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Berkson's Paradox: A Common Statistical Error in Genomics Analyses

The paper identifies Berkson's paradox as a common statistical error in genomics analyses and provides examples and approaches to avoid misinterpreting spurious correlations.

Chromosome-scale nuclear and mitochondrial genome assemblies reveal extreme genome compartmentalization in the hazelnut pathogen Anisogramma anomala

The paper presents a chromosome-scale genome assembly of Anisogramma anomala, revealing extreme genome compartmentalization and unique mitochondrial features.

Dynamics of cell states and alternative splicing following kidney ischemia-reperfusion injury

The paper analyzes bulk RNA-seq data from a kidney IRI mouse experiment to identify temporal phases and alternatively spliced genes, revealing potential splicing regulators involved in injury and repair.

Early Prenatal Cell-Free DNA Methylation Landscape Informs Epigenetic Purification of the Circulating Fetal Genome

The paper develops an epigenetic enrichment method for fetal cfDNA using a first-trimester methylome reference, increasing fetal fraction from 5.1% to 28.4%.

Cross-Tissue Concordance of Blood-Trained Protein EpiScores in Donor-Matched GTEx Tissues

This study evaluates how well blood-trained protein EpiScores predict protein levels in non-blood GTEx tissues, finding broad concordance in lung but covariate-sensitive results in other tissues.

A finished, telomere-to-telomere assembly for Botrytis cinerea strain B05.10

The paper presents an improved genome assembly for Botrytis cinerea strain B05.10 with added telomeres and error corrections.

Multimodal functional characterization of the LDLR noncoding landscape

This study uses multiple functional genomic approaches to identify and characterize cis-regulatory elements (CREs) influencing LDLR expression, revealing overlapping yet distinct CREs across methods.

Gene-poor, repeat-rich Y chromosomes in two Neotropical malaria vectors, Anopheles cruzii and Anopheles aquasalis

The paper identifies Y-linked sequences in two Neotropical malaria vectors using YGS and CQ methods, revealing gene-poor, repeat-rich Y chromosomes with no intact protein-coding genes.

Robust Chromosome Segmentation in Sparse Single-Cell Whole-Genome Sequencing Using a k-Segment Constrained Hidden Markov Model

The paper develops a k-segment constrained HMM for LOH detection in sparse single-cell WGS data, achieving high recall and precision.

Maternal E-cigarette Exposure Augments Murine Abdominal Aortic Aneurysm

This study shows maternal e-cigarette vaping increases AAA growth in offspring mice and causes transgenerational DNA methylation and accessibility changes.

Differential k-mer distributions enable identification of tetrapod subterminal heterochromatin

The paper identifies subterminal heterochromatin in tetrapods using k-mer distributions, revealing ancient subgenome-specific repeats in Xenopus laevis.

ONT-LibQC: rapid quality control of chromatin assay libraries using shallow nanopore sequencing

ONT-LibQC uses shallow nanopore sequencing to rapidly assess chromatin assay library quality before deep sequencing, showing consistent results with Illumina sequencing.

Exploring DNA movement through the application of droplet based high efficient chromatin conformation capture (DropHiChew) and loop velocity

This paper introduces DropHiChew and loop velocity to study DNA movement dynamics, enabling accurate trajectory estimation with shallow sequencing.

RNA-sequencing of butyrate-treated human lymphoblastoid cell lines shows dysregulated genes of multiple disease-related pathways

This study uses RNA-seq to analyze the transcriptomic effects of butyrate on human lymphoblastoid cell lines, identifying dysregulated genes in multiple disease-related pathways.

Dissecting cellular and molecular networks of aging and senescence in the human hippocampus

This study identifies spatially resolved aging and senescence signatures in the human hippocampus using multi-omics approaches, revealing cell-type and sex-specific gene expression changes.

Haplotype-resolved genetic mapping using selfed progeny enables simultaneous genome assembly validation and trait dissection in a heterozygous plant

This paper introduces HRGM, a method that uses selfed progeny and haplotype-resolved assemblies to create genetic maps and validate genome assemblies in plants, identifying loci associated with root development.

Relaxed evolutionary constraints on mitochondrial electron-transfer-associated variants in human cancers

The paper predicts how MT-CYB mutations affect electron transfer in cancer and finds they are depleted in germline but enriched in tumors.

Copy number variants (CNV) interfere with human Accelerated Regions (HARs) to cause neurodevelopmental disorders: a large-scale cohort study

This study investigates the role of copy number variants (CNVs) disrupting Human Accelerated Regions (HARs) in neurodevelopmental disorders (NDDs) using a large cohort of 821 children, identifying three recurrent HAR loci associated with NDDs.

Regulation by partition predicts enhancer target selection in mammalian genomes

The paper introduces SPIE-seq to study enhancer target selection, finding that genomic context and distance-weighted competition, not enhancer identity, determine target choice.

Evolution of CTCF underlies the establishment of loop extrusion as a predominant chromatin folding mechanism in vertebrates

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.