1,742 results match your criteria Bioinformation[Journal]


Linking gut microbiota with the human diseases.

Bioinformation 2020 29;16(2):196-208. Epub 2020 Feb 29.

Department of Biotechnology, Assam University, Silchar, Assam, India.

The human gut is rich in microbes. Therefore, it is of interest to document data to link known human diseases with the gut microbiota. Various factors like hormones, metabolites and dietary habitats are responsible for shaping the microbiota of the gut. Read More

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http://dx.doi.org/10.6026/97320630016196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196170PMC
February 2020

Molecular docking analysis of phytochemicals from ethanolic extract of crescentia cujete with the auto inhibited parkin catalytic domain.

Bioinformation 2020 29;16(2):189-195. Epub 2020 Feb 29.

Michael Job College of Arts and Science for Women, Coimbatore,Tamilnadu, India.

The autoinhibited Parkin catalytic domain (PDB ID: 4BM9) receptor has been described to have a role in the ubiquitination of α-syn in Parkinson's disease. Therefore, it is of interest to discuss the molecular docking analysis data of phytochemicals from ethanolic extract of Crescentia cujete with the auto inhibited Parkin catalytic domain. We report the docking features of the phytochemical named 1, 2-Ethanediamine, N-(2-aminoethyl) with the target protein for further consideration towards the design and development of anti-Parkinson agents. Read More

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http://dx.doi.org/10.6026/97320630016189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196166PMC
February 2020

Molecular modeling and docking analysis of aspirin with pde7b in the context of neuro-inflammation.

Bioinformation 2020 29;16(2):183-188. Epub 2020 Feb 29.

Department of Pharmacology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai-116, Tamil Nadu, India.

The PDE7B gene encodes 3'5'-cyclic nucleotide phosphodiesterase (PDE) and a known target in cognitive impairments. Therefore, it is of interest to design and development of potential inhibitors with PDE7B with improved binding features. We document that the amino acid residues such as H186, K190, and G113 of PDE7B protein showed crucial interactions with aspirin for further consideration in this context. Read More

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http://dx.doi.org/10.6026/97320630016183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196167PMC
February 2020

Increased Gonadotropins and prolactin are linked to infertility in males.

Bioinformation 2020 29;16(2):176-182. Epub 2020 Feb 29.

Division of Endocrinology, Central Drug Research Institute, Lucknow, U.P.,India.

Infertility has become a significant issue among married couples worldwide. The association of variations in reproductive hormones with infertility is evaluated at a tertiary care hospital in North India. A total of 220 infertile males having infertility longer than one year (cases) and 220 age-matched fertile males with confirmed paternity in past two to three years (controls) were enrolled for the study. Read More

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http://dx.doi.org/10.6026/97320630016176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196164PMC
February 2020

CpGDB : A Comprehensive Database of Chloroplast Genomes.

Bioinformation 2020 29;16(2):171-175. Epub 2020 Feb 29.

Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, India.

Chloroplast Genome Database (CpGDB) is user friendly, web-based, freely available and dynamic relational database which provides a platform for researchers to search and download complete chloroplast genome sequences, individual gene sequences and feature records of plant species belonging to same or different families of spermatophytes. Presently, the database consists of genome sequences, individual gene sequences and feature records of chloroplast genomes of 3823 plant species belonging to 1527 genera from 256 families, which will be updated regularly with the availability of new sequences at NCBI. Extensive data mining of feature records from GenBank files, uniform nomenclature for majority of genes, enriched intron/exon feature records makes CpGDB a valuable resource for studies in chloroplast genomics while complementing existing chloroplast databases. Read More

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http://dx.doi.org/10.6026/97320630016171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196173PMC
February 2020

Decoding the vital segments in human ATP-dependent RNA helicase.

Bioinformation 2020 29;16(2):160-170. Epub 2020 Feb 29.

Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India.

An analysis of the ATP-dependent RNA helicase using known functionally close analogs helps disclose the structural and functional information of the enzyme. The enzyme plays several interlinked biological functions and there is an urgent need to interpret its key active-site residues to infer function and establish role. The human protein q96c10. Read More

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http://dx.doi.org/10.6026/97320630016160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196165PMC
February 2020

Docking analysis of importin-11 homology model with the phyto compounds towards colorectal cancer treatment.

Bioinformation 2020 29;16(2):153-159. Epub 2020 Feb 29.

Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai-600 123, Tamil Nadu, India.

Colorectal cancer (CRC) is the most familiar malignancy worldwide. Hence, searching for novel therapeutic options is of highest priority. Therefore, it is of interest to design inhibitors to the protein target importin-11, which transports β-catenin linked to colon cancer cells. Read More

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http://dx.doi.org/10.6026/97320630016153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196172PMC
February 2020

GenPop-An Online Tool to Analyze Human Population Genetic Data.

Bioinformation 2020 29;16(2):149-152. Epub 2020 Feb 29.

Department of Bioinformatics, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai ,Tamilnadu, India- 600116.

GenPop is a web based online cross platform tool developed to help Geneticist and Epidemiologist to deal with association studies in analyzing human population genetic data. The tool features include descriptive analysis such as Hardy-Weinberg equilibrium test, chi-square p-value and analysis of single nucleotide polymorphisms (SNPs) with multiple inheritance models such as dominant, recessive, allelic, genotype, odd's ratio and relative risk at 95% confidence interval and analysis of multiple SNPs including haplotype frequencies and linkage disequilibrium for a pair of biallelic markers. This is a user-driven human population genetic data analysis tool that is easily scalable and acceptable with multiple implementations of different algorithms. Read More

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http://dx.doi.org/10.6026/97320630016149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196168PMC
February 2020

Classification of thyroid nodules using ultrasound images.

Bioinformation 2020 29;16(2):145-148. Epub 2020 Feb 29.

Department of Computer Applications, Alagappa University, Karaikudi, Tamilnadu, India.

Medical imaging using image sensors play an essential role in effective diagnosis. Therefore, it is of interest to use medical imaging techniques for the diagnosis of thyroid-linked dysfunction. Ultrasound is the low-cost image processing technique to study internal organs and blood flow in blood vessels. Read More

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http://dx.doi.org/10.6026/97320630016145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196169PMC
February 2020

2019-nCoV - Towards a 4th generation vaccine.

Bioinformation 2020 12;16(2):139-144. Epub 2020 Feb 12.

UCLA Center for the Health Sciences, Los Angeles, CA, USA, Francesco.

The first report of the unusual manifestation of pneumonia-like symptoms in Wuhan City, China was made on 31 December 2019. Within one week, the Chinese authorities reported that they had identified the causative agent as a new member of the Coronavirus family, the same family of that was responsible for MERS and SARS not so many years ago. The new virus was called Novel Coronavirus 2019 (2019-nCoV). Read More

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http://dx.doi.org/10.6026/97320630016139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196171PMC
February 2020

Molecular docking analysis of alkaloid compounds with beta-catenin towards the treatment of colon cancer.

Bioinformation 2020 31;16(3):283-287. Epub 2020 Mar 31.

Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600 077, India.

It is known that beta-catenin is associated with fibromatosis, sarcoma and mesenchymal tumor. Therefore, it is of interest to design an effective inhibtitor to the target protein beta-catenin. In this study, we report the molecular docking analysis of alkaloid compounds (aristolochicacid, cryptopleurine, demecolcine, fagaronine and thalicarpine) with beta-catenin for further consideration towards the design and development of potential inhintors for the treatmnet of colon cancer. Read More

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http://dx.doi.org/10.6026/97320630016283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147492PMC

Towards the revival of oscillation from complete cessation in stochastic systems for application in molecular biology.

Bioinformation 2020 31;16(3):274-282. Epub 2020 Mar 31.

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

Delay and noise are inevitable in complex systems that are common in biochemical networks. The system is often disturbed at various states irrespective of the size (small or large) of delay and noise. Therefore, it is of interest to describe the significance of delay and noise in stochastic Willamowski-Rossler chemical oscillator model using a delay stochastic (having random probability distribution) simulation algorithm. Read More

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http://dx.doi.org/10.6026/97320630016274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147491PMC

A comparative study of antibacterial and antifungal activities of extracts from four indigenous plants.

