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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.

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.

This study identifies organized vulnerability in the aging genome, showing that certain genes and pathways are less mutated while others accumulate more mutations, suggesting a network-based mechanism for cellular decline.

The paper identifies rhabdoviral sequences in alfalfa genomes through bioinformatics analysis, suggesting their integration into the host genome.

This study identifies eukaryotic retrotransposons that encode prokaryotic-like DNA adenine methyltransferases and shows their adaptation to host 6mA-associated chromatin.

The paper identifies autoimmune disease-associated variants that disrupt transcription factor-cofactor complex assembly and enhancer activity using the CASCADE method in Jurkat T cells.

The paper identifies a new bZIP protein motif, BPabZIP, that facilitates nucleosome displacement and binding near nucleosomes in human cells.

The paper compares somatic mutation accumulation in two coral species, finding distinct patterns suggesting different cell lineage development mechanisms.

The paper identifies sex-specific regulatory dynamics in adolescent brain development that may contribute to depression vulnerability through hormone-sensitive gene expression and chromatin accessibility patterns.