DeepNeo identifies major histocompatibility complex (MHC) I or MHC II neoepitopes that are immunogenically compatible with the T cell repertoire. It can predict neoepitopes most likely to be depleted through spontaneous immunity or through immune checkpoint blockade from untreated and immunotherapy-treated tumor datasets.

A single-cell transcriptomic analysis of endometriosis, endometriomas, eutopic endometrial samples and uninvolved ovary tissues highlights cell populations characteristic of these tissue types. Transcriptional and cellular heterogeneity across tissues suggests novel therapeutic targets and biomarkers for this disease.

In aging mouse livers, 40% of elongating RNA polymerases are stalled, biasing transcriptional output dependent on gene length. This transcriptional stress appears to be caused by endogenous DNA damage.

De novo genome assembly and analyses of 12 maize FILs provide insights into genomic and phenotypic differentiation of various heterotic groups and the molecular basis of heterosis in maize.

A graph-based pan-genome constructed using de novo genome assemblies of ten pearl millet accessions adapted to different climates worldwide identifies structural variations and their contribution to heat tolerance in pearl millet.

MERVL transcripts, but not MERVL-encoded proteins, are essential for mouse preimplantation development. Depletion of MERVL RNA perturbs early lineage specification and leads to increased chromatin accessibility at, and transcription of, two-cell-specific genes.

Arabidopsis sperm cells exhibit widespread chromatin bivalency. Incorporation of histone variant H3.10 regulates sperm chromatin identity. In contrast, in vegetative cells, repressed genes are marked by H3K27me3, while pollination-related genes are active and marked by broad H3K4me3 domains.

Multiple samples collected at autopsy from women with homologous recombination-deficient high-grade serous ovarian cancer highlight substantial inter- and intratumoral heterogeneity. A plethora of resistance mechanisms were identified within and between patients.

Network expansion of trait-associated genes for 1,002 human phenotypes identifies pleiotropic gene modules and biological processes associated with multiple traits, and potential opportunities for drug repurposing and development.

Brain expression quantitative trait locus (eQTL) and network analyses encompassing 8,613 RNA-sequencing samples from 14 eQTL datasets reveal downstream effects and putative drivers for brain-related diseases.