes, including mammals, and ultimately our species, depends upon their ability to adapt to changes in their micro-environmental milieu and to the challenges of their surrounding macro-environment. Read More

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September 2018
1 Read

analysis of onion chitinases using transcriptome data.

Bioinformation 2018 31;14(8):440-445. Epub 2018 Aug 31.

Center for Biotechnology, Siksha 'O' Anusandhan University, Bhubaneswar, Odisha 751003, India.

Chitinases are glycoside hydrolase (GH) family of proteins having multifaceted roles in plants. It is of interest to identify and characterize chitinase-encoding genes from the popular bulbous plant onion ( L.). Read More

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August 2018
6 Reads

Phytochemical analysis and broad spectrum antimicrobial activity of ethanolic extract of Hance leaves and its solventpartitioned fractions.

Bioinformation 2018 31;14(8):430-439. Epub 2018 Aug 31.

School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.

Hance (yellow jasmine, Family Oleaceae) belongs to an important subclass of family whose biological significance is under explored. The current study pertains to isolation of various solvent extracts fractions and their anti-bacterial effects on the Gram-positive and Gram-negative bacterial pathogens. Ethanolic extract of Hance leaves was subjected to further partitioning using different solvents with increasing polarity to get different solvent fractions. Read More

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August 2018
2 Reads

Screening and analysis of acetyl-cholinesterase (AChE) inhibitors in the context of Alzheimer's disease.

Bioinformation 2018 31;14(8):414-428. Epub 2018 Aug 31.

Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry-605014, India.

Acetyl-cholinesterase enzyme (AChE) is a known target for identifying potential inhibitors against Alzheimer diseases (AD). Therefore, it is of interest to screen AChE with the CNS-BBB database. An AChE enzyme is a member of hydrolase family is activated by acetylcholine (ACh), so, targeting the AChE enzyme with the potential inhibitor may block the binding of the ACh. Read More

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August 2018
1 Read

Identification of therapeutic targets for inflammation in sickle cell disease (SCD) among Indian patients using gene expression data analysis.

Bioinformation 2018 31;14(7):408-413. Epub 2018 Jul 31.

Pt. J.N.M. Medical College, Raipur, India.

Sickle cell disease (SCD) is life-threatening hemoglobinopathy prevalent in India, Sub-Saharan Africa and Middle East. Inflammation plays a pivotal role in disease process and involves intricate interaction among leukocytes, platelets, sickle erythrocytes and vascular endothelium. Available disease modifying therapies are hydroxyl-urea and blood transfusion. Read More

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July 2018
7 Reads

A rapid identification technique for drug-resistant isolates using mismatch specific cleavage enzyme.

Bioinformation 2018 31;14(7):404-407. Epub 2018 Jul 31.

Laboratorio de Biotecnologia y Biologia Molecular, Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru.

The emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) strains is a major health problem for high Tuberculosis (TB) incidence countries. Therefore, it is of interest to identify antibiotic resistant bacteria by mismatch detection using DNA hybridization. We generated PCR products for five genes (rpoB, inhA, katG, gyrA and rrs) associated with drug resistance TB from MDR and XDR Mycobacterium tuberculosis (MTB) DNA samples. Read More

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July 2018
6 Reads

Analysis of Hepatitis E virus (HEV) X-domain structural model.

Bioinformation 2018 31;14(7):398-403. Epub 2018 Jul 31.

Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, (HP) India.

Hepatitis E viral infection is now emerging as a global health concern, which needs to be addressed. Mechanism of viral replication and release is attributed by the different genomic component of HEV. However, few proteins/domain like X and Y domain remain unexplored, so we aim to explore the physiochemical, structural and functional features of HEV ORF-1 X domain. Read More

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July 2018
2 Reads

Transcriptome wide identification and characterization of Starch Synthase enzyme in finger millet.

Bioinformation 2018 31;14(7):393-397. Epub 2018 Jul 31.

Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, 248016, India.

Finger millet is a calcium-rich cereal crop of the grass family. The transcriptome data for finger millet is available at NCBI. It is of interest to annotate and characterize starch synthase enzyme from finger millet transcriptome data. Read More

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July 2018
1 Read

A specific QSAR model for proteasome inhibitors from Oleaeuropaea and Ficuscarica.

