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Publisher: Inderscience Publishers   (Total: 434 journals)

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Showing 1 - 200 of 434 Journals sorted alphabetically
African J. of Accounting, Auditing and Finance     Hybrid Journal   (Followers: 12)
African J. of Economic and Sustainable Development     Hybrid Journal   (Followers: 14)
Afro-Asian J. of Finance and Accounting     Hybrid Journal   (Followers: 7, SJR: 0.205, h-index: 3)
American J. of Finance and Accounting     Hybrid Journal   (Followers: 21)
Asian J. of Management Science and Applications     Hybrid Journal   (Followers: 4)
Atoms for Peace: an Intl. J.     Hybrid Journal   (Followers: 3, SJR: 0.103, h-index: 1)
Electronic Government, an Intl. J.     Hybrid Journal   (Followers: 17, SJR: 0.185, h-index: 23)
EuroMed J. of Management     Hybrid Journal  
European J. of Cross-Cultural Competence and Management     Hybrid Journal   (Followers: 7)
European J. of Industrial Engineering     Hybrid Journal   (Followers: 9, SJR: 0.987, h-index: 16)
European J. of Intl. Management     Hybrid Journal   (Followers: 1, SJR: 0.258, h-index: 10)
Global Business and Economics Review     Hybrid Journal   (Followers: 1, SJR: 0.13, h-index: 7)
Interdisciplinary Environmental Review     Hybrid Journal   (Followers: 3)
Intl. J. of Abrasive Technology     Hybrid Journal   (Followers: 2, SJR: 0.207, h-index: 10)
Intl. J. of Accounting and Finance     Hybrid Journal   (Followers: 14)
Intl. J. of Accounting, Auditing and Performance Evaluation     Hybrid Journal   (Followers: 14, SJR: 0.143, h-index: 9)
Intl. J. of Ad Hoc and Ubiquitous Computing     Hybrid Journal   (Followers: 8, SJR: 0.245, h-index: 13)
Intl. J. of Adaptive and Innovative Systems     Hybrid Journal   (Followers: 1)
Intl. J. of Additive and Subtractive Materials Manufacturing     Hybrid Journal   (Followers: 4)
Intl. J. of Advanced Intelligence Paradigms     Hybrid Journal   (Followers: 3, SJR: 0.39, h-index: 5)
Intl. J. of Advanced Mechatronic Systems     Hybrid Journal   (Followers: 2, SJR: 0.212, h-index: 7)
Intl. J. of Advanced Media and Communication     Hybrid Journal   (Followers: 21, SJR: 0.103, h-index: 9)
Intl. J. of Advanced Operations Management     Hybrid Journal   (Followers: 8, SJR: 0.24, h-index: 4)
Intl. J. of Aerodynamics     Hybrid Journal   (Followers: 24)
Intl. J. of Agent-Oriented Software Engineering     Hybrid Journal   (Followers: 3)
Intl. J. of Agile and Extreme Software Development     Hybrid Journal   (Followers: 5)
Intl. J. of Agile Systems and Management     Hybrid Journal   (Followers: 6, SJR: 0.212, h-index: 8)
Intl. J. of Agricultural Resources, Governance and Ecology     Hybrid Journal   (Followers: 2, SJR: 0.125, h-index: 17)
Intl. J. of Alternative Propulsion     Hybrid Journal   (Followers: 8, SJR: 0.103, h-index: 9)
Intl. J. of Applied Cryptography     Hybrid Journal   (Followers: 10, SJR: 0.401, h-index: 9)
Intl. J. of Applied Decision Sciences     Hybrid Journal   (Followers: 1, SJR: 0.455, h-index: 11)
Intl. J. of Applied Management Science     Hybrid Journal   (Followers: 4, SJR: 0.369, h-index: 10)
Intl. J. of Applied Nonlinear Science     Hybrid Journal   (Followers: 1)
Intl. J. of Applied Pattern Recognition     Hybrid Journal   (Followers: 5)
Intl. J. of Applied Systemic Studies     Hybrid Journal   (SJR: 0.138, h-index: 5)
Intl. J. of Arab Culture, Management and Sustainable Development     Hybrid Journal   (Followers: 7)
Intl. J. of Artificial Intelligence and Soft Computing     Hybrid Journal   (Followers: 10)
Intl. J. of Arts and Technology     Hybrid Journal   (Followers: 6, SJR: 0.114, h-index: 10)
Intl. J. of Auditing Technology     Hybrid Journal   (Followers: 5)
Intl. J. of Automation and Control     Hybrid Journal   (Followers: 8, SJR: 0.297, h-index: 7)
