Andrew Nishida

Epigenetic progression of pancreatic cancer to aggressive subtypes involves alternate routes of lineage reprogramming in subtype-intermediate progenitor cells

The paper identifies subtype-intermediate progenitor cells in pancreatic cancer with distinct epigenetic profiles linked to clinical outcomes and lineage reprogramming.

The ENCODE Uniform Analysis Pipelines

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

Integrating de novo and inherited variants in over 42,607 autism cases identifies mutations in new moderate risk genes

The paper identifies 60 new moderate risk genes for autism by integrating de novo and inherited variants across 42,607 cases and 236,000 controls.

Cas12a-Capture: a novel, low-cost, and scalable method for targeted sequencing

The paper introduces Cas12a-Capture, a low-cost, scalable targeted sequencing method that reduces GC bias and improves variant calling accuracy.

Spatially-mapped single-cell chromatin accessibility

The paper introduces sciMAP-ATAC, a method for spatially resolved single-cell chromatin accessibility profiling, and applies it to study cortical lamination, spatial trajectories, and ischemic infarct progression in mouse and human tissues.

Chromatin dynamics during hematopoiesis reveal discrete regulatory modules instructing differentiation

This study maps chromatin dynamics and gene expression during human erythropoiesis, revealing regulatory modules that guide lineage commitment and maturation.