Bioinformation 2020 31;16(3):267-273. Epub 2020 Mar 31.

Department of Botany, Guru Ghasidas University, Bilaspur, India 495009.

A repetitive and wide use of chemical antibiotics has brought a serious threat in the biomedical and clinical sectors by the emergence of multidrug resistant pathogens. Plants have secondary metabolites that make them suitable candidate for natural antimicrobial agent without any side effect. In this study, we assessed comparative antibacterial and antifungal effects of extracts from four Indigenous plants (Nerium sp; Mentha sp; Aloe vera and Eucalyptus sp). Read More

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http://dx.doi.org/10.6026/97320630016267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147494PMC

Distinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae.

Bioinformation 2020 31;16(3):256-268. Epub 2020 Mar 31.

Department of Microbiology, Assam University, Silchar 788011, Assam, India.

It is of interest to describe the distinctive features gleaned from the comparative genome analysis of clinical and non-clinical isolates of Klebsiella pneumoniae. The core genome of K. pneumoinae consisted of 3568 genes. Read More

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http://dx.doi.org/10.6026/97320630016256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147497PMC

Mining of miRNAs from EST data in Dendrobium nobile.

Bioinformation 2020 31;16(3):245-255. Epub 2020 Mar 31.

Department of Botany, Gauhati University, Guwahati, Assam, India - 7810014.

Dendrobium nobile is an orchid species highly popular for its therapeutic properties and is often used as a medicinal herb. Documenting miRNA-target associations in D. nobile is an important step to facilitate functional genomics studies in this species. Read More

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http://dx.doi.org/10.6026/97320630016245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147496PMC

Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus.

Bioinformation 2020 31;16(3):236-244. Epub 2020 Mar 31.

Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq.

Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved drugs with the recently known 2019-nCoV main protease structure having high sequence homology with that from SARS-CoV. We document the binding features of top 10 drugs with the target protein. Read More

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http://dx.doi.org/10.6026/97320630016236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147498PMC

Analysis of methyltransferase (MTase) domain from Zika virus (ZIKV).

Bioinformation 2020 31;16(3):229-235. Epub 2020 Mar 31.

Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.

A comprehensive analysis of methyltransferase (MTase) from Zika virus (ZIKV) is of interest in the development of drugs and biomarkers in the combat and care of ZIKA fever with impulsive joint pain and conjunctivitis. MTase sequence is homologous in several viral species. We analyzed the MTase domain from ZIKV using Bioinformatics tools such as SMART, PROSITE, PFAM, PANTHER, and InterProScan to glean insights on the sequence to structure to function data. Read More

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http://dx.doi.org/10.6026/97320630016229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147495PMC

Analysis of predicted proteasomal cleavages in the methyltransferase domain from JEV.

Bioinformation 2020 31;16(3):223-228. Epub 2020 Mar 31.

Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.

The methyltransferase (MTase, a 265 amino acid residues long region at the N-terminal end of the viral nonfunctional supermolecule NS5 domain) is key for viral replication in Japanese Encephalitis Virus (JEV). Sequence to structure to functional information with adequate knowledge on MTase from JEV is currently limited. Therefore, it is of interest to document a report on the comprehensive analysis of predicted proteasomal cleavage data in the methyltransferase domain from JEV. Read More

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http://dx.doi.org/10.6026/97320630016223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147493PMC

CoViD-19 Immunopathology and Immunotherapy.

Bioinformation 2020 31;16(3):219-222. Epub 2020 Mar 31.

Pre-M.D. Student, Rappaport Faculty of Medicine,Technion-Israel Institute of Technology, Haifa, Israel.

New evidence on the T-cell immuno-pathology in patient's with Corona Virus Disease 2019 (CoViD-19) was reported by Diao et al. in MedRxiv (doi: 10.1101/2020. Read More

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http://dx.doi.org/10.6026/97320630016219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147500PMC

Molecular dynamics analysis of conserved water mediated inter-domain recognition of His667-Trp669 in human ceruloplasmin.

Bioinformation 2020 31;16(3):209-218. Epub 2020 Mar 31.

Department of Chemistry, National Institute of Technology-Durgapur, West Bengal, Durgapur - 713209, India.

