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BIOTECHNOLOGY (244 journals)                  1 2 | Last

Showing 1 - 200 of 244 Journals sorted alphabetically
3 Biotech     Open Access   (Followers: 8)
Advanced Biomedical Research     Open Access  
Advances in Bioscience and Biotechnology     Open Access   (Followers: 17)
Advances in Genetic Engineering & Biotechnology     Hybrid Journal   (Followers: 9)
Advances in Regenerative Medicine     Open Access   (Followers: 3)
African Journal of Biotechnology     Open Access   (Followers: 6)
Algal Research     Partially Free   (Followers: 11)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 69)
American Journal of Bioinformatics Research     Open Access   (Followers: 7)
American Journal of Polymer Science     Open Access   (Followers: 33)
Amylase     Open Access  
Anadolu University Journal of Science and Technology : C Life Sciences and Biotechnology     Open Access  
Animal Biotechnology     Hybrid Journal   (Followers: 8)
Annales des Sciences Agronomiques     Full-text available via subscription  
Applied Biochemistry and Biotechnology     Hybrid Journal   (Followers: 45)
Applied Biosafety     Hybrid Journal  
Applied Food Biotechnology     Open Access   (Followers: 3)
Applied Microbiology and Biotechnology     Hybrid Journal   (Followers: 67)
Applied Mycology and Biotechnology     Full-text available via subscription   (Followers: 4)
Arthroplasty Today     Open Access   (Followers: 1)
Artificial Cells, Nanomedicine and Biotechnology     Hybrid Journal   (Followers: 1)
Asia Pacific Biotech News     Hybrid Journal   (Followers: 2)
Asian Journal of Biotechnology     Open Access   (Followers: 9)
Asian Pacific Journal of Tropical Biomedicine     Open Access   (Followers: 2)
Australasian Biotechnology     Full-text available via subscription   (Followers: 1)
Banat's Journal of Biotechnology     Open Access  
BBR : Biochemistry and Biotechnology Reports     Open Access   (Followers: 5)
Beitr?ge zur Tabakforschung International/Contributions to Tobacco Research     Open Access   (Followers: 3)
Bio-Algorithms and Med-Systems     Hybrid Journal   (Followers: 2)
Bio-Research     Full-text available via subscription   (Followers: 4)
Bioactive Materials     Open Access   (Followers: 1)
Biocatalysis and Agricultural Biotechnology     Hybrid Journal   (Followers: 4)
Biocybernetics and Biological Engineering     Full-text available via subscription   (Followers: 5)
Bioethics UPdate     Hybrid Journal   (Followers: 1)
Biofuels     Hybrid Journal   (Followers: 11)
Biofuels Engineering     Open Access   (Followers: 1)
Biological & Pharmaceutical Bulletin     Full-text available via subscription   (Followers: 4)
Biological Cybernetics     Hybrid Journal   (Followers: 10)
Biomarkers and Genomic Medicine     Open Access   (Followers: 3)
Biomaterials Research     Open Access   (Followers: 4)
BioMed Research International     Open Access   (Followers: 4)
Biomédica     Open Access  
Biomedical and Biotechnology Research Journal     Open Access  
Biomedical Engineering Research     Open Access   (Followers: 6)
Biomedical Glasses     Open Access  
Biomedical Reports     Full-text available via subscription  
BioMedicine     Open Access  
Biomedika     Open Access  
Bioprinting     Hybrid Journal   (Followers: 1)
Bioresource Technology Reports     Hybrid Journal   (Followers: 1)
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 21)
Biosensors Journal     Open Access  
Biosimilars     Open Access   (Followers: 1)
Biosurface and Biotribology     Open Access  
Biotechnic and Histochemistry     Hybrid Journal   (Followers: 1)
BioTechniques : The International Journal of Life Science Methods     Full-text available via subscription   (Followers: 28)
Biotechnologia Acta     Open Access   (Followers: 1)
Biotechnologie, Agronomie, Société et Environnement     Open Access   (Followers: 2)
Biotechnology     Open Access   (Followers: 8)
Biotechnology & Biotechnological Equipment     Open Access   (Followers: 4)
Biotechnology Advances     Hybrid Journal   (Followers: 34)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 44)
Biotechnology and Bioengineering     Hybrid Journal   (Followers: 159)
