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  1. Article ; Online: Single-cell transcriptional profiling in brain reward structures.

    Day, Jeremy J / Martinowich, Keri

    Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology

    2022  Volume 48, Issue 1, Page(s) 243–244

    MeSH term(s) Reward ; Brain
    Language English
    Publishing date 2022-08-02
    Publishing country England
    Document type News ; Research Support, N.I.H., Extramural
    ZDB-ID 639471-1
    ISSN 1740-634X ; 0893-133X
    ISSN (online) 1740-634X
    ISSN 0893-133X
    DOI 10.1038/s41386-022-01394-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2379: 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)

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  2. Article: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies.

    Yao, Jianing / Yu, Jinglun / Caffo, Brian / Page, Stephanie C / Martinowich, Keri / Hicks, Stephanie C

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Recent advances in spatially-resolved single-omics and multi-omics technologies have led to the emergence of computational tools to detect or predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining of proteins and ... ...

    Abstract Recent advances in spatially-resolved single-omics and multi-omics technologies have led to the emergence of computational tools to detect or predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining of proteins and cell types provide multiple perspectives and a more complete understanding of tissue architecture. Here, we introduce Proust, a scalable tool to predict discrete domains using spatial multi-omics data by combining the low-dimensional representation of biological profiles based on graph-based contrastive self-supervised learning. Our scalable method integrates multiple data modalities, such as RNA, protein, and H&E images, and predicts spatial domains within tissue samples. Through the integration of multiple modalities, Proust consistently demonstrates enhanced accuracy in detecting spatial domains, as evidenced across various benchmark datasets and technological platforms.
    Language English
    Publishing date 2024-02-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.02.578662
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Neuropsychopharmacology (NPP) 2020 report on gender balance among corresponding authors and reviewers: before and during the COVID-19 pandemic.

    Hupalo, Sofiya / Martinowich, Keri / Carlezon, William A / Jordan, Chloe J

    Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology

    2022  Volume 47, Issue 5, Page(s) 973–975

    MeSH term(s) Bibliometrics ; COVID-19 ; Gender Identity ; Humans ; Pandemics
    Language English
    Publishing date 2022-02-21
    Publishing country England
    Document type Editorial
    ZDB-ID 639471-1
    ISSN 1740-634X ; 0893-133X
    ISSN (online) 1740-634X
    ISSN 0893-133X
    DOI 10.1038/s41386-022-01288-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2379: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Neuropsychopharmacology (NPP): update on relationships between online attention and citation counts.

    Jordan, Chloe J / Martinowich, Keri / Carlezon, William A

    Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology

    2021  Volume 46, Issue 6, Page(s) 1061–1063

    MeSH term(s) Attention ; Bibliometrics ; Journal Impact Factor
    Language English
    Publishing date 2021-02-18
    Publishing country England
    Document type Editorial
    ZDB-ID 639471-1
    ISSN 1740-634X ; 0893-133X
    ISSN (online) 1740-634X
    ISSN 0893-133X
    DOI 10.1038/s41386-021-00983-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2379: 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)

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  5. Article ; Online: Evaluation of Na

    Martinowich, Keri / Das, Debamitra / Sripathy, Srinidhi Rao / Mai, Yishan / Kenney, Rakaia F / Maher, Brady J

    Molecular psychiatry

    2022  Volume 28, Issue 1, Page(s) 76–82

    Abstract: Pitt Hopkins Syndrome (PTHS) is a rare syndromic form of autism spectrum disorder (ASD) caused by autosomal dominant mutations in the Transcription Factor 4 (TCF4) gene. TCF4 is a basic helix-loop-helix transcription factor that is critical for ... ...

