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

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Dynamic regulation of nucleolar architecture

(2018) Attila Németh et al.   CURRENT OPINION IN CELL BIOLOGY

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

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Condensin II drives large-scale folding and spatial partitioning of interphase chromosomes in Drosophila nuclei

(2018) Leah F. Rosin et al.   PLoS Genetics

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy

(2017) Agnel Praveen Joseph et al.   JOURNAL OF STRUCTURAL BIOLOGY

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

(2017) Sharmistha Kundu et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Profiling the transcriptome with RNA SPOTs

(2017) Chee-Huat Linus Eng et al.   NATURE METHODS

Super-resolution microscopy with DNA-PAINT

(2017) Joerg Schnitzbauer et al.   Nature Protocols

Ten principles of heterochromatin formation and function

(2017) Robin C. Allshire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ultraaccurate genome sequencing and haplotyping of single human cells

(2017) Wai Keung Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

(2017) Marie Trussart et al.   Nature Communications

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

Pairing and anti-pairing: a balancing act in the diploid genome

(2016) Eric F Joyce et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Optical imaging of individual biomolecules in densely packed clusters

(2016) Mingjie Dai et al.   Nature Nanotechnology

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Two distinct trimeric conformations of natively membrane-anchored full-length herpes simplex virus 1 glycoprotein B

(2016) Tzviya Zeev-Ben-Mordehai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

(2016) Harianto Tjong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries

(2015) Yusuf Murgha et al.   BIOTECHNIQUES

Restraint-based three-dimensional modeling of genomes and genomic domains

(2015) François Serra et al.   FEBS LETTERS

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

(2015) Marie Trussart et al.   NUCLEIC ACIDS RESEARCH

Determination of localization accuracy based on experimentally acquired image sets: applications to single molecule microscopy

(2015) Amir Tahmasbi et al.   OPTICS EXPRESS

Nanoscale spatial organization of theHoxDgene cluster in distinct transcriptional states

(2015) Pierre J. Fabre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes

(2015) Wahab A. Khan et al.   Molecular Cytogenetics

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction

(2015) Jonas Paulsen et al.   PLoS Computational Biology

TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits

(2015) Irene Farabella et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Models of chromosome structure

(2014) Mario Nicodemi et al.   CURRENT OPINION IN CELL BIOLOGY

A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment

(2014) Ulrike Endesfelder et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

(2014) Ralf Jungmann et al.   NATURE METHODS

Precisely and accurately localizing single emitters in fluorescence microscopy

(2014) Hendrik Deschout et al.   NATURE METHODS

Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes

(2014) Wahab A Khan et al.   Molecular Cytogenetics

DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation

(2013) Radhika Das et al.   BMC GENOMICS

The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses

(2013) S Lukic et al.   CELL DEATH AND DIFFERENTIATION

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

ViSP: representing single-particle localizations in three dimensions

(2013) Mohamed El Beheiry et al.   NATURE METHODS

On the design of clone-based haplotyping

(2013) Christine Lo et al.   GENOME BIOLOGY

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

(2012) Davide Baù et al.   METHODS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Optimizing the specificity of nucleic acid hybridization

(2012) David Yu Zhang et al.   Nature Chemistry

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

(2012) Magda Bienko et al.   NATURE METHODS

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Random and Non-Random Monoallelic Expression

(2012) Andrew Chess   NEUROPSYCHOPHARMACOLOGY

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking

(2012) Ignacio Izeddin et al.   OPTICS EXPRESS

A public resource facilitating clinical use of genomes

(2012) Madeleine P. Ball et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

(2011) Shelagh Boyle et al.   CHROMOSOME RESEARCH

Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH

(2011) N.A. Yamada et al.   CYTOGENETIC AND GENOME RESEARCH

Scoring functions for cryoEM density fitting

(2011) Daven Vasishtan et al.   JOURNAL OF STRUCTURAL BIOLOGY

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Sample drift correction in 3D fluorescence photoactivation localization microscopy

(2011) Michael J. Mlodzianoski et al.   OPTICS EXPRESS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Single-Molecule Kinetics and Super-Resolution Microscopy by Fluorescence Imaging of Transient Binding on DNA Origami

(2010) Ralf Jungmann et al.   NANO LETTERS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A resolution measure for three-dimensional microscopy

(2009) Jerry Chao et al.   OPTICS COMMUNICATIONS

Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy

(2009) Michael J. Mlodzianoski et al.   OPTICS EXPRESS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes

(2008) Mike Heilemann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples

(2008) Manuel F Juette et al.   NATURE METHODS

Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy

(2008) B. Huang et al.   SCIENCE

Protein Structure Fitting and Refinement Guided by Cryo-EM Density

(2008) Maya Topf et al.   STRUCTURE