bioRxiv Genomics
@biorxiv_genomic
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Joined June 2016
Integrated QTL mapping and CRISPR screening in pooled iPSC-derived microglia reveals genetic drivers of neurodegenerative risk #biorxiv_genomic.
biorxiv.org
Mounting evidence implicates microglia in neurodegeneration, but linking disease-associated genetic variants to target genes and cellular phenotypes is hindered by the inaccessibility of these cells....
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spa-ChIP-seq enables the comprehensive profiling of chromatin #biorxiv_genomic.
biorxiv.org
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a well-established method for studying the genomic localization of DNA-associated proteins. Yet, while useful, most ChIP-seq...
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Extracellular Vesicle Gene Expression Enables Sensitive Detection of Colorectal Neoplasia #biorxiv_genomic.
biorxiv.org
BACKGROUND & AIMS: Extracellular vesicles (EVs), including exosomes, are emerging as promising carriers of disease-specific biomarkers due to their molecular cargo reflective of cellular origin....
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Preservation and Clonal Behavior of Extrachromosomal DNA in Patient-Derived Xenograft Models of Childhood Cancers #biorxiv_genomic.
biorxiv.org
Extrachromosomal DNA (ecDNA) is a powerful oncogenic driver linked to poor prognosis in pediatric cancers. Whole-genome sequencing of 338 patient-derived xenograft (PDX) samples and 127 matched...
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Cellular and Molecular Architecture of Renin-Angiotensin System Signaling in the PVN Under Cardiometabolic Stress #biorxiv_genomic.
biorxiv.org
The hypothalamic paraventricular nucleus (PVN) integrates neuroendocrine and autonomic signals that regulate blood pressure and metabolism. Although the renin-angiotensin system (RAS) is implicated...
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Insulin modulates mPFC gene expression and emotional behavior in a sex-specific manner following fetal growth restriction #biorxiv_genomic.
biorxiv.org
Exposure to prenatal adversity (e.g., stress, malnutrition) is a major risk factor for lifelong vulnerability to neuropsychiatric and metabolic disorders, and alterations in the function of periphe...
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Semi-supervised detection of natural selection with positive-unlabeled learning #biorxiv_genomic.
biorxiv.org
Identifying genomic regions shaped by natural selection is a central goal in evolutionary genomics. Existing machine learning methods for this task are typically trained using simulated genomic data...
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NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable Representations #biorxiv_genomic.
biorxiv.org
Pre-training large language models on genomic sequences has become a powerful approach for learning biologically meaningful representations. While masked language modeling (MLM)-based approaches,...
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Genome-wide analysis of social behaviour in context: a meta-regression approach across social domains, reporters and developmental stages #biorxiv_genomic.
biorxiv.org
Social behaviour is a heritable, context-dependent trait that changes across social settings and development, influencing wellbeing and mental health. We present the first genome-wide meta-regression...
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Epigenetic markers of middle-age: non-linear DNA methylation changes with aging in humans #biorxiv_genomic.
biorxiv.org
Background: Human DNA is known to exhibit an overall tendency toward demethylation with aging. However, assuming a simple linear relationship between DNA methylation and age does not align with the...
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A prognostic signature for lung adenocarcinoma in people who have never smoked #biorxiv_genomic.
biorxiv.org
Knowledge of tumor cell dynamics can inform prognosis and treatment yet is largely lacking for lung adenocarcinoma in people who have never smoked (NS-LUAD). With RNA-seq data from 684 NS-LUAD and...
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Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification #biorxiv_genomic.
biorxiv.org
Genetics-informed proteome-wide association studies (PWAS) provide an effective way to map the complex molecular landscape of biological mechanisms for complex diseases. PWAS relies on an ancestry-...
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Uncovering Functional Sequence Gaps in Human Reference Genomes using African Pan Genome Contig Sequences #biorxiv_genomic.
biorxiv.org
Predominantly used human reference genomes, including GRCh38 and the gapless T2T-CHM13 references, remain limited in their representation of African genomic diversity. We analyzed African Pan-Genome...
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Rapid turnover and recurrent structural variation at the 17q21.31 locus in modern and ancient human genomes, and primates #biorxiv_genomic.
biorxiv.org
The 17q21.31 locus in humans harbors several complex structural haplotypes including a ~970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions...
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A laser capture microdissection-based method for high-sensitivity transcriptomics from archived FFPE tissue slides with single-cell . #biorxiv_genomic.
biorxiv.org
Understanding gene expression within its spatial context is essential for unravelling biological processes. Laser Capture Microdissection (LCM) has emerged as a transformative technology, enabling...
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Autosomal Allelic Inactivation: Variable Replication and Dosage Sensitivity #biorxiv_genomic.
biorxiv.org
Autosomal monoallelic gene expression and asynchronous replication between alleles are well-established features of imprinted genes and genes regulated by allelic exclusion. Inactivation/Stability...
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Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus #biorxiv_genomic.
biorxiv.org
Genome size expansions are common among eukaryotic lineages. Enlarged genomes can be bioenergetically demanding, and active mobile elements can trigger chromosomal rearrangements and loss of gene...
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A functional annotation of a selected protein-coding gene in the Olimarabadopsis pumila genome: Oxysterol-binding . #biorxiv_genomic.
biorxiv.org
Olimarabidopsis pumila, a spring ephemeral from Asia, is closely related to the well-studied model organism Arabidopsis thaliana, though with various important differences. O. pumila has evolved to...
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Characterization of interindividual DNA methylation variability in rainbow trout (Oncorhynchus mykiss) #biorxiv_genomic.
biorxiv.org
Interindividual epigenetic variability, particularly in DNA methylation, is now recognized as a significant contributor to phenotypic diversity in humans and mammals. These epivariable regions, which...
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Whole-genome single-cell multimodal history tracing to reveal cell identity transition #biorxiv_genomic.
biorxiv.org
Advances in single-cell sequencing have deepened our understanding of cellular identities. However, because they inherently capture only static snapshots, after which no further observations are...
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