47 Matching Annotations
  1. Nov 2024
  2. pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov
    Replication stress induces POLQ-mediated structural variant formation throughout common fragile sites after entry into mitosis
    1
    1. scibot 10 Nov 2024
      RRID:CVCL_7526

      DOI: 10.1038/s41467-024-53917-8

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    pmc.ncbi.nlm.nih.gov/articles/PMC11541566/
  3. Sep 2024
  4. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    SJPedPanel: A pan-cancer gene panel for childhood malignancies to enhance cancer monitoring and early detection
    1
    1. scibot 25 Sep 2024
      RRID:CVCL_7526

      DOI: 10.1158/1078-0432.CCR-24-1063

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    ncbi.nlm.nih.gov/pmc/articles/PMC11393547/
  5. Jul 2024
  6. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells
    1
    1. scibot 03 Jul 2024
      RRID:CVCL_7526

      DOI: 10.1371/journal.pgen.1011311

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    ncbi.nlm.nih.gov/pmc/articles/PMC11189215/
  7. Jun 2024
  8. www.biorxiv.org www.biorxiv.org
    POLQ mediates replication-stress induced structural variant formation throughout common fragile sites during mitosis
    1
    1. scibot 06 Jun 2024
      RRID:CVCL_7526

      DOI: 10.1101/2024.05.28.596214

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    biorxiv.org/content/10.1101/2024.05.28.596214v1
  9. Apr 2024
  10. www.sciencedirect.com www.sciencedirect.com
    Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans
    1
    1. scibot 11 Apr 2024
      RRID:CVCL_7526

      DOI: 10.1016/j.xgen.2024.100536

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    sciencedirect.com/science/article/pii/S2666979X24000922
  11. Sep 2023
  12. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells
    1
    1. scibot 23 Sep 2023
      RRID:CVCL_7526

      DOI: 10.12688/wellcomeopenres.18653.2

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    ncbi.nlm.nih.gov/pmc/articles/PMC10509606/
  13. Aug 2023
  14. www.biorxiv.org www.biorxiv.org
    A Computational Approach for the Identification of Novel L1 Transcriptional Regulators
    1
    1. scibot 29 Aug 2023
      RRID:CVCL_7526

      DOI: 10.1101/2023.08.15.553416

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    biorxiv.org/content/10.1101/2023.08.15.553416v1
  15. www.biorxiv.org www.biorxiv.org
    Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
    1
    1. scibot 18 Aug 2023
      RRID:CVCL_7526

      DOI: 10.1101/2023.08.07.552289

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    biorxiv.org/content/10.1101/2023.08.07.552289v1
  16. Jun 2023
  17. www.nature.com www.nature.com
    Chromatin alternates between A and B compartments at kilobase scale for subgenic organization
    1
    1. scibot 08 Jun 2023
      RRID:CVCL_7526

      DOI: 10.1038/s41467-023-38429-1

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    nature.com/articles/s41467-023-38429-1
  18. Dec 2022
  19. www.sciencedirect.com www.sciencedirect.com
    Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq
    1
    1. scibot 24 Dec 2022
      RRID:CVCL_7526

      DOI: 10.1016/j.xgen.2022.100233

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    sciencedirect.com/science/article/pii/S2666979X22001914
  20. Jun 2022
  21. www.nature.com www.nature.com
    Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing
    1
    1. scibot 01 Jun 2022
      RRID:CVCL_7526

      DOI: 10.1038/s41587-022-01289-z

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    nature.com/articles/s41587-022-01289-z
  22. Apr 2022
  23. www.sciencedirect.com www.sciencedirect.com
    Benchmarking challenging small variants with linked and long reads
    2
    1. scibot 29 Apr 2022
      RRID: CVCL_7526

      DOI: 10.1016/j.xgen.2022.100128

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    2. scibot 29 Apr 2022
      RRID:CVCL_7526

      DOI: 10.1016/j.xgen.2022.100128

      Resource: (Coriell Cat# GM12878, RRID:CVCL_7526)

