Bound2Learn: a machine learning approach for classification of DNA-bound proteins from single-molecule tracking experiments

Processive Activity of Replicative DNA Polymerases in the Replisome of Live Eukaryotic Cells

(2020) Nitin Kapadia et al.   MOLECULAR CELL

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

(2019) Andrea Callegari et al.   PLoS Genetics

The Impact of the C-Terminal Region on the Interaction of Topoisomerase II Alpha with Mitotic Chromatin

(2019) Melissa Antoniou-Kourounioti et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells

(2019) Han N. Ho et al.   BIOPHYSICAL JOURNAL

Single-Molecule Kinetics in Living Cells

(2018) Johan Elf et al.   Annual Review of Biochemistry

Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast

(2018) Gunjan D. Mehta et al.   MOLECULAR CELL

TrackMate: An open and extensible platform for single-particle tracking

(2017) Jean-Yves Tinevez et al.   METHODS

Smooth 2D manifold extraction from 3D image stack

(2017) Asm Shihavuddin et al.   Nature Communications

A tunable refractive index matching medium for live imaging cells, tissues and model organisms

(2017) Tobias Boothe et al.   eLife

Frequent exchange of the DNA polymerase during bacterial chromosome replication

(2017) Thomas R Beattie et al.   eLife

Single-Molecule Studies in Live Cells

(2016) Ji Yu   Annual Review of Physical Chemistry

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Bright photoactivatable fluorophores for single-molecule imaging

(2016) Jonathan B Grimm et al.   NATURE METHODS

Single molecule tracking of Ace1p inSaccharomyces cerevisiaedefines a characteristic residence time for non-specific interactions of transcription factors with chromatin

(2016) David A. Ball et al.   NUCLEIC ACIDS RESEARCH

Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid

(2015) Mathew Stracy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

(2014) Petter Hammar et al.   NATURE GENETICS

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

(2014) Thomas J. Etheridge et al.   NUCLEIC ACIDS RESEARCH

Persistent super-diffusive motion of Escherichia coli chromosomal loci

(2014) Avelino Javer et al.   Nature Communications

Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells

(2014) M. Charl Moolman et al.   Nature Communications

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

(2013) Houssam Hajjoul et al.   GENOME RESEARCH

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

(2013) J Christof M Gebhardt et al.   NATURE METHODS

Single-molecule DNA repair in live bacteria

(2013) S. Uphoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Optimal diffusion coefficient estimation in single-particle tracking

(2012) Xavier Michalet et al.   PHYSICAL REVIEW E

mMaple: A Photoconvertible Fluorescent Protein for Use in Multiple Imaging Modalities

(2012) Ann L. McEvoy et al.   PLoS One

Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein

(2011) C. F. Kurat et al.   GENES & DEVELOPMENT

FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

(2010) Florian Mueller et al.   CURRENT OPINION IN CELL BIOLOGY

Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm

(2010) Stephanie C. Weber et al.   PHYSICAL REVIEW LETTERS

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Single-Molecule Approach to Molecular Biology in Living Bacterial Cells

(2008) X. Sunney Xie et al.   Annual Review of Biophysics

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

(2008) Suliana Manley et al.   NATURE METHODS

Regulation of TATA-binding protein dynamics in living yeast cells

(2008) R. O. Sprouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA