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GenFlow: generic flow for integration, management and analysis of molecular biology data

this task is the integration of large volumes of data stored in highly heterogeneous repositories of genomic and cDNA sequences, as well as gene expression results. Solving this problem requires ... analysis.     Introduction Computational molecular biology uses computational power to analyze genetic, molecular and biochemical data from multiple biological species in a genome scale. Presently

Normalization of large-scale behavioural data collected from zebrafish

Many contemporary neuroscience experiments utilize high-throughput approaches to simultaneously collect behavioural data from many animals. The resulting data are often complex in structure and are ... same scale for meaningful comparisons between different conditions. In this study, we present a normalization approach for VMR data based on linear-regression modeling. This model-based normalization

Hi-C analysis: from data generation to integration

In the epigenetics field, large-scale functional genomics datasets of ever-increasing size and complexity have been produced using experimental techniques based on high-throughput sequencing. In ... . Hi-C data availability: increasing size and resolution Hi-C data allows examining the genome 3D organization at multiple scales (Rocha et al. 2015; Fraser et al. 2015). On a large scale, the genome is

Machine Learning and Deep Learning frameworks and libraries for large-scale data mining: a survey

The combined impact of new computing resources and techniques with an increasing avalanche of large datasets, is transforming many research areas and may lead to technological breakthroughs that can ... overview of massive parallelism support that is capable of scaling computation effectively and efficiently in the era of Big Data. KeywordsMachine Learning Deep Learning Large-scale data mining Artificial

Scalar asymptotic charges and dual large gauge transformations

asymptotic charges can be understood as canonical generators of large gauge symmetries. Such a symmetry interpretation has been so far missing for scalar soft theorems. We remedy this situation by treating the

Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets

human cell cultures offer alternatives for systematic and large-scale profiling of drug effects on gene expression level, as typically found in the so-called toxicogenomics datasets. However, the ... , Kim J , et al. Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of DrugInduced Toxicity . PLoS One . 2015 ; 10 ( 9

TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences

phenotypic trait. Using simulated data of modular and pleiotropic regulatory elements, we show that TFforge can identify the correct TFs for many different evolutionary scenarios. We applied TFforge to ... between the sequenced species. By utilizing the ever-growing list of TF binding motifs to detect such TFs based on a large-scale binding site decay signature, our approach is complementary to predicting

Molecular and genomic typing for tuberculosis surveillance: A survey study in 26 European countries

integration of molecular and genomic typing data into TB surveillance; ii) Cross-border cluster investigation and international collaboration, and iii) Perception and evaluation of public health benefits of ... TB notification databases. Sixteen of 20 countries integrated the molecular/genomic typing data into the TB notification database on a case-based level. This integration occurred mostly at national

Human H4 tail stimulates HIV-1 integration through binding to the carboxy-terminal domain of integrase

The integration of the retroviral genome into the chromatin of the infected cell is catalysed by the integrase (IN)•viral DNA complex (intasome). This process requires functional association between ... initially refractory compact chromatin (16). Taken together, these data suggest that specific intasome/nucleosome contacts are required for optimal integration and may be regulated by chromatin compaction and

MRCS: matrix recovery-based communication-efficient compressive sampling on temporal-spatial data of dynamic-scale sparsity in large-scale environmental IoT networks

In the past few years, a large variety of IoT applications has been witnessed by fast proliferation of IoT devices (e.g., environment surveillance devices, wearable devices, city-wide NB-IoT devices ... method. 5.1 Recovery quality and robustness study on data with large-scale events As shown in Figs. 1 and 2, the proposed method achieves high recovery quality with large-range event in Figs. 1c and 2c

Logistics of Implementing a Large-scale Typhoid Vaccine Trial in Kathmandu, Nepal

typhoid. TyVAC-Nepal is a large-scale, participant- and observer-blind, individually randomized, controlled trial evaluating the efficacy of a newly developed typhoid conjugate vaccine in an urban setting ... culture–confirmed typhoid fever in the vaccination arm as compared to the control arm. The experience of conducting this large-scale vaccine trial suggests that comprehensive planning, continuous monitoring

Integration of persistent scatterer interferometry and ground data for landslide monitoring: the Pianello landslide (Bovino, Southern Italy)

these sensors during the following years were then compared and integrated with more recent PSI data from a series of Sentinel-1 images, acquired from March 2014 to October 2016. The integration allows ... the synoptic view (large area coverage) and relatively low costs of remotely sensed images (Wasowski and Bovenga 2014). While optical sensors remain the most used kind of data to identify landslide

Large-scale predictive modeling and analytics through regression queries in data management systems

within data management systems (DMS). Linear regression queries are fundamental to exploratory analytics and predictive modeling. However, computing their exact answers leaves a lot to be desired in terms ... statistically efficient are computationally slow and prohibited for large-scale data sets, i.e., the running time for a given data subspace scales at least quadratically with the size of data points n in the

Aerodynamic drag determination of a full-scale cyclist mannequin from large-scale PTV measurements

The aerodynamic drag of a human-scale wind tunnel model is obtained from large-scale particle tracking velocimetry measurements invoking the conservation of momentum in a control volume surrounding ... measurements (Bosbach et al. 2009; Scarano et al. 2015) allowed a dramatic increase in measurement size (square meters and liters for planar and volumetric PIV, respectively), making ‘large-scale’ PIV

Lucid Data Dreaming for Video Object Segmentation

and multiple object segmentation. Instead of using large training sets hoping to generalize across domains, we generate in-domain training data using the provided annotation on the first frame of each ... annotation effort. In this work we aim to reduce the necessity for such large volumes of training data. It is traditionally assumed that convnets require large training sets to perform best. We show that for

Identification of potential blood biomarkers for Parkinson’s disease by gene expression and DNA methylation data integration analysis

′ (CpGs) or all gene regions CpGs in PD. Gene set enrichment analysis was then applied to DEGs and DMGs. Subsequently, data integration analysis was performed to identify robust PD-associated blood ... and specificity need to be improved, and methods for the integration of gene expression with epigenetic data need to be developed in order to make this feasible. Methods Whole blood gene expression

Large data and Bayesian modeling—aging curves of NBA players

Researchers interested in changes that occur as people age are faced with a number of methodological problems, starting with the immense time scale they are trying to capture, which renders ... , once we adjusted the slope for every player in the data, the general slope of the function lost statistical significance. Even though we are not primarily interested in p values and the interpretation of

Characterization of Large Isoperimetric Regions in Asymptotically Hyperbolic Initial Data

characterization result for large isoperimetric regions in the asymptotically hyperbolic setting that does not assume exact rotational symmetry at infinity. ... )MathSciNetCrossRefzbMATHGoogle Scholar 14. Eichmair M., Metzger J.: On large volume preserving stable CMC surfaces in initial data sets. J. Differ. Geom. 91(1), 81–102 (2012)MathSciNetCrossRefzbMATHGoogle Scholar 15. Eichmair

Integrating social values with other value dimensions: parallel use vs. combination vs. full integration

present a framework building on two key factors deciding the integration potential: logical commensurability of values, and technical compatibility of valuation methods. Using this framework, we analyse the ... the literature) of the individual methods, the data they use and the areas where they have been applied. Our examples sketch out potential ways for integration and do not necessarily refer to thorough

InDel markers: An extended marker resource for molecular breeding in chickpea

several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant ... chickpea [ 1, 26, 27 ] has resulted in vast genome information and further paved the way for various large scale resequencing initiatives ([ 28,29 ], unpublished data) making it easy to capture the