https://wiki.4dnucleome.org/ 2026-04-19T03:30:57-0700 https://wiki.4dnucleome.org/ https://wiki.4dnucleome.org/_media/wiki:favicon.ico text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:3d_multicolor_nanoscopy_at_10000_cells_a_day?rev=1745364087&do=diff 3D Multicolor Nanoscopy at 10,000 Cells a Day Single-molecule switching (SMS) nanoscopy techniques like STORM/(F)PALM circumvent the diffraction limit to enable 3D fluorescence imaging with resolutions in the range of 10-75 nanometers, an order of magnitude better than conventional light microscopes. This increased spatial resolution affords many opportunities to investigate sub-cellular function and organization (for example of the interphase nucleus) but is achieved by sacrificing temporal re… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:avacado?rev=1745364087&do=diff Avocado: Multi-scale Deep Tensor Factorization for the Imputation of Missing Human Epigenomics Datasets <Abstract> Contact Authors * Jacob Schreiber (jmschr@uw.edu) * Timothy Durham (tdurham@uw.edu) * Jeffrey Bilmes (bilmes@uw.edu) * William Noble (wnoble@uw.edu) text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:chromemt?rev=1745364087&do=diff ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells INTRODUCTION In human cells, 2 m of DNA are compacted in the nucleus through assembly with histones and other proteins into chromatin structures, megabase three-dimensional (3D) domains, and chromosomes that determine the activity and inheritance of our genomes. The long-standing textbook model is that primary 11-nm DNA–core nucleosome polymers assemble into 30-nm fibers that further fold into 120-nm ch… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:cocbreview_pombo2020?rev=1745364087&do=diff Evolving methodologies and concepts in 4D nucleome research The genome requires tight regulation in space and time to maintain viable cell functions. Advances in our understanding of the 3D genome show a complex hierarchical network of structures, involving compartments, membraneless bodies, topologically associating domains, lamina associated domains, protein- or RNA-mediated loops, enhancer–promoter contacts, and accessible chromatin regions, with chromatin state regulation through epigenetic… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:diploid_hic?rev=1745364087&do=diff Inferring diploid 3D chromatin structures from Hi-C data The 3D organization of the genome plays a key role in many cellular processes, such as gene regulation, differentiation, and replication. Assays like Hi-C measure DNA-DNA contacts in a genome high-throughput fashion. Inferring accurate 3D models of how chromosomes fold from such data can yield insights that are hidden in the raw data. While many methods exist to infer the 3D structure of haploid genomes, inferring a diploid structure from… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:electric_tomography?rev=1745364087&do=diff 3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography Transmission electron microscopy allows the collection of multiple views of specimens and their computerized three-dimensional reconstruction and analysis with electron tomography. Here we describe development of methods for automated multi-tilt data acquisition, tilt-series processing, and alignment which allow assembly of electron tomographic data fr… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:firenano_chromemt?rev=1745364087&do=diff FIREnano and ChromEMT: Visualizing the structural basis of gene activation and silencing in the nucleus <Abstract> Contact Authors * Jingwen Yin (<Email>) * Guillaume Castillon (<Email>) * Sebastien Phan (<Email>) * Horng D. Ou (<Email>) * text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:live_cell_imaging_crispr?rev=1745364087&do=diff Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9 Imaging chromatin dynamics is crucial to understand genome organization and its role in transcriptional regulation. Recently, the RNA-guidable feature of CRISPR-Cas9 has been utilized for imaging of chromatin within live cells. However, these methods are mostly applicable to highly repetitive regions, whereas imaging regions with low or no repeats remains as a challenge. To address this challenge, we design single-gu… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:loss_ctcf_mouse_es?rev=1745364087&do=diff Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells The CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of the impact of loss of CTCF on genome architecture has been difficult due to its essential role in cell proliferation and early embryogenesis. Here, using auxin-inducible degron techniques to acutely deplete CTCF in mouse embryonic stem cells, we show that cell growt… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:multicolor_electron_microscopy?rev=1745364087&do=diff Multicolor electron microscopy for simultaneous visualization of multiple molecular species Electron microscopy (EM) remains the primary method for imaging cellular and tissue ultrastructure, although simultaneous localization of multiple specific molecules continues to be a challenge for EM. We present a method for obtaining multicolor EM views of multiple subcellular components. The method uses sequential, localized deposition of different lanthanides by photosensitizers, small-molecule probe… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:sample_manuscript?rev=1745364087&do=diff Sample Manuscript: A Demonstration <Abstract> <- Contact Authors * <Name> (<Email>) <- * <Name> (<Email>) * <Name> (<Email>) * … Citation Information <include citation information or at least PubMed ID> <- text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:single_molecule_imaging_of_transcription_dynamics_in_somatic_stem_cells?rev=1745364087&do=diff Single Molecule Imaging of Transcription Dynamics in Somatic Stem Cells Molecular noise is a natural phenomenon inherent to all biological systems1,2. How stochastic processes give rise to the robust outcomes supportive of tissue homeostasis is a conundrum. Here, to quantitatively investigate this issue, we use single-molecule mRNA FISH (smFISH) on stem cells derived from hematopoietic tissue to measure the transcription dynamics of three key transcription factor (TF) genes: PU.1, Gata1 and Gat… text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:single_molecule_localization_microscopy?rev=1745364087&do=diff Photon count estimation in single-molecule localization microscopy Recently, Franke, Sauer and van de Linde introduced a way to estimate the axial position of single molecules (TRABI). To this end they compared the detected photon count from a temporal radial-aperture-based intensity estimation to the estimated count from Gaussian Point Spread Function (PSF) fitting to the data. Empirically they found this photometric ratio to be around 0.7-0.8 close to focus and decreasing away from it. Here, … text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:manuscript_tracking:structure_to_function?rev=1745364087&do=diff From structure to function, how bioinformatics help to reveal functions of our genomes This is an invited meeting report. The full manuscript is attached here[:4dn:manuscript_tracking:edits-ibw-mr_xiaoqi0905-sz-clean.docx]. Submission date is uncertain. (9/5)