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  1. Article ; Online: Cell-Type Transcriptomes of the Multicellular Green Alga

    Matt, Gavriel Y / Umen, James G

    G3 (Bethesda, Md.)

    2018  Volume 8, Issue 2, Page(s) 531–550

    Abstract: Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. ...

    Abstract Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood.
    MeSH term(s) Algal Proteins/classification ; Algal Proteins/genetics ; Cell Differentiation/genetics ; Energy Metabolism/genetics ; Evolution, Molecular ; Gene Expression Profiling ; Gene Ontology ; Light-Harvesting Protein Complexes/classification ; Light-Harvesting Protein Complexes/genetics ; Phylogeny ; Volvox/cytology ; Volvox/genetics ; Volvox/metabolism
    Chemical Substances Algal Proteins ; Light-Harvesting Protein Complexes
    Language English
    Publishing date 2018-02-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.117.300253
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping.

    Paul, Robin / Wang, Jian / Reilly, Colleen / Sioson, Edgar / Patel, Jaimin / Matt, Gavriel / Acić, Aleksandar / Zhou, Xin

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 5

    Abstract: Summary: ProteinPaint BAM track (ppBAM) is designed to assist variant review for cancer research and clinical genomics. With performant server-side computing and rendering, ppBAM supports on-the-fly variant genotyping of thousands of reads using Smith- ... ...

    Abstract Summary: ProteinPaint BAM track (ppBAM) is designed to assist variant review for cancer research and clinical genomics. With performant server-side computing and rendering, ppBAM supports on-the-fly variant genotyping of thousands of reads using Smith-Waterman alignment. To better visualize support for complex variants, reads are realigned against the mutated reference sequence using ClustalO. ppBAM also supports the BAM slicing API of the NCI Genomic Data Commons (GDC) portal, letting researchers conveniently examine genomic details of vast amounts of cancer sequencing data and reinterpret variant calls.
    Availability and implementation: BAM track examples, tutorial, and GDC file access links are available at https://proteinpaint.stjude.org/bam/. Source code is available at https://github.com/stjude/proteinpaint.
    MeSH term(s) Sequence Analysis, DNA ; Genotype ; Sequence Alignment ; Software ; Genomics ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2023-05-04
    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/btad300
    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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  3. Article ; Online: Volvox: A simple algal model for embryogenesis, morphogenesis and cellular differentiation.

    Matt, Gavriel / Umen, James

    Developmental biology

    2016  Volume 419, Issue 1, Page(s) 99–113

    Abstract: Patterning of a multicellular body plan involves a coordinated set of developmental processes that includes cell division, morphogenesis, and cellular differentiation. These processes have been most intensively studied in animals and land plants; however, ...

    Abstract Patterning of a multicellular body plan involves a coordinated set of developmental processes that includes cell division, morphogenesis, and cellular differentiation. These processes have been most intensively studied in animals and land plants; however, deep insight can also be gained by studying development in simpler multicellular organisms. The multicellular green alga Volvox carteri (Volvox) is an excellent model for the investigation of developmental mechanisms and their evolutionary origins. Volvox has a streamlined body plan that contains only a few thousand cells and two distinct cell types: reproductive germ cells and terminally differentiated somatic cells. Patterning of the Volvox body plan is achieved through a stereotyped developmental program that includes embryonic cleavage with asymmetric cell division, morphogenesis, and cell-type differentiation. In this review we provide an overview of how these three developmental processes give rise to the adult form in Volvox and how developmental mutants have provided insights into the mechanisms behind these events. We highlight the accessibility and tractability of Volvox and its relatives that provide a unique opportunity for studying development.
    MeSH term(s) Cell Cycle ; Cell Lineage ; Cell Size ; Cellular Senescence ; Models, Biological ; Morphogenesis ; Mutation ; Phylogeny ; Reproduction, Asexual ; Seeds ; Volvox/cytology ; Volvox/genetics ; Volvox/physiology
    Language English
    Publishing date 2016-07-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2016.07.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 508: Show issues Location:
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  4. Article: Volvox: A simple algal model for embryogenesis, morphogenesis and cellular differentiation

    Matt, Gavriel / James Umen

    Developmental biology. 2016,

    2016  

    Abstract: Patterning of a multicellular body plan involves a coordinated set of developmental processes that includes cell division, morphogenesis, and cellular differentiation. These processes have been most intensively studied in animals and land plants; however, ...

