Donald E. Brown

WHAT IS NORMAL? MULTIMODAL CHARACTERIZATION OF NON-DISEASED PEDIATRIC DUODENAL BIOPSIES USING MACHINE LEARNING IMAGE ANALYSIS AND TRANSCRIPTOMICS

The paper characterizes non-diseased pediatric duodenal biopsies across multiple domains, finding clinical and transcriptomic heterogeneity but limited histologic differences.

Development of the Early Childhood Duodenum across Ancestry, Geography and Environment

The paper creates a cellular and spatial map of the duodenum in children, revealing environmental and developmental influences on intestinal cell states.

Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings

The paper introduces scEmbed, a framework for fast clustering and cell-type annotation of scATAC-seq data using pre-trained embeddings, showing improved performance and transferability.

Joint representation learning for retrieval and annotation of genomic interval sets

The paper develops a system for fast and flexible genomic interval retrieval using joint representation learning of region sets and metadata.

Embeddings of genomic region sets capture rich biological associations in lower dimensions

The paper introduces a method to represent genomic region sets as embeddings using a modified word2vec approach, showing it effectively captures biological associations in lower dimensions.