FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

(2016) Antonino Ingargiola et al.   BIOPHYSICAL JOURNAL

A Quick Introduction to Version Control with Git and GitHub

(2016) John D. Blischak et al.   PLoS Computational Biology

No more hidden solutions in bioinformatics

(2015) Mauno Vihinen   NATURE

Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements

(2015) Gil Rahamim et al.   PLoS One

Bayesian Inference of Accurate Population Sizes and FRET Efficiencies from Single Diffusing Biomolecules

(2014) Rebecca R. Murphy et al.   ANALYTICAL CHEMISTRY

Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule FRET Experiments

(2014) Jan-Willem van de Meent et al.   BIOPHYSICAL JOURNAL

Kinetics of Fast Changing Intramolecular Distance Distributions Obtained by Combined Analysis of FRET Efficiency Kinetics and Time-Resolved FRET Equilibrium Measurements

(2014) E. Lerner et al.   BIOPHYSICAL JOURNAL

Interactive notebooks: Sharing the code

(2014) Helen Shen   NATURE

Best Practices for Scientific Computing

(2014) Greg Wilson et al.   PLOS BIOLOGY

Alternating-laser excitation: single-molecule FRET and beyond

(2013) Johannes Hohlbein et al.   CHEMICAL SOCIETY REVIEWS

Detailed Study of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by DNA Origami

(2013) Roman Tsukanov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

BOBA FRET: Bootstrap-Based Analysis of Single-Molecule FRET Data

(2013) Sebastian L. B. König et al.   PLoS One

Disentangling Subpopulations in Single-Molecule FRET and ALEX Experiments with Photon Distribution Analysis

(2012) Toma E. Tomov et al.   BIOPHYSICAL JOURNAL

The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection

(2012) Nicole C. Robb et al.   JOURNAL OF MOLECULAR BIOLOGY

Classic Maximum Entropy Recovery of the Average Joint Distribution of Apparent FRET Efficiency and Fluorescence Photons for Single-Molecule Burst Measurements

(2012) Matthew S. DeVore et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The case for open computer programs

(2012) Darrel C. Ince et al.   NATURE

Development of new photon-counting detectors for single-molecule fluorescence microscopy

(2012) X. Michalet et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data

(2012) Max Greenfeld et al.   PLoS One

Ten Simple Rules for the Open Development of Scientific Software

(2012) Andreas Prlić et al.   PLoS Computational Biology

Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis

(2011) Joseph P. Torella et al.   BIOPHYSICAL JOURNAL

How, when and why proteins collapse: the relation to folding

(2011) Gilad Haran   CURRENT OPINION IN STRUCTURAL BIOLOGY

Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP)

(2011) Armin Hoffmann et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Characterizing Single-Molecule FRET Dynamics with Probability Distribution Analysis

(2010) Yusdi Santoso et al.   CHEMPHYSCHEM

On the Origin of Broadening of Single-Molecule FRET Efficiency Distributions beyond Shot Noise Limits

(2010) Stanislav Kalinin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

FRET Efficiency Distributions of Multistate Single Molecules

(2010) Irina V. Gopich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational science: ...Error

(2010) Zeeya Merali   NATURE

Probing Biomolecular Structures and Dynamics of Single Molecules Using In-gel Alternating-Laser Excitation

(2009) Yusdi Santoso et al.   ANALYTICAL CHEMISTRY

Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data

(2009) Jonathan E. Bronson et al.   BIOPHYSICAL JOURNAL

Förster transfer outside the weak-excitation limit

(2009) Brian A. Camley et al.   JOURNAL OF CHEMICAL PHYSICS

Decoding the Pattern of Photon Colors in Single-Molecule FRET

(2009) Irina V. Gopich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein folding studied by single-molecule FRET

(2008) Benjamin Schuler et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds†

(2008) Daniel Nettels et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS

Concentration Effects in “Single-Molecule” Spectroscopy†

(2007) Irina V. Gopich   JOURNAL OF PHYSICAL CHEMISTRY B