Biotechnology and Bioprocess Engineering     Hybrid Journal   (Followers: 6)
Biotechnology and Genetic Engineering Reviews     Hybrid Journal   (Followers: 13)
Biotechnology and Health Sciences     Open Access   (Followers: 1)
Biotechnology and Molecular Biology Reviews     Open Access   (Followers: 2)
Biotechnology Annual Review     Full-text available via subscription   (Followers: 5)
Biotechnology for Biofuels     Open Access   (Followers: 10)
Biotechnology Frontier     Open Access   (Followers: 2)
Biotechnology Journal     Hybrid Journal   (Followers: 17)
Biotechnology Law Report     Hybrid Journal   (Followers: 4)
Biotechnology Letters     Hybrid Journal   (Followers: 34)
Biotechnology Progress     Hybrid Journal   (Followers: 41)
Biotechnology Reports     Open Access  
Biotechnology Research International     Open Access   (Followers: 1)
Biotechnology Techniques     Hybrid Journal   (Followers: 10)
Biotecnología Aplicada     Open Access  
Bioteknologi (Biotechnological Studies)     Open Access  
BIOTIK : Jurnal Ilmiah Biologi Teknologi dan Kependidikan     Open Access  
Biotribology     Hybrid Journal   (Followers: 1)
BMC Biotechnology     Open Access   (Followers: 17)
Cell Biology and Development     Open Access  
Chinese Journal of Agricultural Biotechnology     Full-text available via subscription   (Followers: 4)
Communications in Mathematical Biology and Neuroscience     Open Access  
Computational and Structural Biotechnology Journal     Open Access   (Followers: 2)
Computer Methods and Programs in Biomedicine     Hybrid Journal   (Followers: 8)
Copernican Letters     Open Access   (Followers: 1)
Critical Reviews in Biotechnology     Hybrid Journal   (Followers: 20)
Crop Breeding and Applied Biotechnology     Open Access   (Followers: 3)
Current Bionanotechnology     Hybrid Journal  
Current Biotechnology     Hybrid Journal   (Followers: 4)
Current Opinion in Biomedical Engineering     Hybrid Journal   (Followers: 1)
Current Opinion in Biotechnology     Hybrid Journal   (Followers: 55)
Current Pharmaceutical Biotechnology     Hybrid Journal   (Followers: 9)
Current Research in Bioinformatics     Open Access   (Followers: 13)
Current Trends in Biotechnology and Chemical Research     Open Access   (Followers: 3)
Current trends in Biotechnology and Pharmacy     Open Access   (Followers: 8)
DNA and RNA Nanotechnology     Open Access  
EBioMedicine     Open Access  
Electronic Journal of Biotechnology     Open Access  
Entomologia Generalis     Full-text available via subscription   (Followers: 1)
Environmental Science : Processes & Impacts     Full-text available via subscription   (Followers: 4)
Experimental Biology and Medicine     Hybrid Journal   (Followers: 3)
Folia Medica Indonesiana     Open Access  
Food Bioscience     Hybrid Journal  
Food Biotechnology     Hybrid Journal   (Followers: 9)
Food Science and Biotechnology     Hybrid Journal   (Followers: 8)
Frontiers in Bioengineering and Biotechnology     Open Access   (Followers: 6)
Frontiers in Systems Biology     Open Access   (Followers: 2)
Fungal Biology and Biotechnology     Open Access   (Followers: 2)
GM Crops and Food: Biotechnology in Agriculture and the Food Chain     Full-text available via subscription   (Followers: 1)
GSTF Journal of BioSciences     Open Access  
HAYATI Journal of Biosciences     Open Access  
Horticultural Biotechnology Research     Open Access  
Horticulture, Environment, and Biotechnology     Hybrid Journal   (Followers: 11)
IEEE Transactions on Molecular, Biological and Multi-Scale Communications     Hybrid Journal   (Followers: 1)
IET Nanobiotechnology     Hybrid Journal   (Followers: 2)
IN VIVO     Full-text available via subscription   (Followers: 4)
Indian Journal of Biotechnology (IJBT)     Open Access   (Followers: 2)
Indonesia Journal of Biomedical Science     Open Access   (Followers: 2)
Indonesian Journal of Biotechnology     Open Access   (Followers: 1)
Indonesian Journal of Medicine     Open Access  
Industrial Biotechnology     Hybrid Journal   (Followers: 18)
International Biomechanics     Open Access  
