Maxim Imakaev

This study proposes that cohesin bridging, not spatial proximity, mediates enhancer-promoter communication and develops a model to validate this mechanism through engineered cell systems.

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

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

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

The paper identifies three inactive chromatin states in HCT116 cells and shows how H3K9me3-HP1/β heterochromatin influences genome compartmentalization and loop extrusion barriers through DNA methylation.

The paper introduces the 4DN Data Portal, a resource for searching and visualizing curated nucleomics data, including Hi-C and other chromosome architecture datasets.

The paper introduces a spatial modeling approach for detecting differentially interacting genomic regions in Hi-C data with false discovery control, demonstrating its ability to reveal biologically meaningful changes in chromatin architecture.

This paper challenges the predictive value of tumor mutational burden (TMB) for immunotherapy response, finding little evidence of its association and suggesting previous studies had methodological flaws.

This paper introduces a non-parametric polygenic risk prediction method using GWAS summary statistics, improving prediction accuracy for several diseases.

A haplotype-resolved Hi-C approach reveals structured homolog pairing in early Drosophila embryos, correlated with Zelda-mediated chromatin accessibility.

This study develops a method to probe mRNA 3D structures and finds that pre-translational mRNPs form linear rod-like structures without strong end interactions.

This paper investigates the mechanism of nuclear inversion in rod photoreceptors by combining Hi-C, microscopy, and polymer modeling, revealing that heterochromatin interactions drive phase separation and that lamina interactions maintain conventional nuclear organization.

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

This paper examines the differences between 3C and FISH in measuring chromosomal contacts and spatial distances, highlighting implications for integrating these methods.

The paper reviews polymer models and experimental evidence supporting loop extrusion as a mechanism for chromosome folding, focusing on CTCF and cohesin perturbations in interphase.

This paper proposes that loop extrusion by cohesins and boundary proteins like CTCF forms Topologically Associating Domains (TADs) through dynamic loop creation and stabilization.

The paper uses polymer simulations to show that chromatin loops can either insulate or facilitate enhancer-promoter interactions, depending on their location relative to the pair.