Bioinformation 2018 31;14(7):384-392. Epub 2018 Jul 31.

Laboratory of Biochemistry, Environment and Agri-Food (URAC 36)-Faculty of sciences and techniques - Mohammedia, Hassan II university Casablanca Morocco.

and are widely used in traditional medicine for the treatment of cancer. Therefore, it is of interest to develop a QSAR model for screening proteasome inhibitors from plant source. Hence, a QSAR model was developed using multiple linear regressions; partial least squares regression and principal component regression methods. Read More

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July 2018
3 Reads

Molecular docking analysis of phytoconstituent from Momordica charantia with Guanylate Cyclase catalytic domain.

Bioinformation 2018 31;14(7):378-383. Epub 2018 Jul 31.

Centre for Advanced Studies in Botany and Centre for Herbal Sciences, University of Madras, Guindy Campus, Chennai-600 025, Tamil Nadu, India.

Soluble guanylate cyclase (sGC) is a type of lyase enzyme with profoundly increasing importance in treatments of cardiovascular and neurodegenerative disorders. Modulation of sGC activity demonstrated beneficial effects against Parkinson's disease by reducing glutamate excitotoxicity. It is of interest to evaluate the pharmacological activity of Momordica charantia phytoconstituent (DGalacturonic acid) and ODQ with catalytic domain of sGC enzyme, using Autodock version 4. Read More

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July 2018
6 Reads

Toxic Dose prediction of Chemical Compounds to Biomarkers using an ANOVA based Gene Expression Analysis.

Bioinformation 2018 31;14(7):369-377. Epub 2018 Jul 31.

Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.

The aim of toxicogenomic studies is to optimize the toxic dose levels of chemical compounds (CCs) and their regulated biomarker genes. This is also crucial in drug discovery and development. There are popular online computational tools such as ToxDB and Toxygates to identify toxicogenomic biomarkers using t-test. Read More

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July 2018
8 Reads

Phylogenetic Analysis of the vesicular fusion SNARE machinery revealing its functional divergence across Eukaryotes.

Bioinformation 2018 31;14(7):361-368. Epub 2018 Jul 31.

School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India-110067.

Proteins of the SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptors) family play a significant role in all vesicular fusion events involved in endocytic and exocytic pathways. These proteins act as molecular machines that assemble into tight four-helix bundle complex, bridging the opposing membranes into close proximity forming membrane fusion. Almost all SNARE proteins share a 53 amino acid coiled-coil domain, which is mostly linked to the transmembrane domain at the C-terminal end. Read More

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July 2018
9 Reads

tRNA diversification among uncultured archeon clones.

Bioinformation 2018 31;14(7):357-360. Epub 2018 Jul 31.

Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh.

Whole genome sequences (DNA sequences) of four uncultured archeon clones (1B6:CR626858.1, 4B7:CR626856.1, 22i07:JQ768096. Read More

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July 2018
1 Read

A statistical geometry analysis of simulated water-DMSO and water-MeCN binary mixtures for biomolecular studies.

Bioinformation 2018 31;14(7):350-356. Epub 2018 Jul 31.

School of Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India.

Water-Dimethylsulfoxide (DMSO) and water-Acetonitrile (MeCN) binary mixtures at various molar ratios ranging from 0 to 1 are studied using Molecular Dynamics (MD) simulations. Hydration properties of water in different regions of MeCN/DMSO are investigated by using the statistical geometry approach. The obtained results reveal that in water-DMSO simulations both water and solvent molecules prefer to be in mixed cluster forms, depending upon the concentration of DMSO. Read More

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July 2018
1 Read

Astrobiology - an opposing view.

Authors:
Paul Shapshak

Bioinformation 2018 30;14(6):346-349. Epub 2018 Jun 30.

Division of Infectious Diseases and International Health, Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, FL 33606, USA.

The use of quantum computers and Artificial Intelligence (AI) is imperative for use in space exploration and astrobiology investigations. Considerable progress has been made since the commencement of origin of life laboratory and theoretical studies in the mid 20th century. However, the sheer amount of data amassed to date in all these studies including exoplanetary and astrobiological studies is enormous and increasing steadily. Read More

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June 2018
12 Reads

Linking common non-coding RNAs of human lung cancer and M. tuberculosis.

