LKB1 inactivation modulates chromatin accessibility to drive metastatic progression

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

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High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

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Regenerative lineages and immune-mediated pruning in lung cancer metastasis

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Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases

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Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma

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Comprehensive Integration of Single-Cell Data

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An Lkb1-Sik axis suppresses lung tumor growth and controls differentiation

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The AMPK-related kinases SIK1 and SIK3 mediate key tumor suppressive effects of LKB1 in NSCLC

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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs

(2019) William A. Flavahan et al.   NATURE

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

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The PLAG1-GDH1 Axis Promotes Anoikis Resistance and Tumor Metastasis through CamKK2-AMPK Signaling in LKB1-Deficient Lung Cancer

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Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

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Minimal functional driver gene heterogeneity among untreated metastases

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PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

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The chromatin accessibility landscape of primary human cancers

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Molecular definition of a metastatic lung cancer state reveals a targetable CD109–Janus kinase–Stat axis

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chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

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Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2

(2017) Haikuo Zhang et al.   Nature Communications

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

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A Transcriptional Signature Identifies LKB1 Functional Status as a Novel Determinant of MEK Sensitivity in Lung Adenocarcinoma

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A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

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LKB1 loss links serine metabolism to DNA methylation and tumorigenesis

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Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

(2016) David W Morgens et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Metastasis as an evolutionary process

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Immunohistochemical Loss of LKB1 Is a Biomarker for More Aggressive Biology in KRAS-Mutant Lung Adenocarcinoma

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Whole genomes redefine the mutational landscape of pancreatic cancer

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Recombinase-based conditional and reversible gene regulation via XTR alleles

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Class IIa HDACs - new insights into their functions in physiology and pathology

(2014) Maribel Parra   FEBS Journal

The Tumor Suppressor Kinase LKB1 Activates the Downstream Kinases SIK2 and SIK3 to Stimulate Nuclear Export of Class IIa Histone Deacetylases

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

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Suppression of lung adenocarcinoma progression by Nkx2-1

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Integrative Genomic and Proteomic Analyses Identify Targets for Lkb1-Deficient Metastatic Lung Tumors

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