Intl. J. of Automation and Logistics     Hybrid Journal   (Followers: 5)
Intl. J. of Automotive Composites     Hybrid Journal   (Followers: 3)
Intl. J. of Automotive Technology and Management     Hybrid Journal   (Followers: 6, SJR: 0.356, h-index: 15)
Intl. J. of Autonomic Computing     Hybrid Journal   (Followers: 1)
Intl. J. of Autonomous and Adaptive Communications Systems     Hybrid Journal   (Followers: 3, SJR: 0.125, h-index: 10)
Intl. J. of Aviation Management     Hybrid Journal   (Followers: 5)
Intl. J. of Banking, Accounting and Finance     Hybrid Journal   (Followers: 13, SJR: 0.153, h-index: 5)
Intl. J. of Behavioural Accounting and Finance     Hybrid Journal   (Followers: 8)
Intl. J. of Behavioural and Healthcare Research     Hybrid Journal   (Followers: 8)
Intl. J. of Bibliometrics in Business and Management     Hybrid Journal   (Followers: 2)
Intl. J. of Big Data Intelligence     Hybrid Journal   (Followers: 18)
Intl. J. of Bio-Inspired Computation     Hybrid Journal   (Followers: 1, SJR: 0.77, h-index: 25)
Intl. J. of Bioinformatics Research and Applications     Hybrid Journal   (Followers: 13, SJR: 0.231, h-index: 13)
Intl. J. of Biomechatronics and Biomedical Robotics     Hybrid Journal   (Followers: 4)
Intl. J. of Biomedical Engineering and Technology     Hybrid Journal   (Followers: 4, SJR: 0.213, h-index: 10)
Intl. J. of Biomedical Nanoscience and Nanotechnology     Hybrid Journal   (Followers: 6)
Intl. J. of Biometrics     Hybrid Journal   (Followers: 4, SJR: 0.244, h-index: 10)
Intl. J. of Biotechnology     Hybrid Journal   (Followers: 5, SJR: 0.128, h-index: 15)
Intl. J. of Bonds and Derivatives     Hybrid Journal   (Followers: 1)
Intl. J. of Business and Emerging Markets     Hybrid Journal   (Followers: 2)
Intl. J. of Business and Globalisation     Hybrid Journal   (Followers: 2, SJR: 0.21, h-index: 7)
Intl. J. of Business and Systems Research     Hybrid Journal   (Followers: 1, SJR: 0.205, h-index: 11)
Intl. J. of Business Competition and Growth     Hybrid Journal   (Followers: 5)
Intl. J. of Business Continuity and Risk Management     Hybrid Journal   (Followers: 13)
Intl. J. of Business Environment     Hybrid Journal   (Followers: 2)
Intl. J. of Business Excellence     Hybrid Journal   (Followers: 3, SJR: 0.333, h-index: 12)
Intl. J. of Business Forecasting and Marketing Intelligence     Hybrid Journal   (Followers: 6)
Intl. J. of Business Governance and Ethics     Hybrid Journal   (Followers: 4, SJR: 0.222, h-index: 8)
Intl. J. of Business Information Systems     Hybrid Journal   (Followers: 15, SJR: 0.264, h-index: 18)
Intl. J. of Business Innovation and Research     Hybrid Journal   (Followers: 10, SJR: 0.273, h-index: 13)
Intl. J. of Business Intelligence and Data Mining     Hybrid Journal   (Followers: 30, SJR: 0.196, h-index: 13)
Intl. J. of Business Intelligence and Systems Engineering     Hybrid Journal  
Intl. J. of Business Performance and Supply Chain Modelling     Hybrid Journal   (Followers: 16)
Intl. J. of Business Performance Management     Hybrid Journal   (Followers: 8, SJR: 0.194, h-index: 15)
Intl. J. of Business Process Integration and Management     Hybrid Journal   (Followers: 12, SJR: 0.172, h-index: 15)
Intl. J. of Chinese Culture and Management     Hybrid Journal   (Followers: 4)
Intl. J. of Circuits and Architecture Design     Hybrid Journal   (Followers: 6)
Intl. J. of Cloud Computing     Hybrid Journal   (Followers: 25)
Intl. J. of Cognitive Biometrics     Hybrid Journal   (Followers: 2)
Intl. J. of Cognitive Performance Support     Hybrid Journal   (Followers: 3)
Intl. J. of Collaborative Engineering     Hybrid Journal  
Intl. J. of Collaborative Enterprise     Hybrid Journal  
Intl. J. of Collaborative Intelligence     Hybrid Journal   (Followers: 1)
Intl. J. of Communication Networks and Distributed Systems     Hybrid Journal   (Followers: 7, SJR: 0.262, h-index: 9)