Bioinformation 2018 30;14(6):337-345. Epub 2018 Jun 30.

Laboratorio de Genetica Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciencias Biologicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil.

Lung cancer and pulmonary tuberculosis caused by Mycobacterium are two major causes of deaths worldwide. Tuberculosis linked lung cancer is known. However, the precise molecular mechanism of Mycobacterium associated increased risk of lung cancer is not understood. Read More

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Designing novel inhibitors against Mycobacterium tuberculosis FadA5 (acetyl-CoA acetyltransferase) by virtual screening of known anti-tuberculosis (bioactive) compounds.

Bioinformation 2018 30;14(6):327-336. Epub 2018 Jun 30.

School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.

By-products of fatty acid degradation are extensively utilized by Mycobacterium tuberculosis (Mtb) for lipid synthesis and energy production during the infection phase. Cholesterol from host is scavenged by Mtb to fulfill its metabolic requirements, evade host immunity and invade macrophages. Blocking cholesterol catabolic pathways leads to bacteriostasis. Read More

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Comparative analysis of prokaryotic and eukaryotic transcription factors using machine-learning techniques.

Bioinformation 2018 30;14(6):315-326. Epub 2018 Jun 30.

Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, India.

The DNA-protein interactions play vital roles in the central dogma of molecular biology. Proper interactions between DNA and protein would lead to the onset of various biological phenomena like transcription, translation, and replication. However, the mechanisms of these well-known processes vary between prokaryotic and eukaryotic organisms. Read More

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Screening, isolation and characterization of biosurfactant producing strain ANSKLAB03.

Bioinformation 2018 30;14(6):304-314. Epub 2018 Jun 30.

Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India.

Biosurfactants are surface-active compounds produced by a wide range of microorganisms. They have both hydrophobic and hydrophilic domains and can decrease the surface tension and the interfacial tension of growth medium. Biosurfactants have different chemical structures like-lipopeptides, glycolipids, neutral lipids and fatty acids. Read More

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Computational studies on Begomoviral AC2/C2 proteins.

Bioinformation 2018 30;14(6):294-303. Epub 2018 Jun 30.

Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India.

Geminiviridae is a large family of circular, single stranded DNA viruses, which infects and causes devastating diseases on economically important crops. They are subdivided into nine genera. Members of the genus begomovirus encode a pathogenic protein called AC2/C2 which interacts that inactivates many plant proteins and trans-activates a number of host genes via the C-terminal transactivation domain. Read More

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Screening, Purification and Characterization of Protease Inhibitor from .

Bioinformation 2018 30;14(6):285-293. Epub 2018 Jun 30.

Department of Biotechnology, University of Calicut - 673635, Kerala, India.

Plants are rich in protease inhibitors (PI) and trypsin inhibitors are the most common. Therefore, it is of interest to screen PI from plant sources. We report the screening, purification and characterization of PI from Capsicum frutescenes. Read More

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Binding property of HIV p24 and Reverse transcriptase by chalcones from Pongamia pinnata seeds.

Bioinformation 2018 30;14(6):279-284. Epub 2018 Jun 30.

Central Research Laboratory, Sri Manakula Vinayagar Medical College & Hospital, Madagadipet, Puducherry- 605107.

HIV remains a challenging life threatening viral agent for humans despite available anti HIV drugs. The known effective drug named HAART clears the circulating viruses but not the intracellular viruses. Therefore, it is of interest to identify molecules with improved anti-HIV activity from natural plant sources. Read More

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Biodegradation effects of o-cresol by SHY on mustard seed germination.

Bioinformation 2018 30;14(6):271-278. Epub 2018 Jun 30.

Department of Microbiology, Karpagam academy of higher education, Eachinary, Coimbatore- 641 021.

Cresols are ubiquitous due to industrial production and natural presence. o-cresol (2-methyl phenol) is highly toxic to both fauna and flora. It has been included in the EPA list as one of the priority pollutants. Read More

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June 2018
3 Reads

A review on the nutritional, medicinal, molecular and genome attributes of Durian (Durio zibethinus L.), the King of fruits in Malaysia.

