LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 13

Search options

  1. Article ; Online: Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser.

    Li, Daofeng / Harrison, Jessica K / Purushotham, Deepak / Wang, Ting

    Nature methods

    2022  Volume 19, Issue 8, Page(s) 909–910

    MeSH term(s) Chromatin/genetics ; Epigenome ; Genome ; Genomics ; Software
    Chemical Substances Chromatin
    Language English
    Publishing date 2022-07-21
    Publishing country United States
    Document type Letter ; Research Support, N.I.H., Extramural
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01550-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6022: 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.

  2. Article ; Online: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.

    Zhuo, Xiaoyu / Hsu, Silas / Purushotham, Deepak / Kuntala, Prashant Kumar / Harrison, Jessica K / Du, Alan Y / Chen, Samuel / Li, Daofeng / Wang, Ting

    Genome research

    2023  Volume 33, Issue 5, Page(s) 824–835

    Abstract: Genome browsers have become an intuitive and critical tool to visualize and analyze genomic features and data. Conventional genome browsers display data/annotations on a single reference genome/assembly; there are also genomic alignment viewer/browsers ... ...

    Abstract Genome browsers have become an intuitive and critical tool to visualize and analyze genomic features and data. Conventional genome browsers display data/annotations on a single reference genome/assembly; there are also genomic alignment viewer/browsers that help users visualize alignment, mismatch, and rearrangement between syntenic regions. However, there is a growing need for a comparative epigenome browser that can display genomic and epigenomic data sets across different species and enable users to compare them between syntenic regions. Here, we present the WashU Comparative Epigenome Browser. It allows users to load functional genomic data sets/annotations mapped to different genomes and display them over syntenic regions simultaneously. The browser also displays genetic differences between the genomes from single-nucleotide variants (SNVs) to structural variants (SVs) to visualize the association between epigenomic differences and genetic differences. Instead of anchoring all data sets to the reference genome coordinates, it creates independent coordinates of different genome assemblies to faithfully present features and data mapped to different genomes. It uses a simple, intuitive genome-align track to illustrate the syntenic relationship between different species. It extends the widely used WashU Epigenome Browser infrastructure and can be expanded to support multiple species. This new browser function will greatly facilitate comparative genomic/epigenomic research, as well as support the recent growing needs to directly compare and benchmark the T2T CHM13 assembly and other human genome assemblies.
    MeSH term(s) Humans ; Epigenomics ; Epigenome ; Software ; Genomics ; Genome, Human ; Databases, Genetic ; Internet
    Language English
    Publishing date 2023-05-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.277550.122
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3729: 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)
    Zs.MG 8: 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.

  3. Article ; Online: The qBED track: a novel genome browser visualization for point processes.

    Moudgil, Arnav / Li, Daofeng / Hsu, Silas / Purushotham, Deepak / Wang, Ting / Mitra, Robi D

    Bioinformatics (Oxford, England)

    2020  Volume 37, Issue 8, Page(s) 1168–1170

    Abstract: Summary: Transposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here, we describe the qBED format, an open, text-based standard for encoding and analyzing calling card ... ...

    Abstract Summary: Transposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here, we describe the qBED format, an open, text-based standard for encoding and analyzing calling card data. In parallel, we introduce the qBED track on the WashU Epigenome Browser, a novel visualization that enables researchers to inspect calling card data in their genomic context. Finally, through examples, we demonstrate that qBED files can be used to visualize non-calling card datasets, such as Combined Annotation-Dependent Depletion scores and GWAS/eQTL hits, and thus may have broad utility to the genomics community.
    Availability and implementation: The qBED track is available on the WashU Epigenome Browser (http://epigenomegateway.wustl.edu/browser), beginning with version 46. Source code for the WashU Epigenome Browser with qBED support is available on GitHub (http://github.com/arnavm/eg-react and http://github.com/lidaof/eg-react). A complete definition of the qBED format is available as part of the WashU Epigenome Browser documentation (https://eg.readthedocs.io/en/latest/tracks.html#qbed-track). We have also released a tutorial on how to upload qBED data to the browser (http://dx.doi.org/10.17504/protocols.io.bca8ishw).
    MeSH term(s) Epigenome ; Genome ; Genomics ; Protein Binding ; Software
    Language English
    Publishing date 2020-09-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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/btaa771
    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.

  4. Article ; Online: WashU Epigenome Browser update 2019.

    Li, Daofeng / Hsu, Silas / Purushotham, Deepak / Sears, Renee L / Wang, Ting

    Nucleic acids research

    2019  Volume 47, Issue W1, Page(s) W158–W165

    Abstract: The WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including the Roadmap ... ...

    Abstract The WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including the Roadmap Epigenomics and the ENCODE projects. Recently, we refactored the codebase, redesigned the user interface, and developed various novel features. New features include: (i) visualization using virtual reality (VR), which has implications in biology education and the study of 3D chromatin structure; (ii) expanded public data hubs, including data from the 4DN, ENCODE, Roadmap Epigenomics, TaRGET, IHEC and TCGA consortia; (iii) a more responsive user interface; (iv) a history of interactions, which enables undo and redo; (v) a feature we call Live Browsing, which allows multiple users to collaborate remotely on the same session; (vi) the ability to visualize local tracks and data hubs. Amazon Web Services also hosts the redesign at https://epigenomegateway.org/.
    MeSH term(s) Databases, Genetic ; Datasets as Topic ; Epigenome/genetics ; Epigenomics ; Genome, Human ; Humans ; Internet ; Software ; User-Computer Interface ; Web Browser
    Language English
    Publishing date 2019-06-05
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkz348
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: 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.