The human ceruloplasmin (hCP) is the copper containing ferroxidase enzyme with multifunctional activities (NO-oxidase, NO2-synthase,oxidation of neurotransmitters including antioxidants). Therefore, it is of interest to probe the multi-domain hCP using moleculardynamics simulation. Results explain the role played by several conserved water centers in the intra and inter-domain recognition throughH-bond interaction with the interacting residues. Read More

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http://dx.doi.org/10.6026/97320630016209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147499PMC

Protein interaction studies of curli fimbriae in Escherichia coli biofilms.

Bioinformation 2019 31;15(12):918-921. Epub 2019 Dec 31.

Department of Bioinformatics, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai-600 116, India.

Catheter-associated urinary tract infections (CAUTIs) caused by biofilms on indwelling medical devices are the most common type of nosocomial infections, a major health concern due to complications and frequent recurrence. The infections are most often caused by Escherichia coli. Curli are proteinaceous components of a complex extracellular matrix produced by various strains of Enterobacteriaceae. Read More

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http://dx.doi.org/10.6026/97320630015918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088426PMC
December 2019

Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs).

Bioinformation 2019 31;15(12):907-917. Epub 2019 Dec 31.

Dept. of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar-751022, Odisha, India.

MicroRNAs are small non-coding RNAs of 21-24 nucleotides in length that acts as important modulators of gene expression related to numerous biological processes including development and defense response in eukaryotes. However, only a limited report on onion (Allium cepa) miRNAs is available and their associated role in growth and development of onion is not yet clear. Therefore, it is of interest to identify miRNAs and their targets in Allium cepa using the genome survey sequences (GSSs) and expressed sequence tags (ESTs) and deduce the functions of the target genes using gene ontology (GO) terms. Read More

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http://dx.doi.org/10.6026/97320630015907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088424PMC
December 2019

Molecular docking analysis of a secondary metabolite with the glycoprotein receptors of HSV 1 and HSV 2.

Bioinformation 2019 31;15(12):887-895. Epub 2019 Dec 31.

Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore Tamil Nadu, India.

Herpes simplex viruses (HSV) are alpha herpes viruses, which causes life-threatening illness. Therefore, it is of interest to design and develop potential drugs to treat HSV infections. We show the optimal molecular docking properties of a secondary metabolite (3, 7, 11, 15 tetra methyl-2-2-hexadecen-'1-ol) with the glycoprotein receptors of HSV1 and HSV 2 for further consideration. Read More

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http://dx.doi.org/10.6026/97320630015887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088423PMC
December 2019

Life science database cross search: A single window system for dispersed biological databases.

Bioinformation 2019 31;15(12):883-886. Epub 2019 Dec 31.

Japan Science and Technology Agency, National Bioscience Database Center, Japan.

A comprehensive search system for the bioscience databases is in progress. We constructed a search service, Life science database cross search system (https://biosciencedbc.jp/dbsearch/index. Read More

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http://dx.doi.org/10.6026/97320630015883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088429PMC
December 2019

Semi supervised data mining model for the prognosis of pre-diabetic conditions in type 2 Diabetes Mellitus.

Bioinformation 2019 31;15(12):875-882. Epub 2019 Dec 31.

Department of Computer Science Engineering, SASTRA Deemed To be University, Srinivasa Ramanujan Centre (SRC), Kumbakonam, Tamil Nadu, India.

Diabetic Mellitus is the leading disease in the world irrespective of age and geographical location. It is estimated that 43% of the overall population is affected by the disease. The reasons for the disease include inappropriate diet lifestyle with allied symptoms like obesity. Read More

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http://dx.doi.org/10.6026/97320630015875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088425PMC
December 2019

SubmitoLoc: Identification of mitochondrial sub cellular locations of proteins using support vector machine.

Bioinformation 2019 31;15(12):863-868. Epub 2019 Dec 31.

Department of Animal Health Management, Alagappa University, Karaikudi-630003, India.

Mitochondria are important sub-cellular organelles in eukaryotes. Defects in mitochondrial system lead to a variety of disease. Therefore, detailed knowledge of mitochondrial proteome is vital to understand mitochondrial system and their function. Read More

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http://dx.doi.org/10.6026/97320630015863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088428PMC
December 2019

Genomic profiling of Nipah virus using NGS driven RNA-Seq expression data.