Bioinformation 2018 30;14(6):265-270. Epub 2018 Jun 30.

Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling 08100 Bedong, Kedah, Malaysia.

Durian (Durio zibethinus L.; Family Bombacaceae) is an iconic tropical fruit plant cultivated in Malaysia and the Southeast Asian countries. In Malaysia, durian is recognised as the King of fruits and well known as a rich source of volatile sulphur compounds that make it unique. Read More

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Detection of severity in Alzheimer's disease (AD) using computational modeling.

Authors:
Hyunjo Kim

Bioinformation 2018 31;14(5):259-264. Epub 2018 May 31.

Department of Life Science, University of Gachon, Seungnam, Kyeonggido, Korea.

The prevalent cause of dementia - Alzheimer's disease (AD) is characterized by an early cholinergic deficit that is in part responsible for the cognitive deficits (especially memory and attention defects). Prolonged AD leads to moderate-to-severe AD, which is one of the leading causes of death. Placebo-controlled, randomized clinical trials have shown significant effects of Acetyl cholin esterase inhibitors (ChEIs) on function, cognition, activities of daily living (ADL) and behavioral symptoms in patients. Read More

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May 2018
1 Read

Polymorphism studies on microRNA targetome of thalassemia.

Bioinformation 2018 31;14(5):252-258. Epub 2018 May 31.

Thalassemia & Hemoglobinopathy Research center, research institute of Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Thalassemia is one of the most prevalent hemoglobin disorders. It is caused by the decreased or absent synthesis of one globin chain that leads to moderate to severe hemolytic anemia in clinical complications. Some genetic factors cause these phenotypic variations by the alteration of gene expression. Read More

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May 2018
2 Reads

Study on Regulation of Low Density Lipoprotein Cholesterol Metabolism using PCSK9 Gene Silencing: A computational Approach.

Bioinformation 2018 31;14(5):248-251. Epub 2018 May 31.

Department of Medical Biochemistry, Division of Biomedical Sciences, School of Medicine, College of Health Sciences, Mekelle University (Ayder Campus), Mekelle, Ethiopia.

Combating and preventing abnormality in lipid metabolism becomes a pivotal criterion for research. Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a circulating protein; it promotes the degradation of low-density lipoprotein receptors (LDL-R) and hence increases LDL-C levels. Silencing the gene PCSK9 at post-transcriptional level with the help of small interfering Ribo nucleic acid (siRNA) gives a new insight and a novel therapeutic way to regulate LDL-C metabolism. Read More

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May 2018
7 Reads

Selection of Luteolin as a potential antagonist from molecular docking analysis of EGFR mutant.

Bioinformation 2018 31;14(5):241-247. Epub 2018 May 31.

Babcock University Teaching Hospital, Ilesan, Ogun State.

The life-threatening sides effect of the current EGFR mutant inhibitors (drugs) such as the eruption of rash which can be seen on the face, chest, back and even the trunk, diarrhea, nausea, vomiting, anorexia and stomatitis, necessitates the discovery of new potent and safe compounds as a chemo-therapeutic measure against lung cancer. Approximately about 10% of patients with Non-small cell lung cancer (NSCLC) in the US and about 35% in East Asia have tumor associated EGFR. These mutations occur within EGFR exon 18-21, which encodes a portion of the EGFR kinase domain and enables researchers to identify compounds that only recognizes and binds to the cancer cells. Read More

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May 2018
5 Reads

Comparative evaluation of anti-angiogenic effects of noscapine derivatives.

Bioinformation 2018 31;14(5):236-240. Epub 2018 May 31.

Department of Pharmacology, VSS Institute of Medical Science & Research, Burla, Sambalpur, Odisha.

