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This paper introduces wSIR, a scalable supervised dimensionality reduction method for spatial transcriptomics data, which retains predictive power of spatial coordinates and is demonstrated on breast cancer and embryonic development datasets.

The paper examines short-term, long-term, and genetic factors influencing human plasma proteome variability using longitudinal cohort data.

The paper presents an integrated analysis of somatic mosaicism across 25 individuals, revealing tissue-specific mutational processes and epigenetic states.

The paper develops a low-cost genotyping panel for Yesso scallops to support breeding and disease resistance studies.

This study shows that Med15 variants from wine yeast enhance fermentation efficiency by upregulating glycolytic, fermentation, and amino acid biosynthesis genes.

The paper examines the genomic effects of genetic rescue in a sand lizard population, finding increased diversity and reduced genetic load after admixture.

This study identifies region-specific pigment gene expression patterns in a coral colony, showing higher expression of photoconvertible proteins in the orange oral region compared to the green body.

The paper shows that chromatin in living S. pombe cells is generally accessible, challenging the idea that heterochromatin represses DNA access.

The paper uses human-trained neural networks to predict chromatin annotations in non-human species, showing varying accuracy across species and genomic features.

The paper presents a high-quality genome assembly of the sea anemone Aiptasia strain F003, enhancing its use as a model for studying symbiosis, microbiomes, and thermal stress in cnidarians.

The paper introduces perplexity as a metric to quantify isoform diversity in the human transcriptome using long-read RNA-sequencing data, showing it provides interpretable and reproducible measurements.

This study combines HiFi long-read and short-read sequencing to improve MAG recovery and binning accuracy in soil microbiomes.

The paper identifies de novo mutations in siblings and finds no differences in mutation rates by ancestry or smoking status, but links disruptions in REV1 and LIG1 to increased germline mutation rates.

The paper improves the SNS-seq protocol to better detect DNA replication origins and reduce non-origin biases in yeast.

The paper identifies genomic signatures of convergent evolution in spiders that build funnel webs, highlighting shared genetic changes in genes related to nervous system function.

This study identifies HIF1A's role in recruiting primate-specific endogenous retroviruses into hypoxic and immune responses, revealing their regulatory impact on gene expression.

The paper uses sequence-to-function models to predict the functional impact of archaic hominin introgression in Papuan individuals, identifying genes associated with introgressed haplotypes.

This study shows that insecticide-resistant Drosophila suzukii exhibits increased global alternative splicing events, enriched in stress response and resistance processes, even without substantial differential gene expression.

This paper introduces LagTag, a method to recover both earlier and endpoint chromatin states in mammalian cells, and applies it to study dynamic chromatin transitions during stem cell differentiation.

SCADR assesses PTEN missense variants' effects on signaling pathways through single-cell phospho-antibody analysis, revealing variant-specific dysfunction profiles.