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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: 70)
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: 160)
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
Current Research in Bioinformatics
Number of Followers: 13  

  This is an Open Access Journal Open Access journal
ISSN (Print) 1948-9862 - ISSN (Online) 1948-9870
Published by Science Publications Homepage  [31 journals]
  • In Silico Prediction and Functional Characterization of Genes Related to
           Abiotic and Biotic Stresses in Chickpea (Cicer arietinum)

    • Abstract: Chickpea (Cicer arietinum L.) is second largest grown legumes worldwide contributing 75% of total pulse production. It is a cool season legume crop and grown in tropical and subtropical areas. Due to drastic climatic changes, chickpea suffers from many biotic (blight and wilt) and abiotic (salinity, drought, cold) stresses that directly impact the growth and yield. In our study, we predicted and annotated the genes related to biotic and abiotic stresses. Total 20162 ESTs for salinity, 34346 for drought and 191 for cold stress were downloaded. For biotic stresses, viz., wilt and blight disease, 7866 and 56 ESTs were collected, respectively from public domain. All these ESTs were assembled into contigs and blast against protein non-redundant database. Each blast results were mapped to get the corresponding GO terms. Total 1631, 3133 and 13 contigs for salinity, drought and cold stress showed 1333, 2693 and 7 GO terms respectively, while 1144 contigs for Fusarium wilt and 6 contigs for Ascochyta blight disease showed 955 and 4 GO terms. These GO terms describe biological process, molecular function and cellular components of corresponding stresses. Remaining 298 (salinity), 440 (drought), 6 (cold), 189 (wilt) and 2 (blight) contigs were mapped to reference genome and further used for annotation using gene prediction methods and promoter analysis. This study provide insight to novel gene related to abiotic and biotic stress mechanism that can be further analyzed in molecular biology studies for breeding programs.
  • An Efficient Distributed Bioinformatics Computing System for DNA Sequence
           Analysis on Encoding System

    • Abstract: This study provides an effective design of search technique of a distributed bioinformatics computing system for analysis of DNA sequences using OPTSDNA algorithm. This system could be used for disease detection, criminal forensic analysis, gene prediction, genetic system and protein analysis. Different types of distributed algorithms for the search and identification for DNA segments and repeat pattern in a given DNA sequence are developed. The search algorithm was developed to compute the number of DNA sequence which contains the same consecutive types of DNA segments. A distributed subsequence identifications algorithm was designed and implemented to detect the segment containing DNA sequences. Sequential and distributed implementation of these algorithms was executed with different length of search segments patterns and genetic sequences. OPTSDNA algorithm is used for storing various sizes of DNA sequence into database. DNA sequences of different lengths were tested by using this algorithm. These input DNA sequences varied in size from very small to very large. The performance of search technique distributed system is compared with sequential approach.
  • Micrornas as Double Edged Sword in Cancer

    • Abstract: Cancer is the leading causes of death world wide. Basically it can be defined as the disease of the cell. One among the mechanism of transfer of a normal cell to cancerous is the alteration in the genetic material DNA. Treatment for cancer remains as a biggest challenge. Here comes the importance of miRNAs. They are endogenous RNA which regulates a wide range of cellular processes such as proliferation, differentiation, development and apoptosis by suppressing the expression of target mRNA thus playing a central role in various human diseases including cancer. Hence advancement in miRNA research is necessary to develop it as a powerful therapeutic tool in cancer. Oncomirs are miRNAs acts as double edged sword in cancer because up-regulation and down-regulation of miRNAs are observed in cancerous cells and hence acts as oncogenes and tumor suppressors respectively. miRNAs can act as potential biomarkers. Studies shows that the change in level of miRNA are directly associated with cancer. Hence till-date reviewing as onco-miRs is necessary which further the researcher to develop it as a specific and potential target in cancer treatment. miRNAs are promising therapeutic tools for cancer because in humans, 50% of miRNA genes were localized in cancer-associated genomic regions which include minimal regions of amplification, loss of heterozygosity, fragile sites and common breakpoint regions. miRNA are found to be up-regulated and down-regulated in almost all cancer cells. Hence, in this article an attempt is made to review the evidence of microRNAs in cancer as both oncogenes and tumor suppressors.
  • Bioinformatics Analysis of Some Functional Genes and Proteins Involved in
           Obesity-Induced Type 2 Diabetes

