Julia Zeitlinger

AlphaGenome Atlas: in silico mutagenesis of the entire human genome improves prioritization and interpretation of non-coding variants

AlphaGenome Atlas predicts regulatory effects of non-coding variants across the human genome, improving their prioritization and interpretation.

Temporal regulation of a spatial patterning factor in Drosophila neurogenesis

The paper shows that the same selector transcription factor can be regulated by different patterning axes through distinct enhancers in Drosophila neurogenesis, revealing a cis-regulatory mechanism for neuronal diversity.

Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs

The paper maps and interprets low-affinity transcription factor motifs in mESCs, showing they enhance chromatin accessibility and regulatory potential through cooperative interactions.

Positional Interpretation of Cis-Regulatory Code and Nucleosome Organization with Deep Learning Models

This paper introduces PISA, a tool for interpreting sequence-to-function neural networks, enabling the discovery of nucleosome-positioning motifs and understanding cis-regulatory code through MNase-seq data.

High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo

The paper uses ChIP-nexus to analyze TFIID subunit binding in Drosophila, revealing promoter-specific differences in TBP and TAF interactions.

GAME: Genomic API for Model Evaluation

GAME provides a standardized framework for benchmarking genomics models across tasks, enabling consistent evaluation and community contributions.

Interpretable deep learning reveals the sequence rules of Hippo signaling

The paper uses interpretable deep learning to identify sequence rules governing Hippo signaling in mouse trophoblast stem cells, revealing how transcription factors influence enhancer activity.

Gene regulatory network co-option is sufficient to induce a morphological novelty in Drosophila

This study shows that co-opting the trichome genetic network in Drosophila can induce large apical projections on the phallus, demonstrating the flexibility of gene regulatory networks in evolving new morphologies.

Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation

The paper uses deep learning to analyze chromatin accessibility in Drosophila embryos, revealing a two-phase process driven by pioneer TFs and enhancer-activating TFs.

De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding

The paper introduces Affinity Distillation (AD), a method to extract thermodynamic affinities from deep learning models of in vivo TF binding, showing it outperforms motif-based methods in predicting sequence variation impacts.

Lola-I is a developmentally regulated promoter pioneer factor

The paper shows that Lola-I, a Drosophila zinc finger transcription factor, regulates promoter accessibility and paused Pol II during development, similar to enhancer regulation by pioneer factors.

The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

The paper investigates the role of the SAGA core module during Drosophila oogenesis and finds it is genetically essential despite the enzymatic modules being dispensable.

Base-resolution models of transcription factor binding reveal soft motif syntax

The paper introduces BPNet, a deep learning model that predicts base-resolution ChIP-nexus binding profiles of TFs and identifies soft syntax rules for cooperative TF binding.

TATA and paused promoters active in differentiated tissues have distinct expression characteristics

The paper compares TATA and paused promoters in Drosophila embryos, finding that TATA promoters show Pol II occupancy only when active, while paused promoters have consistent Pol II levels regardless of gene expression.

An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia

The paper maps transcription factor expression in Drosophila melanogaster pupal terminalia using RNA-seq and in situ hybridization, revealing structured patterns and creating an online database for future research.

High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing

This study generates high-quality genome assemblies for 15 Drosophila species using Nanopore sequencing, closing gaps in existing references and demonstrating cost-effective long-read sequencing.

Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets

The paper identifies combinatorial binding of Hoxa1 and TALE proteins on genome-wide targets and reveals their cross-regulatory interactions.

Drosophila poised enhancers are generated during tissue patterning with the help of repression

The paper investigates the generation of poised enhancers during Drosophila tissue patterning and suggests they may result from repression rather than being a precursor to activation.