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Jul 2021
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Atlas of Subcellular RNA Localization Revealed by APEX-Seq

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  DOI: 10.1016/j.cell.2019.05.027
  
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Untitled document

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academic.oup.com/gigascience/article/8/5/giz036/5484800
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Untitled document

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Untitled document

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Untitled document

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academic.oup.com/gigascience/article/7/2/gix128/4750781
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Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome

1
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academic.oup.com/gbe/article/11/4/1033/5378701
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PI3K Inhibition Activates SGK1 via a Feedback Loop to Promote Chromatin-Based Regulation of ER-Dependent Gene Expression

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  DOI: 10.1016/j.celrep.2019.02.111
  
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RNA Polymerase II CTD Tyrosine 1 Is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

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  DOI: 10.1016/j.molcel.2018.12.002
  
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currentprotocols.onlinelibrary.wiley.com currentprotocols.onlinelibrary.wiley.com

High‐Resolution Chromatin Profiling Using CUT&RUN

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currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpmb.85
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Untitled document

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academic.oup.com/gigascience/article/6/8/gix049/3888813
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A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis.

2
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  DOI: 10.7554/eLife.28383
  
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Untitled document

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  DOI: 10.1002/cne.24282
  
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onlinelibrary.wiley.com/doi/10.1002/cne.24282/full
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Human biallelic MFN2 mutations induce mitochondrial dysfunction, upper body adipose hyperplasia, and suppression of leptin expression

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Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

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1. scibot 27 Jul 2021
  
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  DOI: 10.1016/j.cels.2018.09.003
  
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sciencedirect.com/science/article/pii/S2405471218303892
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Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

1
1. scibot 27 Jul 2021
  
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  DOI: 10.1016/j.molcel.2018.10.011
  
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sciencedirect.com/science/article/pii/S1097276518308438
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Spatiotemporal m(i)RNA Architecture and 3′ UTR Regulation in the C. elegans Germline

1
1. scibot 27 Jul 2021
  
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  DOI: 10.1016/j.devcel.2018.10.005
  
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sciencedirect.com/science/article/pii/S1534580718308268
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Merkel Cells Activate Sensory Neural Pathways through Adrenergic Synapses

1
1. scibot 27 Jul 2021
  
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  DOI: 10.1016/j.neuron.2018.10.034
  
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sciencedirect.com/science/article/pii/S0896627318309425
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MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis

1
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  DOI: 10.1016/j.molcel.2018.09.031
  
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sciencedirect.com/science/article/pii/S1097276518308025
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Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

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  DOI: 10.1016/j.molcel.2018.09.033
  
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sciencedirect.com/science/article/pii/S1097276518308323
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Distinct Regulation of Th17 and Th1 Cell Differentiation by Glutaminase-Dependent Metabolism

1
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  DOI: 10.1016/j.cell.2018.10.001
  
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sciencedirect.com/science/article/pii/S0092867418313096
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Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

1
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  DOI: 10.1016/j.cell.2018.10.038
  
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N6-methyladenine DNA Modification in Glioblastoma

1
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  DOI: 10.1016/j.cell.2018.10.006
  
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sciencedirect.com/science/article/pii/S009286741831314X
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BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

2
1. scibot 27 Jul 2021
  
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  DOI: 10.1186/s13073-018-0528-3
  
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2. scibot 27 Jul 2021
  
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  DOI: 10.1186/s13073-018-0528-3
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5859752/
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RNA Binding to CBP Stimulates Histone Acetylation and Transcription

2
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  DOI: 10.1016/j.cell.2016.12.020
  
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2. scibot 27 Jul 2021
  
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  DOI: 10.1016/j.cell.2016.12.020
  
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sciencedirect.com/science/article/pii/S0092867416317366
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Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors

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sciencedirect.com/science/article/pii/S1535610818300060
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Untitled document

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  DOI: 10.1093/gigascience/gix112
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5751067/
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Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

1
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  RRID:SCR_00210
  
  DOI: 10.7554/eLife.47891
  
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A molecular portrait of maternal sepsis from Byzantine Troy

2
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  DOI: 10.7554/eLife.20983
  
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  DOI: 10.7554/eLife.20983
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5224923/
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Transcriptome profiling of developing photoreceptor subtypes reveals candidate genes involved in avian photoreceptor diversification