International Journal of Bioinformatics Research and Applications     Hybrid Journal   (Followers: 14)
International Journal of Biomechatronics and Biomedical Robotics     Hybrid Journal   (Followers: 4)
International Journal of Biomedical Research     Open Access   (Followers: 2)
International Journal of Biotechnology     Hybrid Journal   (Followers: 5)
International Journal of Biotechnology and Molecular Biology Research     Open Access   (Followers: 4)
International Journal of Biotechnology for Wellness Industries     Partially Free   (Followers: 1)
International Journal of Environment, Agriculture and Biotechnology     Open Access   (Followers: 5)
International Journal of Functional Informatics and Personalised Medicine     Hybrid Journal   (Followers: 4)
International Journal of Medicine and Biomedical Research     Open Access   (Followers: 1)
International Journal of Nanotechnology and Molecular Computation     Full-text available via subscription   (Followers: 3)
International Journal of Radiation Biology     Hybrid Journal   (Followers: 4)
Iranian Journal of Biotechnology     Open Access  
ISABB Journal of Biotechnology and Bioinformatics     Open Access  
Italian Journal of Food Science     Open Access   (Followers: 1)
JMIR Biomedical Engineering     Open Access  
Journal of Biometrics & Biostatistics     Open Access   (Followers: 3)
Journal of Bioterrorism & Biodefense     Open Access   (Followers: 6)
Journal of Petroleum & Environmental Biotechnology     Open Access   (Followers: 1)
Journal of Advanced Therapies and Medical Innovation Sciences     Open Access  
Journal of Advances in Biotechnology     Open Access   (Followers: 5)
Journal Of Agrobiotechnology     Open Access  
Journal of Analytical & Bioanalytical Techniques     Open Access   (Followers: 7)
Journal of Animal Science and Biotechnology     Open Access   (Followers: 4)
Journal of Applied Biomedicine     Open Access   (Followers: 2)
Journal of Applied Biotechnology     Open Access   (Followers: 2)
Journal of Applied Biotechnology Reports     Open Access   (Followers: 2)
Journal of Applied Mathematics & Bioinformatics     Open Access   (Followers: 5)
Journal of Biologically Active Products from Nature     Hybrid Journal   (Followers: 1)
Journal of Biomaterials and Nanobiotechnology     Open Access   (Followers: 6)
Journal of Biomedical Photonics & Engineering     Open Access  
Journal of Biomedical Practitioners     Open Access  
Journal of Bioprocess Engineering and Biorefinery     Full-text available via subscription  
Journal of Bioprocessing & Biotechniques     Open Access  
Journal of BioScience and Biotechnology     Open Access  
Journal of Biosecurity Biosafety and Biodefense Law     Hybrid Journal   (Followers: 3)
Journal of Biotechnology     Hybrid Journal   (Followers: 63)
Journal of Biotechnology and Strategic Health Research     Open Access   (Followers: 1)
Journal of Chemical and Biological Interfaces     Full-text available via subscription   (Followers: 1)
Journal of Chemical Technology & Biotechnology     Hybrid Journal   (Followers: 9)
Journal of Chitin and Chitosan Science     Full-text available via subscription   (Followers: 1)
Journal of Colloid Science and Biotechnology     Full-text available via subscription  
Journal of Commercial Biotechnology     Full-text available via subscription   (Followers: 6)
Journal of Crop Science and Biotechnology     Hybrid Journal   (Followers: 3)
Journal of Ecobiotechnology     Open Access  
Journal of Essential Oil Research     Hybrid Journal   (Followers: 2)
Journal of Experimental Biology     Full-text available via subscription   (Followers: 25)
Journal of Genetic Engineering and Biotechnology     Open Access   (Followers: 5)
Journal of Ginseng Research     Open Access  
Journal of Industrial Microbiology and Biotechnology     Hybrid Journal   (Followers: 18)
Journal of Integrative Bioinformatics     Open Access  
Journal of Medical Imaging and Health Informatics     Full-text available via subscription  
Journal of Molecular Biology and Biotechnology     Open Access  
Journal of Molecular Microbiology and Biotechnology     Full-text available via subscription   (Followers: 13)
