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Machine learning-based identification of a transcriptomic blood signature discriminating between systemic autoimmunity and infection

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sciencedirect.com/science/article/pii/S2666634025002673
Jul 2025
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Circulating tumor DNA monitoring detects minimal residual disease and predicts outcomes in patients with esophageal adenocarcinoma or squamous cell carcinoma after esophagectomy

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1. scibot 30 Jul 2025
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12290085/
Jun 2025
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A hexamer tandem repeat RNA embedded within an SVA retrotransposon drives R-loop formation and neurodegeneration

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sciencedirect.com/science/article/pii/S2211124725005832
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Satb1 directs the differentiation of TH17 cells through suppression of IL-2 expression

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sciencedirect.com/science/article/pii/S2211124725006370
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RNA shielding of P65 is required to potentiate oncogenic inflammation in TET2 mutated clonal hematopoiesis

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pmc.ncbi.nlm.nih.gov/articles/PMC11611684/
May 2025
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The human proteome with direct physical access to DNA

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sciencedirect.com/science/article/pii/S0092867425005070
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Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex

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sciencedirect.com/science/article/pii/S0896627325003083
Dec 2024
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A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

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1. scibot 22 Dec 2024
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11651654/
Oct 2024
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An in vitro approach reveals molecular mechanisms underlying endocrine disruptor-induced epimutagenesis

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1. scibot 05 Oct 2024
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11449486/
Jul 2024
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The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1

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1. scibot 23 Jul 2024
  
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  DOI: 10.1126/sciadv.adk1296
  
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science.org/doi/10.1126/sciadv.adk1296
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Rapid Dynamics of Signal-Dependent Transcriptional Repression by Capicua

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1. scibot 13 Jul 2024
  
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  DOI: 10.1016/j.devcel.2020.02.004
  
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2. scibot 13 Jul 2024
  
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  DOI: 10.1016/j.devcel.2020.02.004
  
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ncbi.nlm.nih.gov/pmc/articles/PMC7161736/
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The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1

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1. scibot 02 Jul 2024
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11204300/
Apr 2024
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A senescence restriction point acting on chromatin integrates oncogenic signals

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1. scibot 04 Apr 2024
  
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  DOI: 10.1016/j.celrep.2024.114044
  
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sciencedirect.com/science/article/pii/S2211124724003723
Feb 2024
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PHF6-altered T-ALL harbor epigenetic repressive switch at bivalent promoters and respond to 5-azacitidine and venetoclax

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1. scibot 24 Feb 2024
  
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  DOI: 10.1158/1078-0432.CCR-23-2159
  
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aacrjournals.org/clincancerres/article/30/1/94/732070/PHF6-altered-T-ALL-Harbor-Epigenetic-Repressive
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Parkinson’s Disease Risk Enhancers in Microglia

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1. scibot 08 Feb 2024
  
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  DOI: 10.1016/j.isci.2024.108921
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10845915/
Dec 2023
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ccr-23-2159-html.html

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  DOI: 10.1158/1078-0432.ccr-23-2159
  
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52.53.155.43/50002159f66eedc909bd4e89525af95101f094c9/ccr-23-2159-html.html
Nov 2023
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Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly

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1. scibot 28 Nov 2023
  
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  DOI: 10.1016/j.molcel.2023.10.037
  
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sciencedirect.com/science/article/pii/S1097276523009085
Aug 2023
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AmpSeqR: an R package for amplicon deep sequencing data analysis

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1. scibot 12 Aug 2023
  
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  DOI: 10.12688/f1000research.129581.1
  
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52.53.155.43/f4ad8e205573ef3fe7246a88a0ec9b2de25b754b/d0899e17-cfa5-450f-9f7b-901b4cd3503e_129581_-_melanie_bahlo-html.html
Jul 2023
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Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition

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1. scibot 22 Jul 2023
  
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sciencedirect.com/science/article/pii/S0896627323004786
Jun 2023
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Comprehensive DNA methylation analysis indicates that pancreatic intraepithelial neoplasia lesions are acinar-derived and epigenetically primed for carcinogenesis

