@string{AW = "Addison-Wesley Longman Publishing Co., Inc."}
@string{AdvExpMedBiol = "Advances in Experimental Medicine and Biology"}
@string{SAinavarapu = "Ainavarapu, Sri Rama Koti"}
+@string{DAioanei = "Aioanei, Daniel"}
@string{TRAlbrecht = "Albreacht, T.~R."}
@string{FAli = "Ali, F."}
@string{JFAllemand = "Allemand, Jean-Fran\c{c}ois"}
@string{FWBartels = "Bartels, Frank Wilco"}
@string{BBarz = "Barz, Bogdan"}
@string{TBasche = "Basche, Th."}
+@string{PBaschieri = "Baschieri, Paolo"}
@string{ABasu = "Basu, A."}
@string{LBaugh = "Baugh, Loren"}
@string{BBaumgarth = "Baumgarth, Birgit"}
@string{BBullard = "Bullard, Belinda"}
@string{RBunk = "Bunk, Richard"}
@string{DBusam = "Busam, D."}
+@string{GBussi = "Bussi, Giovanni"}
@string{CBustamante = "Bustamante, Carlos"}
@string{YBustanji = "Bustanji, Yasser"}
@string{HJButt = {Butt, Hans-J\"urgen}}
@string{CDewhurst = "Dewhurst, Charles"}
@string{VDiFrancesco = "Di Francesco, V."}
@string{KDiemer = "Diemer, K."}
+@string{GDietler = "Dietler, Giovanni"}
@string{HDietz = "Dietz, Hendrik"}
@string{SDietz = "Dietz, S."}
@string{EDijkstra = "Dijkstra, Edsger Wybe"}
@string{CKHu = "Hu, Chin-Kun"}
@string{BHuang = "Huang, Baiqu"}
@string{HHuang = "Huang, Hector Han-Li"}
+@string{MHubain = "Hubain, Maurice"}
@string{AJHudspeth = "Hudspeth, A.~J."}
@string{KHuff = "Huff, Katy"}
@string{JHughes = "Hughes, John"}
@string{JBT = "J Biotechnol"}
@string{JEChem = "Journal of Electroanalytical Chemistry"}
@string{JMathBiol = "J Math Biol"}
+@string{JMicro = "Journal of microscopy"}
@string{JPhysio = "Journal of physiology"}
@string{JStructBiol = "Journal of structural biology"}
@string{JTB = "J Theor Biol"}
@string{WJang = "Jang, W."}
+@string{HJanovjak = "Janovjak, H."}
@string{LJanosi = "Janosi, Lorant"}
@string{AJanshoff = "Janshoff, Andreas"}
@string{JJAP = "Japanese Journal of Applied Physics"}
@string{TAKucaba = "Kucaba, T. A."}
@string{Kucherlapati = "Kucherlapati"}
@string{JKudoh = "Kudoh, J."}
+@string{MKuhn = "Kuhn, Michael"}
@string{MKulke = "Kulke, Michael"}
@string{CKwok = "Kwok, Carol H."}
@string{RLevy = "L\'evy, R"}
@string{MMartin = "Martin, M. J."}
@string{YMartin = "Martin, Y."}
@string{HMassa = "Massa, H."}
+@string{DMaterassi = "Materassi, Donatello"}
@string{JMathe = "Math\'e, J\'er\^ome"}
@string{AMatouschek = "Matouschek, Andreas"}
@string{BMatthews = "Matthews, Brian W."}
@string{NMetropolis = "Metropolis, Nicholas"}
@string{GMeyer = "Meyer, Gerhard"}
@string{HMi = "Mi, H."}
+@string{CMicheletti = "Micheletti, Cristian"}
@string{MMickler = "Mickler, Moritz"}
@string{AMiller = "Miller, A."}
@string{NMilshina = "Milshina, N."}
@string{MMoy = "Moy, M."}
@string{VMoy = "Moy, Vincent T."}
@string{SMukamel = "Mukamel, Shaul"}
+@string{DJMuller = "M{\"u}ller, Daniel J."}
@string{PMundel = "Mundel, P."}
@string{EMuneyuki = "Muneyuki, Eiro"}
@string{RJMural = "Mural, R. J."}
@string{JScott = "Scott, J."}
@string{RScott = "Scott, R."}
@string{USeifert = "Seifert, Udo"}
+@string{SKSekatskii = "Sekatskii, Sergey K."}
@string{MSekhon = "Sekhon, M."}
@string{TSekiguchi = "Sekiguchi, T."}
@string{BSenger = "Senger, B."}
@string{SThornton = "Thornton, S."}
@string{RWTillmann = "Tillmann, R.~W."}
@string{NNTint = "Tint, N. N."}
+@string{BTiribilli = "Tiribilli, Bruno"}
@string{TTlusty = "Tlusty, Tsvi"}
@string{JTocaHerrera = "Toca-Herrera, Jose L."}
@string{AToyoda = "Toyoda, A."}
@string{RCZinober = "Zinober, Rebecca C."}
@string{JZlatanova = "Zlatanova, Jordanka"}
@string{PZou = "Zou, Peng"}
+@string{GZuccheri = "Zuccheri, Giampaolo"}
@string{RZwanzig = "Zwanzig, R."}
@string{arXiv = "arXiv"}
@string{PGdeGennes = "de Gennes, P. G."}
language = "eng",
}
+@article{ kuhn05,