1
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  nlx_154607
  
  DOI: 10.1002/cne.23702
  
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onlinelibrary.wiley.com/doi/10.1002/cne.23702/full
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Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination

1
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  DOI: 10.1016/j.molcel.2021.06.016
  
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Patient-derived iPSC-cerebral organoid modeling of the 17q11.2 microdeletion syndrome establishes CRLF3 as a critical regulator of neurogenesis

1
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  DOI: 10.1016/j.celrep.2021.109315
  
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sciencedirect.com/science/article/pii/S2211124721006914
Jun 2021
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Pharmacologic modulation of RNA splicing enhances anti-tumor immunity

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  DOI: 10.1016/j.cell.2021.05.038
  
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A drastic shift in the energetic landscape of toothed whale sperm cells

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Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation

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SORBS2 is a genetic factor contributing to cardiac malformation of 4q deletion syndrome patients

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Sublayer- and cell-type-specific neurodegenerative transcriptional trajectories in hippocampal sclerosis

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Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)

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ZC3H4 restricts non-coding transcription in human cells

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Integrated sensing of host stresses by inhibition of a cytoplasmic two-component system controls M. tuberculosis acute lung infection

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BiSulfite Bolt: A bisulfite sequencing analysis platform

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The Meishan pig genome reveals structural variation mediated gene expression and phenotypic divergence underlying Asian pig domestication

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Cell of Origin Influences Pancreatic Cancer Subtype

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Alterations in BAP1 are Associated with Cisplatin Resistance Through Inhibition of Apoptosis in Malignant Pleural Mesothelioma (MPM).

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Derivation of Intermediate Pluripotent Stem Cells Amenable to Primordial Germ Cell Specification

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Adult Neural Stem Cells Are Alerted by Systemic Inflammation through TNF-α Receptor Signaling

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Repetitive Elements Trigger RIG-I-like Receptor Signaling that Regulates the Emergence of Hematopoietic Stem and Progenitor Cells

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A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin

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A single-cell analysis of the Arabidopsis vegetative shoot apex

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How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

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Whole-genome analysis of giraffe supports four distinct species

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Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis

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Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts

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Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass

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Recording of DNA-binding events reveals the importance of a repurposed Candida albicans regulatory network for gut commensalism

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5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer’s disease

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Efficient RNA polymerase II pause release requires U2 snRNP function

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A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer

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Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants

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The genome of Tripterygium wilfordii and characterization of the celastrol biosynthesis pathway

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A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes

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Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form

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Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance

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The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr

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Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

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Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium

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ncbi.nlm.nih.gov/pmc/articles/PMC8007386/
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Genomic exploration of the targets of FOXL2 and ESR2 unveils their implication in cell migration, invasion, and adhesion

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Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery

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Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing

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  DOI: 10.1093/gigascience/giab014
  
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Twelve years of SAMtools and BCFtools

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HTSlib: C library for reading/writing high-throughput sequencing data

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New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples

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Germline EGFR variants are over-represented in adolescents and young adults (AYA) with adrenocortical carcinoma

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The glucocorticoid receptor recruits the COMPASS complex to regulate inflammatory transcription at macrophage enhancers

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Interferon-λ Mediates Non-redundant Front-Line Antiviral Protection against Influenza Virus Infection without Compromising Host Fitness

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The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages

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Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Flowering Time in Brassica napus L.

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Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

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Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

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Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development

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A microbial gene catalog of anaerobic digestion from full-scale biogas plants

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The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

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Failures of nerve regeneration caused by aging or chronic denervation are rescued by restoring Schwann cell c-Jun

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Protocol for assaying chromatin accessibility using ATAC-seq in plants

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Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism

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A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

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Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation

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Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest

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Circadian VIPergic Neurons of the Suprachiasmatic Nuclei Sculpt the Sleep-Wake Cycle

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Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments

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Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

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Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes

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Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

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Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2

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TARGET-Seq: A Protocol for High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing

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Host-induced spermidine production in motile Pseudomonas aeruginosa triggers phagocytic uptake

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Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing

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Changes in the transcriptional fingerprint of satellite glial cells following peripheral nerve injury

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Construction of a chromosome-scale long-read reference genome assembly for potato

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Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods

