Search results for " Mapping"

Long read alignment based on maximal exact match seeds

2012

Abstract Motivation: The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger. Results: We present CUSHAW2, a parallelized, accurate, and memory-efficient long read aligner. Our aligner is based on the seed-and-extend approach and uses maximal exact matches as seeds to find gapped alignments. We have evaluated and compared CUSHAW2 to the three other long read aligners BWA-SW, Bowtie2 an…

Basic networks: Definition and applications

2009

7 pages, 4 figures, 1 table.-- PMID: 19490867 [PubMed]

An extended continuous mapping theorem for outer almost sure weak convergence

2019

International audience; We prove an extended continuous mapping theorem for outer almost sure weak convergence in a metric space, a notion that is used in bootstrap empirical processes theory. Then we make use of those results to establish the consistency of several bootstrap procedures in empirical likelihood theory for functional parameters.

Spatio-temporal small area surveillance of the COVID-19 pandemic

2022

Abstract The emergence of COVID-19 requires new effective tools for epidemiological surveillance. Spatio-temporal disease mapping models, which allow dealing with small units of analysis, are a priority in this context. These models provide geographically detailed and temporally updated overviews of the current state of the pandemic, making public health interventions more effective. These models also allow estimating epidemiological indicators highly demanded for COVID-19 surveillance, such as the instantaneous reproduction number R t , even for small areas. In this paper, we propose a new spatio-temporal spline model particularly suited for COVID-19 surveillance, which allows estimating a…

Flexible strategic planning of transport systems

2012

Abstract This paper presents a decision support methodology for long-range planning of transport systems that exhibits strategic flexibility and stochastic system parameters. Unlike one-off strategic decisions, flexible decisions should be dynamically reformulated with time. The proposed methodology is based on the construction of a tree structure of multiple interlinked tactical planning problems, each associated with a scenario in the tree, where problems under scenarios at intermediate dates incorporate in their formulation the solution of the corresponding problems associated with past (future) connected scenarios. The resulting tree structure of interconnected planning decisions become…

Protein-membrane interaction probed by single plasmonic nanoparticles.

2008

We present a nanosized and addressable sensor platform based on membrane coated plasmonic particles and show unequivocally the covering with lipid bilayers as well as the subsequent detection of streptavidin binding to biotinylated lipids. The binding is detected on membrane covered gold nanorods by monitoring the spectral shift by fast single particle spectroscopy (fastSPS) on many particles in parallel. Our approach allows for local analysis of protein interaction with biological membranes as a function of the lateral composition of phase separated membranes.

Molecular cloning and nucleotide sequence of chicken avidin-related genes 1-5.

1994

Using avidin cDNA as a hybridisation probe, we detected a gene family whose putative products are related to the chicken egg-white avidin. Two overlapping genomic clones were found to contain five genes (avidin-related genes 1–5, avrl-avr5), which have been cloned, characterized and sequenced. All of the genes have a four-exon structure with an overall identity with the avidin cDNA of 88–92%. The genes appear to have no pseudogenic features and, in fact, two of these genes have been shown to be transcribed. The putative proteins share a sequence identity of 68–78% with avidin. The amino acid residues responsible for the biotin-binding activity of avidin and the bacterial biotin-binding prot…

A course of coordinated sciences: The structure of matter

1976

Machine learning for a combined electroencephalographic anesthesia index to detect awareness under anesthesia

2020

Spontaneous electroencephalogram (EEG) and auditory evoked potentials (AEP) have been suggested to monitor the level of consciousness during anesthesia. As both signals reflect different neuronal pathways, a combination of parameters from both signals may provide broader information about the brain status during anesthesia. Appropriate parameter selection and combination to a single index is crucial to take advantage of this potential. The field of machine learning offers algorithms for both parameter selection and combination. In this study, several established machine learning approaches including a method for the selection of suitable signal parameters and classification algorithms are a…

HD-RTI: an adaptive multi-light imaging approach for the quality assessment of manufactured surfaces

2021

International audience; Reflectance Transformation Imaging (RTI) is a technique for estimating surface local angular reflectance from a set of stereo-photometric images captured with variable lighting directions. The digitization of this information fully fits into the industry 4.0 approach and makes it possible to characterize the visual properties of a surface. The proposed method, namely HD-RTI, is based on the coupling of RTI and HDR imaging techniques. This coupling is carried out adaptively according to the response at each angle of illumination. The proposed method is applied to five industrial samples which have high local variations of reflectivity because of their heterogeneity of…