Search results for "Throughput"
showing 10 items of 483 documents
How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)
2022
Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coa…
Joint routing and per-flow fairness in wireless multihop networks
2008
In wireless multihop networks communication between two end-nodes is carried out by hopping over multiple short wireless links. Traditional CSMA/CA based media access control does not work satisfactory in a multihop scenario, since an intended target of a communication may be subject to mutual interference imposed by concurrent transmissions from nodes which cannot directly sense each other, causing unfair throughput allocation. Although TDMA seems to be a more promising solution, careful transmission scheduling is needed in order to achieve error-free communication and fairness. In our previous work, a TDMA scheduling algorithm has been proposed that schedules the transmissions in a fair m…
In Search of Pathogens: Transcriptome-Based Identification of Viral Sequences from the Pine Processionary Moth (Thaumetopoea pityocampa)
2015
Thaumetopoea pityocampa (pine processionary moth) is one of the most important pine pests in the forests of Mediterranean countries, Central Europe, the Middle East and North Africa. Apart from causing significant damage to pinewoods, T. pityocampa occurrence is also an issue for public and animal health, as it is responsible for dermatological reactions in humans and animals by contact with its irritating hairs. High throughput sequencing technologies have allowed the fast and cost-effective generation of genetic information of interest to understand different biological aspects of non-model organisms as well as the identification of potential pathogens. Using these technologies, we have o…
Next-generation sequencing: big data meets high performance computing
2017
The progress of next-generation sequencing has a major impact on medical and genomic research. This high-throughput technology can now produce billions of short DNA or RNA fragments in excess of a few terabytes of data in a single run. This leads to massive datasets used by a wide range of applications including personalized cancer treatment and precision medicine. In addition to the hugely increased throughput, the cost of using high-throughput technologies has been dramatically decreasing. A low sequencing cost of around US$1000 per genome has now rendered large population-scale projects feasible. However, to make effective use of the produced data, the design of big data algorithms and t…
Downlink radio resource allocation for coordinated cellular OFDMA networks
2010
Base station coordination is considered as a promising technique to mitigate inter-cell interference and improve the cell-edge performance in cellular orthogonal frequency division multiple-access (OFDMA) networks. The problem to design an efficient radio resource allocation scheme for coordinated cellular OFDMA networks incorporating base station coordination has been only partially investigated. In this contribution, a novel radio resource allocation algorithm with universal frequency reuse is proposed to support base station coordinated transmission. Firstly, with the assumption of global coordination between all base station sectors in the network, a coordinated subchannel assignment al…
Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma
2013
Background Tumor models are critical for our understanding of cancer and the development of cancer therapeutics. Here, we present an integrated map of the genome, transcriptome and immunome of an epithelial mouse tumor, the CT26 colon carcinoma cell line. Results We found that Kras is homozygously mutated at p.G12D, Apc and Tp53 are not mutated, and Cdkn2a is homozygously deleted. Proliferation and stem-cell markers, including Top2a, Birc5 (Survivin), Cldn6 and Mki67, are highly expressed while differentiation and top-crypt markers Muc2, Ms4a8a (MS4A8B) and Epcam are not. Myc, Trp53 (tp53), Mdm2, Hif1a, and Nras are highly expressed while Egfr and Flt1 are not. MHC class I but not MHC class…
Towards Efficient Control of Mobile Network-Enabled UAVs
2019
| openaire: EC/H2020/815191/EU//PriMO-5G The efficient control of mobile network-enabled unmanned aerial vehicles (UAVs) is targeted in this paper. In particular, a downlink scenario is considered, in which control messages are sent to UAVs via cellular base stations (BSs). Unlike terrestrial user equipment (UEs), UAVs perceive a large number of BSs, which can lead to increased interference causing poor or even unacceptable throughput. This paper proposes a framework for efficient control of UAVs. First, a communication model is introduced for flying UAVs taking into account interference, path loss and fast fading. The characteristics of UAVs make such model different compared to traditiona…
Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines
2021
Abstract Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the e…
Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae.
2020
In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain in…
AIOC2: A deep Q-learning approach to autonomic I/O congestion control in Lustre
2021
Abstract In high performance computing systems, I/O congestion is a common problem in large-scale distributed file systems. However, the current implementation mainly requires administrator to manually design low-level implementation and optimization, we proposes an adaptive I/O congestion control framework, named AIOC 2 , which can not only adaptively tune the I/O congestion control parameters, but also exploit the deep Q-learning method to start the training parameters and optimize the tuning for different types of workloads from the server and the client at the same time. AIOC 2 combines the feedback-based dynamic I/O congestion control and deep Q-learning parameter tuning technology to …