Anna R. Poetsch

The paper compares regulatory changes in larval and adult zebrafish spinal progenitors after injury, showing they converge to a lesion-reactive state with distinct gene expression patterns.

This study identifies Nup153's role in repressing neuronal genes through HDAC1-mediated epigenetic regulation, influencing chromatin states and neuronal responsiveness.

The paper uses GROVER to analyze how DNA sequence, chromatin, and regulatory features influence genome stability by predicting DSB locations and identifying sequence tokens associated with DSB sensitivity.

This study uses deep learning to predict replication timing and finds DNA sequence provides sufficient information for prediction, with epigenetic features adding complementary value.

The paper improves click-code-seq for mapping DNA oxidation and depurination in human genomes, revealing strand bias in oxidized guanines and apurinic sites.

The paper investigates tumor clone dynamics in gastro-esophageal cancer organoids after neoadjuvant chemotherapy, finding that NFκB signaling downregulation contributes to non-genetic transcriptional reprogramming.

The paper evaluates DNA language models by assessing their ability to distinguish sequence context from token identity, finding that overlapping k-mer tokenization limits context learning.

This study shows NK cells influence all phases of cancer immunoediting in B-ALL, promoting resistant clones through selective pressure and identifying LY6E as a marker of poor prognosis.

This paper introduces GROVER, a DNA language model trained on the human genome to generate a dictionary of tokens and analyze genomic sequence context and functional annotations.

OpenPBTA provides a collaborative platform to genomically characterize 1,074 pediatric brain tumors and 22 cell lines, offering analysis modules and somatic datasets for research and clinical applications.

The paper analyzes CRISPR-Cas9 editing precision in human cells, finding that indel profiles vary by site and can be predicted based on sequence and chromatin features.

The paper maps oxidative DNA damage and repair across the genome, revealing regioselective protection of regulatory and coding regions from mutations.