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The paper identifies differentially expressed lncRNAs in Crohn's disease using genome-guided RNA-seq and links them to nearby protein-coding genes involved in immune response and tissue regeneration.

The paper shows that Med15's activator-binding domains are necessary but not sufficient for UAS recruitment, and its disordered C-terminus is critical for directing genome targeting.

The paper identifies common differentially regulated microRNAs in skeletal aging and radiation-induced bone deterioration, linking them to WNT pathway modulation and senescence.

This study analyzes genomic divergence in three large falcon species, linking chromosomal rearrangements to patterns of recombination, diversity, and differentiation.

The paper develops predictors to functionally characterize human phosphosites using integrated data, revealing novel functions and connections to DNA repair and cell survival.

The paper identifies convergent gene loss in the chemical defensome across marine mammals, highlighting adaptation to aquatic environments and reduced detoxification capacity.

This paper introduces a generative AI framework to design target-specific siRNAs for RNAi-based drug design, showing improved specificity and reduced off-target effects compared to existing methods.

This paper develops a Bayesian method to estimate mosaic loss of chromosome Y from bulk RNA-seq data, showing it can detect large LOY events with moderate accuracy.

OpenSplice quantifies the impact of over 590,000 variants on the splicing of 600 human exons, providing insights into splicing regulatory mechanisms and enabling machine learning model evaluation.

PerturbPlan provides an analytical framework to design single-cell CRISPR screens by calculating statistical power and enabling interactive experiment planning.

The paper introduces mwMCC, a method to detect multi-way chromatin interactions at sub-nucleosome resolution, revealing synergistic nano-scale interactions within super-enhancers and their role in gene regulation.

The paper investigates the diversity and distribution of Apicomplexa across marine environments using metabarcoding data, revealing previously unknown diversity and biogeographic patterns.

The paper develops a polymer simulation framework to distinguish specific-folding interactions from polymer compaction in E. coli, revealing SFIs shape chromosome organization and gene expression.

CMAPS performs causal mediation analysis on perturbation screens to identify molecular intermediates, showing accurate mediation estimates and robust mediator identification in Perturb-seq data.

This paper develops ultra-CNA, a high-resolution single-cell analysis pipeline for copy-number alterations, revealing sex-divergent aging trajectories and accelerated aging in cancer.

This study analyzes the evolutionary distribution of trehalose breakdown pathways across 4000 genomes, revealing ancestral origins and lineage-specific losses.

The paper analyzes corallicolid parasites in Pocillopora corals across the Pacific Ocean, finding their widespread presence and linking their abundance to environmental factors and host immune responses.

The paper identifies a unique T-cell inflammatory signature in AGA+ schizophrenia-related disorder patients using scRNA-seq, linking it to increased severity of negative symptoms.

This study identifies 239 snoRNAs in Drosophila S2 cells and maps 2-O-methylation sites using RibOxi-seq2, revealing widespread Nm modifications in rRNAs and mRNAs.

This paper evaluates generalist large language models (LLMs) in tumor genomic interpretation tasks, finding they can complement or outperform task-specific models in some cases.