T Gingeras

The paper identifies bi-directionally expressed enhancers in maize with domestication signatures using integrated epigenomic and transcriptomic data from multiple tissues and inbred lines.

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.

The paper uses single-cell RNA-seq to map the maize root transcriptome and identifies a mechanism regulating cortex layer number through the SHR signaling pathway.

This study constructs high-quality sorghum genome assemblies and identifies structural variations and resistance genes associated with sugarcane aphid resistance.

The paper identifies five major cell types based on transcriptional programs in human tissues and shows their composition correlates with tissue morphology and disease.

The paper describes the development of a cloud-based platform for managing, analyzing, and distributing MaizeCODE data, enhancing reproducibility and accessibility.

The paper analyzes miRNA expression dynamics across mouse embryonic development, identifying tissue-specific clusters and their regulatory roles.

This study evaluates STAR aligner performance across alignment parameters and biological tasks, finding technical metrics uninformative and performance mostly robust except in challenging genomic regions.

The paper profiles promoter activity in 5 Drosophila species to show core promoters restrict developmental timing of gene expression and reveal widespread noncoding transcription.

The paper introduces RNA Capture Long Seq (CLS) to annotate full-length lncRNAs with high throughput and accuracy, doubling annotated complexity compared to short-read methods.

Filtering STAR's chimeric alignments against gene annotations outscored 15 other fusion callers on 60 cancer cell lines and ran fastest, averaging 2.3 single-core hours per sample.

Maximum mappable seed search in uncompressed suffix arrays, then seed clustering and stitching, aligns 550 million paired-end reads per hour on 12 cores with better sensitivity and precision.