Bioinformation 2019 31;15(12):853-862. Epub 2019 Dec 31.

Institute of Bangladesh Studies, University of Rajshahi, Rajshahi, Bangladesh.

Nipah virus (NiV) is an ssRNA, enveloped paramyxovirus in the genus Henipaveridae with a case fatality rate >70%. We analyzed the NGS RNA-Seq gene expression data of NiV to detect differentially expressed genes (DEGs) using the statistical R package limma. We used the Cytoscape, Ensembl, and STRING tools to construct the gene-gene interaction tree, phylogenetic gene tree and protein-protein interaction networks towards functional annotation. Read More

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http://dx.doi.org/10.6026/97320630015853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088422PMC
December 2019

Insights into the metabolic responses of two contrasting Tibetan hulless barley genotypes under low nitrogen stress.

Bioinformation 2019 31;15(12):845-852. Epub 2019 Dec 31.

State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China.

Nitrogen (N) is an essential macronutrient for plants. However, excessive use of N fertilizer for cultivation is an environmental hazard. A good adaption to N deficiency is known in the Tibetan hulless barley. Read More

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http://dx.doi.org/10.6026/97320630015845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088427PMC
December 2019

Science for service in a society is the success story of scientists with serenity.

Bioinformation 2020 25;16(1):34-38. Epub 2020 Jan 25.

Biomedical Informatics (P) Ltd.

Available data on science is constantly gleaned for gathering valuable information to create concise yet precise knowledge on specific subjects (especially, the biology oriented agriculture and biomedicine) for service in the society. These sacrifices surmounts as success stories for scientists worldwide. Data in the form of known literature plays a radical role in serving the society with improved infrastructure and facilities making associated resources available, accessible and affordable. Read More

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http://dx.doi.org/10.6026/97320630016034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986937PMC
January 2020

Importance of customized (task oriented) software tools for biomedical applications.

Authors:
Haseeb A Khan

Bioinformation 2020 15;16(1):30-33. Epub 2020 Jan 15.

Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.

Biomedical scientists and clinicians often require customized and user-friendly software tools due to the unavailability of specific software, complexity of existing software or high cost of commercial software. This editorial provides a short update on recently published task-oriented biomedical software tools. The novelty and applications of some customized software tools including CALCFISHER, CALCNTCP, CALCDOSE, and SCEW are also summarized in this editorial. Read More

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http://dx.doi.org/10.6026/97320630016030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986938PMC
January 2020

Impact of airway dysfunction on dental health.

Authors:
Juliette Tamkin

Bioinformation 2020 15;16(1):26-29. Epub 2020 Jan 15.

Dental Group of Sherman Oaks, California, CA 1403, USA.

The airway encompasses the mouth, jaw, nasal passages, tongue, and throat. Dentists in collaboration with other health professionals can recognize the early signs of the disorder, perform proper assessment of facial and dental structures, and provide treatment to help prevent and manage the dysfunction. Therefore, it is of interest to discuss the impact of airway development and dysfunction on dental health. Read More

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http://dx.doi.org/10.6026/97320630016026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986941PMC
January 2020

Identification of tunnels as in potato hydrolases.

Bioinformation 2020 15;16(1):21-25. Epub 2020 Jan 15.

Department of bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530 Krakow, Poland.

Enzymes with an active center hidden in the middle of the molecule in a tunnel-like cavity constitute an interesting object of analysis due to the highly specialized environment for the course of the catalytic reaction. Identifying the tunnel is a challenge in itself. Moreover, the structural conditioning for the course of the reaction provides information on the diversity of the environment, which must necessarily meet the conditions of high specificity. Read More

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http://dx.doi.org/10.6026/97320630016021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986939PMC
January 2020

Gaining new insights on the Hsp90 regulatory network.

Bioinformation 2020 1;16(1):17-20. Epub 2020 Jan 1.

Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Monte d'Ago, 60131, Ancona, Italy.