    • Abstract: The incidence of type-2 diabetes is rising rapidly worldwide, mainly because of the increase in the incidence of obesity, which is an important risk factor for this condition. Both obesity and type-2 diabetes are complex genetic traits but they also share some nongenetic risk factors. Differences among individuals in their susceptibility to both these conditions probably reflect their genetic constitutions. The dramatic improvements in genomic and bioinformatic resources are accelerating the pace of gene discovery. It is tempting to speculate the key susceptible genes/proteins that bridges diabetes mellitus and obesity. In this regard, we evaluated the role of several genes/proteins that are believed to be involved in the evolution of obesity associated diabetes through thorough literature search. Also we analyzed the data pertaining to genes of these proteins extracted from the databases that are available online for free access. The functional cDNA sequences of these genes/proteins are extracted from National Center for Biotechnology Information (NCBI) and Ensembl Genome Browser. Our bioinformatic analysis reports 21 genes as ominous link with obesity associated diabetes. Also this study indicated that, adipose tissue is now known to express and secrete a variety of metabolites, hormones and cytokines that have been implicated in the development of insulin resistance.This bioinformatic study will be useful for future studies towards therapeutic inventions of obesity associated type-2 diabetes.
  • Homology Modeling of Buffalo (Bubalus bubalis) Interferon-Tau Protein

    • Abstract: Interferon-tau (IFNt) contributes towards maternal recognition of pregnancy in ruminants (like, cattle, buffalo, goat, giraffe). IFNt has been extensively studied in most of the ruminants except for buffalo Bubalus bubalis). The present study has been undertaken to predict the secondary structure of Interferon-tau in buffalo. The available amino acid sequence of bubaline IFNt (sequence database of SwissProt) was subjected to protein-BLAST to find similar sequences with high scores and low e-values. The ovine IFNt sequence (PDB code: 1B5L) was selected for further computational analysis of the bubaline IFNt sequence to predict the secondary and tertiary structure. The secondary structure of the modeled bubaline IFNt was predicted using STRIDE. The 3D structure was generated using academic version of MODELER9v6. The Probability Density Functions (PDF) was used to restrain Cα-Cα distances, main chain N-O distances as well as main-chain and side-chain dihedral angles. The energy minimization and van der waal contacts were taken care of using ACCELRYS DS Modeling 2.0. The residue profiles of the obtained three-dimensional models were checked by VERIFY3D. The energetic architecture and the correctness of the generated model revealed that the predicted secondary model was correct and acceptable. The predicted structure of the bubaline IFNt constructed through homology modeling from ovine IFNt, can be used for functional characterization of bubaline IFNt.
  • Bayesian Exploration of Multilocus Interactions on the Genome-Wide Scale

    • Abstract: Problem statement: Recent technological and scientific advances propelled the field of Genome-Wide Association Study (GWAS), which promises to be instrumental in linking many common complex diseases to their genetic origin. While so far such large-scale surveys have been moderately successful in identifying disease related genetic variants, much of disease heritability is still not accounted for by the discovered loci. There is an urgent need for advanced statistical methods for efficient automatic detection of complicated multilocus interactions on significant scales. Approach: Novel statistical methods based on Bayesian data analysis ideas, specifically Bayesian modeling, Bayesian variable partitioning, graphical and network models are promising to aid in search for missing disease heritability and shed light on complex biological processes involved in disease development. First crucial difference setting these methods apart from all the mainstream previous approaches (hypothesis testing methods) is their joint disease mapping capability via the simultaneous fitting of a statistical model for the whole case-control data set. Additionally, such Bayesian methods allow for the construction of complicated data models and quantitative incorporation of diverse prior information into the final statistical model. Results: The use of Bayesian techniques has already yielded new insights into the details of epistatic interactions across the genome associated with various important diseases. Conclusion/Recommendations: Bayesian approaches provide a way to detect and understand complicated multilocus interactions that already started to elucidate important disease pathways. As the field of GWAS matures, Bayesian strategies can surely aid in converting such multiple surveys into useful biomedical information.
  • An Optimal Approach for Medical Image Analysis