Journal of Nano Education     Full-text available via subscription  
Journal of Nanobiotechnology     Open Access   (Followers: 4)
Journal of Nanofluids     Full-text available via subscription   (Followers: 1)
Journal of Organic and Biomolecular Simulations     Open Access  
Journal of Plant Biochemistry and Biotechnology     Hybrid Journal   (Followers: 4)
Journal of Science and Applications : Biomedicine     Open Access  
Journal of the Mechanical Behavior of Biomedical Materials     Hybrid Journal   (Followers: 13)
Journal of Trace Elements in Medicine and Biology     Hybrid Journal   (Followers: 1)
Journal of Tropical Microbiology and Biotechnology     Full-text available via subscription  
Journal of Yeast and Fungal Research     Open Access   (Followers: 1)
Marine Biotechnology     Hybrid Journal   (Followers: 4)
Meat Technology     Open Access  
Messenger     Full-text available via subscription  
Metabolic Engineering Communications     Open Access   (Followers: 4)
Metalloproteinases In Medicine     Open Access  
Microbial Biotechnology     Open Access   (Followers: 10)
MicroMedicine     Open Access   (Followers: 3)
Molecular and Cellular Biomedical Sciences     Open Access   (Followers: 1)
Molecular Biotechnology     Hybrid Journal   (Followers: 13)
Molecular Genetics and Metabolism Reports     Open Access   (Followers: 3)
Nanobiomedicine     Open Access  
Nanobiotechnology     Hybrid Journal   (Followers: 2)

        1 2 | Last

Journal Cover
American Journal of Bioinformatics Research
Number of Followers: 7  

  This is an Open Access Journal Open Access journal
ISSN (Print) 2167-6992 - ISSN (Online) 2167-6976
Published by SAP Homepage  [105 journals]
  • Computational Analysis of Deleterious Single Nucleotide Polymorphisms
           (SNPs) in Human CALR Gene

    • Abstract: Publication year: 2018Source: American Journal of Bioinformatics Research, Volume 8, Number 1Sahar G. Elbager, Hadeel F. Gad Mahgoob, Mohamed Y. Basher, Asia M. Elrashid, Hazem Abdo, Shazalia K. Babiker, Ali I. Alsaid, Mohamed A. I. Alfaki, Safinaz I. Khalil, Amar A. Dowd, Magdi A. BayoumiBackground: The human Calreticulin (CRT) is a multifunctional protein encoded by CALR gene (CALR) located on chromosome 19. Calreticulin plays an important role in protein folding and calcium homeostasis. It’s also has been associated with cell proliferation, cell cycle progression and immunogenic cell death. High CRT serum levels were reported in various cancer like prostate cancer and breast carcinoma. Being observed as an important molecule in biological responses and its association with various diseases, we aimed to systematically explore the probable effects of CALR genetic variants on functions and structure of calreticulin using in silico prediction softwares. Methods: The data on human CALR gene was retrieved from dbSNP/NCBI. Eleven different prediction algorithms; SIFT, Polyphen, PROVEAN, SNAP2, Condel, Pmut, nsSNPs Analyzer, PhD-SNP, I-Mutant, Mutpred and Project Hope were used to analyzing the effect of nsSNPs on functions and structure of the CRT protein. STRING and KEGG database were used for CRT protein-protein interaction. Results: As per dbSNP database, the human CALR gene investigated in this work contained a total of 682SNPs:53 SNPs in 3′ UTR region, 25 SNPs in 5′ UTR region, 343 SNPs in intron region, 103 SNPs in coding synonymous regions and 154 non-synonymous SNPs (nsSNPs) which comprises of 150 missense mutations, 3 frameshift mutations and one nonsense mutation. We selected missense nsSNPs for our investigation. A total of 4 nsSNPs P216L, R73C, W261G and Y128C were predicted to have the most damaging effects on CRT protein's structure and function. STRING and KEGG revealed that CRT protein had strong interactions with proteins that involved in protein processing and presentation networks. Therefore, any structural alterations in the CRT protein that interfere or harm these networks interactions would probably increase susceptibility to diseases. Conclusion: Based on these analyses, the present study suggested that the reported functional SNPs may act as potential targets in genetic association studies.