Angiogenesis, the formation of new capillaries from pre-existing vessels, is essential for tumor progression. Synthetic derivatives of anti-cancer compound, noscapine (an opium alkaloid) such as Cl-noscapine, Br-noscapine and Folate-noscapine along with two of the reference compounds, TNP-470 and paclitaxel were examined for anti-angiogenic activities by using human umbilical vein endothelial cells (HUVECs). The noscapine derivatives showed anti-angiogenic activity albeit at high concentration compared to the reference compounds. Read More

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May 2018
2 Reads

Molecular Docking Analysis of Pyrimethamine Derivatives with Plasmodium falciparum Dihydrofolate Reductase.

Bioinformation 2018 31;14(5):232-235. Epub 2018 May 31.

Laboratory of Bioinformatics, Department of Biotechnology, IFTM University, Delhi Road (NH 24), Moradabad 244 102, Uttar Pradesh, India.

DHFR from Pf is a known target for malaria. There is a continued effort for the design and development of the potent inhibitor for PfDHFR in the control of malaria. Therefore it is of interest to screen PfDHFR with the derivatives of Pyrimethamine. Read More

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May 2018
1 Read

Insights from the Molecular modeling, docking analysis of illicit drugs and Bomb Compounds with Honey Bee Odorant Binding Proteins (OBPs).

Bioinformation 2018 31;14(5):219-231. Epub 2018 May 31.

Department of Botany, Alagappa University, Karaikudi - 630 003.

Analysis of honeybee PBPs is of interest in the development of Biosensor applications. We described the predicted binding of 19 such compounds with 43-honey bee OBPs using molecular modeling, docking and phylogenetic analysis. Therefore, training the honeybees using preferred compounds formulate the bees to identify the illicit drugs and bomb compounds. Read More

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May 2018
1 Read

Prediction of Protein Acetylation Sites using Kernel Naive Bayes Classifier Based on Protein Sequences Profiling.

Bioinformation 2018 31;14(5):213-218. Epub 2018 May 31.

Data Science for Knowledge Creation Research Center, Seoul National University, Korea.

Lysine acetylation is one of the decisive categories of protein post-translational modification (PTM), it is convoluted in many significant cellular developments and severe diseases in the biological system. The experimental identification of protein-acetylated sites is painstaking, time-consuming and expensive. Hence, there is significant interest in the development of computational approaches for consistent prediction of acetylation sites using protein sequences. Read More

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May 2018
7 Reads

Structure modeling to function prediction of Uncharacterized Human Protein C15orf41.

Bioinformation 2018 31;14(5):206-212. Epub 2018 May 31.

Data Science for Knowledge Creation Research Center, Seoul National University, Korea.

The dyserythropoietic anemia disease is a genetic disorder of erythropoiesis characterized by morphological abnormalities of erythroblasts. This is caused by human gene C15orf41 mutation. The uncharacterized C15orf41 protein is involved in the formation of a functional complex structure. Read More

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May 2018
1 Read

Future Innovations in Viral Immune Surveillance: A Novel Place for Bioinformation and Artificial Intelligence in the Administration of Health Care.

Bioinformation 2018 31;14(5):201-205. Epub 2018 May 31.

UCLA Center for the Health Sciences, School of Dentistry, Los Angeles, CA.

Novel developments in bioinformation, bioinformatics and biostatistics, including artificial intelligence (AI), play a timely and critical role in translational care. Case in point, the extent to which viral immune surveillance is regulated by immune cells and soluble factors, and by non-immune factors informs the administration of health care. The events by which health is regained following viral infection is an allostatic process, which can be modeled using Hilbert's and Volterra's mathematical biology criteria, and biostatistical methodologies such as linear multiple regression. Read More

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May 2018
1 Read

Insights from the sequence similarity of Zika virus proteins with the Human nerve proteins.

Bioinformation 2018 31;14(5):194-200. Epub 2018 May 31.

CODEWEL Nireekshana ACET, Narayanaguda, Hyderabad -500029, Telangana, India.

Massive peptide sharing between the Zika virus polyprotein and host tissue proteins could elicit significant host-pathogen interactions and cross-reactions leading to autoimmune diseases. This study found similarities in the Zika V proteins and human nerve tissue proteins. 63 human nerve proteins were screened for similarities with the Zika V of which Neuromodulin, Nestin, Galanin, Bombesin, Calcium-binding protein were found to have similarities to the Zika V poly protein C at different sequence regions. Read More

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May 2018
16 Reads

PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins.