Intl. J. of Comparative Management     Hybrid Journal  
Intl. J. of Competitiveness     Hybrid Journal   (Followers: 2)
Intl. J. of Complexity in Applied Science and Technology     Hybrid Journal  
Intl. J. of Complexity in Leadership and Management     Hybrid Journal   (Followers: 28)
Intl. J. of Computational Biology and Drug Design     Hybrid Journal   (Followers: 1, SJR: 0.272, h-index: 8)
Intl. J. of Computational Complexity and Intelligent Algorithms     Hybrid Journal   (Followers: 1)
Intl. J. of Computational Economics and Econometrics     Hybrid Journal   (Followers: 3)
Intl. J. of Computational Intelligence in Bioinformatics and Systems Biology     Hybrid Journal   (Followers: 10)
Intl. J. of Computational Intelligence Studies     Hybrid Journal   (Followers: 2)
Intl. J. of Computational Materials Science and Surface Engineering     Hybrid Journal   (Followers: 6, SJR: 0.159, h-index: 6)
Intl. J. of Computational Science and Engineering     Hybrid Journal   (Followers: 1, SJR: 0.34, h-index: 12)
Intl. J. of Computational Systems Engineering     Hybrid Journal   (Followers: 1)
Intl. J. of Computational Vision and Robotics     Hybrid Journal   (Followers: 4, SJR: 0.123, h-index: 4)
Intl. J. of Computer Aided Engineering and Technology     Hybrid Journal   (Followers: 2, SJR: 0.112, h-index: 7)
Intl. J. of Computer Applications in Technology     Hybrid Journal   (Followers: 2, SJR: 0.309, h-index: 20)
Intl. J. of Computers in Healthcare     Hybrid Journal   (Followers: 2)
Intl. J. of Computing Science and Mathematics     Hybrid Journal   (Followers: 1, SJR: 0.385, h-index: 10)
Intl. J. of Continuing Engineering Education and Life-Long Learning     Hybrid Journal   (Followers: 3, SJR: 0.217, h-index: 16)
Intl. J. of Convergence Computing     Hybrid Journal   (Followers: 1)
Intl. J. of Corporate Governance     Hybrid Journal   (Followers: 4)
Intl. J. of Corporate Strategy and Social Responsibility     Hybrid Journal   (Followers: 3)
Intl. J. of Creative Computing     Hybrid Journal   (Followers: 1)
Intl. J. of Critical Accounting     Hybrid Journal   (Followers: 2)
Intl. J. of Critical Computer-Based Systems     Hybrid Journal   (SJR: 0.22, h-index: 6)
Intl. J. of Critical Infrastructures     Hybrid Journal   (Followers: 2, SJR: 0.277, h-index: 18)
Intl. J. of Data Analysis Techniques and Strategies     Hybrid Journal   (Followers: 3, SJR: 0.381, h-index: 10)
Intl. J. of Data Mining and Bioinformatics     Hybrid Journal   (Followers: 15, SJR: 0.289, h-index: 13)
Intl. J. of Data Mining, Modelling and Management     Hybrid Journal   (Followers: 13, SJR: 0.152, h-index: 8)
Intl. J. of Data Science     Hybrid Journal   (Followers: 8)
Intl. J. of Decision Sciences, Risk and Management     Hybrid Journal   (Followers: 9)
Intl. J. of Decision Support Systems     Hybrid Journal  
Intl. J. of Design Engineering     Hybrid Journal   (Followers: 12)
Intl. J. of Digital Culture and Electronic Tourism     Hybrid Journal   (Followers: 5)
Intl. J. of Digital Signals and Smart Systems     Hybrid Journal  
Intl. J. of Diplomacy and Economy     Hybrid Journal   (Followers: 5)
Intl. J. of Dynamical Systems and Differential Equations     Hybrid Journal   (Followers: 1, SJR: 0.173, h-index: 9)
Intl. J. of Earthquake and Impact Engineering     Hybrid Journal   (Followers: 4)
Intl. J. of Economic Policy in Emerging Economies     Hybrid Journal   (Followers: 2, SJR: 0.228, h-index: 5)
Intl. J. of Economics and Accounting     Hybrid Journal   (Followers: 1)
Intl. J. of Economics and Business Research     Hybrid Journal   (Followers: 3, SJR: 0.102, h-index: 1)
Intl. J. of Education Economics and Development     Hybrid Journal   (Followers: 5, SJR: 0.193, h-index: 2)
Intl. J. of Electric and Hybrid Vehicles     Hybrid Journal   (Followers: 9, SJR: 0.234, h-index: 9)
Intl. J. of Electronic Banking     Hybrid Journal   (Followers: 5)
