Vadim Backman

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

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

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.

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.

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

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

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.

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

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.

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

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.

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.

The paper compares lamin B and DNA levels in nuclear blebs across cell types and perturbations, finding DNA concentration is more consistently reduced than lamin B levels.

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

This study shows that formamide in 3D FISH distorts nanoscale chromatin structure, while alternative methods like RASER-FISH and CRISPR-Sirius have minimal impact.

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.

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.

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.

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.

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.

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

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.