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Publisher: Inderscience Publishers   (Total: 424 journals)

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Showing 1 - 200 of 424 Journals sorted alphabetically
African J. of Accounting, Auditing and Finance     Hybrid Journal   (Followers: 12)
African J. of Economic and Sustainable Development     Hybrid Journal   (Followers: 11)
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: 18)
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: 15, SJR: 0.185, h-index: 23)
EuroMed J. of Management     Hybrid Journal  
European J. of Cross-Cultural Competence and Management     Hybrid Journal   (Followers: 6)
European J. of Industrial Engineering     Hybrid Journal   (Followers: 8, 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: 11)
Intl. J. of Accounting, Auditing and Performance Evaluation     Hybrid Journal   (Followers: 13, 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  
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: 22, SJR: 0.103, h-index: 9)
Intl. J. of Advanced Operations Management     Hybrid Journal   (Followers: 7, SJR: 0.24, h-index: 4)
Intl. J. of Aerodynamics     Hybrid Journal   (Followers: 19)
Intl. J. of Agent-Oriented Software Engineering     Hybrid Journal   (Followers: 4)
Intl. J. of Agile and Extreme Software Development     Hybrid Journal   (Followers: 4)
Intl. J. of Agile Systems and Management     Hybrid Journal   (Followers: 7, 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: 5, 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: 4, SJR: 0.455, h-index: 11)
Intl. J. of Applied Management Science     Hybrid Journal   (Followers: 5, 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: 3)
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: 8)
Intl. J. of Artificial Intelligence and Soft Computing     Hybrid Journal   (Followers: 7)
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: 9, SJR: 0.297, h-index: 7)
Intl. J. of Automation and Logistics     Hybrid Journal   (Followers: 5)
Intl. J. of Automotive Composites     Hybrid Journal   (Followers: 2)
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: 4, 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: 12, SJR: 0.153, h-index: 5)
Intl. J. of Behavioural Accounting and Finance     Hybrid Journal   (Followers: 7)
Intl. J. of Behavioural and Healthcare Research     Hybrid Journal   (Followers: 7)
Intl. J. of Bibliometrics in Business and Management     Hybrid Journal  
Intl. J. of Big Data Intelligence     Hybrid Journal   (Followers: 12)
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: 14, 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: 1, 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: 6)
Intl. J. of Business Continuity and Risk Management     Hybrid Journal   (Followers: 14)
Intl. J. of Business Environment     Hybrid Journal   (Followers: 3)
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: 18, SJR: 0.264, h-index: 18)
Intl. J. of Business Innovation and Research     Hybrid Journal   (Followers: 9, SJR: 0.273, h-index: 13)
Intl. J. of Business Intelligence and Data Mining     Hybrid Journal   (Followers: 29, 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: 13)
Intl. J. of Business Performance Management     Hybrid Journal   (Followers: 6, SJR: 0.194, h-index: 15)
Intl. J. of Business Process Integration and Management     Hybrid Journal   (Followers: 13, SJR: 0.172, h-index: 15)
Intl. J. of Chinese Culture and Management     Hybrid Journal   (Followers: 5)
Intl. J. of Circuits and Architecture Design     Hybrid Journal   (Followers: 6)
Intl. J. of Cloud Computing     Hybrid Journal   (Followers: 26)
Intl. J. of Cognitive Biometrics     Hybrid Journal   (Followers: 1)
Intl. J. of Cognitive Performance Support     Hybrid Journal   (Followers: 4)
Intl. J. of Collaborative Engineering     Hybrid Journal  
Intl. J. of Collaborative Enterprise     Hybrid Journal  
Intl. J. of Collaborative Intelligence     Hybrid Journal  
Intl. J. of Communication Networks and Distributed Systems     Hybrid Journal   (Followers: 7, SJR: 0.262, h-index: 9)
Intl. J. of Competitiveness     Hybrid Journal   (Followers: 1)
Intl. J. of Complexity in Applied Science and Technology     Hybrid Journal  
Intl. J. of Complexity in Leadership and Management     Hybrid Journal   (Followers: 23)
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: 5)
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: 2, SJR: 0.34, h-index: 12)
Intl. J. of Computational Systems Engineering     Hybrid Journal  
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: 3, 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: 2, 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: 1)
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: 3, SJR: 0.277, h-index: 18)
Intl. J. of Data Analysis Techniques and Strategies     Hybrid Journal   (Followers: 5, SJR: 0.381, h-index: 10)
Intl. J. of Data Mining and Bioinformatics     Hybrid Journal   (Followers: 17, SJR: 0.289, h-index: 13)
Intl. J. of Data Mining, Modelling and Management     Hybrid Journal   (Followers: 14, SJR: 0.152, h-index: 8)
