Yinxiu Zhan
YOU?
Author Swipe
View article: MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics
MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics Open
Mitochondrial single-cell lineage tracing (MT-scLT) has recently emerged as a scalable and non-invasive tool to trace somatic cell lineages. However, the reliability and resolution of MT-scLT remains highly debated. Here, we present MiTo ,…
View article: Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis
Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis Open
The establishment of germ layers during early development is crucial for body formation. The Drosophila zygote serves as a model for investigating these transitions in relation to the chromatin landscape. However, the cellular heterogeneit…
View article: Molecular tumour board in gastrointestinal cancers
Molecular tumour board in gastrointestinal cancers Open
View article: A rationale for the poor response to alectinib in a patient with adenocarcinoma of the lung harbouring a STRN-ALK fusion by artificial intelligence and molecular modelling: a case report
A rationale for the poor response to alectinib in a patient with adenocarcinoma of the lung harbouring a STRN-ALK fusion by artificial intelligence and molecular modelling: a case report Open
Our model calculations suggested that the effect of the translocation was to induce the dimerization of ALK into a complex that distorted the binding pocket, which is the same for alectinib, lorlatinib and crizotinib. The distortion…
View article: Is precision medicine the solution to improve organ preservation in laryngeal/hypopharyngeal cancer? A position paper by the Preserve Research Group
Is precision medicine the solution to improve organ preservation in laryngeal/hypopharyngeal cancer? A position paper by the Preserve Research Group Open
In locally advanced (LA) laryngeal/hypopharyngeal squamous cell carcinoma (LHSCC), larynx preservation (LP) strategies aim at the cure of the disease while preserving a functional larynx, thus avoiding total laryngectomy and the associated…
View article: Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos
Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos Open
View article: An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors Open
View article: Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes
Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes Open
View article: Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin
Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin Open
Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean-square displac…
View article: Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin
Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin Open
Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean square displac…
View article: Cohesin and CTCF control the dynamics of chromosome folding
Cohesin and CTCF control the dynamics of chromosome folding Open
In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they dep…
View article: Cohesin and CTCF control the dynamics of chromosome folding
Cohesin and CTCF control the dynamics of chromosome folding Open
The dataset contains all the tracking data from Mach et al 2022 paper. Each file has the following header: x,y,z: spot coordinate. For dual color imaging, the distance along x,y and z across channels track: track id frame: time frame cell:…
View article: Cohesin and CTCF control the dynamics of chromosome folding
Cohesin and CTCF control the dynamics of chromosome folding Open
The dataset contains all the tracking data from Mach et al 2022 paper. Each file has the following header: x,y,z: spot coordinate. For dual color imaging, the distance along x,y and z across channels track: track id frame: time frame cell:…
View article: Cohesin and CTCF control the dynamics of chromosome folding
Cohesin and CTCF control the dynamics of chromosome folding Open
The dataset contains all the tracking data from Mach et al 2022 paper. Each file has the following header: x,y,z: spot coordinate. For dual color imaging, the distance along x,y and z across channels track: track id frame: time frame cell:…
View article: Cohesin and CTCF control the dynamics of chromosome folding
Cohesin and CTCF control the dynamics of chromosome folding Open
The dataset contains all the tracking data from Mach et al 2022 paper. Each file has the following header: x,y,z: spot coordinate. For dual color imaging, the distance along x,y and z across channels track: track id frame: time frame cell:…
View article: Cohesin and CTCF control the dynamics of chromosome folding
Cohesin and CTCF control the dynamics of chromosome folding Open
The dataset contains all the tracking data from Mach et al 2022 paper. Each file has the following header: x,y,z: spot coordinate. For dual color imaging, the distance along x,y and z across channels track: track id frame: time frame cell:…
View article: Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication
Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication Open
The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors (e.g. CTCF) underlying topologically associating domains (TADs) leads to modest alterati…
View article: Nonlinear control of transcription through enhancer–promoter interactions
Nonlinear control of transcription through enhancer–promoter interactions Open
Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs) 1–4 . Howev…
View article: Live-cell imaging and physical modeling reveal control of chromosome folding dynamics by cohesin and CTCF
Live-cell imaging and physical modeling reveal control of chromosome folding dynamics by cohesin and CTCF Open
Physical proximity between genomic sequences in mammalian chromosomes controls key biological processes such as transcriptional regulation and DNA repair. Yet it is currently unknown if chromosomal contacts are rare and stable or instead f…
View article: Inversion of a topological domain leads to restricted changes in its gene expression and affects inter-domain communication
Inversion of a topological domain leads to restricted changes in its gene expression and affects inter-domain communication Open
The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors underlying genome topology, such as CTCF and cohesin, leads to modest alterations in gen…
View article: deepBlink: threshold-independent detection and localization of diffraction-limited spots
deepBlink: threshold-independent detection and localization of diffraction-limited spots Open
Detection of diffraction-limited spots in single-molecule microscopy images is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and n…
View article: Nonlinear control of transcription through enhancer-promoter interactions
Nonlinear control of transcription through enhancer-promoter interactions Open
Chromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated interactions and topologically associating domains (TADs) …
View article: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
HP1 drives de novo 3D genome reorganization in early Drosophila embryos Open
View article: deepBlink: Threshold-independent detection and localization of diffraction-limited spots
deepBlink: Threshold-independent detection and localization of diffraction-limited spots Open
Detection of diffraction-limited spots is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and not always reliable. We have developed…
View article: Effective model of loop extrusion predicts chromosomal domains
Effective model of loop extrusion predicts chromosomal domains Open
An active loop-extrusion mechanism is regarded as the main out-of-equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fiber by solving…
View article: Datasets
Datasets Open
The benchmarking datasets used for deepBlink. The npz files contain train/valid/test splits inside and can be used directly. The files belong to the following challenges / classes:- ISBI Particle tracking challenge: microtubule, vesicle, r…
View article: A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary
A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary Open
View article: Bifractal nature of chromosome contact maps
Bifractal nature of chromosome contact maps Open
Modern biological techniques such as Hi–C permit to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualised as matrices called contact maps. In this paper, we introduce a multifrac…
View article: DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
DamC reveals principles of chromatin folding in vivo without crosslinking and ligation Open
View article: Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response
Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response Open