    • Abstract: Problem statement: Image segmentation is the process that subdivides an image into its constituent parts and extracts the objects. It is one of the most critical tasks in automatic image analysis because the subdivided results will affect all the subsequent processes of image analysis, such as object representation and description, feature measurement and even the following higher level tasks such as object classification and scene interpretation by optimized results. Approach: In this study, we proposed an optimal approach for medical image segmentation based on the combination of Particle Swarm Optimization (PSO) and Global Minimization by Active Contour (GMAC) methods. PSO is a population based new evolutionary algorithm in the field of image segmentation where the image homogeneous part can be detected. The grouped part from PSO is again treated with GMAC to reduce the complex region of image parts. Results: The feasibility of these algorithms for analyzing is presented through experimental investigation. The simulation results givethat the proposed optimal approach gives efficient results for image segmentation. Conclusion/Recommendation: The performance of the proposed study is compared with the existing traditional algorithm and real time medical diagnosis image.
  • Providing Collaborative Algorithms Support for Personal Health Care

    • Abstract: Problem statement: Today, there is a growing interest towards the adoption of novel technology in the field of medical monitoring and personal health care systems in general. This is especially case with certain categories of people suffering from chronicle diseases that need 24 h access to medical care. Approach: To solve this challenging issue, a model of a system containing three levels: bionetwork, social community and primary and secondary health-care centers, was developed. The main purpose of the proposed methodology is to find the dependency of the users’ health condition (obtained by bionetwork) and physical activity he/she perform (get by mobile application). To achieve this we consider datasets from the health history of users (obtained from clinical centers) and use classification algorithms on these datasets for grouping the users based on their similarity. Results: Developed model of a system which enables 24 h monitoring of the condition of patients and the possibility of sending an emergency call for sudden deterioration of his/her medical condition. In addition, the system enables the patient (system user) to contact other people with similar condition and exchange their experience. Conclusion: The system improves the terms of home care treatment of the patient and increases the medical capacity of the appropriate healthcare institutions which results in significant reduction of the overall costs for patients and hospitals.
  • Using Threads to Overcome Synchronization Delays in Parallel Multiple
           Progressive Alignment Algorithms

    • Abstract: Problem statement: The parallelization of multiple progressive alignment algorithms is a difficult task. All known methods have strong bottlenecks resulting from synchronization delays. This is even more constraining in distributed memory systems, where message passing also delays the interprocess communication. Despite these drawbacks, parallel computing is becoming increasingly necessary to perform multiple sequence alignment. Approach: In this study, it is introduced a solution for parallelizing multiple progressive alignments in distributed memory systems that overcomes such delays. Results: The proposed approach uses threads to separate actual alignment from synchronization and communication. It also uses a different approach to schedule independent tasks. Conclusion/Recommendations: The approach was intensively tested, producing a performance remarkably better than a largely used algorithm. It is suggested that it can be applied to improve the performance of some multiple alignment tools, as CLUSTALW and MUSCLE.
  • Use of Enterobacterial Repetitive Intergenic Consensus PCR in Detecting
           Target(s) of Hapalindole-T, From a Cyanobacterium, in Escherichia Coli: In
           Silico Validation

    • Abstract: Problem statement: Identification of newer biomolecule as well as targets are a rising concern because of increasing drug resistance in bacteria. We have isolated a broad spectrum antibiotic biomolecule Hapalindole-T from a cyanobacterium, Fisherella sp. growing on local Azadirachta indica tree bark. A model bacterium E. coli was screened spontaneously for Hap-T resistance. These resistant strains of E. coli were used to identify Hap-T target(s). Approach: These strains were subjected to Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR analysis and compared with the sensitive one. We have used different bioinformatic tools like Clustalw, NJ Plot and Docking server. The Swiss-model server was used for homology modelling. Predicted 3D structure was refined by energy minimization and quality was assessed by Procheck. The model protein hailed from fimbrial biogenesis outer membrane usher protein (ADK89122.1). The interaction between the predicted structure of Model-1 protein and Hap-T biomolecule was analysed in silico using Autodock and Mopac parameters. Results: An additional band of DNA fragment (~500 base pairs) was found on agarose gel run after amplified genome of resistant strain. The results indicated that certain residues (Tyr-28), (Phe-54), (Leu-36) and (Val-52) were highly conserved and present in active sites. Conclusion/Recommendations: Thus understanding of microbial adhesion can act as an alternative approach in development of broad spectrum antibiotics.
  • Bayesian Determination of Disease Associated Differences in Haplotype

