Ashley Mae Conard

EPIC: An open community challenge for sequence-based prediction of transcription initiation in five non-model metazoans

EPIC challenges teams to predict transcription initiation from DNA sequence in non-model metazoans, aiming to assess generalizability beyond human and model species.

The transcription factor CLAMP is required for neurogenesis in Drosophila melanogaster.

This study identifies CLAMP as a transcription factor essential for Drosophila NSC differentiation and optic lobe development by regulating Notch and Tailless.

The Evidence Aggregator: AI reasoning applied to rare disease diagnostics

The Evidence Aggregator (EvAgg) uses generative AI to streamline rare disease diagnostics by extracting and summarizing genetic variant and clinical information from literature, improving efficiency and accuracy.

Predicting evolutionary rate as a pretraining task improves genome language model representations

This paper introduces a pretraining task for genome language models that predicts evolutionary rate, showing improved performance over sequence-only pretraining.

A dual DNA/RNA-binding factor regulates co-transcriptional splicing through target RNA interaction and modulates splicing factor dynamics

The paper shows CLAMP, a DNA-binding factor, regulates sex-specific splicing by interacting with RNA and modulating RBP dynamics.

Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks

Multioviz enables in silico perturbation and analysis of gene regulatory networks to guide experimental decisions using a real dataset from mice.

Sex-specific transcript diversity is regulated by a maternal pioneer factor in early Drosophila embryos

The paper identifies mechanisms by which the CLAMP TF regulates sex-specific splicing in Drosophila embryos through interactions with RBPs and gene regulation.

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data

TIMEOR identifies temporal regulatory mechanisms from multi-omics data by inferring gene regulatory relationships across time, revealing a link between insulin stimulation and circadian rhythm.

Neuromolecular and behavioral effects of ethanol deprivation in Drosophila

This study investigates how ethanol deprivation affects behavior and gene expression in Drosophila, identifying molecular and neural changes associated with negative affect states.