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    sciencedirect.com/science/article/pii/S2666979X2200057X
  24. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment
    1
    1. scibot 27 Apr 2022
      RRID:CVCL_7526

      DOI: 10.1016/j.crmeth.2022.100188

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    ncbi.nlm.nih.gov/pmc/articles/PMC9017139/
  25. Feb 2022
  26. www.sciencedirect.com www.sciencedirect.com
    HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization
    1
    1. scibot 23 Feb 2022
      RRID:CVCL_7526

      DOI: 10.1016/j.molcel.2022.01.023

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    sciencedirect.com/science/article/pii/S1097276522000983
  27. www.sciencedirect.com www.sciencedirect.com
    Gene architecture directs splicing outcome in separate nuclear spatial regions
    1
    1. scibot 22 Feb 2022
      RRID:CVCL_7526

      DOI: 10.1016/j.molcel.2022.02.001

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    sciencedirect.com/science/article/pii/S109727652200106X
  28. www.nature.com www.nature.com
    Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture
    1
    1. scibot 12 Feb 2022
      RRID:CVCL_7526

      DOI: 10.1038/s41596-021-00651-w

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    nature.com/articles/s41596-021-00651-w
  29. Jan 2022
  30. www.sciencedirect.com www.sciencedirect.com
    Construction of Strand-seq libraries in open nanoliter arrays
    1
    1. scibot 26 Jan 2022
      RRID:CVCL_7526

      DOI: 10.1016/j.crmeth.2021.100150

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    sciencedirect.com/science/article/pii/S2667237521002277
  31. www.nature.com www.nature.com
    SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding
    1
    1. scibot 15 Jan 2022
      RRID:CVCL_7526

      DOI: 10.1038/s41596-021-00633-y

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    nature.com/articles/s41596-021-00633-y
  32. Oct 2021
  33. www.nature.com www.nature.com
    Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)
    1
    1. scibot 23 Oct 2021
      RRID:CVCL_7526

      DOI: 10.1038/s41596-021-00507-3

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    nature.com/articles/s41596-021-00507-3
  34. Aug 2021
  35. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Untitled document
    1
    1. scibot 11 Aug 2021
      RRID:CVCL_7526

      DOI: 10.1093/gigascience/gix024

      Resource: (Coriell Cat# GM12878, RRID:CVCL_7526)

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    ncbi.nlm.nih.gov/pmc/articles/PMC5467036/
  36. academic.oup.com academic.oup.com
    A reference human genome dataset of the BGISEQ-500 sequencer
    1
    1. scibot 11 Aug 2021
      RRID:CVCL_7526

      DOI: 10.1093/gigascience/gix024

      Resource: (Coriell Cat# GM12878, RRID:CVCL_7526)

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    academic.oup.com/gigascience/article/6/5/gix024/3098240
  37. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Untitled document
    1
    1. scibot 04 Aug 2021
      RRID:CVCL_7526

      DOI: 10.7554/eLife.23203

      Resource: (Coriell Cat# GM12878, RRID:CVCL_7526)

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    ncbi.nlm.nih.gov/pmc/articles/PMC5487215/
  38. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Untitled document
    1
    1. scibot 03 Aug 2021
      CVCL_7526

      DOI: 10.1186/s13072-016-0100-6

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    ncbi.nlm.nih.gov/pmc/articles/PMC5097419/
  39. www.sciencedirect.com www.sciencedirect.com
    Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF
    1
    1. scibot 01 Aug 2021
      RRID:CVCL_7526

      DOI: 10.1016/j.cels.2019.05.011

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      Curator: @ethanbadger

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    sciencedirect.com/science/article/pii/S2405471219301929
  40. Jul 2021
  41. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Continuous-trait probabilistic model for comparing multi-species functional genomic data
    1
    1. scibot 30 Jul 2021
      RRID:CVCL_7526

