Computational analysis for functional and evolutionary aspects of BACE-1 and associated Alzheimer's related proteins

Panigrahi, Priya P.; Singh, Tiratha Raj

doi:10.1504/ijcistudies.2012.050355

Cited by 5 publications

(1 citation statement)

References 20 publications

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“…Systems biology studies the way in which interaction of different types of molecules results in complex behavior at the cellular, organism, disease and higher levels (Krasnogor et al 2005;Melke et al 2010;Panigrahi and Singh 2012;Ulas et al 2012). It approaches these questions using a combination of high-throughput experiments, mathematical and computational models, and information storage in specialized databases.…”

Section: Introductionmentioning

confidence: 99%

A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing

Kumar

Singh

2013

Syst Synth Biol

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Quorum sensing (QS) is a process which allows a population of bacteria to coordinately regulate gene expression of their entire community. Bacillus subtilis is a soil organism which uses QS to alternate between competence for DNA uptake and sporulation. We propose a model to describe the components involved in QS and to analyze reaction species involved in the regulation of QS machinery. We targeted only those QS phenotypes for which the genetic organization and molecular characterization of the components are fully elucidated. We have analyzed simulations for concentration of different species involved in competence as well as sporulation pathways at diverse time period using quantitative methods. It was observed that there is possibility of achieving different measurement from reactions taken place between species by applying irreversible Michaelis-Menten kinetic law. We obtain variation in measurement on changing parameters such as concentrations ranging from 0.3 to 50 lM in stepwise manner by setting end time in the range of 0.1-100 ms. Additionally we observe covariance between different reaction species involved in QS by fluctuating their quantities in real-time simulations. Our model mimics correctly the phenotype for competence and virulence. We concluded that time factor play major role to determine rate kinetics of diverse reaction species as compared to their concentrations and support the hypothesis of getting genetic stability while colonies are in synchronization.

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Section: Introductionmentioning

confidence: 99%

A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing

Kumar

Singh

2013

Syst Synth Biol

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Nmdb: Network Motif Database Envisaged and Explicated From Human Disease Specific Pathways

2014

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The study of network motifs for large number of networks can aid us to resolve the functions of complex biological networks. In biology, network motifs that reappear within a network more often than expected in random networks include negative autoregulation, positive autoregulation, single-input modules, feedforward loops, dense overlapping regulons and feedback loops. These network motifs have their different dynamical functions. In this study, our main objective is to examine the enrichment of network motifs in different biological networks of human disease specific pathways. We characterize biological network motifs as biologically significant sub-graphs. We used computational and statistical criteria for efficient detection of biological network motifs, and introduced several estimation measures. Pathways of cardiovascular, cancer, infectious, repair, endocrine and metabolic diseases, were used for identifying and interlinking the relation between nodes. 3–8 sub-graph size network motifs were generated. Network Motif Database was then developed using PHP and MySQL. Results showed that there is an abundance of autoregulation, feedforward loops, single-input modules, dense overlapping regulons and other putative regulatory motifs in all the diseases included in this study. It is believed that the database will assist molecular and system biologists, biotechnologists, and other scientific community to encounter biologically meaningful information. Network Motif Database is freely available for academic and research purpose at: http://www.bioinfoindia.org/nmdb .

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Data Mining, Big Data, Data Analytics

Panigrahi

Singh

2017

Library and Information Services for Bioinformatics Education and Research

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In this digital and computing world, data formation and collection rate are growing very rapidly. With these improved proficiencies of data storage and fast computation along with the real-time distribution of data through the internet, the usual everyday ingestion of data is mounting exponentially. With the continuous advancement in data storage and accessibility of smart devices, the impact of big data will continue to develop. This chapter provides the fundamental concepts of big data, its benefits, probable pitfalls, big data analytics and its impact in Bioinformatics. With the generation of the deluge of biological data through next generation sequencing projects, there is a need to handle this data trough big data techniques. The chapter also presents a discussion of the tools for analytics, development of a novel data life cycle on big data, details of the problems and challenges connected with big data with special relevance to bioinformatics.

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Computational analysis for functional and evolutionary aspects of BACE-1 and associated Alzheimer's related proteins

Cited by 5 publications

References 20 publications

A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing

A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing

Nmdb: Network Motif Database Envisaged and Explicated From Human Disease Specific Pathways

Data Mining, Big Data, Data Analytics

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