James A. Birchler

This paper presents genome and epigenome analyses of Lemnaceae plants, identifying genes related to clonal reproduction and CO2 sequestration, and highlights their potential for biotechnology.

The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.

The paper investigates how extrachromosomal DNA (eccDNA) contributes to glufosinate resistance in Palmer amaranth by amplifying the GS2 gene.

The paper analyzes transcriptome data from human aneuploidies to show inverse or proportional trans-modulation of genes on unvaried chromosomes and compensation on varied chromosomes, with differences observed between autosomal and sex chromosome aneuploidies.

This paper introduces DeepGRN, an attention-based model for transcription factor binding site prediction, showing improved performance on ENCODE-DREAM datasets.

The paper develops a universal chromosome identification system for maize and wild Zea species using FISH probes, enabling accurate identification and revealing chromosomal differences between species.

The paper describes a transgenerational epigenetic decline in vigor and viability in maize-teosinte backcross populations, termed 'hybrid decay', characterized by genomic instability and altered gene expression.