Intl. J. of Data Science     Hybrid Journal   (Followers: 6)
Intl. J. of Decision Sciences, Risk and Management     Hybrid Journal   (Followers: 8)
Intl. J. of Decision Support Systems     Hybrid Journal  
Intl. J. of Design Engineering     Hybrid Journal   (Followers: 14)
Intl. J. of Digital Culture and Electronic Tourism     Hybrid Journal   (Followers: 7)
Intl. J. of Diplomacy and Economy     Hybrid Journal   (Followers: 3)
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: 1)
Intl. J. of Economic Policy in Emerging Economies     Hybrid Journal   (Followers: 3, 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: 5, SJR: 0.102, h-index: 1)
Intl. J. of Education Economics and Development     Hybrid Journal   (Followers: 3, 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   (Followers: 1, SJR: 0.383, h-index: 9)
Intl. J. of Electronic Healthcare     Hybrid Journal   (Followers: 3, 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: 10, 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: 25, SJR: 0.238, h-index: 15)
Intl. J. of Entrepreneurship and Small Business     Hybrid Journal   (Followers: 23, SJR: 0.294, h-index: 16)
Intl. J. of Environment and Health     Hybrid Journal   (Followers: 9, SJR: 0.147, h-index: 10)
Intl. J. of Environment and Pollution     Hybrid Journal   (Followers: 6, SJR: 0.241, h-index: 35)
Intl. J. of Environment and Sustainable Development     Hybrid Journal   (Followers: 17, SJR: 0.142, h-index: 14)
Intl. J. of Environment and Waste Management     Hybrid Journal   (Followers: 7, SJR: 0.142, h-index: 11)
Intl. J. of Environment, Workplace and Employment     Hybrid Journal   (Followers: 4)
Intl. J. of Environmental Engineering     Hybrid Journal   (Followers: 6)
Intl. J. of Environmental Policy and Decision Making     Hybrid Journal   (Followers: 8)
Intl. J. of Environmental Technology and Management     Hybrid Journal   (Followers: 1, SJR: 0.13, h-index: 15)
Intl. J. of Exergy     Hybrid Journal   (Followers: 3, 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  
Intl. J. of Financial Engineering and Risk Management     Hybrid Journal   (Followers: 3)
Intl. J. of Financial Innovation in Banking     Hybrid Journal   (Followers: 3)
Intl. J. of Financial Markets and Derivatives     Hybrid Journal   (Followers: 3)
Intl. J. of Financial Services Management     Hybrid Journal   (Followers: 2)
Intl. J. of Food Safety, Nutrition and Public Health     Hybrid Journal   (Followers: 13)
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: 7, SJR: 0.219, h-index: 14)
Intl. J. of Functional Informatics and Personalised Medicine     Hybrid Journal   (Followers: 6, 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: 3)
Intl. J. of Global Energy Issues     Hybrid Journal   (Followers: 8, SJR: 0.18, h-index: 19)
Intl. J. of Global Environmental Issues     Hybrid Journal   (Followers: 3, SJR: 0.149, h-index: 15)
Intl. J. of Global Warming     Hybrid Journal   (Followers: 1, SJR: 0.431, h-index: 10)
Intl. J. of Globalisation and Small Business     Hybrid Journal   (Followers: 10, SJR: 0.293, h-index: 9)
Intl. J. of Granular Computing, Rough Sets and Intelligent Systems     Hybrid Journal   (Followers: 2)
Intl. J. of Green Economics     Hybrid Journal   (Followers: 4, 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: 5)
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: 6, 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: 3)
Intl. J. of Hospitality and Event Management     Hybrid Journal   (Followers: 3)
Intl. J. of Human Factors and Ergonomics     Hybrid Journal   (Followers: 15)
Intl. J. of Human Factors Modelling and Simulation     Hybrid Journal   (Followers: 15)
Intl. J. of Human Resources Development and Management     Hybrid Journal   (Followers: 23, SJR: 0.148, h-index: 11)
Intl. J. of Human Rights and Constitutional Studies     Hybrid Journal   (Followers: 11)
Intl. J. of Hydrology Science and Technology     Hybrid Journal   (Followers: 4, SJR: 0.181, h-index: 3)
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   (Followers: 1)
Intl. J. of Industrial and Systems Engineering     Hybrid Journal   (Followers: 9, 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  
Intl. J. of Information and Communication Technology     Hybrid Journal   (Followers: 6, SJR: 0.144, h-index: 5)
Intl. J. of Information and Computer Security     Hybrid Journal   (Followers: 19, SJR: 0.134, h-index: 8)
Intl. J. of Information and Decision Sciences     Hybrid Journal   (Followers: 18, 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: 27)
Intl. J. of Information Quality     Hybrid Journal   (Followers: 5, SJR: 0.103, h-index: 8)
Intl. J. of Information Systems and Change Management     Hybrid Journal   (Followers: 9, SJR: 0.112, h-index: 8)
Intl. J. of Information Systems and Management     Hybrid Journal   (Followers: 2)
Intl. J. of Information Technology and Management     Hybrid Journal   (Followers: 15, SJR: 0.128, h-index: 11)
Intl. J. of Information Technology, Communications and Convergence     Hybrid Journal   (Followers: 19)