+ author = MKuhn #" and "# HJanovjak #" and "# MHubain #" and "# DJMuller,
+ title = {Automated alignment and pattern recognition of
+ single-molecule force spectroscopy data.},
+ year = 2005,
+ month = may,
+ address = {Division of Computer Science, California Institute of
+ Technology, Pasadena, California 91125, USA.},
+ journal = JMicro,
+ volume = 218,
+ number = 2,
+ pages = {125--132},
+ ISSN = {0022-2720},
+ doi = {10.1111/j.1365-2818.2005.01478.x},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/15857374},
+ language = {eng},
+ keywords = {Algorithms},
+ keywords = {Bacteriorhodopsins},
+ keywords = {Data Interpretation, Statistical},
+ keywords = {Escherichia coli Proteins},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Protein Folding},
+ keywords = {Sodium-Hydrogen Antiporter},
+ keywords = {Software},
+ abstract = {Recently, direct measurements of forces stabilizing
+ single proteins or individual receptor-ligand bonds became
+ possible with ultra-sensitive force probe methods like the atomic
+ force microscope (AFM). In force spectroscopy experiments using
+ AFM, a single molecule or receptor-ligand pair is tethered between
+ the tip of a micromachined cantilever and a supporting
+ surface. While the molecule is stretched, forces are measured by
+ the deflection of the cantilever and plotted against extension,
+ yielding a force spectrum characteristic for each biomolecular
+ system. In order to obtain statistically relevant results, several
+ hundred to thousand single-molecule experiments have to be
+ performed, each resulting in a unique force spectrum. We developed
+ software and algorithms to analyse large numbers of force
+ spectra. Our algorithms include the fitting polymer extension
+ models to force peaks as well as the automatic alignment of
+ spectra. The aligned spectra allowed recognition of patterns of
+ peaks across different spectra. We demonstrate the capabilities of
+ our software by analysing force spectra that were recorded by
+ unfolding single transmembrane proteins such as bacteriorhodopsin
+ and NhaA. Different unfolding pathways were detected by
+ classifying peak patterns. Deviant spectra, e.g. those with no
+ attachment or erratic peaks, can be easily identified. The
+ software is based on the programming language C++, the GNU
+ Scientific Library (GSL), the software WaveMetrics IGOR Pro and
+ available open-source at http://bioinformatics.org/fskit/.},
+ note = {Development stalled in 2005 after Michael graduated.},
+}
+
@article{ sandal09,
author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "#
AGomezCasado #" and "# BSamori,
language = "eng",
}
+@article{ materassi09,
+ author = DMaterassi #" and "# PBaschieri #" and "# BTiribilli #" and "#
+ GZuccheri #" and "# BSamori,
+ title = {An open source/real-time atomic force microscope
+ architecture to perform customizable force spectroscopy
+ experiments},
+ year = 2009,
+ month = aug,
+ address = {Department of Electrical and Computer Engineering,
+ University of Minnesota, 200 Union St. SE, Minneapolis,
+ Minnesota 55455, USA. mater013@umn.edu},
+ journal = RSI,
+ volume = 80,
+ number = 8,
+ pages = 084301,
+ issn = "1089-7623",
+ doi = "10.1063/1.3194046",
+ url = "http://www.ncbi.nlm.nih.gov/pubmed/19725671",
+ language = "eng",
+ keywords = {Algorithms},
+ keywords = {Animals},
+ keywords = {Calibration},
+ keywords = {Gold},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Muscle Proteins},
+ keywords = {Myocardium},
+ keywords = {Optics and Photonics},
+ keywords = {Ownership},
+ keywords = {Protein Kinases},
+ keywords = {Software},
+ keywords = {Spectrum Analysis},
+ keywords = {Time Factors},
