LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 16

Search options

  1. Article ; Online: OSCAA: A two-dimensional Gaussian mixture model for copy number variation association analysis.

    Yu, Xuanxuan / Luo, Xizhi / Cai, Guoshuai / Xiao, Feifei

    Genetic epidemiology

    2024  

    Abstract: Copy number variants (CNVs) are prevalent in the human genome and are found to have a profound effect on genomic organization and human diseases. Discovering disease-associated CNVs is critical for understanding the pathogenesis of diseases and aiding ... ...

    Abstract Copy number variants (CNVs) are prevalent in the human genome and are found to have a profound effect on genomic organization and human diseases. Discovering disease-associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome-wide assessment of such variation. In this article, we developed One-Stage CNV-disease Association Analysis (OSCAA), a flexible algorithm to discover disease-associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the PCs from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signals. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.
    Language English
    Publishing date 2024-03-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 605785-8
    ISSN 1098-2272 ; 0741-0395
    ISSN (online) 1098-2272
    ISSN 0741-0395
    DOI 10.1002/gepi.22558
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1969: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article: OSCAA: A Two-Dimensional Gaussian Mixture Model for Copy Number Variation Association Analysis.

    Yu, Xuanxuan / Luo, Xizhi / Cai, Guoshuai / Xiao, Feifei

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Copy number variants (CNVs) are prevalent in the human genome which provide profound effect on genomic organization and human diseases. Discovering disease associated CNVs is critical for understanding the pathogenesis of diseases and aiding their ... ...

    Abstract Copy number variants (CNVs) are prevalent in the human genome which provide profound effect on genomic organization and human diseases. Discovering disease associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome wide assessment of such variation. In this article, we developed OSCAA, a flexible algorithm to discover disease associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the principal components from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signal. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.
    Language English
    Publishing date 2023-09-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.25.559392
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: PlantRep: a database of plant repetitive elements.

    Luo, Xizhi / Chen, Shiyu / Zhang, Yu

    Plant cell reports

    2022  Volume 41, Issue 4, Page(s) 1163–1166

    Abstract: Key message: We re-annotated repeats of 459 plant genomes and released a new database: PlantRep ( http://www.plantrep.cn/ ). PlantRep sheds lights of repeat evolution and provides fundamental data for deep exploration of genome. ...

    Abstract Key message: We re-annotated repeats of 459 plant genomes and released a new database: PlantRep ( http://www.plantrep.cn/ ). PlantRep sheds lights of repeat evolution and provides fundamental data for deep exploration of genome.
    MeSH term(s) DNA Transposable Elements ; Evolution, Molecular ; Genome, Plant/genetics ; Repetitive Sequences, Nucleic Acid/genetics
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2022-01-03
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 8397-5
    ISSN 1432-203X ; 0721-085X ; 0721-7714
    ISSN (online) 1432-203X
    ISSN 0721-085X ; 0721-7714
    DOI 10.1007/s00299-021-02817-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 85/705: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data.

    Luo, Xizhi / Qin, Fei / Xiao, Feifei / Cai, Guoshuai

    Briefings in bioinformatics

    2022  Volume 23, Issue 6

    Abstract: Gene expression in mammalian cells is inherently stochastic and mRNAs are synthesized in discrete bursts. Single-cell transcriptomics provides an unprecedented opportunity to explore the transcriptome-wide kinetics of transcriptional bursting. However, ... ...

    Abstract Gene expression in mammalian cells is inherently stochastic and mRNAs are synthesized in discrete bursts. Single-cell transcriptomics provides an unprecedented opportunity to explore the transcriptome-wide kinetics of transcriptional bursting. However, current analysis methods provide limited accuracy in bursting inference due to substantial noise inherent to single-cell transcriptomic data. In this study, we developed BISC, a Bayesian method for inferring bursting parameters from single cell transcriptomic data. Based on a beta-gamma-Poisson model, BISC modeled the mean-variance dependency to achieve accurate estimation of bursting parameters from noisy data. Evaluation based on both simulation and real intron sequential RNA fluorescence in situ hybridization data showed improved accuracy and reliability of BISC over existing methods, especially for genes with low expression values. Further application of BISC found bursting frequency but not bursting size was strongly associated with gene expression regulation. Moreover, our analysis provided new mechanistic insights into the functional role of enhancer and superenhancer by modulating both bursting frequency and size. BISC also formulated a downstream framework to identify differential bursting (in frequency and size separately) genes in samples under different conditions. Applying to multiple datasets (a mouse embryonic cell and fibroblast dataset, a human immune cell dataset and a human pancreatic cell dataset), BISC identified known cell-type signature genes that were missed by differential expression analysis, providing additional insights in understanding the cell-specific stochastic gene transcription. Applying to datasets of human lung and colon cancers, BISC successfully detected tumor signature genes based on alterations in bursting kinetics, which illustrates its value in understanding disease development regarding transcriptional bursting. Collectively, BISC provides a new tool for accurately inferring bursting kinetics and detecting differential bursting genes. This study also produced new insights in the role of transcriptional bursting in regulating gene expression, cell identity and tumor progression.
    MeSH term(s) Animals ; Humans ; Mice ; Transcriptome ; In Situ Hybridization, Fluorescence ; Reproducibility of Results ; Bayes Theorem ; Kinetics ; Neoplasms ; Transcription, Genetic ; Mammals/genetics
    Language English
    Publishing date 2022-11-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbac464
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6262: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article: PlantRep: a database of plant repetitive elements

