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The multiscale distribution of radiation-induced DNA damage and its impact on local genome structure

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1. scibot 03 Sep 2025
  
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  DOI: 10.1101/2025.08.25.672161
  
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biorxiv.org/content/10.1101/2025.08.25.672161v1
Jul 2025
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Scalable screening of ternary-code DNA methylation dynamics associated with human traits

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1. scibot 04 Jul 2025
  
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  DOI: 10.1016/j.xgen.2025.100929
  
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sciencedirect.com/science/article/pii/S2666979X25001855
Jun 2025
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Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D

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1. scibot 28 Jun 2025
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41594-025-01512-w
  
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nature.com/articles/s41594-025-01512-w
Dec 2024
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Mapping protein–DNA interactions with DiMeLo-seq

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1. scibot 29 Dec 2024
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41596-024-01032-9
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11674881/
Nov 2024
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Replication stress induces POLQ-mediated structural variant formation throughout common fragile sites after entry into mitosis

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1. scibot 10 Nov 2024
  
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  DOI: 10.1038/s41467-024-53917-8
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11541566/
Sep 2024
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SJPedPanel: A pan-cancer gene panel for childhood malignancies to enhance cancer monitoring and early detection

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1. scibot 25 Sep 2024
  
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  DOI: 10.1158/1078-0432.CCR-24-1063
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11393547/
Jul 2024
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An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells

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1. scibot 03 Jul 2024
  
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  DOI: 10.1371/journal.pgen.1011311
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11189215/
Jun 2024
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POLQ mediates replication-stress induced structural variant formation throughout common fragile sites during mitosis

1
1. scibot 06 Jun 2024
  
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  RRID:CVCL_7526
  
  DOI: 10.1101/2024.05.28.596214
  
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biorxiv.org/content/10.1101/2024.05.28.596214v1
Apr 2024
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Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans

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1. scibot 11 Apr 2024
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.xgen.2024.100536
  
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sciencedirect.com/science/article/pii/S2666979X24000922
Sep 2023
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Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells

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1. scibot 23 Sep 2023
  
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  RRID:CVCL_7526
  
  DOI: 10.12688/wellcomeopenres.18653.2
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10509606/
Aug 2023
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A Computational Approach for the Identification of Novel L1 Transcriptional Regulators

1
1. scibot 29 Aug 2023
  
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  RRID:CVCL_7526
  
  DOI: 10.1101/2023.08.15.553416
  
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biorxiv.org/content/10.1101/2023.08.15.553416v1
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Single-cell somatic copy number variants in brain using different amplification methods and reference genomes

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1. scibot 18 Aug 2023
  
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  RRID:CVCL_7526
  
  DOI: 10.1101/2023.08.07.552289
  
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biorxiv.org/content/10.1101/2023.08.07.552289v1
Jun 2023
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Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

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1. scibot 08 Jun 2023
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41467-023-38429-1
  
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nature.com/articles/s41467-023-38429-1
Dec 2022
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Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq

1
1. scibot 24 Dec 2022
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.xgen.2022.100233
  
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sciencedirect.com/science/article/pii/S2666979X22001914
Jun 2022
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Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

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1. scibot 01 Jun 2022
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41587-022-01289-z
  
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nature.com/articles/s41587-022-01289-z
Apr 2022
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Benchmarking challenging small variants with linked and long reads

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1. scibot 29 Apr 2022
  
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  RRID: CVCL_7526
  
  DOI: 10.1016/j.xgen.2022.100128
  
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  Curator: @sophiastull
  
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2. scibot 29 Apr 2022
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.xgen.2022.100128
  
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sciencedirect.com/science/article/pii/S2666979X2200057X
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
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.crmeth.2022.100188
  
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ncbi.nlm.nih.gov/pmc/articles/PMC9017139/
Feb 2022
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HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization

1
1. scibot 23 Feb 2022
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.molcel.2022.01.023
  
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sciencedirect.com/science/article/pii/S1097276522000983
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Gene architecture directs splicing outcome in separate nuclear spatial regions

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1. scibot 22 Feb 2022
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.molcel.2022.02.001
  
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sciencedirect.com/science/article/pii/S109727652200106X
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Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

1
1. scibot 12 Feb 2022
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41596-021-00651-w
  
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nature.com/articles/s41596-021-00651-w
Jan 2022
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Construction of Strand-seq libraries in open nanoliter arrays

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1. scibot 26 Jan 2022
  
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  DOI: 10.1016/j.crmeth.2021.100150
  
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sciencedirect.com/science/article/pii/S2667237521002277
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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
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41596-021-00633-y
  
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nature.com/articles/s41596-021-00633-y
Oct 2021
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Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

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1. scibot 23 Oct 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41596-021-00507-3
  