The heat shock protein Hsp90 is a molecular chaperon that uses ATP and interacts with various co-chaperone proteins, acting as adapters, in order to carry out the maturation of its target proteins. In physiological conditions, the heat shock proteins (HSPs) favour post-translational modification, protein folding and sub-cellular transport of their "client" proteins. In stress conditions, many misfolded proteins accumulate exposing their hydrophobic residues and these are recognized by HSPs which prevent the aggregation and favour the correct folding. Read More

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http://dx.doi.org/10.6026/97320630016017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986935PMC
January 2020

Bioinformatics drives discovery in Biomedicine.

Bioinformation 2020 1;16(1):13-16. Epub 2020 Jan 1.

Division of Vaccine Discovery, La Jolla Institute for Immunology, CA 92037, USA.

Bioinformatics has evolved from providing basic solutions, such as sequence alignment, structure predictions, and phylogenetic analysis to an independent data-driven field. The unprecedented growth of genomic technologies and the enormous data have opened an avenue for bioinformaticians (Bioinformatics professionals) never been seen before in the history of mankind. The novel opportunity also requires creative solutions that need skills to deal with noisy, unstructured information to offer valuable biological insights. Read More

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http://dx.doi.org/10.6026/97320630016013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986933PMC
January 2020

Revisiting the Micropipetting Techniques in Biomedical Sciences: A Fundamental Prerequisite in Good Laboratory Practice.

Bioinformation 2020 1;16(1):8-12. Epub 2020 Jan 1.

Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah-21589, Kingdom of Saudi Arabia.

The underlying technical and operational knowledge of micro-pipetting is essential for scientists, technicians, and students to achieve precise results from their experiments in Biomedical Sciences and other related disciplines. Since it is one of the crucial prerequisites for Good Laboratory Practices (GLPs), the key fundamentals of the micro-pipetting methods, such as forward and reverse pipetting and the importance of ergonomics and maintenance etc., are revisited in this Editorial report. Read More

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http://dx.doi.org/10.6026/97320630016008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986936PMC
January 2020

Metascience in Bioinformation.

Bioinformation 2020 1;16(1):4-7. Epub 2020 Jan 1.

Center for the Health Sciences, University of California Los Angeles, USA.

Metascience refers to the systematic process that uncovers, builds, evaluates, organizes and disseminates scientific advances. It is the principal tool at the disposal of the society to combat the debilitating effects of "false information" on health related data and its constituents. Read More

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http://dx.doi.org/10.6026/97320630016004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986940PMC
January 2020

Drug Discovery: Today and Tomorrow.

Authors:
Darren R Flower

Bioinformation 2020 1;16(1):1-3. Epub 2020 Jan 1.

Independent Interdisciplinary Consultant, Oxford, United Kingdom.

Drug discovery continues to underperform relative to unmet medical need. Driven by profit not societal need, the search for new drugs is neither properly funded nor sufficiently systematic. Many innovative approaches are significantly underused yet extant methodology is replete with problems. Read More

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http://dx.doi.org/10.6026/97320630016001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986934PMC
January 2020

Molecular modelling and docking analysis of pleurocidin (an antimicrobial peptide) like peptides with enterotoxin H from Klebsilla pneumonia.

Bioinformation 2019 17;15(11):838-844. Epub 2019 Dec 17.

Department of Human genetics and molecular biology, Bharathiyar University, Coimbatore, Tamilnadu, India.

Enterotoxin H is a key molecular target for replication and establishment of Klebsilla pneumonia in the host. Therefore, it is of interest to study the interaction of enterotoxin H with pleurocidin like peptides using molecular modelling (template PDB ID: 1YCE), Lig-Plot (ligand construction) and docking tools for therapeutic consideration. The hydrophobic pocket and the active site residues (Val 13, Met 16, Gly 25, Ala 25, and Ile 28) were identified using Cast P, Molegro and Sitehound tools. Read More

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http://dx.doi.org/10.6026/97320630015838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936665PMC
December 2019

Molecular docking analysis of timepidium with Acetylcholine and lumacaftor with GABA(A) activator.

Bioinformation 2019 16;15(11):832-837. Epub 2019 Dec 16.

Department of Biomedical Engineering, NED University of Engineering and Technology Karachi, Pakistan.

