当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > EnSVMB: Metagenomics Fragments Classification using Ensemble SVM and BLAST.

EnSVMB: Metagenomics Fragments Classification using Ensemble SVM and BLAST.

Abstract：

:Metagenomics brings in new discoveries and insights into the uncultured microbial world. One fundamental task in metagenomics analysis is to determine the taxonomy of raw sequence fragments. Modern sequencing technologies produce relatively short fragments and greatly increase the number of fragments, and thus make the taxonomic classification considerably more difficult than before. Therefore, fast and accurate techniques are called to classify large-scale fragments. We propose EnSVM (Ensemble Support Vector Machine) and its advanced method called EnSVMB (EnSVM with BLAST) to accurately classify fragments. EnSVM divides fragments into a large confident (or small diffident) set, based on whether the fragments get consistent (or inconsistent) predictions from linear SVMs trained with different k-mers. Empirical study shows that sensitivity and specificity of EnSVM on confident set are higher than 90% and 97%, but on diffident set are lower than 60% and 75%. To further improve the performance on diffident set, EnSVMB takes advantage of best hits of BLAST to reclassify fragments in that set. Experimental results show EnSVM can efficiently and effectively divide fragments into confident and diffident sets, and EnSVMB achieves higher accuracy, sensitivity and more true positives than related state-of-the-art methods and holds comparable specificity with the best of them.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Jiang Y,Wang J,Xia D,Yu G

doi

10.1038/s41598-017-09947-y

subject

Has Abstract

pub_date

2017-08-25 00:00:00

pages

9440

issue

1

issn

2045-2322

pii

10.1038/s41598-017-09947-y

journal_volume

7

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • Efficient production of adenovirus vector lacking genes of virus-associated RNAs that disturb cellular RNAi machinery.

    abstract：:First-generation adenovirus vectors (FG AdVs) are widely used in basic studies and gene therapy. However, virus-associated (VA) RNAs that act as small-interference RNAs are indeed transcribed from the vector genome. These VA RNAs can trigger the innate immune response. Moreover, VA RNAs are processed to functional vir...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep01136

    authors： Maekawa A,Pei Z,Suzuki M,Fukuda H,Ono Y,Kondo S,Saito I,Kanegae Y

    更新日期：2013-01-01 00:00:00

  • Chaotic optical power dropouts driven by low frequency bias forcing in a mid-infrared quantum cascade laser.

    abstract：:Mid-infrared quantum cascade lasers operating under external optical feedback and external periodic bias forcing are shown to exhibit a deterministic chaotic pattern composed of frequencies which are linked to the one of the forcing. Results also show that both the amplitude and the frequency of the forcing play a key...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-40861-7

    authors： Spitz O,Wu J,Carras M,Wong CW,Grillot F

    更新日期：2019-03-14 00:00:00

  • Statistical modeling and optimization of heterogeneous Fenton-like removal of organic pollutant using fibrous catalysts: a full factorial design.

    abstract：:This work focuses on the optimization of heterogeneous Fenton-like removal of organic pollutant (dye) from water using newly developed fibrous catalysts based on a full factorial experimental design. This study aims to approximate the feasibility of heterogeneous Fenton-like removal process and optionally make predict...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-72401-z

    authors： Morshed MN,Pervez MN,Behary N,Bouazizi N,Guan J,Nierstrasz VA

    更新日期：2020-09-30 00:00:00

  • Significantly enhanced creep resistance of low volume fraction in-situ TiBw/Ti6Al4V composites by architectured network reinforcements.

    abstract：:We present a new class of TiBw/Ti6Al4V composites with a network reinforcement architecture that exhibits a significant creep resistance compared to monolithic Ti6Al4V alloys. Creep tests performed at temperatures between 773 K and 923 K and stress range of 100 MPa-300 MPa indicate both a significant improvement of th...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep40823

    authors： Wang S,Huang LJ,Geng L,Scarpa F,Jiao Y,Peng HX

    更新日期：2017-01-17 00:00:00

  • Few-cycle Regime Atomic Force Microscopy.