    • Abstract: Problem statement: While experimental ascertainment of haplotype blocks in the genome-scale case-control studies is expensive, accurate computational phasing is still a daunting task for bioinformatics approaches. We used a statistical method to determine differences, potentially associated with a certain disease, in linkage disequilibrium block boundaries in whole-genome Single Nucleotide Polymorphisms (SNPs) data. Approach: We utilized a Bayesian model for calculating the posterior probabilities of the block boundaries in the SNPs data and used Metropolis-Hastings algorithm to sample from that posterior distribution. Our method was applied to search for haplotype-block boundary differences associated with two autoimmune diseases: Type I Diabetes (T1D) and Rheumatoid Arthritis (RA). Results: We located the regions on chromosome 6 with significant control-case difference in haplotype blocks around the SNPs and genes that were previously known to be associated with T1D and RA (in the HLA complex), as well as around genes whose association with the autoimmune diseases should be further explored in future studies. Conclusion/Recommendations: The statistical approach explored in this study provides an efficient and accurate way to study connection of haplotype-block differences to multiple important diseases.
  • Bioinformatics-Assisted Microbiological Research: Tasks, Developments and
           Upcoming Challenges

    • Abstract: Problem statement: Bioinformatics in the present day microbiological research is an inevitable subject area that encompasses biological resources and high end computational skills to unravel the coded and encrypted information within the life. We have produced a brief account of the developments and tasks in the subject and upcoming challenges in the subject. The area has seen tremendous developmental pattern in the last few decades due to the emerging computational technologies dedicated for uncovering the complex but vital biological information that not only essentially constitute the basis of life but entails about the evolutionary diversification and multiphasic interaction among the organisms with their own environment. Now, with the technological advancements, bioinformatics has completely changed microbiological domain for researchers. Conclusion/Recommendations: In Future, the ultimate goal of bioinformatics will be such kind of integration of the biological databases and genomic resources that can result in a computer representation of living cells and organisms whereby any aspect of biology can be examined computationally.
  • Homology Modeling of Buffalo (Bubalus bubalis) Interferon-Tau Protein

    • Abstract: Interferon-Tau (IFNt) contributes towards maternal recognition of pregnancy in ruminants (like, cattle, buffalo, goat, giraffe). IFNt has been extensively studied in most of the ruminants except for buffalo Bubalus bubalis). The present study has been undertaken to predict the secondary structure of Interferon-tau in buffalo. The available amino acid sequence of bubaline IFNt (sequence database of SwissProt) was subjected to protein-BLAST to find similar sequences with high scores and low e-values. The ovine IFNt sequence (PDB code: 1B5L) was selected for further computational analysis of the bubaline IFNt sequence to predict the secondary and tertiary structure. The secondary structure of the modeled bubaline IFNt was predicted using STRIDE. The 3D structure was generated using academic version of MODELER9v6. The probability density functions (pdf) were used to restrain Cα-Cα distances, main chain N-O distances as well as main-chain and side-chain dihedral angles. The energy minimization and van der waal contacts were taken care of using ACCELRYS DS Modeling 2.0. The residue profiles of the obtained three-dimensional models were checked by VERIFY3D. The energetic architecture and the correctness of the generated model revealed that the predicted secondary model was correct and acceptable. The predicted structure of the bubaline IFNt constructed through homology modeling from ovine IFNt, could be used for further profiling the species specific difference in IFNt activity.
  • Swarm Optimization Techniques for Segmenting Gel Electrophoresis Images

    • Abstract: Gel Electrophoresis (GE) are discussed as the main tool to dissociate DNA sequences. It helps in analyzing the genome such that each image resulting from it consists of lanes that include several bands. Image segmentation plays the foremost role in image processing. It helps in producing accurate results in medical diagnosis. Image segmentation works by dividing an image into regions that cover the full image. Image segmentation methods can be implemented, but still have certain defects that cannot produce accurate results. On the other hand, Swarm Optimization methods produce results with high efficiency in image segmentation. In this study, swarm optimization techniques for image segmentation are proposed. The proposed technique depends on applying different segmentation methods as Fuzzy C-Means (FCM) and Particle Swarm Optimization (PSO) is an extensively used in computer science considered a simple and easy algorithm to implement. It also depends on swarm intelligence. PSO useful in image segmentation because the result is more exact and efficient. Furthermore, Darwinian PSO (DPSO) and Fractional Order Darwinian PSO (FODPSO) produced precise results. The efficiency of the proposed approach is compared with other by computing image quality measurement parameters like Peak Signal to Noise Ratio (PSNR), Mean Square Error (MSE) and others. The proposed technique, especially FODPSO produces more accurate results to segment GE image.
  • Structure Prediction and Binding Site Analysis of Hepatotoxic
           Microcystin-LR Degrading MlrC-Like Protein from Burkholderia sp. using
           Computational Approaches

