Lila Rieber

Machine Learning-Driven Optimization of Specific, Compact, and Efficient Base Editors via Single-Round Diversification

This paper develops novel base editors by diversifying TadA orthologs and using generative models to optimize specificity and efficiency.

Structure-Led Exploration of the Metagenome Yields Novel RNA-Guided Nucleases with Broad PAM Diversity

The paper identifies novel RNA-guided nucleases with broad PAM diversity using structure-led metagenomic analysis, expanding genome editing capabilities.

Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation

The paper uses synthetic genomic reconstitution to study Hox cluster regulation, finding that distal enhancers are required for full transcriptional output while chromatin remodeling can occur without them.

Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map

The paper introduces a SOM-based method to visualize and analyze relationships between chromatin interactions and regulatory genomic activities using Hi-C data.

Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types

The paper develops MultiMDS to compare 3D chromosomal structures across Hi-C datasets, revealing compartment-independent relocalizations of loci.

miniMDS: 3D structural inference from high-resolution Hi-C data

miniMDS improves 3D genome structure inference from high-resolution Hi-C data by combining high- and low-resolution MDS for efficiency and accuracy.