    abstract：:Traditionally, dynamic atomic force microscopy (AFM) techniques are based on the analysis of the quasi-steady state response of the cantilever deflection in terms of Fourier analysis. Here we describe a technique that instead exploits the often disregarded transient response of the cantilever through a relatively mode...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-49104-1

    authors： López-Guerra EA,Somnath S,Solares SD,Jesse S,Ferrini G

    更新日期：2019-09-03 00:00:00

  • Nanofibrous asymmetric collagen/curcumin membrane containing aspirin-loaded PLGA nanoparticles for guided bone regeneration.

    abstract：:The goal of the current study was to develop an asymmetric guided bone regeneration (GBR) membrane benefiting from curcumin and aspirin. The membrane was prepared using electrospinning technique and then was physic-chemically characterized by the conventional methods. The release profile of aspirin from the prepared m...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-75454-2

    authors： Ghavimi MA,Bani Shahabadi A,Jarolmasjed S,Memar MY,Maleki Dizaj S,Sharifi S

    更新日期：2020-10-23 00:00:00

  • Determinants of PCR performance (Xpert MTB/RIF), including bacterial load and inhibition, for TB diagnosis using specimens from different body compartments.

    abstract：:The determinants of Xpert MTB/RIF sensitivity, a widely used PCR test for the diagnosis of tuberculosis (TB) are poorly understood. We compared culture time-to-positivity (TTP; a surrogate of bacterial load), MTB/RIF TB-specific and internal positive control (IPC)-specific C(T) values, and clinical characteristics in ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep05658

    authors： Theron G,Peter J,Calligaro G,Meldau R,Hanrahan C,Khalfey H,Matinyenya B,Muchinga T,Smith L,Pandie S,Lenders L,Patel V,Mayosi BM,Dheda K

    更新日期：2014-07-11 00:00:00

  • Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity.

    abstract：:The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Fl...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep41906

    authors： Kuhn BM,Nodzyński T,Errafi S,Bucher R,Gupta S,Aryal B,Dobrev P,Bigler L,Geisler M,Zažímalová E,Friml J,Ringli C

    更新日期：2017-02-06 00:00:00

  • Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas.

    abstract：:The fungal microbiota is an important component of the human gut microbiome and may be linked to gastrointestinal disease. In this study, the fungal microbiota of biopsy samples from adenomas and adjacent tissues was characterized by deep sequencing. Ascomycota, Glomeromycota and Basidiomycota were identified as the d...

    journal_title：Scientific reports

    pub_type： 临床试验,杂志文章

    doi：10.1038/srep07980

    authors： Luan C,Xie L,Yang X,Miao H,Lv N,Zhang R,Xiao X,Hu Y,Liu Y,Wu N,Zhu Y,Zhu B

    更新日期：2015-01-23 00:00:00

  • Investigation on energy bandgap states of amorphous SiZnSnO thin films.

    abstract：:The variation in energy bandgaps of amorphous oxide semiconducting SiZnSnO (a-SZTO) has been investigated by controlling the oxygen partial pressure (Op). The systematic change in Op during deposition has been used to control the electrical characteristics and energy bandgap of a-SZTO. As Op increased, the electrical ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-55807-2

    authors： Lee BH,Cho KS,Lee DY,Sohn A,Lee JY,Choo H,Park S,Kim SW,Kim S,Lee SY

    更新日期：2019-12-17 00:00:00

  • Silencing of Glutathione S-Transferase Pi Inhibits Cancer Cell Growth via Oxidative Stress Induced by Mitochondria Dysfunction.

    abstract：:Antitumor drug development based on the concept of intervening in the antioxidant system of cancer cells has been gaining increased interest. In this study, we propose a promising strategy for cancer treatment using modulation of oxidative stress by suppression of glutathione S-transferases (GSTs), a typical antioxida...