    • Abstract: Microcystin-LR (MCYST-LR) is a well characterized hepatotoxic heptapeptide produced by various species of cyanobacteria including Microcystis aeruginosa. Burkholderia is a genus of bacteria with cyanobacterial toxins degrading property. This study predicts the structure of microcystin degrading MlrC-like protein from Burkholderia sp. strain CCGE1002 that has microcystin degradation capability. Binding interaction of MlrC-like protein with MCYST-LR was studied. Three-dimensional model of MlrC-like protein was generated using composite modeling based I-TASSER server. The model was further assessed through different computational approaches. The generated model was found comparable to experimental structures. MCYST-LR was used for docking with predicted model to investigate ligand-protein interaction. The study provides the structural insight into the binding mode of MlrC-like protein of Burkholderia sp. with MCYST-LR and could be further helpful in designing modeling inhibitors for MCYST-LR.
  • BIS-CATTLE: A Web Server for Breed Identification using Microsatellite DNA

    • Abstract: Domestic cow, Bos taurus is one of the important species selected by humans for various traits, viz. milk yield, meat quality, draft ability, resistance to disease and pests and social and religious reasons. Since cattle domestication from Neolithic (8,000-10,000 years ago) today the population has reached 1.5 billion and further it’s likely to be 2.6 billion by 2050. High magnitude of numbers, breed management, market need of traceability of breed product, conservation prioritization and IPR issues due to germplasm flow/exchange, has created a critical need for accurate and rapid breed identification. Since ages the defined breed descriptors has been used in identification of breed but due to lack of phenotypic description especially in ova, semen, embryos and breed products molecular approach is indispensable. Further the degree of admixture and non-descript animals characterization, needs of molecular approach is imperative. Till date breed identification methods based on molecular data analysis has great limitations like lack of reference data availability and need of computational expertise. To overcome these challenges we developed a web server for maintaining reference data and facility for breed identification. The reference data used for developing prediction model were obtained from8 cattle breeds and 18 microsatellite DNA markers yielding 18000 allele data. In this study various algorithms were used for reducing number of loci or for identification of important loci. Minimization up to 5 loci was achieved using memory-based learning algorithm without compromising with accuracy of 95%. This model approach and methodology can play immense role in all domestic animal species across globe in breed identification and conservation programme. This can also be modelled even for all flora and fauna to identify their respective variety or breed needed in germplasm management.
  • In-silico Rational Protein Engineering and Design Approach to Improve
           Thermostability of a Haloalkane Dehalogenase Enzyme

    • Abstract: Thermostability of enzymes is a major prerequisite for use in industrial enzymology. There are as such no simple general principles for achieving thermostability in case of enzymes as many factors are required to fulfil for different enzymes. The present study describes computational methods to design thermostable haloalkane dehalogenase enzyme using the crystal structure available Protein Data Bank (PDB ID: 1EDE). In in silico design strategy rule-based approaches such as disulfide bond geometry, new hydrophobic pocket design, new salt bridge construction and multiple mutations (combination of the above approaches) were introduced to the original enzyme. After each design strategy the functional effect was confirmed in terms of enzyme substrate binding by molecular docking using Autodock vina tool. Best design strategy was evaluated by comparative molecular dynamics simulation applying simulated annealing method at 8 ns using GROMACS tool. The surface hydrophobicity which is the key factor for thermostability in haloalkane dehalogenase was obtained from the simulation result. Upon optimizing the parameters, thermostability of mutant enzyme under consideration was also confirmed by the 5 ns molecular dynamics simulation at 400, 500 and 600 K.
  • BioInfoKnowledgeBase: Comprehensive Information Resource for
           Bioinformatics Tools