    Luo, Xizhi / Chen, Shiyu / Zhang, Yu

    Plant cell reports. 2022 Apr., v. 41, no. 4

    2022  

    Abstract: KEY MESSAGE: We re-annotated repeats of 459 plant genomes and released a new database: PlantRep (http://www.plantrep.cn/). PlantRep sheds lights of repeat evolution and provides fundamental data for deep exploration of genome. ...

    Abstract KEY MESSAGE: We re-annotated repeats of 459 plant genomes and released a new database: PlantRep (http://www.plantrep.cn/). PlantRep sheds lights of repeat evolution and provides fundamental data for deep exploration of genome.
    Keywords databases ; evolution ; genome
    Language English
    Dates of publication 2022-04
    Size p. 1163-1166.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ZDB-ID 8397-5
    ISSN 1432-203X ; 0721-085X ; 0721-7714
    ISSN (online) 1432-203X
    ISSN 0721-085X ; 0721-7714
    DOI 10.1007/s00299-021-02817-y
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 85/705: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: SCRIP: an accurate simulator for single-cell RNA sequencing data.

    Qin, Fei / Luo, Xizhi / Xiao, Feifei / Cai, Guoshuai

    Bioinformatics (Oxford, England)

    2021  

    Abstract: Motivation: Recent advancements in single-cell RNA sequencing (scRNA-seq) have enabled time-efficient transcriptome profiling in individual cells. To optimize sequencing protocols and develop reliable analysis methods for various application scenarios, ... ...

    Abstract Motivation: Recent advancements in single-cell RNA sequencing (scRNA-seq) have enabled time-efficient transcriptome profiling in individual cells. To optimize sequencing protocols and develop reliable analysis methods for various application scenarios, solid simulation methods for scRNA-seq data are required. However, due to the noisy nature of scRNA-seq data, currently available simulation methods cannot sufficiently capture and simulate important properties of real data, especially the biological variation. In this study, we developed SCRIP, a novel simulator for scRNA-seq that is accurate and enables simulation of bursting kinetics.
    Results: Compared to existing simulators, SCRIP showed a significantly higher accuracy of stimulating key data features, including mean-variance dependency in all experiments. SCRIP also outperformed other methods in recovering cell-cell distances. The application of SCRIP in evaluating differential expression analysis methods showed that edgeR outperformed other examined methods in differential expression analyses, and ZINB-WaVE improved the AUC at high dropout rates. Collectively, this study provides the research community with a rigorous tool for scRNA-seq data simulation.
    Availability and implementation: https://CRAN.R-project.org/package=SCRIP.
    Supplementary information: Supplementary files are available at Bioinformatics online.
    Language English
    Publishing date 2021-12-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btab824
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article ; Online: Shall genomic correlation structure be considered in copy number variants detection?

    Qin, Fei / Luo, Xizhi / Cai, Guoshuai / Xiao, Feifei

    Briefings in bioinformatics

    2021  Volume 22, Issue 6

    Abstract: Copy number variation has been identified as a major source of genomic variation associated with disease susceptibility. With the advent of whole-exome sequencing (WES) technology, massive WES data have been generated, allowing for the identification of ... ...

    Abstract Copy number variation has been identified as a major source of genomic variation associated with disease susceptibility. With the advent of whole-exome sequencing (WES) technology, massive WES data have been generated, allowing for the identification of copy number variants (CNVs) in the protein-coding regions with direct functional interpretation. We have previously shown evidence of the genomic correlation structure in array data and developed a novel chromosomal breakpoint detection algorithm, LDcnv, which showed significantly improved detection power through integrating the correlation structure in a systematic modeling manner. However, it remains unexplored whether the genomic correlation exists in WES data and how such correlation structure integration can improve the CNV detection accuracy. In this study, we first explored the correlation structure of the WES data using the 1000 Genomes Project data. Both real raw read depth and median-normalized data showed strong evidence of the correlation structure. Motivated by this fact, we proposed a correlation-based method, CORRseq, as a novel release of the LDcnv algorithm in profiling WES data. The performance of CORRseq was evaluated in extensive simulation studies and real data analysis from the 1000 Genomes Project. CORRseq outperformed the existing methods in detecting medium and large CNVs. In conclusion, it would be more advantageous to model genomic correlation structure in detecting relatively long CNVs. This study provides great insights for methodology development of CNV detection with NGS data.
    MeSH term(s) Algorithms ; Computational Biology/methods ; DNA Copy Number Variations ; Genetic Association Studies/methods ; Genetic Predisposition to Disease ; Genetic Testing/methods ; Genomics/methods ; Humans ; Software ; Whole Exome Sequencing ; Workflow
    Language English
    Publishing date 2021-04-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbab215
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6262: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: Integrating genomic correlation structure improves copy number variations detection.

