Guy Nir

Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D

The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

The paper shows lineage-determining transcription factors position enhancers and promoters to enable multi-enhancer regulation of oncogenes in lymphoma and T-cell leukemia.

Restored rigidity sensing fails to induce anoikis in cancer cells due to Akt activation and cell cell interactions

This study shows that restoring rigidity sensing in cancer cells via Tpm2.1 overexpression does not induce anoikis due to Akt activation and cell-cell interactions.

Oncogenic drivers shape the tumor microenvironment in human gliomas

This study investigates how oncogenic mutations in gliomas influence the tumor microenvironment through integrative multiomic and spatial transcriptomic analysis of glioma samples.

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos

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

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

The paper uses super-resolution imaging and integrative modeling to achieve 10 kb resolution of chromosome folding.

OligoMiner: A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

OligoMiner designs genome-scale oligo FISH probes with customizable parameters and evaluates probe specificity using supervised learning, demonstrating scalability across model organisms.