Vadim Backman

Heterochromatin protein 1α acts as an essential stabilizer of chromatin packing domains

This study shows that HP1 stabilizes chromatin packing domains by maintaining their structure and enabling efficient transcriptional responses to stress.

Genome-Wide Mapping of Major Histone Modifications Reveals Distinct Epigenetic Regulatory States in a Reef-Building Coral

The paper maps major histone modifications in a reef-building coral to understand chromatin regulation of gene expression and identifies distinct epigenetic states.

Bounded ecological memory in coral reefs: divergent demographic pathways under recurrent heatwaves and collapse under extreme thermal stress

The paper shows coral reefs exhibit bounded ecological memory, with reduced bleaching under predictable heatwaves but collapse under extreme thermal stress due to demographic shifts and loss of resilience.

One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization

This paper introduces the SR-EV model to interpret chromatin organization as ensemble-level statistical patterns rather than fixed structures, showing how TADs and contact enrichments emerge from geometric rules and heterogeneity.

Chromatin architecture and physical constriction cooperate in phenotype switching and cancer cell dissemination

This study shows that chromatin architecture and physical constriction together drive phenotype switching and metastasis in melanoma by altering CTCF positioning and heterochromatin structure.

Gene transcription and chromatin packing domains form a self-organizing system

The paper shows that Pol-II regulates chromatin packing domains through transcriptional loops, linking RNA synthesis to genome organization and gene expression.

Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome

The paper proposes that introns, intergenic segments, and exons are positioned geometrically within chromatin domains to sustain transcriptional memory and reconcile epigenetic patterns and mutation non-randomness.

Leveraging chromatin packing domains to target chemoevasion in vivo

This study develops a physics-based model linking chromatin organization to chemoevasion, identifies TPR compounds that enhance chemotherapy efficacy in ovarian cancer.

Three-color single-molecule localization microscopy in chromatin

This paper develops a three-color single-molecule localization microscopy protocol to study chromatin structure, revealing that heterochromatin and euchromatin are not distinct territories but are spatially coupled.

Nuclear blebs are associated with destabilized chromatin packing domains

The paper investigates how nuclear blebs alter chromatin packing domains, finding fragmentation of nanoscopic heterochromatin domains within blebs.

The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle

This study theoretically examines how intranuclear factors like salt concentration and pH affect the charge state of nucleosome core particles, highlighting the role of magnesium ions and molecular details.

Deep Learning-driven Automatic Nuclei Segmentation of Label-free Live Cell Chromatin-sensitive Partial Wave Spectroscopic Microscopy Imaging

This paper introduces csPWS-seg, a deep learning model for automated nuclei segmentation in label-free live cell csPWS microscopy, achieving high accuracy with median IoU 0.80 and DSC 0.88.

mRNA expression is co-regulated by non-nucleolar RNA polymerase I

The paper shows that RNA polymerase I co-regulates chromatin domains and mRNA synthesis with RNA polymerase II, affecting genome connectivity and gene expression.

Chromatin packing domains persist after RAD21 depletion in 3D.

The paper shows that RAD21 depletion reduces but does not eliminate chromatin packing domains in electron microscopy, suggesting non-cohesin mechanisms largely control 3D structure.

Statistical Analysis of Three-Dimensional Chromatin Packing Domains Determined by Chromatin Scanning Transmission Electron Microscopy (ChromSTEM)

The paper introduces ChromSTEM, a method for high-resolution 3D imaging of chromatin structure, and finds that chromatin forms well-defined domains around 100 nm in radius with radially decreasing mass-density.

Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anti-cancer drug response

This study uses spike-in normalization in single-cell RNA-seq to reveal dynamic transcriptional changes in cancer cells responding to anti-cancer drugs, identifying gene states and regulatory modules linked to drug efficacy.

Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function

The paper introduces a nano-ChIA platform that combines electron tomography and superresolution imaging to study chromatin structure and dynamics at the single-nucleosome level in live cells.

Quantifying Three-dimensional Chromatin Organization Utilizing Scanning Transmission Electron Microscopy: ChromSTEM

The paper introduces ChromSTEM, a method to quantify 3D chromatin organization using electron microscopy, and finds chromatin is densely packed with heterochromatin having higher density than euchromatin.

Interphase chromatin as a self-returning random walk: Can DNA fold into liquid trees?

The paper proposes a self-returning random walk model to explain interphase chromatin structure, reconciling high contact frequency and structural heterogeneity.

Live Cell Partial Wave Spectroscopic microscopy: Label-free Imaging of the Native, Living Cellular Nanoarchitecture

This paper develops live cell Partial Wave Spectroscopic (PWS) microscopy to study chromatin nano-architecture dynamics in real-time, showing changes in chromatin structure due to DNA damage and linking it to mitochondrial membrane potential.