Epilepsy is a chronic disorder characterized by disturbed tissue related molecular activity within the brain irrespective of age. The cause is very difficult to understand towards a suitable treatment. However, its symptoms like seizures are treated and suppressed by known medications. Read More

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http://dx.doi.org/10.6026/97320630015832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936661PMC
December 2019

Genome-wide identification, characterization and phylogenetic analysis of Dicer-like (DCL) gene family in Coffea arabica.

Bioinformation 2019 11;15(11):824-831. Epub 2019 Dec 11.

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

A fine-tuned RNA interference (RNAi) pathway has been developed by plants to restrain distinct biological processes in various life stages including stress responses, development and maintenance of genome integrity. The Dicer-Like (DCL) proteins starts the RNAi process by producing complementary double-stranded RNAs (dsRNAs) into small RNA duplexes (21-24 nucleotides) trigger the RNAi process. Nevertheless, these members of RNAi pathway have not been deciphered in one of the most economically important plant coffee (). Read More

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http://dx.doi.org/10.6026/97320630015824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936657PMC
December 2019

An updated data portal for fungal allergens with curated information.

Bioinformation 2019 11;15(11):820-823. Epub 2019 Dec 11.

Koshien University Ringgold Standard Institution, School of Nutrition Sciences, Department of Food Design Takarazuka, Hyogo Japan.

Allergens originating from fungal components abundantly exist in and around human life. We constructed a data portal specific for fungal allergens that includes genomic data from four Aspergillus species used by beverage industries. The fungal database contains the information of nucleotide sequences, which are similar to the coding region of already known allergens in the public database. Read More

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http://dx.doi.org/10.6026/97320630015820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936663PMC
December 2019

Genotype based Risk Predictors for Polycystic Ovary Syndrome in Western Saudi Arabia.

Bioinformation 2019 10;15(11):812-819. Epub 2019 Dec 10.

Biochemistry Department, King Abdulaziz University, Jeddah, P.O. Box 80218, Saudi Arabia.

Polycystic ovary syndrome (PCOS) is the most common endocrine disease among premenopausal women. The genetic risk of PCOS in the Saudi population is still unclear. Therefore, it is of interest to study the genotype and allele frequency for six gene variants (THADA rs13429458, TOX3 rs4784165, FSHR rs2268361, YAP1 rs1894116, RAB5B rs705702, and HMGA2 rs2272046) in patients with PCOS in western Saudi population. Read More

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http://dx.doi.org/10.6026/97320630015812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936662PMC
December 2019

Genetic association of MBL-2 gene polymorphisms with Filarial chyluria.

Bioinformation 2019 10;15(11):806-811. Epub 2019 Dec 10.

Department of Microbiology, King George's Medical University, Lucknow, UP, India.

Lymphatic filariasis has become a significant public health issue in North India. The association of polymorphisms in MBL2 gene with filarial chyluria (FC) is evaluated in the North Indian patients for the first time. Hence, a tertiary care hospital based case-control study was conducted in north India where FC is endemic. Read More

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http://dx.doi.org/10.6026/97320630015806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936659PMC
December 2019

Towards the early detection of ductal carcinoma (a common type of breast cancer) using biomarkers linked to the PPAR(γ) signaling pathway.

Bioinformation 2019 9;15(11):799-805. Epub 2019 Dec 9.

Department of Biomedical Science and Environmental Biology, KMU-Kaohsiung Medical University, Kaohsiung, Taiwan.

Breast cancer is a leading cause of morbidity and mortality among women comprising about 12% females worldwide. The underlying alteration in the gene expression, molecular mechanism and metabolic pathways responsible for incidence and progression of breast tumorigenesis are yet not completely understood. In the present study, potential biomarker genes involved in the early progression for early diagnosis of breast cancer has been detailed. Read More

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http://dx.doi.org/10.6026/97320630015799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936658PMC
December 2019

Data Mining Technology Enabled Anti Retroviral Therapy (ART) for HIV Positive Patients in Gondar University Hospital, Ethiopia.

Bioinformation 2019 8;15(11):790-798. Epub 2019 Dec 8.

Department of Computer Science, College of Computing and Informatics, Haramaya University, Ethiopia.

