Daniel J. Cotter

FLASH predicts phenotype from sequence using deep learning, achieving high accuracy on unseen variants and identifying new virulence predictors across microbes.

The paper uses spatial CODEX experiments to show early colorectal cancer microenvironment changes in FAP, including CAFs, immune suppression, and beta-catenin nuclear translocation.

The paper describes the development of a course on genetics, ethics, and society designed by trainees to address the lack of ethics training in scientific education.

The paper derives the limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating, showing different effects based on consanguinity type.

The paper maps cell organization and function across human intestine regions using single nuclear RNA and open chromatin assays, revealing distinct cell neighborhoods and regulatory differences.

The paper examines how mutation, recombination, selection, and demography shape genetic variation across different regions of the human X chromosome using data from 26 populations.

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

The paper quantifies protein levels across 32 human tissues and compares them to transcriptome data, revealing insights into post-transcriptional regulation and disease mechanisms.