Intl. J. of Electronic Business     Hybrid Journal   (Followers: 1)
Intl. J. of Electronic Customer Relationship Management     Hybrid Journal   (Followers: 2, SJR: 0.192, h-index: 8)
Intl. J. of Electronic Democracy     Hybrid Journal   (Followers: 1)
Intl. J. of Electronic Finance     Hybrid Journal   (Followers: 4, SJR: 0.2, h-index: 1)
Intl. J. of Electronic Governance     Hybrid Journal   (SJR: 0.383, h-index: 9)
Intl. J. of Electronic Healthcare     Hybrid Journal   (Followers: 2, SJR: 0.195, h-index: 18)
Intl. J. of Electronic Marketing and Retailing     Hybrid Journal   (Followers: 7, SJR: 0.148, h-index: 7)
Intl. J. of Electronic Security and Digital Forensics     Hybrid Journal   (Followers: 9, SJR: 0.221, h-index: 8)
Intl. J. of Embedded Systems     Hybrid Journal   (Followers: 5, SJR: 0.252, h-index: 9)
Intl. J. of Emergency Management     Hybrid Journal   (Followers: 11, SJR: 0.492, h-index: 17)
Intl. J. of Energy Technology and Policy     Hybrid Journal   (Followers: 7, SJR: 0.131, h-index: 11)
Intl. J. of Engineering Management and Economics     Hybrid Journal   (Followers: 4)
Intl. J. of Engineering Systems Modelling and Simulation     Hybrid Journal   (Followers: 9, SJR: 0.192, h-index: 9)
Intl. J. of Enterprise Network Management     Hybrid Journal   (SJR: 0.118, h-index: 6)
Intl. J. of Entrepreneurial Venturing     Hybrid Journal   (Followers: 1, SJR: 0.213, h-index: 7)
Intl. J. of Entrepreneurship and Innovation Management     Hybrid Journal   (Followers: 27, SJR: 0.238, h-index: 15)
Intl. J. of Entrepreneurship and Small Business     Hybrid Journal   (Followers: 26, SJR: 0.294, h-index: 16)
Intl. J. of Environment and Health     Hybrid Journal   (Followers: 5, SJR: 0.147, h-index: 10)
Intl. J. of Environment and Pollution     Hybrid Journal   (Followers: 2, SJR: 0.241, h-index: 35)
Intl. J. of Environment and Sustainable Development     Hybrid Journal   (Followers: 15, SJR: 0.142, h-index: 14)
Intl. J. of Environment and Waste Management     Hybrid Journal   (Followers: 4, SJR: 0.142, h-index: 11)
Intl. J. of Environment, Workplace and Employment     Hybrid Journal   (Followers: 3)
Intl. J. of Environmental Engineering     Hybrid Journal   (Followers: 5)
Intl. J. of Environmental Policy and Decision Making     Hybrid Journal   (Followers: 3)
Intl. J. of Environmental Technology and Management     Hybrid Journal   (Followers: 1, SJR: 0.13, h-index: 15)
Intl. J. of Exergy     Hybrid Journal   (Followers: 2, SJR: 0.667, h-index: 20)
Intl. J. of Experimental and Computational Biomechanics     Hybrid Journal   (Followers: 8)
Intl. J. of Experimental Design and Process Optimisation     Hybrid Journal   (Followers: 5)
Intl. J. of Export Marketing     Hybrid Journal   (Followers: 2)
Intl. J. of Financial Engineering and Risk Management     Hybrid Journal   (Followers: 4)
Intl. J. of Financial Innovation in Banking     Hybrid Journal   (Followers: 3)
Intl. J. of Financial Markets and Derivatives     Hybrid Journal   (Followers: 4)
Intl. J. of Financial Services Management     Hybrid Journal   (Followers: 1)
Intl. J. of Food Safety, Nutrition and Public Health     Hybrid Journal   (Followers: 15)
Intl. J. of Forensic Engineering     Hybrid Journal   (Followers: 2)
Intl. J. of Forensic Engineering and Management     Hybrid Journal   (Followers: 3)
Intl. J. of Foresight and Innovation Policy     Hybrid Journal   (Followers: 5, SJR: 0.219, h-index: 14)
Intl. J. of Functional Informatics and Personalised Medicine     Hybrid Journal   (Followers: 4, SJR: 0.101, h-index: 7)
Intl. J. of Fuzzy Computation and Modelling     Hybrid Journal   (Followers: 2)
Intl. J. of Gender Studies in Developing Societies     Hybrid Journal   (Followers: 4)
Intl. J. of Global Energy Issues     Hybrid Journal   (Followers: 9, SJR: 0.18, h-index: 19)
Intl. J. of Global Environmental Issues     Hybrid Journal   (Followers: 2, SJR: 0.149, h-index: 15)
