Publications

Molecular systems biology

Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays.

EMBO reports

Transcription elongation can be sufficient, but is not necessary, to advance replication timing.

Nature

Regulatory grammar in human promoters uncovered by MPRA-based deep learning.

Nature

An integrated view of the structure and function of the human 4D nucleome.

Nature structural & molecular biology

Interactions between the genome and the nuclear lamina are multivalent and cooperative.

Nature reviews. Genetics

Predicting gene expression from DNA sequence using deep learning models.

Nucleic acids research

Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor.

STAR protocols

Protocol for multiplexed transcription factor activity detection using optimized barcoded reporters and an automated computational pipeline.

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Science (New York, N.Y.)

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene.

Nucleic acids research

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers.

Nature biotechnology

Machine learning prediction of prime editing efficiency across diverse chromatin contexts.

Nature biotechnology

Publisher Correction: Machine learning prediction of prime editing efficiency across diverse chromatin contexts.

eLife

Major nuclear locales define nuclear genome organization and function beyond A and B compartments.

bioRxiv : the preprint server for biology

Transcription can be sufficient, but is not necessary, to advance replication timing.

Cell systems

Optimized reporters for multiplexed detection of transcription factor activity.

The EMBO journal

Chromatin protein complexes involved in gene repression in lamina-associated domains.

eLife

Large-scale analysis of the integration of enhancer-enhancer signals by promoters.

bioRxiv : the preprint server for biology

An integrated view of the structure and function of the human 4D nucleome.

Communications biology

Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable localization of heterochromatin in different cell types.

Nucleic acids research

Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing.

bioRxiv : the preprint server for biology

Optimized reporters for multiplexed detection of transcription factor activity.

The regulatory grammar of human promoters uncovered by MPRA-trained deep learning

Nature communications

Widespread chromatin context-dependencies of DNA double-strand break repair proteins.

Cell reports

Perturbations in 3D genome organization can promote acquired drug resistance.

Nucleic acids research

Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements.

Nature

Heritable transcriptional defects from aberrations of nuclear architecture.

Nucleic acids research

Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR.

EMBO reports

Dynamic chromosomal interactions and control of heterochromatin positioning by Ki-67.

DNA repair

From fluorescent foci to sequence: Illuminating DNA double strand break repair by high-throughput sequencing technologies.

Genome biology

CTCF and cohesin promote focal detachment of DNA from the nuclear lamina.

Molecular cell

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.

Nature

Nonlinear control of transcription through enhancer-promoter interactions.

Frontiers in genetics

Protocol: A Multiplexed Reporter Assay to Study Effects of Chromatin Context on DNA Double-Strand Break Repair.

Methods in molecular biology (Clifton, N.J.)

Genome-Wide Mapping and Microscopy Visualization of Protein-DNA Interactions by pA-DamID.

Current opinion in cell biology

Lamina-associated domains: Tethers and looseners.

Science (New York, N.Y.)

3D genomics across the tree of life reveals condensin II as a determinant of architecture type.

Molecular cell

Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.

Open biology

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner.

Genome biology

SPIN reveals genome-wide landscape of nuclear compartmentalization.

EMBO reports

Cell cycle dynamics of lamina-associated DNA.

Developmental cell

Phosphorylated Lamins in Euchromatin: New Clues to Progeria.

The EMBO journal

Local rewiring of genome-nuclear lamina interactions by transcription.

Trends in biochemical sciences

Deciphering Gene Regulation Using Massively Parallel Reporter Assays.

Nature genetics

High-throughput identification of human SNPs affecting regulatory element activity.

Nature reviews. Molecular cell biology

The role of transcription in shaping the spatial organization of the genome.

Cell

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs.

Methods in molecular biology (Clifton, N.J.)

Rapid Quantitative Evaluation of CRISPR Genome Editing by TIDE and TIDER.

The Journal of cell biology

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.

Epigenetics & chromatin

The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a.