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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  [424 journals]
  • Improving de novo metatranscriptome assembly via machine learning
           algorithms
    • Authors: Hussein Mohsen, Haixu Tang, Yuzhen Ye
      Pages: 91 - 107
      Abstract: In this paper, we present DNPipe, a Pipeline that processes and filters the transcript contigs reported by existing De Novo metatranscriptome assembly algorithms, aiming to improve the quality of de novo assembly of metatranscriptomic sequences. DNPipe consists of expectation-maximisation (EM) and sampling approaches that utilise abundance information of transcript contigs. We tested DNPipe on six metatranscriptomic datasets acquired from a mock microbial community dominated by three (among more than 15) known bacterial genomes. Results show that DNPipe can substantially improve the quality of metatranscriptome assembly, producing longer and more accurate transcripts. The N50 of the contigs increases by 19% (from around 1880 bps to 2250 bps), and the precision of the assembly improves by up to 8.7%, achieving about 81%. DNPipe assemblies are of higher quality than those assembled by Trinity as well. The DNPipe tool can be downloaded as open source software at https://sourceforge.net/projects/dnpipe/files/.
      Keywords: de novo; sequence; assembly; expectation-maximisation; EM; metatranscriptomics; RNA-Seq
      Citation: International Journal of Computational Biology and Drug Design, Vol. 10, No. 2 (2017) pp. 91 - 107
      PubDate: 2017-04-25T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2017.083877
      Issue No: Vol. 10, No. 2 (2017)
       
  • Expression quantitative locus mapping for identification of hotspots using
           an empirical Bayes mixture model
    • Authors: Guanglong Jiang, Yingqiang Fu, Pengyue Zhang, Shirin Ardeshir-Rouhani-Fard, Lijun Cheng, Lang Li, Zhigao Li
      Pages: 108 - 122
      Abstract: Identification of genomic regions that regulate gene expression can help our understanding of the mechanisms underlying genetic contributions to phenotypic variations. Hence, we consider a mixture model to locate candidate genomic regions that are more frequently associated with gene expression traits. A modified two-sample t-statistic was used, and single-nucleotide polymorphisms (SNPs) with P-values
      Keywords: genotype; gene expression; expression quantitative trait loci; genome-wide association studies; empirical Bayes; mixture model; transcription factor
      Citation: International Journal of Computational Biology and Drug Design, Vol. 10, No. 2 (2017) pp. 108 - 122
      PubDate: 2017-04-25T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2017.083882
      Issue No: Vol. 10, No. 2 (2017)
       
