Ilya M. Flyamer

Genome-wide absolute quantification of chromatin looping

This study calibrates Micro-C with live imaging to determine absolute chromatin looping probabilities in mouse cells, finding most loops occur at low frequencies.

Analysis of multi-way chromatin interactions at sub-nucleosome resolution identifies synergistic nano-scale interactions within super-enhancers

The paper introduces mwMCC, a method to detect multi-way chromatin interactions at sub-nucleosome resolution, revealing synergistic nano-scale interactions within super-enhancers and their role in gene regulation.

Pairtools: from sequencing data to chromosome contacts

Pairtools processes sequencing data into contact pairs for 3C+ analysis, offering high-performance and flexible tools for various protocols.

Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity

The paper investigates how estrogen receptor activation affects enhancer-promoter contact frequencies and spatial proximity, finding they change independently during gene activation.

Cooltools: enabling high-resolution Hi-C analysis in Python

Cooltools provides scalable and flexible analysis tools for high-resolution Hi-C data, addressing challenges in storage, memory, and customization.

Bioframe: Operations on Genomic Intervals in Pandas Dataframes

Bioframe provides a Python library for efficient genomic interval operations using pandas dataframes, extending the data science stack for computational genomics.

Ultra-long-range interactions between active regulatory elements

The paper identifies ultra-long-range chromatin interactions between active regulatory elements in vertebrate and invertebrate genomes, showing they are driven by three distinct mechanisms independent of RNA polymerase II and some cofactors.

Cohesin is required for long-range enhancer action

This study shows cohesin, but not CTCF, is required for activation of genes by distant enhancers, while close enhancers can function without cohesin.

Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction

This study identifies RIF1 as a molecular hub that co-regulates nuclear organisation and replication timing through its interaction with PP1, revealing distinct functional requirements for these processes.

Low level of expression of C-terminally truncated human FUS causes extensive changes in spinal cord transcriptome of asymptomatic transgenic mice

The paper shows that low-level expression of a pathogenic C-terminally truncated FUS in mice causes transcriptome changes in the spinal cord without motor neuron pathology.

Coolpup.py: versatile pile-up analysis of Hi-C data

Coolpup.py provides a versatile and efficient tool for pile-up analysis of Hi-C data, enabling robust detection of genomic loops and novel insights into 3D genome organization.

A Central Role for Canonical PRC1 in Shaping the 3D Nuclear Landscape

This study investigates the role of PRC1 in shaping 3D nuclear organization in mESCs, showing that PRC1-mediated interactions are independent of CTCF and can occur at a megabase scale.

Developmentally regulated Shh expression is robust to TAD perturbations

The paper shows that Shh expression remains robust to TAD perturbations during development, except when enhancers are deleted.

A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture

The paper shows cohesin-dependent loop extrusion organizes zygotic chromatin into loops and domains, with distinct effects on maternal and paternal genomes.