Papers About QUB

Please cite the software interface as follows:

Milescu, L.S., Nicolai, C., Bannen, J., 2000-2017 QuB Software.

Nicolai, C., Sachs, F. 2013. Solving Ion Channel Kinetics with the QuB Software. Biophysical Reviews and Letters 08:03 1-21. doi:10.1142/S1793048013300053

Also, please cite the appropriate publication for each algorithm utilized:

Publications

Dynamic Clamp:
Milescu, L.S., T. Yamanishi, K. Ptak, M.Z. Mogri, and J.C. Smith. 2008. Real-time kinetic modeling of voltage-gated ion channels using dynamic clamp. Biophysical J. 95(1):66-87.

MacRates (ensemble optimization):
Milescu, L.S., G. Akk, and F. Sachs. 2005. Maximum likelihood estimation of ion channel kinetics from macroscopic currents. Biophysical J. 88(4):2494-2515.

MIL (single-channel idealized optimization):
Qin, F., A. Auerbach, and F. Sachs (1997) Maximum likelihood estimation of aggregated Markov processes. Proceedings of the Royal Society B 264:375-383.

Qin, F., A. Auerbach, and F. Sachs (1996) Estimating single-channel kinetic parameters from idealized patch clamp data. containing missed events. Biophysical Journal 70:264-280.

MPL (single-channel direct optimization):
Qin,F., Auerbach,A. & Sachs,F. A Direct Optimization Approach to Hidden Markov Modeling for Single Channel Kinetics. Biophys. J. 2000 79: 1915-1927

RDF:
Flomenbom, O. Mathematical Treatments That Solve Single Molecules Biophysical Reviews and Letters 2013 08:109-36 doi: 10.1142/S1793048013300016

SKM (idealization):
Qin, F. 2004. Restoration of Single-Channel Currents Using the Segmental k-Means Method Based on Hidden Markov Modeling Biophys. J. 2004 86(3):1488-501

Staircase methods:
Milescu, L.S., A. Yildiz, P.R. Selvin, and F. Sachs. 2006. Extraction of dwell-time sequences from processive molecular motor data. Biophysical J. 91(9):3135-3150.

Milescu, L.S., A. Yildiz, P.R. Selvin, and F. Sachs. 2006. Maximum likelihood estimation of molecular motor kinetics from staircase data. Biophysical J. 91(4):1156-1168.

other:
Li, L., Qin, F. 2004. Model-Based Fitting of Single-Channel Dwell-Time Distributions Biophys J. 87(3):1657-71.

A recent paper on microscopic reversibility, similar to the technique in the 1996 MIL paper :
Colquhoun, D., Dowsland, K., Beato, M. & Plested, A. How to Impose Microscopic Reversibility in Complex Reaction Mechanisms Biophys. J. 2004 86: 3510-3518

Paul H. Edelman & Jim Chen, “Duel Diligence:” Second Thoughts about the Supremes as the Sultans of Swing, 70 S. Cal. L. Rev. 219 (1996), 227
Edelman and Chen use Markovian theory to analyse the outcome of Supreme Court decisions.

Fun with Markov Chains Simulated literature using word transition probabilities from classic texts.