    • Abstract: Bioinformatics is revolutionizing biological sciences and facilitating every area of biology. Right from the start of any biological project, information regarding availability of resources or databases appropriate for the analysis of data repository are becoming essentially required. Biological scientists use to browse across the web for searching tools/softwares and to identify most appropriate one for analysis purpose. Time of any project can be saved and efforts will go in the right direction if the most appropriate analysis tools are selected. With the idea of putting maximally used data resources at a single place, we developed BioInfoKnowledgeBase (BIKB), a comprehensive information resource on softwares and databases applicable for various biological analyses. This database provides information of more than 1000 bioinformatics softwares grouped in six major biological themes and categorized in thirty-one different categories along with information of ~100 biological databases and public repositories. BioInfoKnowledgeBase is online accessible at
  • Illumina-Based De Novo Transcriptome Analysis and Identifications of Genes
           Involved in the Monolignol Biosynthesis Pathway in Acacia koa

    • Abstract: Acacia koa is a leguminous timber tree endemic to the Hawaiian Islands. For breeding projects involved in improving wood quality of A. koa, understanding of genes influencing wood quality is crucial. Therefore, the objective of this study was to identify A. koa genes in the monolignol biosynthesis pathway, which is involved in wood formation and development. In this study, whole transcritpome sequencing of A. koa seedlings was performed through Illumina-based sequencing and over 88 million high-quality paired-end raw reads were generated. Trinity de novo assembly of those reads yielded 85,533 unigenes with an average length of 641 bp. Based on sequence similarity search with known proteins, we annotated 47,038 of the unigenes. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 149 unigenes were assigned to ortholog groups of enzymes involved in the monolignol biosynthesis pathway. In addition, we identified complete coding sequences of genes for all the ten identified enzymes of the pathway. Future studies on expression levels of these genes in A. koa with different wood qualities will provide a tool for selection of desirable types. Comprehensive sequence resources of A. koa generated through this study will contribute to genomic studies and improvement programs for this tree.
  • Reducing Redundancy of Codons through Total Graph

    • Abstract: Inthis study some algebraic connections in genetic code is being discussed.The genetic code is the rule by which DNA stores the geneticinformation about formation of protein molecule. Based on the physico-chemicalproperties of four RNA (or DNA) bases, two orders in the base sets are obtained. This ordering allows us to define a ringstructure on the set of 64 codons. Then the total graph in the genetic codealgebra is being discussed. It is shown that transition mutations (purine (A,G) to purine or pyrimidine (C, T) to pyrimidine) on the third base position ofcodons partitions the whole set of codons into disjoint graphs and therebygenerates the total graph of the genetic code. The redundancy of the 64 codonscoding for the 20 amino acids is reduced by the total graph.
  • Ten Bioinformatics Tools for Single Nucleotide Polymorphisms Detection

    • Abstract: SingleNucleotide Polymorphisms (SNPs) as unique genetic variations are widely used asbiomarkers for drug designing and development for individualized therapy. SNPgenotyping techniques such as SBE with MS detection, SBE with fluorescence intensity detection, The FP-TDI, Pyrosequencing and The TaqMan 5’ nucleaseassay are low-speed, timeconsuming and very expensive. To overcome such disadvantages, bioinformaticstools are emerged as alternative methods for detection of SNPs in differentpopulations for different diseases such as cancer, diabetes, heart diseases, Downsyndrome and other genetic related disorders to help in rapid and low-cost andhigh accuracy detection methods. In this review we have listed 10bioinformatics tools for SNP detection to introduce them for the researcherswho are interested in SNP detection required studies in order to help them insaving time and cost and enhancement of accuracy of their results. The bioinformaticstools are selected in this review are poly phred,HGBASE, Human chromosome 21 cSNPdatabase, Dog Genome SNP Database, JSNP database, Polybays, novoSNP, HaploSNPer,PupaSNP and QualitySNPng, which havetheir own specific performance for detection of SNPs. Researcher can choiceappropriate programs on the basis of their research’s need and application. We hopethis review can be helpful and integrates scientific information withbioinformatics tools in drug discovery processes and other studies involved SNPdetection and lead to short time-low cost and high accuracy biomarker detectionin drug designing and development process.
  • Applying Information Theory Analysis for the Solution of Biomedical Data
           Processing Problems