  5. Article ; Online: WashU Epigenome Browser update 2022.

    Li, Daofeng / Purushotham, Deepak / Harrison, Jessica K / Hsu, Silas / Zhuo, Xiaoyu / Fan, Changxu / Liu, Shane / Xu, Vincent / Chen, Samuel / Xu, Jason / Ouyang, Shinyi / Wu, Angela S / Wang, Ting

    Nucleic acids research

    2022  Volume 50, Issue W1, Page(s) W774–W781

    Abstract: WashU Epigenome Browser (https://epigenomegateway.wustl.edu/browser/) is a web-based genomic data exploration tool that provides visualization, integration, and analysis of epigenomic datasets. The newly renovated user interface and functions have ... ...

    Abstract WashU Epigenome Browser (https://epigenomegateway.wustl.edu/browser/) is a web-based genomic data exploration tool that provides visualization, integration, and analysis of epigenomic datasets. The newly renovated user interface and functions have enabled researchers to engage with the browser and genomic data more efficiently and effectively since 2018. Here, we introduce a new integrated panel design in the browser that allows users to interact with 1D (genomic features), 2D (such as Hi-C), 3D (genome structure), and 4D (time series) data in a single web page. The browser can display three-dimensional chromatin structures with the 3D viewer module. The 4D tracks, called 'Dynamic' tracks, animatedly display time-series data, allowing for a more striking visual impact to identify the gene or genomic region candidates as a function of time. Genomic data, such as annotation features, numerical values, and chromatin interaction data can all be viewed in the dynamic track mode. Imaging data from microscopy experiments can also be displayed in the browser. In addition to software development, we continue to service and expand the data hubs we host for large consortia including 4DN, Roadmap Epigenomics, TaRGET and ENCODE, among others. Our growing user/developer community developed additional track types as plugins, such as qBed and dynseq tracks, which extend the utility of the browser. The browser serves as a foundation for additional genomics platforms including the WashU Virus Genome Browser (for COVID-19 research) and the Comparative Genome Browser. The WashU Epigenome Browser can also be accessed freely through Amazon Web Services at https://epigenomegateway.org/.
    MeSH term(s) Humans ; COVID-19/genetics ; Databases, Genetic ; Epigenome ; Genome, Human ; Internet ; Software ; Web Browser
    Language English
    Publishing date 2022-04-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac238
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: 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.

  6. Article ; Online: Author Correction: Exploring the coronavirus pandemic with the WashU Virus Genome Browser.

    Flynn, Jennifer A / Purushotham, Deepak / Choudhary, Mayank N K / Zhuo, Xiaoyu / Fan, Changxu / Matt, Gavriel / Li, Daofeng / Wang, Ting

    Nature genetics

    2020  Volume 52, Issue 10, Page(s) 1132

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Keywords covid19
    Language English
    Publishing date 2020-09-16
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-020-00714-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: 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)
    Zs.MG 46: 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.

  7. Article ; Online: Exploring the coronavirus pandemic with the WashU Virus Genome Browser.

    Flynn, Jennifer A / Purushotham, Deepak / Choudhary, Mayank N K / Zhuo, Xiaoyu / Fan, Changxu / Matt, Gavriel / Li, Daofeng / Wang, Ting

    Nature genetics

    2020  Volume 52, Issue 10, Page(s) 986–991

    MeSH term(s) Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/virology ; Databases, Genetic ; Genome, Viral/genetics ; Humans ; Internet ; Pandemics ; Pneumonia, Viral/virology ; SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-09-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-020-0697-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: 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)
    Zs.MG 46: 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.

  8. Article: Exploring the coronavirus pandemic with the WashU Virus Genome Browser

    Flynn, Jennifer A / Purushotham, Deepak / Choudhary, Mayank N K / Zhuo, Xiaoyu / Fan, Changxu / Matt, Gavriel / Li, Daofeng / Wang, Ting

    Nat Genet

    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #752475
    Database COVID19

    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.

  9. Article ; Online: Exploring the coronavirus epidemic using the new WashU Virus Genome Browser

    Flynn, Jennifer / Purushotham, Deepak / Choudhary, Mayank NK / Zhuo, Xiaoyu / Fan, Changxu / Matt, Gavriel / Li, Daofeng / Wang, Ting

    bioRxiv

    Abstract: Since its debut in mid-December, 2019, the novel coronavirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the virus have ... ...

    Abstract Since its debut in mid-December, 2019, the novel coronavirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the virus have been sequenced and uploaded to NCBIs GenBank [1], providing insight into the viruss evolutionary history and pathogenesis. Here, we present the WashU Virus Genome Browser, a web-based portal for viewing virus genomic data. The browser is home to 16 complete 2019-nCoV genome sequences, together with hundreds of related viral sequences including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and Ebola virus. In addition, the browser features unique customizability, supporting user-provided upload of novel viral sequences in various formats. Sequences can be viewed in both a track-based representation as well as a phylogenetic tree-based view, allowing the user to easily compare sequence features across multiple strains. The WashU Virus Genome Browser inherited many features and track types from the WashU Epigenome Browser, and additionally incorporated a new type of SNV track to address the specific needs of viral research. Our Virus Browser portal can be accessed at https://virusgateway.wustl.edu, and documentation is available at https://virusgateway.readthedocs.io/.
    Keywords covid19
    Publisher BioRxiv; MedRxiv; WHO
    Document type Article ; Online
    Note WHO #Covidence: #939124
    DOI 10.1101/2020.02.07.939124
    Database COVID19

    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: Author Correction: Exploring the coronavirus pandemic with the WashU Virus Genome Browser

    Flynn, Jennifer A / Purushotham, Deepak / Choudhary, Mayank N K / Zhuo, Xiaoyu / Fan, Changxu / Matt, Gavriel / Li, Daofeng / Wang, Ting

    Nat. genet

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #772955
    Database COVID19

    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.

To top