It is of interest to discuss the feasibility for data mining technology enabled antiretroviral therapy (ART) for HIV positive patients at the University of Gondar Specialized Teaching Hospital, Ethiopia. The Knowledge Discovery in Databases (KDD), which is in an iterative process where evaluation measures enhanced, is used to prepare the data set for ART in HIV positive patients. A decision tree J48 model that is the implementation of algorithm ID3 (Iterative Dichotomiser 3) developed by the WEKA project team is used in this study. Read More

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http://dx.doi.org/10.6026/97320630015790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936664PMC
December 2019

Molecular docking based virtual screening of the breast cancer target NUDT5.

Bioinformation 2019 5;15(11):784-789. Epub 2019 Dec 5.

Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali-3814.

Breast cancer affects one in eight women in Bangladesh and is the most common cancer among women in South Asia next to skin cancer. NUDT5 are nucleotide-metabolizing enzymes (NUDIX hydrolases) linked with the ADP ribose and 8-oxo-guanine metabolism. It is known to be associated with the hormone dependent gene regulation and proliferation in breast cancer cells. Read More

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http://dx.doi.org/10.6026/97320630015784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936656PMC
December 2019

BioDADPep: A Bioinformatics database for anti diabetic peptides.

Bioinformation 2019 13;15(11):780-783. Epub 2019 Nov 13.

Department of Life Science and Bioinformatics, Assam University Diphu Campus, Diphu, Karbi Anglong 782 462, India.

The increasing number of cases for diabetes worldwide is a concern. Therefore, it is of interest to design therapeutic peptides to overcome side effects caused by the available drugs. It should be noted that data on several known anti-diabetic peptides is available in the literature in an organized manner. Read More

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http://dx.doi.org/10.6026/97320630015780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936660PMC
November 2019

Detection and analysis of stable and flexible genes towards a genome signature framework in cancer.

Bioinformation 2019 10;15(10):772-779. Epub 2019 Nov 10.

The University of Leipzig, Faculty of Physics and Earth Science, Peter Debye Institute for Soft Matter Physics, LinnestraBe 5, 04103 Leipzig, Germany.

Comparison and detection of stable cancer genes across cancer types is of interest. The gene expression data of 6 different cancer types (colon, breast, lung, ovarian, brain and renal) and a control group from The Cancer Genome Atlas (TCGA) database were used in this study. The comparison of gene expression data together with the calculation standard deviations of such data was completed using a statistical model for the detection of stable genes. Read More

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http://dx.doi.org/10.6026/97320630015772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6900328PMC
November 2019

From EST to structure models for functional inference of APP, BACE1, PSEN1, PSEN2 genes.

Bioinformation 2019 31;15(10):760-771. Epub 2019 Oct 31.

Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore-641046, Tamil Nadu, India.

Successive oxidative stress and biochemical changes results in neuronal death and neuritic plaques growth in Alzheimer's disease (AD). Therefore, it is interest to analyze amyloid-βeta precursor protein (APP), beta-secretase 1 (BACE1), presenilin (PSEN1 and PSEN2) genes from brain tissues to gain insights. Development of potential inhibitors for these targets is of significance. Read More

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http://dx.doi.org/10.6026/97320630015760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6900319PMC
October 2019

Insights from molecular dynamics simulation of human ceruloplasmin (ferroxidase enzyme) binding with biogenic monoamines.

Bioinformation 2019 31;15(10):750-759. Epub 2019 Oct 31.

Department of Chemistry National Institute of Technology-Durgapur, West Bengal, Durgapur-713209, India.

Human ceruloplasmin (hCP) is a multi-copper oxidase with ferroxidase and amine oxidase activities. Molecular dynamics simulation (MDS) and docking analysis of biogenic monoamines with ceruloplasmin explain the role of Asp1025, Glu935, Glu272, Glu232 and Glu230 together with the binding site water molecules (referred as conserved water molecules) in the stabilization of neurotransmitter (Serotonin, Norepinephrine and Epinephrine) molecules within the binding cavity of hCP. Conserved water molecules are found at specific positions interacting with the protein structures that have sequence similarity. Read More

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http://dx.doi.org/10.6026/97320630015750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6900326PMC
October 2019