    Luo, Xizhi / Qin, Fei / Cai, Guoshuai / Xiao, Feifei

    Bioinformatics (Oxford, England)

    2020  Volume 37, Issue 3, Page(s) 312–317

    Abstract: Motivation: Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as ... ...

    Abstract Motivation: Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e. boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions, such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs, which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic dependence structure (i.e. LD).
    Results: We theoretically demonstrated the correlation structure of CNV data in SNP array, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. Therefore, we developed the LDcnv that integrated the genomic correlation structure with a local search strategy into statistical modeling of the CNV intensities. To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presented high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. This new segmentation algorithm has a wide scope of potential application with data from various high-throughput technology platforms.
    Availability and implementation: https://github.com/FeifeiXiaoUSC/LDcnv.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Algorithms ; DNA Copy Number Variations ; Genome, Human ; Genomics ; Humans ; Models, Statistical ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2020-08-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btaa737
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: Empirical study with structural break on the relationship between financial development and economic growth of Jiangxi province

    Jiang Xinxi / Luo Xizhi

    SHS Web of Conferences, Vol 25, p

    2016  Volume 02020

    Abstract: The empirical study over the period 1978-2011 found that the relationship between real per capita GDP and financial interrelation ratio structurally broke since 2004. From 1978 to 2003, economic growth and financial development had a long-term co- ... ...

    Abstract The empirical study over the period 1978-2011 found that the relationship between real per capita GDP and financial interrelation ratio structurally broke since 2004. From 1978 to 2003, economic growth and financial development had a long-term co-integration, and it showed one-way supply relationship according to the Granger causality test, which means the economic growth have a slowly leading function to the development of finance. From 2004 to 2011, the correlation between them became weaker and had no Granger causality, but there had a long-term co-integration and mutual causality relationship existed between loan and GDP during the whole period. From it we can see loan could boost output more persistently. Therefore, the enhanced economic power of Jiangxi province could promote further development of regional financial service industries, and we would propose some related policy suggestions in this paper.
    Keywords financial development ; economic growth ; structural break ; Jiangxi province ; Social Sciences ; H
    Subject code 339
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  10. Article ; Online: BMI-CNV: a Bayesian framework for multiple genotyping platforms detection of copy number variants.

    Luo, Xizhi / Cai, Guoshuai / Mclain, Alexander C / Amos, Christopher I / Cai, Bo / Xiao, Feifei

    Genetics

    2022  Volume 222, Issue 4

    Abstract: Whole-exome sequencing (WES) enables the detection of copy number variants (CNVs) with high resolution in protein-coding regions. However, variants in the intergenic or intragenic regions are excluded from studies. Fortunately, many of these samples have ...

    Abstract Whole-exome sequencing (WES) enables the detection of copy number variants (CNVs) with high resolution in protein-coding regions. However, variants in the intergenic or intragenic regions are excluded from studies. Fortunately, many of these samples have been previously sequenced by other genotyping platforms which are sparse but cover a wide range of genomic regions, such as SNP array. Moreover, conventional single sample-based methods suffer from a high false discovery rate due to prominent data noise. Therefore, methods for integrating multiple genotyping platforms and multiple samples are highly demanded for improved copy number variant detection. We developed BMI-CNV, a Bayesian Multisample and Integrative CNV (BMI-CNV) profiling method with data sequenced by both whole-exome sequencing and microarray. For the multisample integration, we identify the shared copy number variants regions across samples using a Bayesian probit stick-breaking process model coupled with a Gaussian Mixture model estimation. With extensive simulations, BMI-copy number variant outperformed existing methods with improved accuracy. In the matched data from the 1000 Genomes Project and HapMap project data, BMI-CNV also accurately detected common variants and significantly enlarged the detection spectrum of whole-exome sequencing. Further application to the data from The Research of International Cancer of Lung consortium (TRICL) identified lung cancer risk variant candidates in 17q11.2, 1p36.12, 8q23.1, and 5q22.2 regions.
    MeSH term(s) DNA Copy Number Variations ; Genotype ; Bayes Theorem ; Body Mass Index ; HapMap Project
    Language English
    Publishing date 2022-09-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1093/genetics/iyac147
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.B 767: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top