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1. scibot 03 Jun 2023
  
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  DOI: 10.1158/0008-5472.CAN-22-4052
  
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aacrjournals.org/cancerres/article/83/11/1905/726442/Comprehensive-DNA-Methylation-Analysis-Indicates
May 2023
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Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases

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  DOI: 10.1038/s41531-023-00504-1
  
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nature.com/articles/s41531-023-00504-1
Apr 2023
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

DNA methylation landscapes of prostate cancer brain metastasis are shaped by early driver genetic alterations

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ncbi.nlm.nih.gov/pmc/articles/PMC10102845/
Mar 2023
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In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution

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1. scibot 11 Mar 2023
  
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sciencedirect.com/science/article/pii/S2666979X23000368
Aug 2022
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Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases

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1. scibot 22 Aug 2022
  
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  DOI: 10.1101/2022.05.30.22275781
  
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52.53.155.43/362fce05ea7f85123208e7831722388400cae744/2022.05.30.22275781.full-html.html
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Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegeneration

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1. scibot 10 Aug 2022
  
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  DOI: 10.1016/j.immuni.2022.07.004
  
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sciencedirect.com/science/article/pii/S1074761322003375
Jul 2022
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Transcriptional and Epigenetic Consequences of DMSO Treatment on HepaRG Cells

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1. scibot 30 Jul 2022
  
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  DOI: 10.3390/cells11152298
  
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ncbi.nlm.nih.gov/pmc/articles/PMC9331440/
May 2022
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An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

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1. scibot 14 May 2022
  
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  DOI: 10.1101/2020.02.29.970558
  
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biorxiv.org/content/10.1101/2020.02.29.970558v2
Mar 2022
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Novel insights from a multiomics dissection of the Hayflick limit

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1. scibot 23 Mar 2022
  
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  DOI: 10.7554/eLife.70283
  
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elifesciences.org/articles/70283
Feb 2022
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FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons

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  DOI: 10.7554/eLife.71892
  
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elifesciences.org/articles/71892
Nov 2021
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Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins

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1. scibot 09 Nov 2021
  
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  DOI: 10.1158/1541-7786.MCR-21-0354
  
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ncbi.nlm.nih.gov/pmc/articles/PMC8568690/
Oct 2021
www.nature.com www.nature.com

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

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1. scibot 14 Oct 2021
  
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  DOI: 10.1038/s41586-021-03500-8
  
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nature.com/articles/s41586-021-03500-8
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Morphological diversity of single neurons in molecularly defined cell types

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1. scibot 14 Oct 2021
  
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  DOI: 10.1038/s41586-021-03941-1
  
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nature.com/articles/s41586-021-03941-1
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Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier

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1. scibot 01 Oct 2021
  
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  DOI: 10.1016/j.celrep.2021.109755
  
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sciencedirect.com/science/article/pii/S2211124721012092
Aug 2021
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Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers

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1. scibot 04 Aug 2021
  
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  DOI: 10.1016/j.xcrm.2021.100349
  
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sciencedirect.com/science/article/pii/S2666379121001981
Jul 2021
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast

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1. scibot 14 Jul 2021
  
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  DOI: 10.7554/eLife.65331
  
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ncbi.nlm.nih.gov/pmc/articles/PMC8263057/
Jun 2021
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Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation

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1. scibot 17 Jun 2021
  
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  RRID:SCR_000025
  
  DOI: 10.1016/j.xpro.2021.100609
  
  Resource: GenomicRanges (RRID:SCR_000025)
  
  Curator: @scibot
  
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sciencedirect.com/science/article/pii/S2666166721003166
May 2021
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

ZC3H4 restricts non-coding transcription in human cells

1
1. scibot 26 May 2021
  
  in Public
  
  SCR_000025
  
  DOI: 10.7554/eLife.67305
  
  Resource: GenomicRanges (RRID:SCR_000025)
  