    journal_title：Scientific reports

    pub_type： 杂志文章,收录出版

    doi：10.1038/s41598-019-51462-9

    authors： Fujitani N,Yoneda A,Takahashi M,Takasawa A,Aoyama T,Miyazaki T

    更新日期：2019-10-14 00:00:00

  • Emission of direct-gap band in germanium with Ge-GeSn layers on one-dimensional structure.

    abstract：:In our experiment, it was observed that the emission of direct-gap band in germanium with Ge-GeSn layers on one-dimensional (1D) structure. The results of experiment and calculation demonstrate that the uniaxial tensile strain in the (111) and (110) direction can efficiently transform Ge to a direct bandgap material w...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep24802

    authors： Huang ZM,Huang WQ,Liu SR,Dong TG,Wang G,Wu XK,Qin CJ

    更新日期：2016-04-21 00:00:00

  • NOTCH2 participates in Jagged1-induced osteogenic differentiation in human periodontal ligament cells.

    abstract：:Jagged1 activates Notch signaling and subsequently promotes osteogenic differentiation in human periodontal ligament cells (hPDLs). The present study investigated the participation of the Notch receptor, NOTCH2, in the Jagged1-induced osteogenic differentiation in hPDLs. NOTCH2 and NOTCH4 mRNA expression levels increa...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-70277-7

    authors： Manokawinchoke J,Sumrejkanchanakij P,Boonprakong L,Pavasant P,Egusa H,Osathanon T

    更新日期：2020-08-07 00:00:00

  • A prediction model of outcome of SARS-CoV-2 pneumonia based on laboratory findings.

    abstract：:The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in thousands of deaths in the world. Information about prediction model of prognosis of SARS-CoV-2 infection is scarce. We used machine learning for processing laboratory findings of 110 patients with SARS-CoV-2 pneumonia (including 51 non-s...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-71114-7

    authors： Wu G,Zhou S,Wang Y,Lv W,Wang S,Wang T,Li X

    更新日期：2020-08-20 00:00:00

  • Health-related quality of life amongst people diagnosed with abdominal aortic aneurysm and peripheral artery disease and the effect of fenofibrate.

    abstract：:The aims of this study were, firstly, to assess the effect of concurrent peripheral artery disease (PAD) on the health-related quality of life (QOL) of people diagnosed with a small abdominal aortic aneurysm (AAA); and secondly, to test whether the peroxisome proliferator-activated receptor α agonist fenofibrate impro...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-71454-4

    authors： Golledge J,Pinchbeck J,Rowbotham SE,Yip L,Jenkins JS,Quigley F,Moxon JV

    更新日期：2020-09-03 00:00:00

  • Hyperlipidemia and hepatitis in liver-specific CREB3L3 knockout mice generated using a one-step CRISPR/Cas9 system.

    abstract：:cAMP responsive element binding protein 3-like 3 (CREB3L3), a transcription factor expressed in the liver and small intestine, governs fasting-response energy homeostasis. Tissue-specific CREB3L3 knockout mice have not been generated till date. To our knowledge, this is the first study using the one-step CRISPR/Cas9 s...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep27857

    authors： Nakagawa Y,Oikawa F,Mizuno S,Ohno H,Yagishita Y,Satoh A,Osaki Y,Takei K,Kikuchi T,Han SI,Matsuzaka T,Iwasaki H,Kobayashi K,Yatoh S,Yahagi N,Isaka M,Suzuki H,Sone H,Takahashi S,Yamada N,Shimano H

    更新日期：2016-06-13 00:00:00

  • DXA reference values and anthropometric screening for visceral obesity in Western Australian adults.