Bioinformation 2018 31;14(5):190-193. Epub 2018 May 31.

Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India.

Residues in allelic positions, in the local segment of aligned sequences of proteins show wide variations. Here, we describe PROPAB that computes the propensity tables for helix, strand and coil types from multiple 3D structure files following ab initio statistical procedure. It also classifies them in range specific and chain specific manners. Read More

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May 2018
9 Reads

Design of peptide epitope from the neuraminidase protein of influenza A and influenza B towards short peptide vaccine development.

Bioinformation 2018 31;14(5):183-189. Epub 2018 May 31.

Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore - 632055, Tamil Nadu, India.

Influenza viruses A and B are important human respiratory pathogens causing seasonal, endemic and pandemic infections in several parts of the globe with high morbidity and considerable mortality. The current inactivated and live attenuated vaccines are not effective. Therefore, it is of interest to design universal influenza virus vaccines with high efficacy. Read More

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May 2018
1 Read

LSAT: Liliaceae Simple Sequences Analysis Tool, a web server.

Bioinformation 2018 30;14(4):181-182. Epub 2018 Apr 30.

Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, 57922 South Korea.

LSAT is a web-based microsatellite SSR marker designer tool specific for the Liliaceae family. It is developed using HTML, CSS, PHP, Perl and Java scripts. It works without extra add-ons on standard browsers. Read More

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April 2018
15 Reads

Computer-Aided Multi-Target Management of Emergent Alzheimer's Disease.

Bioinformation 2018 5;14(4):167-180. Epub 2018 May 5.

Department of Informatics, School of Medicine, CHA University, Seongnam, South Korea.

Alzheimer's disease (AD) represents an enormous global health burden in terms of human suffering and economic cost. AD management requires a shift from the prevailing paradigm targeting pathogenesis to design and develop effective drugs with adequate success in clinical trials. Therefore, it is of interest to report a review on amyloid beta (Aβ) effects and other multi-targets including cholinesterase, NFTs, tau protein and TNF associated with brain cell death to be neuro-protective from AD. Read More

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May 2018
26 Reads

ASBAAC: Automated Salt-Bridge and Aromatic-Aromatic Calculator.

Bioinformation 2018 30;14(4):164-166. Epub 2018 Apr 30.

Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research - Indian Institute of Chemical Biology, 4 Raja SC Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India.

Biological systems are made of complex networks non-covalent interactions observed among protein-protein, protein-DNA, proteinlipid complexes using hydrogen-bonds, salt-bridges, aromatic-aromatic, van der Waals (vdW), hydrophobic-interactions and several others using distance criteria. Hence, large-scale data analysis is required to understand the principles of biological complex formation. Therefore, it is of interest to analyze non-covalent interaction namely, salt-bridge and aromatic-aromatic contacts in known and modeled protein complex structures. Read More

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April 2018
4 Reads

Biomarker Identification from RNA-Seq Data using a Robust Statistical Approach.

Bioinformation 2018 30;14(4):153-163. Epub 2018 Apr 30.

Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.

Biomarker identification by differentially expressed genes (DEGs) using RNA-sequencing technology is an important task to characterize the transcriptomics data. This is possible with the advancement of next-generation sequencing technology (NGS). There are a number of statistical techniques to identify DEGs from high-dimensional RNA-seq count data with different groups or conditions such as edgeR, SAMSeq, voom-limma, etc. Read More

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April 2018
3 Reads

Molecular modeling, docking and protein-protein interaction analysis of MAPK signalling cascade involved in Camalexin biosynthesis in Brassica rapa.

Bioinformation 2018 30;14(4):145-152. Epub 2018 Apr 30.

Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India.

Phytoalexins are small antimicrobial molecules synthesized and accumulated by plants upon exposure to pathogens. Camalexin is an indole-derived phytoalexin, which is accumulated in plants including Arabidopsis thaliana, and other Brassicaceae, which plays a major role in disease resistance against fungal pathogens. The productivity of Brassica crops is adversely affected by Alternaria blight disease, which is caused by Alternaria brassicae. Read More

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April 2018
16 Reads

Scale-free networks in metabolomics.