  • In Silico Genetic Variation Analysis of Cytochrome P450 2C19 and Their
           Effect in Certain Drugs Metabolism

    • Abstract: Publication year: 2017Source: American Journal of Bioinformatics Research, Volume 7, Number 2Safinaz Ibrahim Khalil, Toga A. Alaziz Awad Mahmoud, Sahar G. Elbager, Mohamed A. I. Alfaki, Ahmed M. Elmoselhy, Walaa Salah Abdulla MohammedBackground: Cytochrome P450 2C19 (CYP2C19) is the commonest drug metabolizing enzyme, responsible for the oxidation of about 20% of the currently used drugs. Single Nucleotide Polymorphism (SNPs) play a major role in determining the risk of an individual susceptibility to many illnesses and their drug response. Identification of NPs may help in understanding their effects on genes product and their association with diseases and also could help in the development of new medical testing markers. Methods: This study was carried out for Homo sapiens single variation (SNPs) in CYP2C19 gene through coding regions. Variants data was obtained from database of SNP even. A total of 15943 SNPs in CYP2C19 gene were fond; 14307 SNPs were Homosapins; of which 319 were non-synonymous SNPs. Non synonymous SNPs were selected for insilico analysis; SIFT, Polyphen2, and PharmGKB softwares and servers were used to identify SNPs in proteins functions, structures and, pharmacokinetic activity. Results show that, of 319 nsSNPs, 13SNPs were predicted as highly damaging. Pharmacogenomic analysis of this 13 nsSNPS showed clinical annotations with many diseases and affection of efficacy, pharmacokinetics and toxicity of many drugs. In conclude these previous identified SNPs lead to gene alteration, which may be contribute to the distinct pharmacogenetic phenotypes. In conclude these previous identified SNPs could lead to gene alteration, which may be contribute to the distinct pharmacogenetic phenotypes.
  • 3D Structure Modeling of Major Subunit and Chaperone of CS3 Pili:
           Prediction of Residues Conferring Assembly of Fimbriae

    • Abstract: Publication year: 2017Source: American Journal of Bioinformatics Research, Volume 7, Number 2Vajiheh Eskandari, Bagher Yakhchali, Seyed Shahriar ArabThe objective of the current study is to model the three dimensional (3D) structures of major subunit (CstH) and chaperone (CS3-1) of CS3 pili using computational methods, particularly comparative protein modeling. The generated models of CstH and CS3-1 have been deposited into the PMDB database under the ID numbers PM0079873 and PM0078481, respectively. The 3D structures were utilized in the molecular dimerization in order to identify the potential interaction sites in the CstH molecule. The interacting surface areas of the dimer molecules were determined using the PDBePISA server. The interaction affinities and electrostatic potential of the CstH subunit surfaces and its complexes were calculated by PPEPred server and APBS software, respectively. The results indicated that analysis of the 3D models presents an important insight into the permissive sites, binding mode and contact sites of the CstH protein and our method can be a useful tool for other experimental studies in the biology of the pili and their applications.
  • In Silico Analysis of the Structural and Biochemical Features of the
           Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF), Interleukin-3
           (IL-3) and Interleukin-5 (IL-5) Receptors Subunit α

    • Abstract: Publication year: 2017Source: American Journal of Bioinformatics Research, Volume 7, Number 1Elham I. M. Ibrahim, Rihab Ali Omer, Ahmed H. Elsadig, Mohamed Sir Elkhatim, Sofia B. MohamedComputational analysis has become an indispensable bioinformatics approaches for the characterization of proteins regarding the physicochemical properties, prediction of signal peptides and 3D structure. Additionally, computational studies of protein–ligand interactions provide a rational basis for the speedy identification of novel leads for drug. To date no any computational analysis evaluating such parameters for GM-CSF-Rα, IL-3-Rα and IL-5-Rα. Hence, the present work aimed at identifying the theoretical basis of the physicochemical, structural and functional proprieties for these proteins using online computational tools.In the present study, different bioinformatics tools were used to characterize the properties and structure of the GM-CSF-Rα, IL3Rα, and IL5Rα proteins. Firstly, the Physico-chemical characterization was computed by ExPasy’s (ProtParam). Then Fingerprinting analysis was done with ScanProsite. Followed by the functional characterization of the transmembrane regions and phosphorylation sites using SOSUI server and NetPhos server respectively. Afterwards, secondary