Intl. J. of Global Warming     Hybrid Journal   (Followers: 2, SJR: 0.431, h-index: 10)
Intl. J. of Globalisation and Small Business     Hybrid Journal   (Followers: 11, SJR: 0.293, h-index: 9)
Intl. J. of Governance and Financial Intermediation     Hybrid Journal  
Intl. J. of Granular Computing, Rough Sets and Intelligent Systems     Hybrid Journal   (Followers: 2)
Intl. J. of Green Economics     Hybrid Journal   (Followers: 3, SJR: 0.148, h-index: 10)
Intl. J. of Grid and Utility Computing     Hybrid Journal   (SJR: 0.235, h-index: 8)
Intl. J. of Happiness and Development     Hybrid Journal   (Followers: 7)
Intl. J. of Healthcare Technology and Management     Hybrid Journal   (Followers: 7, SJR: 0.155, h-index: 13)
Intl. J. of Heavy Vehicle Systems     Hybrid Journal   (Followers: 7, SJR: 0.154, h-index: 15)
Intl. J. of High Performance Computing and Networking     Hybrid Journal   (Followers: 4, SJR: 0.362, h-index: 10)
Intl. J. of High Performance Systems Architecture     Hybrid Journal   (Followers: 6, SJR: 0.301, h-index: 7)
Intl. J. of Higher Education and Sustainability     Hybrid Journal   (Followers: 5)
Intl. J. of Hospitality and Event Management     Hybrid Journal   (Followers: 4)
Intl. J. of Human Factors and Ergonomics     Hybrid Journal   (Followers: 16)
Intl. J. of Human Factors Modelling and Simulation     Hybrid Journal   (Followers: 13)
Intl. J. of Human Resources Development and Management     Hybrid Journal   (Followers: 25, SJR: 0.148, h-index: 11)
Intl. J. of Human Rights and Constitutional Studies     Hybrid Journal   (Followers: 13)
Intl. J. of Humanitarian Technology     Hybrid Journal  
Intl. J. of Hydrology Science and Technology     Hybrid Journal   (Followers: 5, SJR: 0.181, h-index: 3)
Intl. J. of Hydromechatronics     Hybrid Journal  
Intl. J. of Image Mining     Hybrid Journal   (Followers: 1)
Intl. J. of Immunological Studies     Hybrid Journal   (Followers: 1)
Intl. J. of Indian Culture and Business Management     Hybrid Journal  
Intl. J. of Industrial and Systems Engineering     Hybrid Journal   (Followers: 11, SJR: 0.433, h-index: 19)
Intl. J. of Industrial Electronics and Drives     Hybrid Journal   (Followers: 4)
Intl. J. of Information and Coding Theory     Hybrid Journal   (Followers: 6)
Intl. J. of Information and Communication Technology     Hybrid Journal   (Followers: 8, SJR: 0.144, h-index: 5)
Intl. J. of Information and Computer Security     Hybrid Journal   (Followers: 18, SJR: 0.134, h-index: 8)
Intl. J. of Information and Decision Sciences     Hybrid Journal   (Followers: 10, SJR: 0.323, h-index: 10)
Intl. J. of Information and Operations Management Education     Hybrid Journal   (Followers: 8)
Intl. J. of Information Privacy, Security and Integrity     Hybrid Journal   (Followers: 25)

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Journal Cover International Journal of Computational Biology and Drug Design
  [SJR: 0.272]   [H-I: 8]   [1 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1756-0756 - ISSN (Online) 1756-0764
   Published by Inderscience Publishers Homepage  [434 journals]
  • Evaluation of biological and technical variations in low-input RNA-Seq and
           single-cell RNA-Seq
    • Authors: Fan Gao, Jae Mun Kim, JiHong Kim, Ming-Yi Lin, Charles Y. Liu, Jonathan J. Russin, Christopher P. Walker, William Mack, Oleg V. Evgrafov, Robert H. Chow, James A. Knowles, Kai Wang
      Pages: 5 - 22