Bioinformation 2018 31;14(3):140-144. Epub 2018 Mar 31.

Neonatal Intensive Care Unit, Department of Surgical Sciences, Neonatal Pathology and Neonatal Section, University of Cagliari, Cagliari, Italy.

Metabolomics is an expanding discipline in biology. It is the process of portraying the phenotype of a cell, tissue or species organism using a comprehensive set of metabolites. Therefore, it is of interest to understand complex systems such as metabolomics using a scale-free topology. Read More

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March 2018
2 Reads

Insights from the Molecular Modelling and Docking Analysis of AIF-NLS complex to infer Nuclear Translocation of the Protein.

Bioinformation 2018 31;14(3):132-139. Epub 2018 Mar 31.

Department of Genetic Engineering, School of Bioengineering, SRM University, Kattankulathur, Chennai - 603203.

Apoptosis Inducing Factor protein has a dual role depending on its localization in mitochondrion (energy production) and nucleus (induces apoptosis). Cell damage transports this protein to nucleus which otherwise favors mitochondrion. The alteration of Nuclear Localisation Signal tags could aid nuclear translocation. Read More

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March 2018
2 Reads

Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks.

Bioinformation 2018 31;14(3):123-131. Epub 2018 Mar 31.

National Research Centre on Plant Biotechnology, Indian Agriculture Research Institute, New Delhi, India.

Rice, a staple food crop, is often subjected to drought and salinity stresses thereby limiting its yield potential. Since there is a cross talk between these abiotic stresses, identification of common and/or overlapping regulatory elements is pivotal for generating rice cultivars that showed tolerance towards them. Analysis of the gene interaction network (GIN) facilitates identifying the role of individual genes and their interactions with others that constitute important molecular determinants in sensing and signaling cascade governing drought and/or salinity stresses. Read More

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March 2018
22 Reads

Analysis of antibiotics resistant genes in different strains of .

Bioinformation 2018 31;14(3):113-122. Epub 2018 Mar 31.

Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria.

The control of Staphylococcus aureus infection is being hampered by methicillin and other resistant strains. The identification of the unique antibiotic resistant genes from the genomes of various strains of S. aureus is of interest. Read More

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March 2018
2 Reads

Genetic characterization of Chikungunya virus 2009 isolates from South India.

Bioinformation 2018 31;14(3):106-112. Epub 2018 Mar 31.

Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Chennai, India.

Chikungunya Virus (CHIKV) is a single stranded positive sense enveloped RNA virus. Re-emergence of CHIKV caused a massive outbreak with severe clinical manifestation affecting multiple organs. The genetic diversity of CHIKV, which caused recurring outbreaks in India, was studied. Read More

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March 2018
19 Reads

Molecular dynamics simulation (MDS) analysis of ToxT virulence factor complexed with docked potential inhibitors.

Bioinformation 2018 31;14(3):101-105. Epub 2018 Mar 31.

Molecular Biology Research Center, Systems Biology and Poisonings institute, Baqiyatallah University of Medical Sciences, Tehran, IRAN.

The ToxT transcription factor mediates the transcription of the two major virulence factors in Vibrio cholerae. It has a DNA binding domain made of α4, α5, α6, α7, α8, α9 and α10 helices that is responsible for the transcription of virulence genes. Therefore, it is of interest to screen ToxT against the ZINC ligand database containing data for a million compounds. Read More

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March 2018
4 Reads

physicochemical characterization and topology analysis of Respiratory burst oxidase homolog (Rboh) proteins from Arabidopsis and rice.

Bioinformation 2018 31;14(3):93-100. Epub 2018 Mar 31.

Department of Biotechnology, Guru Nanak Dev University (GNDU), Amritsar 143005, Punjab, India.

NADPH oxidase (NOX) is a key enzyme involved in the production of apoplastic superoxide (O2-), a type of reactive oxygen species (ROS). Plant Noxes are the homologs of mammalian NADPH oxidase's catalytic subunit and are documented as respiratory burst oxidase homologs (Rbohs). A number of studies have reported their diverse functions in combating various stresses and in plant growth and development. Read More

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March 2018
2 Reads
1 Citation