structure prediction and the protein-ligand binding site residues were predicted by PDBSUM, and the detected ligands and their interactions were visualized by LIGPLOT and Protein ligand interaction profiler (PILP) softwares. The residues in GM-CSF-Rα, IL-3Rα and IL-5Rα proteins that may undergo ubiquitination were detected by using the UbPred and BDM-PUB programs, the predicted peptides for sumoylation in GM-CSF-Rα, IL-3Rα and IL-5Rα proteins were detected by GPS-SUMO online service. Finally, the 3D structure of proteins was built by Chimera 1.8 program. In addition, the models were surveyed using ERRAT server; as a confirmation for the quality of the models. Our results revealed that GM-CSF-Rα is stable whereas the IL3Rα and IL5Rα are classified as unstable proteins. All proteins are membrane proteins, acidic and hydrophilic in nature, with serine being the most phosphorylated amino acid. Interestingly, fibronectin type-III (FN3) domain was detected among these proteins. Also, we detected the sequences belonging to the following families: HEMATOPO_REC_S_F2, ASN_GLYCOSYLATION, CK2_PHOSPHO_SITE, PKC_PHOSPHO_SITE, MYRISTYL, CAMP_PHOSPHO_SITE, and TYR_PHOSPHO. Moreover, we detected 9 kinases in GM-CSF-Rα, while 13 kinases in IL-3-Rα and 15 kinases in IL-5-Rα. In GM-CSF-Rα 3 binding sites were detected with two ligands (GOL and NAG), and 5 binding sites in IL-3-Rα and IL-5-Rα with 3ligands (NAG, FUL and BMA) and one ligand (BGC) respectively. Secondary structure prediction showed that Beta sheet dominated all the other conformations. Modeling the 3 D structure of proteins resulted in a quality of less than 90%.computational analysis of GM-CSF-Rα, IL-3-Rα and IL-5-Rα will give a deep insight and provide opportunities for understanding the function of these proteins, and developing novel therapeutics for treating certain leukemia and inflammatory diseases.
  • Bioinformatics Analysis of Single Nucleotide Polymorphism in Multiple Drug
           Resistance Protein 1 (ABCB1) and Multi-Drug Resistance-Associated Protein
           1 (ABCC1) in Bos taurus

    • Abstract: Publication year: 2017Source: American Journal of Bioinformatics Research, Volume 7, Number 1Nuha A. Mahmoud, Elham I. Mohammed, Siham O. Elshafei, Ahmed H. Elsadig, Rihab A. Omer, Sofia B. MohamedThe ABCB1 and ABCC1 genes are a transmembrane active efflux pump for a variety of drugs. They are a putative mechanism of multidrug resistance in a range of diseases. It is postulated that ABCB1 and ABCC1 single nucleotide polymorphism (SNP) contribute to variability in protein functions, and therefore in drug resistance, prognosis, toxicity and disease. However, there are not much attention has been given to SNP in ABCB1 and ABCC1 genes in Bos taurus. In this current study, a comprehensive analysis of the functional and structural impacts of all known SNPs of the genes, was performed using publicly available computational prediction tools. Two different databases were used to retrieve SNP data sets followed by five different in silico algorithms (SIFT, PROVEAN, PANTHER and GO& SNAP2) to screen nsSNPs in ABCB1 and ABCC1 genes. The comparative analysis predicted that 9 and 2 functional SNPs showed damaging effects in ABCB1 and ABCC1 subsequently. The ExPASy-PROSIT program revealed that the deleterious mutations (G516A and V560G) are contained in the ABC Transporter 2, (F707C) in ABC_TM1F domains, (K424E and C422W) in ATP binding cassette in ABCB1. And the (R719W) lay in the ABC_ Transporter2 domain for ABCC1. As well as identifying the putative functional SNPs that may possibly undergo post-translation; it was founded that mutation at K424E can also lead to an alteration in the ubiquitylation site within the ABCB1. The mutation (V1244G) of ABCC1 is also present at a sum interacting motif (SIM). Additionally, MUpro and I. Mutant showed a decrease in stability for high-risk nsSNPs in ABCB1 and ABCC1, suggesting that variants could destabilize the amino acid interactions directly or indirectly. This effect will cause to some extent, functional deviations of proteins. Furthermore, the 3D structure of both proteins using a CPH server and Chimera were also modeled. Finally, the 27 SNPs in 3’ un-translated region was analyzed using an mrSNP tool in an ABCB1 gene the results showed that there were no SNPs lay in 3’UTR. Throughout the review of this study; damaging effect nsSNPs in ABCB1 and ABCC1 genes were detected, and they were altered the structure and function of these genes. They are also may have a relation with ABCB1 and ABCC1 functions in Bos taurus. Recent advances understanding the role and the mechanism of ABCB1 and ABCC1 polymorphisms Tauruss taurus by Next Generation Sequencing are presented.