    Abstract Pitt Hopkins Syndrome (PTHS) is a rare syndromic form of autism spectrum disorder (ASD) caused by autosomal dominant mutations in the Transcription Factor 4 (TCF4) gene. TCF4 is a basic helix-loop-helix transcription factor that is critical for neurodevelopment and brain function through its binding to cis-regulatory elements of target genes. One potential therapeutic strategy for PTHS is to identify dysregulated target genes and normalize their dysfunction. Here, we propose that SCN10A is an important target gene of TCF4 that is an applicable therapeutic approach for PTHS. Scn10a encodes the voltage-gated sodium channel Na
    MeSH term(s) Animals ; Mice ; Autism Spectrum Disorder/drug therapy ; Autism Spectrum Disorder/genetics ; Autism Spectrum Disorder/metabolism ; Facies ; Hyperventilation/genetics ; Intellectual Disability/drug therapy ; Intellectual Disability/genetics ; Intellectual Disability/metabolism ; Transcription Factor 4/genetics ; NAV1.8 Voltage-Gated Sodium Channel/chemistry ; NAV1.8 Voltage-Gated Sodium Channel/metabolism
    Chemical Substances Transcription Factor 4 ; Scn10a protein, mouse ; NAV1.8 Voltage-Gated Sodium Channel
    Language English
    Publishing date 2022-10-12
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1330655-8
    ISSN 1476-5578 ; 1359-4184
    ISSN (online) 1476-5578
    ISSN 1359-4184
    DOI 10.1038/s41380-022-01811-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4812: 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)

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  6. Article: Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments.

    Sriworarat, Chaichontat / Nguyen, Annie / Eagles, Nicholas J / Collado-Torres, Leonardo / Martinowich, Keri / Maynard, Kristen R / Hicks, Stephanie C

    bioRxiv : the preprint server for biology

    2023  

    Abstract: High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we ... ...

    Abstract High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Samui, a performant and interactive image visualization tool that runs completely in the web browser. Samui is specifically designed for fast image visualization and annotation and enables users to browse through large images and their selected features within seconds of receiving a link. We demonstrate the broad utility of Samui with images generated with two platforms: Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression. Samui along with example datasets is available at https://samuibrowser.com.
    Language English
    Publishing date 2023-02-23
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.28.525943
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments.

    Sriworarat, Chaichontat / Nguyen, Annie / Eagles, Nicholas J / Collado-Torres, Leonardo / Martinowich, Keri / Maynard, Kristen R / Hicks, Stephanie C

    Biological imaging

    2023  Volume 3, Page(s) e15

    Abstract: High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we ... ...

    Abstract High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Samui, a performant and interactive image visualization tool that runs completely in the web browser. Samui is specifically designed for fast image visualization and annotation and enables users to browse through large images and their selected features within seconds of receiving a link. We demonstrate the broad utility of Samui with images generated with two platforms: Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression. Samui along with example datasets is available at https://samuibrowser.com.
    Language English
    Publishing date 2023-07-12
    Publishing country England
    Document type Journal Article
    ISSN 2633-903X
    ISSN (online) 2633-903X
    DOI 10.1017/S2633903X2300017X
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Activity-regulated gene expression across cell types of the mouse hippocampus.

    Nelson, Erik D / Maynard, Kristen R / Nicholas, Kyndall R / Tran, Matthew N / Divecha, Heena R / Collado-Torres, Leonardo / Hicks, Stephanie C / Martinowich, Keri

    Hippocampus

    2023  Volume 33, Issue 9, Page(s) 1009–1027

    Abstract: Activity-regulated gene (ARG) expression patterns in the hippocampus (HPC) regulate synaptic plasticity, learning, and memory, and are linked to both risk and treatment responses for many neuropsychiatric disorders. The HPC contains discrete classes of ... ...