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Binding of the Treslin-MTBP Complex to Specific Regions of the Human Genome Promotes the Initiation of DNA Replication

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Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteins

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ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair

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Umbilical cord blood-derived ILC1-like cells constitute a novel precursor for mature KIR+NKG2A- NK cells

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Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs

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Cell-type diversity and regionalized gene expression in the planarian intestine

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Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity

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Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection

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Activin A determines steroid levels and composition in the fetal testis

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Investigating Human Mitochondrial Genomes in Single Cells

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Aire-dependent genes undergo Clp1-mediated 3’UTR shortening associated with higher transcript stability in the thymus

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A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

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Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS

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A Preliminary Study to Investigate the Genetic Background of Longevity Based on Whole-Genome Sequence Data of Two Methuselah Dogs

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Draft Genome of the Asian Buffalo Leech Hirudinaria manillensis

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Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

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Imprinted Maternally Expressed microRNAs Antagonize Paternally Driven Gene Programs in Neurons

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NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency

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Transposase-assisted tagmentation of RNA/DNA hybrid duplexes

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Global genome diversity of the Leishmania donovani complex

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Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

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C/EBPα and GATA-2 Mutations Induce Bilineage Acute Erythroid Leukemia through Transformation of a Neomorphic Neutrophil-Erythroid Progenitor

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INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins

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Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice

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The testis protein ZNF165 is a SMAD3 cofactor that coordinates oncogenic TGFβ signaling in triple-negative breast cancer

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Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits

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Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

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Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity

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S-phase-independent silencing establishment in Saccharomyces cerevisiae

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Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation

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Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs

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Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum

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The role of Rif1 in telomere length regulation is separable from its role in origin firing

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Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons

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A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

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Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18

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Human Herpesvirus 6 Detection in Alzheimer’s Disease Cases and Controls across Multiple Cohorts

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Deletion of Stk11 and Fos in mouse BLA projection neurons alters intrinsic excitability and impairs formation of long-term aversive memory

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Rapid Dynamics of Signal-Dependent Transcriptional Repression by Capicua

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Identification of scavenger receptor B1 as the airway microfold cell receptor for Mycobacterium tuberculosis

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Sphingosine 1-phosphate-regulated transcriptomes in heterogenous arterial and lymphatic endothelium of the aorta

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Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes

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The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates

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

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Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

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CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

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Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation

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The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance

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Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes

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Two Separation-of-Function Isoforms of Human TPP1 Dictate Telomerase Regulation in Somatic and Germ Cells

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Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

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Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

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Genome plasticity in Candida albicans is driven by long repeat sequences

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Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy ( Coilia nasus ) provides novel insights into migratory adaptation

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Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling

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Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa

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Chromosomal-level reference genome of Chinese peacock butterfly ( Papilio bianor ) based on third-generation DNA sequencing and Hi-C analysis

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Active and Repressed Chromatin Domains Exhibit Distinct Nucleosome Segregation during DNA Replication

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The piRNA Response to Retroviral Invasion of the Koala Genome

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Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin–producing Escherichia coli

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Genome-Edited Triple-Recessive Mutation Alters Seed Dormancy in Wheat

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High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing

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Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation

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MicroRNAs Cause Accelerated Decay of Short-Tailed Target mRNAs

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Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop

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CTCF confers local nucleosome resiliency after DNA replication and during mitosis

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Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration

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Chromosomal-level assembly of the blood clam, Scapharca ( Anadara ) broughtonii , using long sequence reads and Hi-C

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Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

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Continuous and Discrete Neuron Types of the Adult Murine Striatum

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Chromosome‐level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

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Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

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DUX4 Suppresses MHC Class I to Promote Cancer Immune Evasion and Resistance to Checkpoint Blockade

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RNA sequencing of isolated cell populations expressing human APOL1 G2 risk variant reveals molecular correlates of sickle cell nephropathy in zebrafish podocytes

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Single-Cell RNA-Seq Reveals Developmental Origins and Ontogenetic Stability of Neurexin Alternative Splicing Profiles

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Combinatorial action of NF–Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish

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Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability

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Oligodendrocyte Intrinsic miR-27a Controls Myelination and Remyelination

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The Dynamics of Cytoplasmic mRNA Metabolism

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Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

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Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data

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Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

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Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy

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Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans

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