Method to Watch |
Featured
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Research Briefing |
Deciphering subcellular organization with multiplexed imaging and deep learning
Our study introduces conditional autoencoder for multiplexed pixel analysis (CAMPA), a deep-learning framework that uses highly multiplexed imaging to identify consistent subcellular landmarks across heterogeneous cell populations and experimental perturbations. Generating interpretable cellular phenotypes revealed links between subcellular organization and perturbations of RNA production, RNA processing and cell size.
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Article
| Open Access
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps
CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis) learns representations of molecular pixel profiles from multiplexed images that can be clustered to quantify subcellular landmarks and capture interpretable cellular phenotypes.
- Hannah Spitzer
- , Scott Berry
- & Fabian J. Theis
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Correspondence |
Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome
- Xiaopeng Zhu
- , Yang Zhang
- & Jian Ma
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Article
| Open Access
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations
The Integrative Genome Modeling platform is a tool for population-based three-dimensional genome structure modeling and analysis by integrating various experimental data sources.
- Lorenzo Boninsegna
- , Asli Yildirim
- & Frank Alber
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Method to Watch |
Greater detail in the nucleus
Probing spatially organized DNA and its interacting elements in single cells will deepen our understanding of cell-type-specific gene regulation.
- Lei Tang
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Research Highlight |
Mapping genome structures in single cells
Researchers develop single-cell SPRITE to detect higher-order 3D genome structures in single cells.
- Lei Tang
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Research Highlight |
Radial genome organization
Sequencing gradually digested chromatin along the nuclear radius enables the mapping of radial organization of chromatin in human cells.
- Lei Tang
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Perspective |
Mechanistic modeling of chromatin folding to understand function
This Perspective highlights recently developed computational models for studying chromosome organization, with a focus on how mechanistic modeling helps biologists to interpret the biological function behind the genome structures.
- Chris A. Brackey
- , Davide Marenduzzo
- & Nick Gilbert
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Article |
3D ATAC-PALM: super-resolution imaging of the accessible genome
3D ATAC-PALM integrates ATAC with super-resolution imaging for nanoscale views of the accessible genome. When combined with FISH, protein fluorescence and genetic perturbation, the method enables investigation of accessible chromatin in situ.
- Liangqi Xie
- , Peng Dong
- & Zhe Liu
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Perspective |
Visualizing the genome in high resolution challenges our textbook understanding
This Perspective highlights how high-resolution imaging has informed our view and helped overturn the textbook understanding of 4D genome organization.
- Melike Lakadamyali
- & Maria Pia Cosma
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Method to Watch |
Liquid phase separation
Tools are needed to study phase behaviors of membraneless compartments in living cells.
- Lei Tang
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Brief Communication |
Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling
After CRISPR-mediated targeting of the peroxidase APEX2 to a genomic locus of interest, the proteins at that locus are labeled, enriched and identified via quantitative proteomics.
- Samuel A. Myers
- , Jason Wright
- & Steven A. Carr
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Brief Communication |
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2
dCas9 fused to ascorbate peroxidase (APEX2) biotinylates proteins around targeted loci so they can be enriched and characterized.
- Xin D. Gao
- , Li-Chun Tu
- & Erik J. Sontheimer
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Correspondence |
hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data
- Caleb A Lareau
- & Martin J Aryee
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Research Highlights |
Multiscale 3D view of the genome
Ultradeep sequencing of Hi-C data from mouse cells in different developmental stages can address outstanding questions about 3D chromatin function.
- Nicole Rusk
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Research Highlights |
Micro-C maps of genome structure
A method using micrococcal nuclease for chromatin fragmentation gives a high-resolution view of 3D genome structure.
- Natalie de Souza
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Methods in Brief |
Intracellular topology
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Research Highlights |
A brief history of nuclear organization
By marking protein-DNA interactions in real time, scientists track chromosomal rearrangements in the nuclei of living cells.
- Michael Eisenstein
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Methods in Brief |
A better look at the nuclear pore
From genome structure to function