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  1. Article ; Online: sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies.

    Miller, Thiago L A / Orpinelli Rego, Fernanda / Buzzo, José Leonel L / Galante, Pedro A F

    Bioinformatics (Oxford, England)

    2020  Volume 37, Issue 3, Page(s) 419–421

    Abstract: Motivation: Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or polymorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) ... ...

    Abstract Motivation: Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These gene duplicates can be fixed, somatically inserted or polymorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and the development of computational tools for effectively identifying and genotyping them is an urgent need.
    Results: Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs in whole-genome or whole-exome sequencing data but also to revealing their insertion sites, zygosity and genomic context and classifying them as somatic or polymorphic events. We show that sideRETRO can identify novel retroCNVs and genotype them, in addition to finding polymorphic retroCNVs in whole-genome and whole-exome data. Therefore, sideRETRO fills a gap in the literature and presents an efficient and straightforward algorithm to accelerate the study of bona fide retroCNVs.
    Availability and implementation: sideRETRO is available at https://github.com/galantelab/sideRETRO.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Base Sequence ; Exome ; Genomics ; Genotype ; Pseudogenes/genetics ; Software
    Language English
    Publishing date 2020-07-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btaa689
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
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  2. Article ; Online: Use of ultraviolet-visible spectrophotometry associated with artificial neural networks as an alternative for determining the water quality index.

    Alves, Edson Marcelino / Rodrigues, Ramon Juliano / Dos Santos Corrêa, Caroline / Fidemann, Tiago / Rocha, José Celso / Buzzo, José Leonel Lemos / de Oliva Neto, Pedro / Núñez, Eutimio Gustavo Fernández

    Environmental monitoring and assessment

    2018  Volume 190, Issue 6, Page(s) 319

    Abstract: The water quality index (WQI) is an important tool for water resource management and planning. However, it has major disadvantages: the generation of chemical waste, is costly, and time-consuming. In order to overcome these drawbacks, we propose to ... ...

    Abstract The water quality index (WQI) is an important tool for water resource management and planning. However, it has major disadvantages: the generation of chemical waste, is costly, and time-consuming. In order to overcome these drawbacks, we propose to simplify this index determination by replacing traditional analytical methods with ultraviolet-visible (UV-Vis) spectrophotometry associated with artificial neural network (ANN). A total of 100 water samples were collected from two rivers located in Assis, SP, Brazil and calculated the WQI by the conventional method. UV-Vis spectral analyses between 190 and 800 nm were also performed for each sample followed by principal component analysis (PCA) aiming to reduce the number of variables. The scores of the principal components were used as input to calibrate a three-layer feed-forward neural network. Output layer was defined by the WQI values. The modeling efforts showed that the optimal ANN architecture was 19-16-1, trainlm as training function, root-mean-square error (RMSE) 0.5813, determination coefficient between observed and predicted values (R
    MeSH term(s) Brazil ; Environmental Monitoring/methods ; Neural Networks (Computer) ; Principal Component Analysis ; Rivers/chemistry ; Spectrophotometry, Ultraviolet ; Ultraviolet Rays ; Water Pollutants, Chemical/analysis ; Water Pollution, Chemical/statistics & numerical data ; Water Quality
    Chemical Substances Water Pollutants, Chemical
    Language English
    Publishing date 2018-05-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 782621-7
    ISSN 1573-2959 ; 0167-6369
    ISSN (online) 1573-2959
    ISSN 0167-6369
    DOI 10.1007/s10661-018-6702-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 5186: Show issues

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  3. Article ; Online: Author Correction: Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil.

    Naslavsky, Michel S / Scliar, Marilia O / Yamamoto, Guilherme L / Wang, Jaqueline Yu Ting / Zverinova, Stepanka / Karp, Tatiana / Nunes, Kelly / Ceroni, José Ricardo Magliocco / de Carvalho, Diego Lima / da Silva Simões, Carlos Eduardo / Bozoklian, Daniel / Nonaka, Ricardo / Dos Santos Brito Silva, Nayane / da Silva Souza, Andreia / de Souza Andrade, Heloísa / Passos, Marília Rodrigues Silva / Castro, Camila Ferreira Bannwart / Mendes-Junior, Celso T / Mercuri, Rafael L V /
    Miller, Thiago L A / Buzzo, Jose Leonel / Rego, Fernanda O / Araújo, Nathalia M / Magalhães, Wagner C S / Mingroni-Netto, Regina Célia / Borda, Victor / Guio, Heinner / Rojas, Carlos P / Sanchez, Cesar / Caceres, Omar / Dean, Michael / Barreto, Mauricio L / Lima-Costa, Maria Fernanda / Horta, Bernardo L / Tarazona-Santos, Eduardo / Meyer, Diogo / Galante, Pedro A F / Guryev, Victor / Castelli, Erick C / Duarte, Yeda A O / Passos-Bueno, Maria Rita / Zatz, Mayana

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 1831

    Language English
    Publishing date 2022-03-30
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-29575-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil.

    Naslavsky, Michel S / Scliar, Marilia O / Yamamoto, Guilherme L / Wang, Jaqueline Yu Ting / Zverinova, Stepanka / Karp, Tatiana / Nunes, Kelly / Ceroni, José Ricardo Magliocco / de Carvalho, Diego Lima / da Silva Simões, Carlos Eduardo / Bozoklian, Daniel / Nonaka, Ricardo / Dos Santos Brito Silva, Nayane / da Silva Souza, Andreia / de Souza Andrade, Heloísa / Passos, Marília Rodrigues Silva / Castro, Camila Ferreira Bannwart / Mendes-Junior, Celso T / Mercuri, Rafael L V /
    Miller, Thiago L A / Buzzo, Jose Leonel / Rego, Fernanda O / Araújo, Nathalia M / Magalhães, Wagner C S / Mingroni-Netto, Regina Célia / Borda, Victor / Guio, Heinner / Rojas, Carlos P / Sanchez, Cesar / Caceres, Omar / Dean, Michael / Barreto, Mauricio L / Lima-Costa, Maria Fernanda / Horta, Bernardo L / Tarazona-Santos, Eduardo / Meyer, Diogo / Galante, Pedro A F / Guryev, Victor / Castelli, Erick C / Duarte, Yeda A O / Passos-Bueno, Maria Rita / Zatz, Mayana

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 1004

    Abstract: As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly ...

    Abstract As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS.
    MeSH term(s) Aged ; Brazil/epidemiology ; Genome, Human/genetics ; Genomics/methods ; Humans ; Metagenomics ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing
    Language English
    Publishing date 2022-03-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-28648-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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