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NicheCorr: Identifying Niche-Specific Differential Gene Co-Expression in Spatial Transcriptomics

NicheCorr identifies niche-specific gene co-expression changes in spatial transcriptomics data, revealing spatially structured signaling interactions in liver and pancreatic cancer datasets.

Transcriptome-wide Differential Expression and Splicing in Inflammatory Bowel Disease Patients

The paper identifies differential expression and splicing in IBD patients, showing distinct molecular mechanisms in CD and UC.

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

Direct effects on gene transcription revealed by global and CRISPR-targeted oxidative DNA damage

The paper shows oxidative DNA damage directly affects gene transcription through repair-dependent mechanisms using RNA-Seq, ChIP-seq, and chemogenetic approaches.

Genome and methylome of the root crop table beet (Beta vulgaris)

The paper presents a chromosome-scale genome and methylome assembly for table beet, identifies candidate genes for geosmin production, and compares it with sugar beet.

A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds

The paper presents a gapless Landrace pig genome assembly that improves resolution of repetitive regions and reveals breed-specific telomere repeat structures.

Unpacking Chromatin Accessibility with Fiber-seq

This paper introduces Fiber-seq, a method for detecting chromatin accessibility on individual DNA fibers, and provides guidelines for its proper use and analysis.

Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

The paper identifies localized chromatin rewiring in rice's stable 3D genome that coordinates rhythmic transcription across the circadian cycle.

De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

This study uses PacBio HiFi sequencing to assemble complete Plasmodium falciparum genomes from natural infections, revealing full repertoires of immune-related genes.

Collapsed Site Coalescent Facilitates Detection of Adaptive Divergences Between Segmental Duplicates

The paper introduces a method to analyze population genetics of segmental duplicates by modeling gene conversion events and detecting adaptive divergence.

Chromosome-level Atlantic switchgrass assemblies reveal a supernumerary B-Chromosome with transcriptional and evolutionary impacts

The paper identifies a supernumerary B-Chromosome in Atlantic switchgrass, showing its evolutionary origin and impact on gene expression and genomic diversity.

A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758)

The paper presents a chromosome-level, haplotype-resolved genome assembly for the European moose, achieving high completeness and gene annotation.

Historical and Contemporary Management of Genetic Diversity in French Local Horse Breeds: Insights from Genomic Data

This study uses genomic data to analyze the genetic diversity and management history of French local horse breeds, showing distinct patterns of kinship and inbreeding linked to different management practices.

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

The paper shows that RNA-seq quantification methods and reference annotations significantly impact eQTL analysis, colocalization, and TWAS results across multiple tissues and phenotypes.

Sequence design for three-dimensional genome folding using Akita Semifreddo

This paper introduces Akita Semifreddo, a framework for designing DNA sequences that produce specific 3D genome folding patterns, demonstrating the ability to create boundaries, dots, and flames with controlled strengths.

Prediction of Systemic Lupus Erythematosus from Genotype and Gene-Expression Data: Batch Correction and Leakage Free Evaluation

This paper evaluates the prediction of SLE using genotype and gene-expression data with batch correction and leakage-free cross-validation, finding that expression data perform better than SNPs but face confounding issues.

Climate-associated genomic variation across life stages reveals population-specific signals of local adaptation in European beech

The paper identifies climate-associated genomic variation in European beech across life stages, revealing population-specific adaptive responses to temperature and precipitation changes.

SPARK: Bayesian structure learning of enhancer-based gene regulatory networks from single-cell multiomics data and prior knowledge

SPARK reconstructs enhancer-based gene regulatory networks using single-cell multiomics data and prior knowledge, revealing regulatory links associated with immune disease GWAS variants.

A molecular framework of chromatin extrusion in plants

This study identifies PDS5A as a key regulator of chromatin loop extrusion and TAD-like domains in Arabidopsis, revealing a promoter- and motif-based mechanism for loop anchoring and transcriptional control.

Genetic control and tissue specificity of transcriptomic rhythmicity

This study identifies genetic regulators of transcriptomic rhythmicity using GTEx data and links them to phenotypes in the Pan-UK Biobank.