    Abstract Activity-regulated gene (ARG) expression patterns in the hippocampus (HPC) regulate synaptic plasticity, learning, and memory, and are linked to both risk and treatment responses for many neuropsychiatric disorders. The HPC contains discrete classes of neurons with specialized functions, but cell type-specific activity-regulated transcriptional programs are not well characterized. Here, we used single-nucleus RNA-sequencing (snRNA-seq) in a mouse model of acute electroconvulsive seizures (ECS) to identify cell type-specific molecular signatures associated with induced activity in HPC neurons. We used unsupervised clustering and a priori marker genes to computationally annotate 15,990 high-quality HPC neuronal nuclei from N = 4 mice across all major HPC subregions and neuron types. Activity-induced transcriptomic responses were divergent across neuron populations, with dentate granule cells being particularly responsive to activity. Differential expression analysis identified both upregulated and downregulated cell type-specific gene sets in neurons following ECS. Within these gene sets, we identified enrichment of pathways associated with varying biological processes such as synapse organization, cellular signaling, and transcriptional regulation. Finally, we used matrix factorization to reveal continuous gene expression patterns differentially associated with cell type, ECS, and biological processes. This work provides a rich resource for interrogating activity-regulated transcriptional responses in HPC neurons at single-nuclei resolution in the context of ECS, which can provide biological insight into the roles of defined neuronal subtypes in HPC function.
    MeSH term(s) Mice ; Animals ; Hippocampus/physiology ; Neurons/physiology ; Learning/physiology ; Gene Expression Regulation/genetics ; Seizures ; Gene Expression
    Language English
    Publishing date 2023-05-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1074352-2
    ISSN 1098-1063 ; 1050-9631
    ISSN (online) 1098-1063
    ISSN 1050-9631
    DOI 10.1002/hipo.23548
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3227: 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)

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  9. Article: Distinct roles of

    Bach, Svitlana V / Bauman, Allison J / Hosein, Darya / Tuscher, Jennifer J / Ianov, Lara / Greathouse, Kelsey M / Henderson, Benjamin W / Herskowitz, Jeremy H / Martinowich, Keri / Day, Jeremy J

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Brain-derived neurotrophic factor ( ...

    Abstract Brain-derived neurotrophic factor (
    Language English
    Publishing date 2023-04-05
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.05.535694
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Distinct roles of Bdnf I and Bdnf IV transcript variant expression in hippocampal neurons.

    Bach, Svitlana V / Bauman, Allison J / Hosein, Darya / Tuscher, Jennifer J / Ianov, Lara / Greathouse, Kelsey M / Henderson, Benjamin W / Herskowitz, Jeremy H / Martinowich, Keri / Day, Jeremy J

    Hippocampus

    2024  Volume 34, Issue 5, Page(s) 218–229

    Abstract: Brain-derived neurotrophic factor (Bdnf) plays a critical role in brain development, dendritic growth, synaptic plasticity, as well as learning and memory. The rodent Bdnf gene contains nine 5' non-coding exons (I-IXa), which are spliced to a common 3' ... ...

    Abstract Brain-derived neurotrophic factor (Bdnf) plays a critical role in brain development, dendritic growth, synaptic plasticity, as well as learning and memory. The rodent Bdnf gene contains nine 5' non-coding exons (I-IXa), which are spliced to a common 3' coding exon (IX). Transcription of individual Bdnf variants, which all encode the same BDNF protein, is initiated at unique promoters upstream of each non-coding exon, enabling precise spatiotemporal and activity-dependent regulation of Bdnf expression. Although prior evidence suggests that Bdnf transcripts containing exon I (Bdnf I) or exon IV (Bdnf IV) are uniquely regulated by neuronal activity, the functional significance of different Bdnf transcript variants remains unclear. To investigate functional roles of activity-dependent Bdnf I and IV transcripts, we used a CRISPR activation system in which catalytically dead Cas9 fused to a transcriptional activator (VPR) is targeted to individual Bdnf promoters with single guide RNAs, resulting in transcript-specific Bdnf upregulation. Bdnf I upregulation is associated with gene expression changes linked to dendritic growth, while Bdnf IV upregulation is associated with genes that regulate protein catabolism. Upregulation of Bdnf I, but not Bdnf IV, increased mushroom spine density, volume, length, and head diameter, and also produced more complex dendritic arbors in cultured rat hippocampal neurons. In contrast, upregulation of Bdnf IV, but not Bdnf I, in the rat hippocampus attenuated contextual fear expression. Our data suggest that while Bdnf I and IV are both activity-dependent, BDNF produced from these promoters may serve unique cellular, synaptic, and behavioral functions.
    Language English
    Publishing date 2024-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1074352-2
    ISSN 1098-1063 ; 1050-9631
    ISSN (online) 1098-1063
    ISSN 1050-9631
    DOI 10.1002/hipo.23600
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3227: 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)

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