    Abstract Patterning of a multicellular body plan involves a coordinated set of developmental processes that includes cell division, morphogenesis, and cellular differentiation. These processes have been most intensively studied in animals and land plants; however, deep insight can also be gained by studying development in simpler multicellular organisms. The multicellular green alga Volvox carteri (Volvox) is an excellent model for the investigation of developmental mechanisms and their evolutionary origins. Volvox has a streamlined body plan that contains only a few thousand cells and two distinct cell types: reproductive germ cells and terminally differentiated somatic cells. Patterning in Volvox is achieved through a stereotyped developmental program that includes embryonic cleavage with asymmetric cell division, morphogenesis, and cell-type differentiation. In this review we provide an overview of how these three developmental processes give rise to the adult form in Volvox and how developmental mutants have provided insights into the mechanisms behind these events. We highlight the accessibility and tractability of Volvox and its relatives that provide a unique opportunity for studying development.
    Keywords Volvox ; adults ; algae ; animals ; cell differentiation ; cell division ; embryogenesis ; embryophytes ; germ cells ; models ; morphogenesis ; mutants ; somatic cells
    Language English
    Size p. .
    Publishing place Elsevier Inc.
    Document type Article
    Note Pre-press version
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2016.07.014
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 76/715: Show issues

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  5. 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

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: Show issues Location:
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    Zs.MG 46: Show issues

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  6. 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

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: Show issues Location:
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  7. Article ; Online: St. Jude Survivorship Portal: sharing and analyzing large clinical and genomic datasets from pediatric cancer survivors.

    Matt, Gavriel Y / Sioson, Edgar / Shelton, Kyla / Wang, Jian / Lu, Congyu / Zaldivar Peraza, Airen / Gangwani, Karishma / Paul, Robin / Reilly, Colleen / Acić, Aleksandar / Liu, Qi / Sandor, Stephanie R / McLeod, Clay / Patel, Jaimin / Wang, Fan / Im, Cindy / Wang, Zhaoming / Sapkota, Yadav / Wilson, Carmen L /
    Bhakta, Nickhill / Ness, Kirsten K / Armstrong, Gregory T / Hudson, Melissa M / Robison, Leslie L / Zhang, Jinghui / Yasui, Yutaka / Zhou, Xin

    Cancer discovery

    2024  

    Abstract: Childhood cancer survivorship studies generate comprehensive datasets comprising demographic, diagnosis, treatment, outcome, and genomic data from survivors. To broadly share this data, we created the St. Jude Survivorship Portal (https://survivorship ... ...

    Abstract Childhood cancer survivorship studies generate comprehensive datasets comprising demographic, diagnosis, treatment, outcome, and genomic data from survivors. To broadly share this data, we created the St. Jude Survivorship Portal (https://survivorship.stjude.cloud), the first data portal for sharing, analyzing, and visualizing pediatric cancer survivorship data. Over 1,600 phenotypic variables and 400 million genetic variants from over 7,700 childhood cancer survivors can be explored on this free, open-access portal. Summary statistics of variables are computed on-the-fly and visualized through interactive and customizable charts. Survivor cohorts can be customized and/or divided into groups for comparative analysis. Users can also seamlessly perform cumulative incidence and regression analyses on the stored survivorship data. Using the portal, we explored the ototoxic effects of platinum-based chemotherapy, uncovered a novel association between mental health, age, and limb amputation, and discovered a novel haplotype in MAGI3 strongly associated with cardiomyopathy specifically in survivors of African ancestry.
    Language English
    Publishing date 2024-04-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2625242-9
    ISSN 2159-8290 ; 2159-8274
    ISSN (online) 2159-8290
    ISSN 2159-8274
    DOI 10.1158/2159-8290.CD-23-1441
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 6916: Show issues Location:
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  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

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  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

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  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

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