      Abstract: Background: Low-input or single-cell RNA-Seq are widely used today, but two technical questions remain: 1) in technical replicates, what proportion of noises comes from input RNA quantity rather than variation of bioinformatics tools?; 2) In single neurons, whether variation in gene expression is attributable to biological heterogeneity or just random noise? To examine the sources of variability, we have generated RNA-Seq data from low-input (10/100/1000pg) reference RNA samples and 38 single neurons from human brains. Results: For technical replicates, the quantity of input RNA is negatively correlated with expression variation. For genes in the medium- and high-expression groups, input RNA amount explains most of the variation, whereas bioinformatic pipelines explain some variation for the low-expression group. The t-distributed stochastic neighbour embedding (t-SNE) method reveals data-inherent aggregation of low-input replicate data, and suggests heterogeneity of single pyramidal neuron transcriptome. Interestingly, expression variation in single neurons is biologically relevant. Conclusions: We found that differences in bioinformatics pipelines do not present a major source of variation.
      Keywords: RNA-Seq; single-cell sequencing; bioinformatics; TopHat; RNA-Seq by expectation maximisation; RSEM; t-distributed stochastic neighbour embedding; t-SNE; principal component analysis; PCA; annotate variation; ANNOVAR; variance
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 5 - 22
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090839
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • Heterogeneity in untreated, stressed and drug-tolerant cells: insights
           into the evolution of cancer resistance
    • Authors: Bhagya K. Wijayawardena, Gopinath Sivasankaran, Lang Li
      Pages: 23 - 38
      Abstract: The evolution of cancer is a Darwinian process, the composition of cancer cell population varying with time, especially after chemotherapy. Such changes occurring in the genetic landscape of tumours are possibly responsible for the chemotherapeutic resistance. Due to the recent advances in single cellular sequencing, the evolution of cancers can be monitored at the single cellular resolution. We reanalysed a previously published dataset composed of single cell RNAseq data, collected before, during and after the establishment of Paclitaxel tolerance, to identify single cell heterogeneity. We used gene expression analysis, gene expression rank correlation analysis, pathway analysis and mutation analysis to identify within group variations of cancer cells after chemotherapy. We identified a decrease in cancer cell within group diversity during the transition to drug-tolerance. Additionally, we observed high mutation rate in stressed single cells, which suggests genetic instability of cancer cells that could ultimately result in the development of drug resistance. Our analysis carries significant implications for developing personalised and efficient therapeutics against cancer.
      Keywords: single cell RNAseq; drug resistance; paclitaxel; chemotherapy; tumour; drug 18 tolerance; Illumina HiSEq; MDA-MB-231
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 23 - 38
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090846
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • A flexible approach to reconstruct the genomic spatial structure by the
           genetic algorithm
    • Authors: Yan Zhang, William Hoskins, Ruofan Xia, Xiya Xia, Jim W. Zheng, Jijun Tang
      Pages: 39 - 51
      Abstract: The 3D structures of the chromosomes play fundamental roles in essential cellular functions, e.g., gene regulation, gene expression, evolution. HiC technique provides the interaction density between loci on chromosomes. Several approaches have been developed to reconstruct the 3D model of the chromosomes from HiC data. However, all of the approaches are based on a particular mathematical model and lack of flexibility for new development. We introduce a novel approach using the genetic algorithm. Our approach is flexible to accept any mathematical models to build a 3D chromosomal structure. Also, our approach outperforms current techniques in accuracy.
