With the advent of fully sequenced genomes, the computational study of orthologous protein relationships in evolution, comparative genomics, but also for substantiating the evolutionary conservation of fundamental cellular processes increased exponentially. (biomedcentral.com)
We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. (biomedcentral.com)
Algorithms2
Other orthology search methods combine sequence-based searches with phylogenetic methods or graph-clustering algorithms to circumvent computationally intense phylogenetic calculations. (biomedcentral.com)
Furthermore, all of the aforementioned DVEPSO configurations are compared against the dynamic multi-objective optimisation (DMOPSO) algorithm that was the winning algorithm of a comprehensive comparative study of dynamic multi-objective optimisation algorithms. (upenn.edu)
ANOVA2
Analysis of variance (ANOVA) is a widely used tool to analyze and rank genes in both one- and dual-color comparative gene expression experiments [ 5 ]. (biomedcentral.com)
Statistical analyses, including ANOVA and Chi-Squared tests, were conducted to test for significant differences between racial groups in quantitative and categorical variables. (preprints.org)
Computationally1
With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. (biomedcentral.com)
Sensitivity4
Furthermore, we compared performance of both ratio- and intensity-based analyses in terms of reproducibility and sensitivity for differential gene expression. (biomedcentral.com)
Intensity-based analysis of dual-color datasets results in more reproducible results and increased sensitivity in the detection of differential gene expression than the analysis of the same dataset with ratio-based analysis. (biomedcentral.com)
Sensitivity analyses were performed using different kidney function surveillance definitions. (cdc.gov)
Treating clinic remained a significant predictor of kidney function surveillance in all sensitivity analyses. (cdc.gov)
Gene expression3
By analyzing three distinct and technically replicated datasets with either ratio- or intensity-based models, we determined that, when applied to the same dataset, intensity-based analysis of dual-color gene expression experiments yields 1) more reproducible results, and 2) is more sensitive in the detection of differentially expressed genes. (biomedcentral.com)
Using these methods on 122 cap analysis of gene expression (CAGE) samples of transcription start sites, we construct genome-wide 'promoteromes' in human and mouse consisting of a three-tiered hierarchy of transcription start sites, transcription start clusters, and transcription start regions. (biomedcentral.com)
There are several advantages that deep-sequencing approaches to gene expression analysis offer over standard micro-array approaches. (biomedcentral.com)
Outcome1
The outcome of comparative microarray experiments is a ranked list of significant genes, possibly involved in the process under investigation. (biomedcentral.com)
Interactions2
If the average number of links per protein is sufficiently large, the result will be a network of interactions, a so-called functional linkage network (FLN). (biomedcentral.com)
High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. (springer.com)
Approaches2
In general, these comparative genomic approaches involve extensive clustering of subsequences of intergenic regions from many organisms followed by structural motif prediction [ 3 , 4 ]. (biomedcentral.com)
This renewed interest is informed by a variety of approaches, which range from studies on the unequal distribution of economic power and resources to analysis of regional endowments, such as human capital or quality of institutions. (upv.es)
Data9
Ratio-based analysis is the current standard for the analysis of dual-color microarray data. (biomedcentral.com)
In the first step, we demonstrate that four commonly used machine learning methods, Linear SVM, Linear Discriminant Analysis, Naïve Bayes, and Neural Network, all combine heterogeneous data to produce reliable and high-coverage FLNs, in which the linkage weight more accurately estimates functional coupling of linked proteins than use individual data sources alone. (biomedcentral.com)
To overcome these drawbacks, multiple data sources are often utilized and integrated using machine learning procedures, such as Bayesian methods, Neural Network, and Decision Tree. (biomedcentral.com)
Meanwhile, based on the panel data from 280 prefecture-level cities in China from 2003 to 2013, the paper thoroughly probed into, and discussed, the effect imposed by industry clustering and specialization on the utilization efficiency of urban land. (preprints.org)
While parameter estimation can be performed efficiently when complete training data is available (i.e., when all variables have been observed), learning the local distributions becomes difficult when latent (hidden) variables are introduced. (upenn.edu)
Here we present a set of rigorous methods for normalization, quantification of noise, and co-expression analysis of deep sequencing data. (biomedcentral.com)