    abstract：:Limited reference values exist for visceral adipose tissue (VAT) mass measured by DXA. The objectives of this study were to provide reference values for DXA-derived VAT mass and compare the association with anthropometry measures. The study cohort comprised 677 men and 738 women aged 18-65 years from Western Australia...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-73631-x

    authors： Staynor JMD,Smith MK,Donnelly CJ,Sallam AE,Ackland TR

    更新日期：2020-10-30 00:00:00

  • Carotenoid metabolite and transcriptome dynamics underlying flower color in marigold (Tagetes erecta L.).

    abstract：:Marigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of flower colors. Despite its economic value, few biochemical and molecular studies have explored the generation of flower color in this species. To study the mechanism underlying marigold petal color, we performed a metabolite analysis ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-73859-7

    authors： Zhang H,Zhang S,Zhang H,Chen X,Liang F,Qin H,Zhang Y,Cong R,Xin H,Zhang Z

    更新日期：2020-10-08 00:00:00

  • Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three-Dimensional Biologically Relevant Spectrum (BRS-3D).

    abstract：:Adenosine receptors (ARs) are potential therapeutic targets for Parkinson's disease, diabetes, pain, stroke and cancers. Prediction of subtype selectivity is therefore important from both therapeutic and mechanistic perspectives. In this paper, we introduced a shape similarity profile as molecular descriptor, namely t...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep36595

    authors： He SB,Ben Hu,Kuang ZK,Wang D,Kong DX

    更新日期：2016-11-04 00:00:00

  • Linoleic and palmitoleic acid block streptokinase-mediated plasminogen activation and reduce severity of invasive group A streptococcal infection.

    abstract：:In contrast to mild infections of Group A Streptococcus (GAS) invasive infections of GAS still pose a serious health hazard: GAS disseminates from sterile sites into the blood stream or deep tissues and causes sepsis or necrotizing fasciitis. In this case antibiotics do not provide an effective cure as the bacteria ar...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-11276-z

    authors： Rox K,Jansen R,Loof TG,Gillen CM,Bernecker S,Walker MJ,Chhatwal GS,Müller R

    更新日期：2017-09-18 00:00:00

  • Controlling Light Transmission Through Highly Scattering Media Using Semi-Definite Programming as a Phase Retrieval Computation Method.

    abstract：:Complex Semi-Definite Programming (SDP) is introduced as a novel approach to phase retrieval enabled control of monochromatic light transmission through highly scattering media. In a simple optical setup, a spatial light modulator is used to generate a random sequence of phase-modulated wavefronts, and the resulting i...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-02716-x

    authors： N'Gom M,Lien MB,Estakhri NM,Norris TB,Michielssen E,Nadakuditi RR

    更新日期：2017-05-31 00:00:00

  • Common variants of ARID1A and KAT2B are associated with obesity in Indian adolescents.

    abstract：:Obesity involves alterations in transcriptional programs that can change in response to genetic and environmental signals through chromatin modifications. Since chromatin modifications involve different biochemical, neurological and molecular signaling pathways related to energy homeostasis, we hypothesize that geneti...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-22231-x

    authors： Giri AK,Parekatt V,Dwivedi OP,Banerjee P,Bandesh K,Prasad G,Tandon N,Bharadwaj D

    更新日期：2018-03-02 00:00:00

  • Three-party quantum private computation of cardinalities of set intersection and union based on GHZ states.

    abstract：:Private Set Intersection Cardinality (PSI-CA) and Private Set Union Cardinality (PSU-CA) are two cryptographic primitives whereby two or more parties are able to obtain the cardinalities of the intersection and the union of their respective private sets, and the privacy of their sets is preserved. In this paper, we pr...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-77579-w

    authors： Zhang C,Long Y,Sun Z,Li Q,Huang Q

    更新日期：2020-12-17 00:00:00

  • Helicobacter pylori chemoreceptor TlpC mediates chemotaxis to lactate.