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ncbi.nlm.nih.gov/pmc/articles/PMC8137146/
Apr 2021
www.cell.com www.cell.com

IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis

1
1. scibot 20 Apr 2021
  
  in Public
  
  RRID:SCR_018096
  
  DOI: 10.1016/j.ccell.2020.06.007
  
  Resource: GenomicRanges (RRID:SCR_000025)
  
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cell.com/cancer-cell/fulltext/S1535-6108(20)30311-1
Feb 2021
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The glucocorticoid receptor recruits the COMPASS complex to regulate inflammatory transcription at macrophage enhancers

1
1. scibot 11 Feb 2021
  
  in Public
  
  RRID:SCR_000025
  
  DOI: 10.1016/j.celrep.2021.108742
  
  Resource: GenomicRanges (RRID:SCR_000025)
  
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  RRIDCUR:Validated RRID:SCR_000025
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sciencedirect.com/science/article/pii/S2211124721000553
Sep 2020
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Rapid Dynamics of Signal-Dependent Transcriptional Repression by Capicua

1
1. scibot 03 Sep 2020
  
  in Public
  
  RRID:SCR_000025
  
  DOI: 10.1016/j.devcel.2020.02.004
  
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ncbi.nlm.nih.gov/pmc/articles/PMC7161736/
Jan 2020
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

1
1. scibot 13 Jan 2020
  
  in Public
  
  RRID:SCR_000025
  
  DOI: 10.7554/eLife.50087
  
  Resource: GenomicRanges (RRID:SCR_000025)
  
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ncbi.nlm.nih.gov/pmc/articles/PMC6890464/
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RAG-Mediated DNA Breaks Attenuate PU.1 Activity in Early B Cells through Activation of a SPIC-BCLAF1 Complex

1
1. scibot 13 Jan 2020
  
  in Public
  
  RRID:SCR_000025
  
  DOI: 10.1016/j.celrep.2019.09.026
  
  Resource: GenomicRanges (RRID:SCR_000025)
  
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sciencedirect.com/science/article/pii/S2211124719312033
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A Unique Epigenomic Landscape Defines Human Erythropoiesis

1
1. scibot 13 Jan 2020
  
  in Public
  
  RRID:SCR_000025
  
  DOI: 10.1016/j.celrep.2019.08.020
  
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sciencedirect.com/science/article/pii/S2211124719310538
elifesciences.org elifesciences.org

FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory

1
1. scibot 13 Jan 2020
  
  in Public
  
  RRID:SCR_000025
  
  DOI: 10.7554/eLife.46919
  
  Resource: GenomicRanges (RRID:SCR_000025)
  
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elifesciences.org/articles/46919
Nov 2018
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EZH2-Mediated Primary Cilium Deconstruction Drives Metastatic Melanoma Formation

1
1. scibot 05 Nov 2018
  
  in Public
  
  GenomicRanges
  
  Curator: @anp055
  
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sciencedirect.com/science/article/pii/S1535610818302290
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The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

1
1. scibot 05 Nov 2018
  
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  RRID:SCR_000025
  
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sciencedirect.com/science/article/pii/S0092867417314940
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner

1
1. scibot 05 Nov 2018
  
  in Public
  
  RRID:SCR_000025
  
  Curator: @evieth
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5786503/
Nov 2017
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TIAM1 Antagonizes TAZ/YAP Both in the Destruction Complex in the Cytoplasm and in the Nucleus to Inhibit Invasion of Intestinal Epithelial Cells

1
1. scibot 08 Nov 2017
  
  in Public
  
  GenomicRanges
  
  Curator: @kaitlinsung
  
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sciencedirect.com/science/article/pii/S1535610817301034
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Human AML-iPSCs Reacquire Leukemic Properties after Differentiation and Model Clonal Variation of Disease

1
1. scibot 08 Nov 2017
  
  in Public
  
  GenomicRanges version 1.18.4
  
  Curator: @Zeljana_Babic
  
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  (GenomicRanges, RRID:SCR_000025)
  
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sciencedirect.com/science/article/pii/S1934590916304544