      Keywords: genome; spatial structure; genetic algorithm; HiC
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 39 - 51
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090825
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • A GPU-CPU heterogeneous algorithm for NGS read alignment
    • Authors: Ahmad Al Kawam, Sunil Khatri, Aniruddha Datta
      Pages: 52 - 66
      Abstract: In the next generation sequencing (NGS) read alignment problem, millions of deoxyribonucleic acid (DNA) fragments, called reads, are mapped to a reference genome. Read alignment is typically carried out using traditional computing platforms, which have become a limiting factor in the speed of the process. The massive scale of the problem makes it an attractive target for acceleration. In this paper, we design a read alignment algorithm designed to run on a heterogeneous system composed of a graphics processing unity (GPU) and a multicore central processing unit (CPU). We introduce novel techniques for the alignment process and construct a computational pipeline of overlapped CPU and GPU stages. We compare our tool with the BWA-mem alignment tool, and the results show substantial speedups.
      Keywords: NGS; next generation sequencing; read alignment; GPU acceleration
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 52 - 66
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090840
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • Signal translational efficiency between mRNA expression and antibody-based
           protein expression for breast cancer and its subtypes from cell lines to
           tissue
    • Authors: Aida Yazdanparast, Lang Li, Milan Radovich, Lijun Cheng
      Pages: 67 - 89
      Abstract: Background: Although gene transcripts and protein expression have been utilised to classify breast cancer subtypes, it is not clear whether the observed measurement of gene transcript abundance can predict its protein expression. Herein, we attempt to address gene transcript/protein associations using publically-available data on breast cancer tumour tissues and cell lines. Method: Correlation analysis between mRNAs and Reverse-phase protein arrays (RPPA) among 421 primary breast tumours and 33 breast cancer cell lines was conducted. Highly concordant proteins/genes were further analysed in different breast cancer subtypes. Results: The overall accordance of mRNA/RPPA correlation between cell lines and primary tissue is R<SUP align="right">2</SUP> = 0.71. Since most of these genes are well known drug targets, highly concordant gene/RPPA associations not only confirm that these gene transcripts can serve as biomarkers for their protein products in drug target selection, but also imply that breast cancer cell lines can serve as good models for primary breast cancer tumours.
      Keywords: breast cancer; reverse-phase protein array; mRNA; cell lines; protein abundance
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 67 - 89
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090833
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • Native state of complement protein C3d analysed via hydrogen exchange and
           conformational sampling
    • Authors: Didier Devaurs, Malvina Papanastasiou, Dinler A. Antunes, Jayvee R. Abella, Mark Moll, Daniel Ricklin, John D. Lambris, Lydia E. Kavraki
      Pages: 90 - 113
      Abstract: Hydrogen/deuterium exchange detected by mass spectrometry (HDX-MS) provides valuable information on protein structure and dynamics. Although HDX-MS data is often interpreted using crystal structures, it was suggested that conformational ensembles produced by molecular dynamics simulations yield more accurate interpretations. In this paper, we analyse the complement protein C3d by performing an HDX-MS experiment, and evaluate several interpretation methodologies using an existing prediction model to derive HDX-MS data from protein structure. To interpret and refine C3d's HDX-MS data, we look for a conformation (or conformational ensemble) of C3d that allows computationally replicating this data. We confirm that crystal structures are not a good choice and suggest that conformational ensembles produced by molecular dynamics simulations might not always be satisfactory either. Finally, we show that coarse-grained conformational sampling of C3d produces a conformation from which its HDX-MS data can be replicated and refined.
      Keywords: complement protein C3d; hydrogen exchange; mass spectrometry; protein conformational sampling; coarse-grained conformational sampling; native state; X-ray crystallography; molecular dynamics; protein structures; conformational ensembles
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 90 - 113
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090834
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • Inhibition of polyamine biosynthesis for toxicity control in Serratia
           marcescens strain WW4 by targeting ornithine decarboxylase: a
           structure-based virtual screening study
    • Authors: Kalyani Dhusia, Pramod K. Yadav, Rohit Farmer, Pramod W. Ramteke
      Pages: 114 - 134
      Abstract: Ornithine decarboxylase (ODC) enzyme, catalyses the decarboxylation of ornithine to form spermidine which is a committed step in the biosynthesis of polyamines. Here, in the present work, structure of ODC was modelled and studied for its active site. The stability of modelled structure was revalidated by the molecular dynamics simulation at 50 nano second time scale. 142 Natural products of Indofine Herbal Ingredient library from ZINC database were screened using Autodock Vina for the identification of potential leading herbal inhibitors. The results obtained from docking showed that Conessine is best inhibiting candidate with docking affinity of -9.7 Kcal/mol. Conessine is an alkaloid which proves its immense importance as metabolites. Thus, polyamine being harmful when synthesised in excess are necessary to be controlled at their genesis. Therefore, conessine might be a potential inhibitor for toxicity control in plant growth promoting rhizobacteria.