    abstract：:It is recently appreciated that many bacterial chemoreceptors have ligand-binding domains (LBD) of the dCACHE family, a structure with two PAS-like subdomains, one membrane-proximal and the other membrane-distal. Previous studies had implicated only the membrane-distal subdomain in ligand recognition. Here, we report ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-14372-2

    authors： Machuca MA,Johnson KS,Liu YC,Steer DL,Ottemann KM,Roujeinikova A

    更新日期：2017-10-26 00:00:00

  • Comprehensive multivariate correlations between climatic effect, metabolite-profile, antioxidant capacity and antibacterial activity of Brazilian red propolis metabolites during seasonal study.

    abstract：:The standardization of apiceutical products like as propolis extracts has been widely debated worldwide and variations in the propolis chemical composition are still very relevant topics for use-standardized of different propolis-type as medication by much of the world's population. The present manuscript discuss impo...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-54591-3

    authors： do Nascimento TG,Dos Santos Arruda RE,da Cruz Almeida ET,Dos Santos Oliveira JM,Basílio-Júnior ID,Celerino de Moraes Porto IC,Rodrigues Sabino A,Tonholo J,Gray A,Ebel RE,Clements C,Zhang T,Watson DG

    更新日期：2019-12-04 00:00:00

  • Coordinated cell motility is regulated by a combination of LKB1 farnesylation and kinase activity.

    abstract：:Cell motility requires the precise coordination of cell polarization, lamellipodia formation, adhesion, and force generation. LKB1 is a multi-functional serine/threonine kinase that associates with actin at the cellular leading edge of motile cells and suppresses FAK. We sought to understand how LKB1 coordinates these...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep40929

    authors： Wilkinson S,Hou Y,Zoine JT,Saltz J,Zhang C,Chen Z,Cooper LA,Marcus AI

    更新日期：2017-01-19 00:00:00

  • Emotional arousal modulates oscillatory correlates of targeted memory reactivation during NREM, but not REM sleep.

    abstract：:Rapid eye movement (REM) sleep is considered to preferentially reprocess emotionally arousing memories. We tested this hypothesis by cueing emotional vs. neutral memories during REM and NREM sleep and wakefulness by presenting associated verbal memory cues after learning. Here we show that cueing during NREM sleep sig...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep39229

    authors： Lehmann M,Schreiner T,Seifritz E,Rasch B

    更新日期：2016-12-16 00:00:00

  • Marine alkaloid monanchoxymycalin C: a new specific activator of JNK1/2 kinase with anticancer properties.

    abstract：:Monanchoxymycalin C (MomC) is a new marine pentacyclic guanidine alkaloid, recently isolated from marine sponge Monanchora pulchra by us. Here, anticancer activity and mechanism of action was investigated for the first time using a human prostate cancer (PCa) model. MomC was active in all PCa cell lines at low micromo...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-69751-z

    authors： Dyshlovoy SA,Kaune M,Kriegs M,Hauschild J,Busenbender T,Shubina LK,Makarieva TN,Hoffer K,Bokemeyer C,Graefen M,Stonik VA,von Amsberg G

    更新日期：2020-08-06 00:00:00

  • Author Correction: Temperature dependence of protein-water interactions in a gated yeast aquaporin.

    abstract：:A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper. ...

    journal_title：Scientific reports

    pub_type： 杂志文章,已发布勘误

    doi：10.1038/s41598-017-17040-7

    authors： Aponte-Santamaría C,Fischer G,Båth P,Neutze R,de Groot BL

    更新日期：2017-12-05 00:00:00

  • Recovering metals from aqueous solutions by biosorption onto phosphorylated dry baker's yeast.

    abstract：:Biosorption is a cost-effective and simple technique for removing heavy metals and rare earth elements from aqueous solution. Here, metals were recovered from aqueous solutions using phosphorylated dry baker's yeast cells. The cells were phosphorylated using cyclo-triphosphate, Na3P3O9. The total P content of the phos...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-36306-2

    authors： Ojima Y,Kosako S,Kihara M,Miyoshi N,Igarashi K,Azuma M

    更新日期：2019-01-18 00:00:00