However, whereas for micro-arrays there has been a large amount of work devoted to the analysis of the data, including issues of normalization, noise analysis, sequence-composition biases, background corrections, and so on, deep sequencing based expression analysis is still in its infancy and no standardized analysis protocols have been developed so far. (biomedcentral.com)
Here we present new mathematical and computational procedures for the analysis of deep sequencing expression data. (biomedcentral.com)
In particular, we have developed rigorous procedures for normalizing the data, a quantitative noise model, and a Bayesian procedure that uses this noise model to join sequence reads into clusters that follow a common expression profile across samples. (biomedcentral.com)
Industry5
It establishes vital linkages and synergy between industry & agriculture, the two building blocks of any economy. (indianclusters.org)
2) theoretically speaking, the relation between industry clustering and urban land utilization efficiency presents an inverted-U shape. (preprints.org)
Consequently, strengthening the industry professional development of Western and Central China and small and medium-sized cities, facilitating diversified development of industries in Eastern China and large cities, and accelerating industrial clustering, all of these measures above will be conducive to improving urban land utilization efficiency in China. (preprints.org)
This study aims to characterize the state of the art and technology about the application of Virtual Reality and Digital Human Modeling for the physical ergonomics analysis in the during product development phases in the industry through a systematic review of the literature and patents. (preprints.org)
The majority of research on the use of VR and DHM technologies for physical ergonomics analysis focus on the automotive industry and the ergonomic assessment of workstations and current processes. (preprints.org)
Multiple1
Sometimes the bars are clustered to allow multiple series to be charted side-by-side, for example yearly sales for 2015 to 2018 might appear against each product category. (peterjamesthomas.com)
Study1
Survival analysis--which is also called event history analysis--is presented as an excellent analytic technique for the study of career timing. (upv.es)
Urban1
Whether it is the chapter on gambling, or on workplace compensation, or on urban neighborhoods, or on the linkages between innovation and population. (abhinavagarwal.net)
Accounting2
Accounting for such an array effect in the analysis of dual-color arrays was initially necessary due to the relatively poor quality of array platforms: researchers were confronted with different levels of background signals across arrays, and the process of spotting cDNAs yielded probes with different shapes and probe concentrations. (biomedcentral.com)
Health Modern State and Development Perspectives of Accounting, Economic Analysis and Audit. (frankponten.de)
Identify1
We used clustering analysis to identify patterns in social equity and energy consumption. (preprints.org)
Recent years1
In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. (springer.com)
Method2
An experimental evaluation method is proposed to find critical nodes of the FPGA-based designs, named "hardness analysis technique" under the proposed RASP-FIT tool. (thesai.org)
2020) introduce a genome-clustering method based on the number of shared identical DNA sequences of length k (or k -mers). (peercommunityin.org)
Focus1
Most of these analyses focus on combinatorial problems, such as path finding. (upenn.edu)
Relationships1
We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. (springer.com)
Technology1
The literature review indicated that Virtual Reality technology complements the Digital Human Modeling during physical ergonomics analysis for manufacturing process already designed. (preprints.org)
Technologies2
Here, we review the current state of the application of these technologies to the analysis of spider communities. (springer.com)
However, even though the huge applications, these technologies are not yet applied by these industries for the analysis of physical ergonomics during product development phases. (preprints.org)
Locations2
A secondary analysis, of prospective cohorts at 12 locations within the U.S. from 2003 to 2009 (n=75,614), were pooled to evaluate sunburn incidence 10-12days after the beach visit. (cdc.gov)
An experimental set-up is developed to verify and validate the criticality of these locations found by using hardness analysis. (thesai.org)
Research1
The DEF seminar series 2022/2023 was organised in collaboration with the project "Individual Behaviour and Economic Performance: Methodological Challenges and Institutional Context" (IBEP) [ www.taltech.ee/en/ibep ], which has received funding from the European Union's Horizon 2020 Research and Innovation programme under Grant Agreement No 952574. (taltech.ee)
Critical1
We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities. (springer.com)