  • Ensemble Learning Methods to Deal with Imbalanced Disease and Left-Skewed
           Cost Data

    • Abstract: Publication year: 2017Source: American Journal of Bioinformatics Research, Volume 7, Number 1Songul CinarogluRare events and class imbalance is very often in classification problems. Rare diseases which are good example for rare events are life-threating and vast majority of them are genetically determined. Moreover, traditionally appropriate analysis of cost data generated by clinical trial is problematic. The distribution of cost data is generally highly skewed because a few patients faced with large costs. Several ensemble learning methods (ELM) were applied to health care datasets such as predicting individual expenditures and disease risks for patients. These methods are consists of a set of individual training classifiers such as Bagging and Boosting. This study aims to compare ELM classification performances applied on thyroid disease dataset. Data came from UCI Machine Learning Repository. Diagnosed as a hyperthyroid determined as a dependent variable for classification. ID.3, C4.5, CART, NB, KNN, RF, SVM, NN were used as ELMs. Bagging and Boosting were implemented to improve prediction performances. “k” 10 fold cross validation and AUC was examined to evaluate classication performances of ELMs. Study results reveal that single ELM have superior prediction performance compared with Bagging and Boosting applications. In addition to that kNN, RF and NN have superior classification performance compared with other ELMs. Future research is needed to better understand the role of ELM to improve prediction performance of rare disease data.
  • Development of Program Architecture of Intelligence Information System for
           Growing Tea Plantation

    • Abstract: Publication year: 2016Source: American Journal of Bioinformatics Research, Volume 6, Number 3Javanshir Mammadov, Gulnara Abbasova, Kurbanova SabinaIn this paper, the problem of program architecture creation for providing collection of intelligence information of growing tea plantation is considered. For efficiensy growing tea plantation in the mountain region of Azerbaijan, program interface of intelligence information system (IIS) is offered. On the stages, all program functions of IIS and its connection with other the special program systems are given, which must provide executive of automation irrigation system, agrotechnical works and collection of quality tea leafs from the tea plantations.
  • Development of Fingerprint Biometrics Verification and Vetting Management

    • Abstract: Publication year: 2016Source: American Journal of Bioinformatics Research, Volume 6, Number 3Joseph Kalunga, Simon TemboThis paper presents the development of fingerprint biometrics verification and vetting management system for Sensitive Organization. The idea behind this study is to improve security in sensitive institutions through integration of fingerprint biometrics into identity database. A fingerprint is a very recognized and acceptable security feature. It is traditionally used for human identification and criminal vetting of newly recruited security staff. There was need to develop Human Identity Authentication System that verify the true identity of people gaining entry into sensitive institution as an additional security layer to existing traditional techniques (National Identification Card, Driving license and passport). Traditional Techniques of human identity verification suffer from security Vulnerabilities such as masquerading identity; mobility issues (include lost, forgery and misplacement) and inaccuracy. The study was conducted using visual studio 2010 on DotNet framework 4.0 with C# object oriented programming language. The backend database used was MySQL relational database management system (RDMBS). The research produced a number of key results include the development of biometric security layer that is able to identify and verify identity of an individual using enrolled fingerprint template. Other results include the ability to capture military police security data, storage, retrieval and dissemination. The developed application performance was evaluated by enrolled ten fingerprints and captured related individual personal information. The result indicated 99.999% biometric accuracy levels attained with error allowance of 0.001% False Acceptance Rate (FAR) and 0.001% False Rejection Rate (FRR). In conclusion, the study shows that the integration of fingerprint biometric system in sensitive institution database can improve security of the organization and alleviate problem associated with traditional identity verification techniques.