      DOI: 10.1016/j.cels.2018.05.022

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    ncbi.nlm.nih.gov/pmc/articles/PMC6107375/
  42. link.springer.com link.springer.com
    BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
    1
    1. scibot 29 Jul 2021
      RRID:CVCL_7526

      DOI: 10.1186/s13059-019-1671-x

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    link.springer.com/article/10.1186/s13059-019-1671-x
  43. May 2021
  44. www.sciencedirect.com www.sciencedirect.com
    Enhancer viruses for combinatorial cell-subclass-specific labeling
    1
    1. scibot 11 May 2021
      RRID:CVCL_7526

      DOI: 10.1016/j.neuron.2021.03.011

      Resource: (Coriell Cat# GM12878, RRID:CVCL_7526)

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    sciencedirect.com/science/article/pii/S0896627321001598
  45. www.sciencedirect.com www.sciencedirect.com
    Novel target capture DNA library preparation method using CircLigase-mediated hook ligation
    1
    1. scibot 08 May 2021
      RRID:CVCL_7526

      DOI: 10.1016/j.nbt.2020.06.007

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    sciencedirect.com/science/article/pii/S1871678420301540
  46. Feb 2021
  47. academic.oup.com academic.oup.com
    Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
    1
    1. scibot 24 Feb 2021
      RRID:CVCL_7526

      DOI: 10.1093/gigascience/giz158

      Resource: (Coriell Cat# GM12878, RRID:CVCL_7526)

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    academic.oup.com/gigascience/article/9/1/giz158/5695848
  48. elifesciences.org elifesciences.org
    Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host–pathogen dynamics in lymphoblastoid cell lines
    1
    1. scibot 11 Feb 2021
      RRID:CVCL_7526

      DOI: 10.7554/eLife.62586

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      Curator: @evieth

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    elifesciences.org/articles/62586
  49. Dec 2020
  50. www.nature.com www.nature.com
    Efficient hybrid de novo assembly of human genomes with WENGAN
    1
    1. scibot 19 Dec 2020
      RRID:CVCL_7526

      DOI: 10.1038/s41587-020-00747-w

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    nature.com/articles/s41587-020-00747-w
  51. Sep 2020
  52. www.sciencedirect.com www.sciencedirect.com
    Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS
    1
    1. scibot 15 Sep 2020
      RRID:CVCL_7526

      DOI: 10.1016/j.cell.2020.03.002

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      Curator: @ethanbadger

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    sciencedirect.com/science/article/pii/S0092867420302646
  53. academic.oup.com academic.oup.com
    TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads
    1
    1. scibot 12 Sep 2020
      RRID:CVCL_7526

      DOI: 10.1093/gigascience/giaa094

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      Curator: @Naa003

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    academic.oup.com/gigascience/article/9/9/giaa094/5902284
  54. www.sciencedirect.com www.sciencedirect.com
    MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning
    1
    1. scibot 06 Sep 2020
      RRID:CVCL_7526

      DOI: 10.1016/j.cels.2020.04.004

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    sciencedirect.com/science/article/pii/S2405471220301472
  55. onlinelibrary.wiley.com onlinelibrary.wiley.com
    Multi‐omics analysis reveals the functional transcription and potential translation of enhancers
    1
    1. scibot 05 Sep 2020
      RRID:CVCL_7526

      DOI: 10.1002/ijc.33132

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    onlinelibrary.wiley.com/doi/10.1002/ijc.33132
  56. Jan 2020
  57. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Assessment of human diploid genome assembly with 10x Linked-Reads data
    1
    1. scibot 13 Jan 2020
      RRID:CVCL_7526

      DOI: 10.1093/gigascience/giz141

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      Curator: @evieth

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    ncbi.nlm.nih.gov/pmc/articles/PMC6879002/
  58. genomebiology.biomedcentral.com genomebiology.biomedcentral.com
    Untitled document
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    1. scibot 13 Jan 2020
      RRID:CVCL_7526

      DOI: 10.1186/s13059-019-1671-x

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    genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1671-x
  59. Apr 2019
  60. academic.oup.com academic.oup.com
    16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
    1
    1. scibot 04 Apr 2019
      RRID:CVCL__7526

