Topological data analysis
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Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic relationship of chromatin structure and gene regulation. We developed a novel computational method HiSIF to identify genome-wide interacting loci.
13p vibransone 28-03-2024 8 2 Download
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The simulation for this purpose will be done using PVSyst V7.0 to estimate the production of the photovoltaic system installation on the building’s rooftop by using the weather data imported from MeteoNorm. Analysis of simulation results confirms the potential of on-site PV system exploitation to provide energy for data center - which is a critical infrastructure in urban area.
4p vistephenhawking 26-04-2022 9 3 Download
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Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming.
19p viarchimedes 26-01-2022 6 0 Download
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A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms.
10p visilicon2711 20-08-2021 8 1 Download
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Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn.
10p vikentucky2711 26-11-2020 13 3 Download
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The analysis of high-throughput data in biology is aided by integrative approaches such as gene-set analysis. Gene-sets can represent well-defined biological entities (e.g. metabolites) that interact in networks (e.g. metabolic networks), to exert their function within the cell.
6p vikentucky2711 26-11-2020 6 0 Download
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Non-small cell lung cancer (NSCLC) is one of the leading causes of death globally, and research into NSCLC has been accumulating steadily over several years. Drug repositioning is the current trend in the pharmaceutical industry for identifying potential new uses for existing drugs and accelerating the development process of drugs, as well as reducing side effects.
14p vioklahoma2711 19-11-2020 9 1 Download
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Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data.
16p vioklahoma2711 19-11-2020 13 2 Download
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Pathway analysis methods, in which differentially expressed genes are mapped to databases of reference pathways and relative enrichment is assessed, help investigators to propose biologically relevant hypotheses.
8p vioklahoma2711 19-11-2020 9 1 Download
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Network component analysis (NCA) became a popular tool to understand complex regulatory networks. The method uses high-throughput gene expression data and a priori topology to reconstruct transcription factor activity profiles. Current NCA algorithms are constrained by several conditions posed on the network topology, to guarantee unique reconstruction (termed compliancy).
13p vioklahoma2711 19-11-2020 13 1 Download
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Analysis of integrated genome-scale networks is a challenging problem due to heterogeneity of high-throughput data. There are several topological measures, such as graphlet counts, for characterization of biological networks.
10p vioklahoma2711 19-11-2020 7 1 Download
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Analysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in which a disease progresses. Identifying topological preservation of modular structure also contributes to that understanding.
23p vioklahoma2711 19-11-2020 13 0 Download
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Biological data comprises various topologies or a mixture of forms, which makes its analysis extremely complicated. With this data increasing in a daily basis, the design and development of efficient and accurate statistical methods has become absolutely necessary.
9p viconnecticut2711 29-10-2020 12 1 Download
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For more than a decade, gene expression data sets have been used as basis for the construction of co-expression networks used in systems biology investigations, leading to many important discoveries in a wide range of subjects spanning human disease to evolution and the development of organisms.
11p vicoachella2711 27-10-2020 12 0 Download
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Pathway enrichment analysis is extensively used in the analysis of Omics data for gaining biological insights into the functional roles of pre-defined subsets of genes, proteins and metabolites. A large number of methods have been proposed in the literature for this task.
14p vicolorado2711 23-10-2020 10 1 Download
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Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network graph based on the data topology.
18p vicolorado2711 22-10-2020 13 0 Download
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In this Smart Grid network, a Smart Grid node can receive and send data to Smart Grid centre through a Smart Grid network gateway. Hardware analysis and design of a Smart Grid node and Smart Grid network gateway are proposed with a goal of low cost and efficient energy consumption. Through a practical test of received signal strength measurement in an urban environment, the reliability of data communications of this Smart Grid wireless device has been proved. And finally, by using NS-2 simulation, packet loss and network delay time for different network topologies are evaluated.
10p minhxaminhyeu4 15-07-2019 20 0 Download
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It’s convenient to describe a data structure in terms of the operations performed, rather than in terms of implementation details. That means we should separate the concepts from particular implementations. When a data structure is defined that way, it’s called an abstract data type (ADT).
124p janeeyre_thanh 12-08-2013 75 15 Download
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The Rv0948c gene fromMycobacterium tuberculosisH37Rv encodes a 90 amino acid protein as the natural gene product with chorismate mutase (CM) activity. The protein, 90-MtCM, exhibits Michaelis–Menten kinetics with akcat of 5.5 ± 0.2 s )1 and a Kmof 1500 ± 100lmat 37C and pH 7.5. The 2.0 A˚ X-ray structure shows that 90-MtCM is an alla-helical homodimer (Protein Data Bank ID: 2QBV) with the topology ofEscheri-chia coliCM (EcCM), and that both protomers contribute to each catalytic site.
12p research12 29-04-2013 35 2 Download
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This paper presents SIENA, an event notification service that we have de- signed and implemented to maximize both expressiveness and scalability. In Section 3we describe the service’s formally defined application programming in- terface,which is an extension of the familiar publish/subscribe protocol [Birman 1993]. Several candidate server topologies and protocols are presented in Sec- tion 4.
210p nhacchovina 22-03-2013 50 10 Download