  • Computational Analysis of Deleterious Single Nucleotide Polymorphisms
           (SNPs) in Human MutS Homolog6 (MSH6) Gene

    • Abstract: Publication year: 2016Source: American Journal of Bioinformatics Research, Volume 6, Number 2Nahla E. Abdelraheem, Marwa Mohamed Osman, Osama Muhieldin Elgemaabi, Afra Abdelhamid Fadl Alla, Mosab Mohamed Ismail, Soada Ahmed Osman, Aisha Ismail Ibrahim, Nihad Elsadig Babekir, Salwa Osman Mekki, Mohamed A. HassanBackground: Point mutations in MSH6 gene had been related to group of cancers called lynch syndrome which accounts for 3% to 5% of all colorectal cancers. Despite the excessively studied MSH6 mutations, the mechanism by which these mutations promote carcinogenesis remains controversial. Methods: MSH6 was investigated in dbSNP/NCBI in December 2015, 3666 SNPs were found in human; 388 were coding synonymous, 937 non synonymous, 201 in frame shift, 63 in 3' un-translated region and 347 in 5' un-translated region. Non synonymous and 3'UTR SNPs were selected for insilico analysis; SIFT, Polyphen2, Imutant3.0, MUpro, PhD-SNP, SNPs & GO, MutPred, ELASPIC, Mutation 3D, UCSF Chimera 1.8, PolymiRTs, and GENEMAIA softwares and servers were used to investigate the effect of SNPs on MSH6 protein's structure and function. Results:21 SNPs were found to be highly damaging for the protein by SIFT and Polyphen, and were further analyzed by I-Mutant, MUpro, PHD-SNP, SNPs & GO, ELASPIS, Mutation 3D and Chimera. 2 SNPs were predicted by PolymiRTs to induce disruption or creation of miR binding sites; rs200412142 contained 2 disrupting and 1 creating functional classes in 3 miRSite, while rs184571821 SNP contained 3 creating functional classes in 3 miRSites. GENEMANIA revealed five genes similar in their expression level with MSH6 and seven genes share the same protein domain with it.Conclusions: 14 nsSNPs (R1217K, H1248D, E1214A, T1219I, K1140R, A1303T, M1137T, A1303G, R915K, H946D, T917I, A1001T, L899F, A1001G) were located at the interface of the MSH6 protein interfering with its relation with MSH2ISO2, MSH3, MSH2 and E9PHA6. Interactions of MSH6 with these proteins are critical for its MMR function and any structural alterations that interfere or harm these networks interactions would probably increase susceptibility to tumors formation and progression. 2 SNPs at the 3UTR; rs200412142 and rs184571821 introduced a change in the micro RNA binding site at the 3UT which might result in deregulation of the gene function.
  • A Comprehensive in Silico Analysis of the Functional and Structural Impact
           of Non-Synonymous Single Nucleotide Polymorphisms in the Human KRAS Gene

    • Abstract: Publication year: 2016Source: American Journal of Bioinformatics Research, Volume 6, Number 2Nahla E. Abdelraheem, Ghada M. El-Tayeb, Lamia O. Osman, Samar A. Abedlrhman, Aisha S. Ali, Ahmed H. Elsadig, Sofia B. MohamedThe protein product of the normal KRAS gene performs an essential function in normal tissue signaling, and the mutation of a KRAS gene is an essential step in the development of many cancers. Despite the reported association of KRAS gene mutations with human disease susceptibility, the comprehensive computational analysis of coding, noncoding and regulatory SNPs, and their functional impacts on protein level, still remains unknown. In this study, we performed a comprehensive analysis of the functional and structural impact of non-synonymous (nsSNP) that are deleterious to KRAS structure and function. A sequence homology-based approach was adopted for screening nsSNPs in KRAS, including nine different in silico prediction algorithms; SIFT, PROVEAN, MutPred, SNP&GO, PhD-SNP, PANTHER, I-Mutant 2.0, MUpo and DUET. Moreover, to understand how mutations can affect the strength of the interactions that bind proteins together we submitted data to ELASPIC servers and evolutionary conservation data was obtained from the ConSurf web server. The PDB structure of KRAS protein was obtained from RCSB Protein Data Bank (PDB ID: 4QL3) and Structural theoretical models of KRAS were created using mutation3D and chimera servers. Our results demonstrate that 14 nsSNPs in the antiviral KRAS gene may be deleterious to KRAS structure and function.14 deleterious and high-risk nsSNPs were identified in KRAS gene. 11 of these are located at highly conserved amino acid sites in the protein domain (RAS). Additionally, we detected 4 nsSNPs in the core residues of the protein and 10 SNPS at interface. Finally, we classified six SNPs as top high-risk (Q61E, A146T, N116S, K147E, G60R and A59V) which may alter the putative structure of KRAS’s domain, particularly in G1, G2, G3, G4 and G5 motif regions. These same regions are critical to the protein's structure and function. This study adopted an extensive in silico analysis of the highly polymorphic KRAS gene and will be a valuable resource for future targeted mechanistic and population-based studies.
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Tel: +00 44 (0)131 4513762
Fax: +00 44 (0)131 4513327
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