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      (Coriell Cat# GM12878, RRID:CVCL_7526)

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    academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/gix045
  61. Nov 2018
  62. www.sciencedirect.com www.sciencedirect.com
    Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data
    1
    1. scibot 05 Nov 2018
      RRID:CVCL_7526

      Curator: @evieth

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      (Coriell Cat# GM12878, RRID:CVCL_7526)

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    sciencedirect.com/science/article/pii/S2405471218302400
  63. www.sciencedirect.com www.sciencedirect.com
    The Epstein-Barr Virus Regulome in Lymphoblastoid Cells
    1
    1. scibot 05 Nov 2018
      GM12878

      Curator: @Jmenke

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      (Coriell Cat# GM12878, RRID:CVCL_7526)

      SciCrunch record: RRID:CVCL_7526

      Alternate resolvers: SciCrunch xml N2T identifiers.org

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      RRID:CVCL_7526 RRIDCUR:Missing
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    sciencedirect.com/science/article/pii/S1931312817303554
  64. www.sciencedirect.com www.sciencedirect.com
    Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
    1
    1. scibot 05 Nov 2018
      RRID:CVCL_7526

      Resource used:

      (Coriell Cat# GM12878, RRID:CVCL_7526)

      SciCrunch record: RRID:CVCL_7526

      Alternate resolvers: SciCrunch xml N2T identifiers.org

      What is this?

      RRID:CVCL_7526
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    sciencedirect.com/science/article/pii/S0092867418306366
  65. www.sciencedirect.com www.sciencedirect.com
    CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals
    1
    1. scibot 05 Nov 2018
      RRID:CVCL_7526

      Resource used:

      (Coriell Cat# GM12878, RRID:CVCL_7526)

      SciCrunch record: RRID:CVCL_7526

      Alternate resolvers: SciCrunch xml N2T identifiers.org

      What is this?

      RRID:CVCL_7526
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    sciencedirect.com/science/article/pii/S240547121730488X
  66. Nov 2017
  67. academic.oup.com academic.oup.com
    16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
    1
    1. scibot 08 Nov 2017
      CVCL_7526

      Curator: @chewbeccax

      Resource used:

      (Coriell Cat# GM12878, RRID:CVCL_7526)

      SciCrunch record: RRID:CVCL_7526

      Alternate resolvers: SciCrunch xml N2T identifiers.org

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      RRID:CVCL_7526
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    academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/gix045
  68. elifesciences.org elifesciences.org
    Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells
    1
    1. scibot 08 Nov 2017
      CVCL_7526

      Curator: @chewbeccax

      Resource used:

      (Coriell Cat# GM12878, RRID:CVCL_7526)

      SciCrunch record: RRID:CVCL_7526

      Alternate resolvers: SciCrunch xml N2T identifiers.org

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      RRID:CVCL_7526 RRIDCUR:Validated
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    elifesciences.org/articles/23203
  69. academic.oup.com academic.oup.com
    A reference human genome dataset of the BGISEQ-500 sequencer
    1
    1. scibot 08 Nov 2017
      RRID:CVCL_7526

      Curator: @bandrow

      Resource used:

      (Coriell Cat# GM12878, RRID:CVCL_7526)

      SciCrunch record: RRID:CVCL_7526

      Alternate resolvers: SciCrunch xml N2T identifiers.org

      What is this?

      RRID:CVCL_7526
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    academic.oup.com/gigascience/article/6/5/gix024/3098240
  70. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs
    1
    1. scibot 08 Nov 2017
      RRID: CVCL_7526

      Curator: @bandrow

      Resource used:

      (Coriell Cat# GM12878, RRID:CVCL_7526)

      SciCrunch record: RRID:CVCL_7526

      Alternate resolvers: SciCrunch xml N2T identifiers.org

      What is this?

      RRID:CVCL_7526
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    ncbi.nlm.nih.gov/pmc/articles/PMC5005034/