    • Abstract: The use of information-theoretical methods can be highly valuable for the solution of biomedical data processing problems. Some of the problems that can be solved by those methods include: The assessment of the influence of diagnostic parameters, biomarkers and risk factors, on the emergence of disease; the discretization of diagnostic parameters; the analysis of a combined influence of a group of parameters; the partition of a group of diagnostic parameters according to the amount of diagnostic information contained in those parameters; the analysis of the parameters’ heterogeneity or variability and more. To illustrate the solution of those problems, we use a data base on diabetes patients. There are grounds to believe that an increasing application of information-theoretical methodologies in biomedical research will lead to significant practical dividends for diagnosis and therapy.
  • In Silico Analysis of Cellulose Synthase Gene (NcCesA1) in Developing
           Xylem Tissues of Neolamarckia Cadamba

    • Abstract: This study reported the isolation and in silico characterization of full-length cellulose synthase (CesA) cDNA from Neolamarckia cadamba, an important tropical plantation tree species. CesA is a member of processive glycosyltransferases that involved in cellulose biosynthesis of plants. CesA acts as a central catalyst in the generation of plant cell wall biomass or cellulose. It also plays an important role in regulating wood formation. The hypothetical full-length CesA cDNA (NcCesA1; JX134621) was assembled by contig mapping approach using the CesA cDNA sequences from NcdbEST and the amplified 5’-and 3’-RACE PCR sequences. The NcCesA1 cDNA has a length of 3,472 bp with 3,126 bp open reading frame encoding a 1,042 amino acid sequence. The predicted NcCesA1 protein contained N-terminal cysteine rich zinc binding domain, 7 putative Transmembrane Helices (TMH), 4 U-motifs that contain a signature D, D, D, QxxRW motif, an alternating Conserved Region (CR-P) and 2 Hypervariable Regions (HVR). These entire shared domain structures suggest the functional role of NcCesA1 is involved in glycosyltransferation of the secondary cell wall cellulose biosynthesis of N. cadamba. Sequence comparison also revealed the high similarity (90%) among NcCesA1 and PtrCesA2 of Populus tremuloides. This further implies the involvement of NcCesA1 that catalyzes the cellulose biosynthesis of secondary cell wall rather than primary cell wall. This full-length NcCesA1 cDNA can serve as good candidate gene in association genetics study which leads to Gene-Assisted Selection (GAS) in the N. cadamba tree breeding programme. Furthermore, the isolation of new CesA genes from tropical tree genomes is essential for enhancing knowledge of cellulose biosynthesis in trees that has many fundamental and commercial implications.
  • Bioinformatics Analysis of Xyloglucan Endotransglycosylase/Hydrolase (XTH)

    • Abstract: This study reported the isolation and in silico characterization of a full-length Xyloglucan endotransglycosylase/Hydrolase (XTH) cDNA from Neolamarckia cadamba, an important tropical light hardwood plantation tree species. XTH is considered as a key agent to regulate cell wall expansion and is believed to be responsible for the incorporation of newly synthesised xyloglucan into the wall matrix. The full-length of NcXTH was firstly predicted using the XTH singletons from the NcdbEST through contig mapping approach. Further validation and confirmation were conducted by amplifying the full-length XTH cDNA using RT-PCR approach. Two full-length XTH cDNAs, namely NcXTH1 (JX134619) and NcXTH2 (JX134620) were discovered and the nucleotide sequences were 893 and 1,024 bp in length, respectively. The open reading frames for NcXTH1 and NcXTH2 were 858 and 915 bp, respectively. Results predicted that NcXTH1 and NcXTH2 proteins carry out XET activity but they are from different XTH family members. This full-length NcXTH cDNA can serve as good candidate genes in association genetics study which leads to Gene-Assisted Selection (GAS) in the N. cadamba tree breeding programme.

    • Abstract: Content-Based Image Retrieval Systems (CBIR) provide effective support to the doctor to find relevant images using their visual content. Current medical systems are unable to provide accurate and precise results. To solve this problem, effective indexing algorithms are required to extract the contents of the images. In this study, the method of indexing image from the energy coefficients of the wavelet transform is tested on the basis of retinal images to find similar images and the results are promising; the search precision is greater than 60%.
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
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