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nature.com/articles/s41596-021-00507-3
Aug 2021
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Untitled document

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1. scibot 11 Aug 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.1093/gigascience/gix024
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5467036/
academic.oup.com academic.oup.com

A reference human genome dataset of the BGISEQ-500 sequencer

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1. scibot 11 Aug 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.1093/gigascience/gix024
  
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academic.oup.com/gigascience/article/6/5/gix024/3098240
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Untitled document

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1. scibot 04 Aug 2021
  
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  DOI: 10.7554/eLife.23203
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5487215/
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Untitled document

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1. scibot 03 Aug 2021
  
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  CVCL_7526
  
  DOI: 10.1186/s13072-016-0100-6
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5097419/
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Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF

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1. scibot 01 Aug 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.cels.2019.05.011
  
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sciencedirect.com/science/article/pii/S2405471219301929
Jul 2021
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Continuous-trait probabilistic model for comparing multi-species functional genomic data

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1. scibot 30 Jul 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.cels.2018.05.022
  
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ncbi.nlm.nih.gov/pmc/articles/PMC6107375/
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BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

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1. scibot 29 Jul 2021
  
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  DOI: 10.1186/s13059-019-1671-x
  
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link.springer.com/article/10.1186/s13059-019-1671-x
May 2021
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Enhancer viruses for combinatorial cell-subclass-specific labeling

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1. scibot 11 May 2021
  
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  DOI: 10.1016/j.neuron.2021.03.011
  
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sciencedirect.com/science/article/pii/S0896627321001598
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Novel target capture DNA library preparation method using CircLigase-mediated hook ligation

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1. scibot 08 May 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.nbt.2020.06.007
  
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sciencedirect.com/science/article/pii/S1871678420301540
Feb 2021
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Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

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1. scibot 24 Feb 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.1093/gigascience/giz158
  
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academic.oup.com/gigascience/article/9/1/giz158/5695848
elifesciences.org elifesciences.org

Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host–pathogen dynamics in lymphoblastoid cell lines

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1. scibot 11 Feb 2021
  
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  RRID:CVCL_7526
  
  DOI: 10.7554/eLife.62586
  
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elifesciences.org/articles/62586
Dec 2020
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Efficient hybrid de novo assembly of human genomes with WENGAN

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1. scibot 19 Dec 2020
  
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  RRID:CVCL_7526
  
  DOI: 10.1038/s41587-020-00747-w
  
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nature.com/articles/s41587-020-00747-w
Sep 2020
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Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS

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1. scibot 15 Sep 2020
  
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  DOI: 10.1016/j.cell.2020.03.002
  
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TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

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1. scibot 12 Sep 2020
  
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  RRID:CVCL_7526
  
  DOI: 10.1093/gigascience/giaa094
  
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academic.oup.com/gigascience/article/9/9/giaa094/5902284
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MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning

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1. scibot 06 Sep 2020
  
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  RRID:CVCL_7526
  
  DOI: 10.1016/j.cels.2020.04.004
  
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Multi‐omics analysis reveals the functional transcription and potential translation of enhancers

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1. scibot 05 Sep 2020
  
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  RRID:CVCL_7526
  
  DOI: 10.1002/ijc.33132
  
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onlinelibrary.wiley.com/doi/10.1002/ijc.33132
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Assessment of human diploid genome assembly with 10x Linked-Reads data

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1. scibot 13 Jan 2020
  
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  RRID:CVCL_7526
  
  DOI: 10.1093/gigascience/giz141
  
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Untitled document

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1. scibot 13 Jan 2020
  
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  RRID:CVCL_7526
  
  DOI: 10.1186/s13059-019-1671-x
  
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genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1671-x
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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

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1. scibot 04 Apr 2019
  
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academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/gix045
Nov 2018
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Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data

1
1. scibot 05 Nov 2018
  
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  RRID:CVCL_7526
  
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The Epstein-Barr Virus Regulome in Lymphoblastoid Cells

1
1. scibot 05 Nov 2018
  
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  GM12878
  
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Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

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  RRID:CVCL_7526
  
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CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals

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  RRID:CVCL_7526
  
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sciencedirect.com/science/article/pii/S240547121730488X
Nov 2017
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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

1
1. scibot 08 Nov 2017
  
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  CVCL_7526
  
  Curator: @chewbeccax
  
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elifesciences.org elifesciences.org

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

1
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  CVCL_7526
  
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A reference human genome dataset of the BGISEQ-500 sequencer

1
1. scibot 08 Nov 2017
  
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  RRID:CVCL_7526
  
  Curator: @bandrow
  
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MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs

1
1. scibot 08 Nov 2017
  
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  RRID: CVCL_7526
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5005034/