HTSeq—a Python framework to work with high-throughput sequencing data

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The Sequence Alignment/Map format and SAMtools

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Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

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Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

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5-Methylcytosine RNA Methylation in Arabidopsis Thaliana

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SMARCB1 is required for widespread BAF complex–mediated activation of enhancers and bivalent promoters

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Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels

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Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution

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α-Ketoglutarate links p53 to cell fate during tumour suppression

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Gene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders

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Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia

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Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells

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Impaired death receptor signaling in leukemia causes antigen-independent resistance by inducing CAR T-cell dysfunction

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Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models

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Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

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Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain

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Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

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Glycine-based treatment ameliorates NAFLD by modulating fatty acid oxidation, glutathione synthesis, and the gut microbiome

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Resolving early mesoderm diversification through single-cell expression profiling

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A core function of EDS1 with PAD4 is to protect the salicylic acid defense sector in Arabidopsis immunity

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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

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Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type

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Myocardial Gene Expression Signatures in Human Heart Failure With Preserved Ejection Fraction

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ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia

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Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation

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Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

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Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

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The evening complex coordinates environmental and endogenous signals in Arabidopsis

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Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

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Dual RNA-Seq of Mtb-Infected Macrophages In Vivo Reveals Ontologically Distinct Host-Pathogen Interactions

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Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

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Rapid magnetic isolation of extracellular vesicles via lipid-based nanoprobes

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Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes

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Niacin Cures Systemic NAD+ Deficiency and Improves Muscle Performance in Adult-Onset Mitochondrial Myopathy

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NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program

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Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

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Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA

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Photosensitivity and type I IFN responses in cutaneous lupus are driven by epidermal-derived interferon kappa

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Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

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Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

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Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring

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Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues

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SCnorm: robust normalization of single-cell RNA-seq data

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Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism

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Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

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Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis

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Embryo model completes gastrulation to neurulation and organogenesis

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Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity

Birkenbihl, R. P., Kracher, B., Roccaro, M., & Somssich, I. E. (2016) · The Plant Cell · doi:10.1105/tpc.16.00681 · Cited by 281

Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells

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Mitochondrial translation requires folate-dependent tRNA methylation

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Capturing human trophoblast development with naive pluripotent stem cells in vitro

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The loss of RNA N6-adenosine methyltransferase Mettl14 in tumor-associated macrophages promotes CD8+ T cell dysfunction and tumor growth

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Initiation and amplification of SnRK2 activation in abscisic acid signaling

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Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

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B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity

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The mid-developmental transition and the evolution of animal body plans

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Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

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An interactive environment for agile analysis and visualization of ChIP-sequencing data

Lerdrup, M., Johansen, J. V., Singh, S. A., & Hansen, K. H. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3180 · Cited by 277

Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells

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Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq

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An efficient KRAB domain for CRISPRi applications in human cells

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The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma

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Soluble ACE2-mediated cell entry of SARS-CoV-2 via interaction with proteins related to the renin-angiotensin system

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The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination

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IL-10 constrains sphingolipid metabolism to limit inflammation

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The Arabidopsis CERK1‐associated kinase PBL27 connects chitin perception to MAPK activation

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TERRA RNA Antagonizes ATRX and Protects Telomeres

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Microglial TREM-1 receptor mediates neuroinflammatory injury via interaction with SYK in experimental ischemic stroke

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