  • Computational tools for genome-wide R-loops identification and
           characterisation
    • Authors: Rongjie Liu, Aparna Gorthi, Yufang Jin, Alexander J.R. Bishop, Yidong Chen
      Pages: 123 - 136
      Abstract: R-loops are physiologically occurring structures in the genome that composed of a DNA/RNA hybrid and a displaced single-stranded DNA. R-loops have been observed in various organisms and shown to play important roles in regulating gene expression, DNA replication, genome stability, and other functions. The recent introduction of the protocol of DNA-RNA Immune-Precipitation (DRIP) followed by next-generation sequencing further propels the data accumulation of R-loop formation in different cellular contexts. In this study, we presented a user-friendly tool, DRIPer, for investigating DRIP-seq data to compare against a collection of publicly available DRIP-seq data and ENCODE ChIP-seq. Such comparisons allow correlation analysis and Kolmogorov-Smirnov tests to study associations via a given gene set, which could be for specific biological pathways, ontological functions, or other co-regulated genes. This powerful method will enable biologists to quickly evaluate the relationship of R-loops to nearby binding protein sites and target gene expression.
      Keywords: DNA/RNA hybrid; R-loops; DRIP-seq; ChIP-seq; binding protein sites; target gene expression; biological pathways; ontological functions; co-regulated genes; DRIPer
      Citation: International Journal of Computational Biology and Drug Design, Vol. 10, No. 2 (2017) pp. 123 - 136
      PubDate: 2017-04-25T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2017.083883
      Issue No: Vol. 10, No. 2 (2017)
       
  • PageRank influence analysis of protein-protein association networks in the
           malaria parasite Plasmodium falciparum
    • Authors: Xinran Yu, Timothy G. Lilburn, Hong Cai, Jianying Gu, Turgay Korkmaz, Yufeng Wang
      Pages: 137 - 156
      Abstract: Malaria has caused millions of deaths over the years and it is still a major scourge in its endemic regions. Resistance to even the most recently developed effective treatments has emerged. A deeper understanding of parasite biology and host-parasite interactions will enable new, robust measures against the malaria parasite. In this paper, we developed a novel PageRank-based network analysis approach to identify proteins that are potentially influential in protein-protein association networks in Plasmodium falciparum. The proteins that were predicted to be most influential are involved in transcriptional regulation, signalling, proteolysis, and heat shock response. They are associated with proteins that may play a role in fundamental processes that range from genetic information processing, metabolism, transport, development, to virulence to the host. Functional characterisation of these proteins may open venues for novel therapeutics for effective malaria eradication.
      Keywords: malaria; plasmodium; PageRank; systems biology; network
      Citation: International Journal of Computational Biology and Drug Design, Vol. 10, No. 2 (2017) pp. 137 - 156
      PubDate: 2017-04-25T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2017.083878
      Issue No: Vol. 10, No. 2 (2017)
       
  • Virtualisation of gene knockout experiments based on kinetic modelling:
           Escherichia coli as an algorithmic case
    • Authors: Rudong Li, Guohui Ding, Yixue Li
      Pages: 157 - 188
      Abstract: Since substantial biological studies focus on molecular essentialities (e.g., gene knockout experiments), virtualisation of such studies saves experimental costs and facilitates knowledge acquisition and bio-engineering. Nevertheless, non-quantitative methods are incompetent and the traditional flux-balance analysis (FBA) is less effective at physiological rather than genome scale. In this respect, kinetic modelling can simulate bio-pathway dynamics and enhance functional characterisations of bio-molecules. However, conventional sensitivity or flux control analysis has limited predictive ability for structural perturbations like gene knockouts. Thus we hereby conceived a novel algorithm for in silico evaluating molecular essentialities based on dynamical systems. Exemplified by E. coli central carbon metabolism, our method was accurate. We found that E. coli central metabolic genes could be categorised into four types of essentiality; moreover, E. coli metabolism might be supported by a minimum of six genes. Additionally, comparing with FBA and a previous kinetic-modelling method, our method was more effective.
      Keywords: gene essentiality; molecular knockout; in silico evaluation; kinetic modelling; system collapse; dysfunctionality; cell survivability; fundamental physiology; E. coli; central metabolism
      Citation: International Journal of Computational Biology and Drug Design, Vol. 10, No. 2 (2017) pp. 157 - 188
      PubDate: 2017-04-25T23:20:50-05:00
      DOI: 10.1504/IJCBDD.2017.083879
      Issue No: Vol. 10, No. 2 (2017)
       
 
 
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