      Keywords: ornithine decarboxylase; herbal inhibitor; molecular dynamics simulation; docking; virtual screening
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 114 - 134
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090837
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • Identifying the dynamic gene regulatory network during latent HIV-1
           reactivation using high-dimensional ordinary differential equations
    • Authors: Jaejoon Song, Michelle Carey, Hongjian Zhu, Hongyu Miao, Juan Camilo Ramírez, Hulin Wu
      Pages: 135 - 153
      Abstract: Reactivation of latently infected cells has emerged as an important strategy for eradication of HIV. However, genetic mechanisms of regulation after reactivation remain unclear. We describe a five-step pipeline to study the dynamics of the gene regulatory network following a viral reactivation using high-dimensional ordinary differential equations. Our pipeline implements a combination of five different methods, by detecting temporally differentially expressed genes (step 1), clustering genes with similar temporal expression patterns into a small number of response modules (step 2), performing a functional enrichment analysis within each gene response module (step 3), identifying a network structure based on the gene response modules using ordinary differential equations (ODE) and a high-dimensional variable selection technique (step 4), and obtaining a gene regulatory model based on refined parameter estimates using nonlinear least squares (step 5). We applied our pipeline to a time course gene expression data of latently infected T-cells following a latency-reversion.
      Keywords: HIV; human immunodeficiency virus; gene regulatory network; ODEs; ordinary differential equations
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 135 - 153
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090844
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • Risk-associated and pathway-based method to detect association
           with Alzheimer's disease
    • Authors: Jeffrey Mitchel, Laszlo Prokai, Youping Deng, Fan Zhang, Robert Barber
      Pages: 154 - 170
      Abstract: Genes do not function alone but through complex biological pathways in complex diseases such as Alzheimer's disease (AD). Unravelling these intricate pathways is essential to understanding biological mechanisms of the AD. Based on the integrated pathway analysis database (IPAD), we developed a pathway-based method to detect association with the AD. First, we performed risk associated allele analysis to determine if a major or minor allele is associated with risk. Then we performed pathway-disease association analysis to identify 133 AD-associated pathways. Lastly, we performed pathway-patient association analysis to investigate the patient's association and distribution among the 133 pathways. We found five AD-associated pathways that have the highest association with patients. We present a pathway-based method to detect AD-associated pathways from GWAS data. Our pathway-based analysis not only provides a technique to identify disease-associated pathways, but also help determine the pathway-patient association.
      Keywords: Alzheimer's disease; pathway analysis; biomarker discovery
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 154 - 170
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090838
      Issue No: Vol. 11, No. 1/2 (2018)
       
  • Neural signature of event-related N200 and P300 modulation in parietal
           lobe during human response inhibition
    • Authors: Rupesh Kumar Chikara, Oleksii Komarov, Li-Wei Ko
      Pages: 171 - 182
      Abstract: Response inhibition is a process of motor control and related to the suppression of the action. The role of inhibition in many studies remains an issue of debate, most researchers nevertheless agree that some sort of inhibition mechanism is involved in the deliberate cessation of a motor response. Therefore, stop-signal task has been designed to investigate the response inhibition. Other aspects also encourage the importance of this study, because deficits in response inhibition is an essence in a variety of neurological disorders such as schizophrenia and attention deficit hyperactivity disorder (ADHD). The aim of present study is to examine the brain modulation of left and right-hand response inhibitions with electroencephalography (EEG). The results indicate response inhibition related neural signatures including the N200 and P300 waves in the frontal, central and parietal regions. This work accomplishes that the independent nature of the inhibitory control of the left-and right-hand.
      Keywords: EEG; electroencephalography; stop-signal task; response inhibition; ERP; event-related potentials; N200; P300
      Citation: International Journal of Computational Biology and Drug Design, Vol. 11, No. 1/2 (2018) pp. 171 - 182
      PubDate: 2018-03-28T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2018.090842
      Issue No: Vol. 11, No. 1/2 (2018)
       
 
 
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