Towards the idea of molecular brains

Y Timsit, SP Grégoire - International Journal of Molecular Sciences, 2021 - mdpi.com
How can single cells without nervous systems perform complex behaviours such as
habituation, associative learning and decision making, which are considered the hallmark of …

Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila

OV Kyrchanova, OV Bylino, PG Georgiev - Frontiers in Genetics, 2022 - frontiersin.org
The spatial organization of chromosomes is involved in regulating the majority of
intranuclear processes in higher eukaryotes, including gene expression. Drosophila was …

Pairtools: from sequencing data to chromosome contacts

Open2C, N Abdennur, G Fudenberg… - PLOS Computational …, 2024 - journals.plos.org
The field of 3D genome organization produces large amounts of sequencing data from Hi-C
and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive …

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

Open2C, N Abdennur, S Abraham… - PLOS Computational …, 2024 - journals.plos.org
Chromosome conformation capture (3C) technologies reveal the incredible complexity of
genome organization. Maps of increasing size, depth, and resolution are now used to probe …

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

DB Brückner, H Chen, L Barinov, B Zoller, T Gregor - Science, 2023 - science.org
Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion of distal …

Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation

D Lin, W Xu, P Hong, C Wu, Z Zhang, S Zhang… - Nature …, 2022 - nature.com
Immunocytes dynamically reprogram their gene expression profiles during differentiation
and immunoresponse. However, the underlying mechanism remains elusive. Here, we …

Single-cell Hi-C data analysis: safety in numbers

AA Galitsyna, MS Gelfand - Briefings in bioinformatics, 2021 - academic.oup.com
Over the past decade, genome-wide assays for chromatin interactions in single cells have
enabled the study of individual nuclei at unprecedented resolution and throughput. Current …

Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system

A Pourmorady, S Lomvardas - Current Opinion in Genetics & Development, 2022 - Elsevier
The mammalian genome possesses> 2000 olfactory receptor (OR) alleles regulated by 63
known OR-Enhancer elements, yet each olfactory sensory neuron (OSN) expresses only a …

Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C

Y Chi, J Shi, D Xing, L Tan - Frontiers in Molecular Biosciences, 2022 - frontiersin.org
The three-dimensional (3D) structure of chromosomes influences essential biological
processes such as gene expression, genome replication, and DNA damage repair and has …

Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D

Y Zheng, S Shen, S Keleş - Genome biology, 2022 - Springer
Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable
profiling of long-range genomic interactions. However, data from these technologies are …