+ abstract = {We describe the realization of an atomic force
+ microscope architecture designed to perform customizable
+ experiments in a flexible and automatic way. Novel technological
+ contributions are given by the software implementation platform
+ (RTAI-LINUX), which is free and open source, and from a functional
+ point of view, by the implementation of hard real-time control
+ algorithms. Some other technical solutions such as a new way to
+ estimate the optical lever constant are described as well. The
+ adoption of this architecture provides many degrees of freedom in
+ the device behavior and, furthermore, allows one to obtain a
+ flexible experimental instrument at a relatively low cost. In
+ particular, we show how such a system has been employed to obtain
+ measures in sophisticated single-molecule force spectroscopy
+ experiments\citep{fernandez04}. Experimental results on proteins
+ already studied using the same methodologies are provided in order
+ to show the reliability of the measure system.},
+ note = {Although this paper claims to present an open source
+ experiment control framework (on Linux!), it doesn't actually link
+ to any source code. This is puzzling and frusterating.},
+}
+
+@article{ aioanei11,
+ author = DAioanei #" and "# MBrucale #" and "# BSamori,
+ title = {Open source platform for the execution and analysis of
+ mechanical refolding experiments.},
+ year = 2011,
+ month = feb,
+ day = 1,
+ address = {Department of Biochemistry G.~Moruzzi,
+ University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
+ aioaneid@gmail.com},
+ journal = BIOINFO,
+ volume = 27,
+ number = 3,
+ pages = {423--425},
+ issn = {1367-4811},
+ doi = {10.1093/bioinformatics/btq663},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21123222},
+ language = {eng},
+ keywords = {Computational Biology},
+ keywords = {Kinetics},
+ keywords = {Protein Denaturation},
+ keywords = {Protein Refolding},
+ keywords = {Software},
+ abstract = {Single-molecule force spectroscopy has facilitated the
+ experimental investigation of biomolecular force-coupled kinetics,
+ from which the kinetics at zero force can be extrapolated via
+ explicit theoretical models. The atomic force microscope (AFM) in
+ particular is routinely used to study protein unfolding kinetics,
+ but only rarely protein folding kinetics. The discrepancy arises
+ because mechanical protein refolding studies are more technically
+ challenging.},
+ note = {\href{http://code.google.com/p/refolding/}{Refolding} is a
+ suite for performing and analyzing double-pulse refolding
+ experiments. The experiment-driver is mostly written in Java with
+ the analysis code in Python. The driver is curious; it uses the
+ NanoScope scripting interface to drive the experiment through the
+ NanoScope software by impersonating a mouse-wielding user (like
+ Selenium does for web browsers). See the
+ \imint{sh}|RobotNanoDriver.java| code for details. There is also
+ support for automatic velocity clamp analysis.},
+}
+
+@article{ benedetti11,
+ author = FBenedetti #" and "# CMicheletti #" and "# GBussi #" and "#
+ SKSekatskii #" and "# GDietler,
+ title = {Nonkinetic modeling of the mechanical unfolding of
+ multimodular proteins: theory and experiments.},
+ year = 2011,
+ month = sep,
+ day = 21,
+ address = {Laboratory of Physics of Living Matter,
+ Ecole Polytechnique F{\'e}d{\'e}rale de Lausanne,
+ Lausanne, Switzerland.},
+ journal = BPJ,
+ volume = 101,
+ number = 6,
+ pages = {1504--1512},
+ issn = {1542-0086},
+ doi = {10.1016/j.bpj.2011.07.047},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21943432},
+ language = {eng},
+ keywords = {Kinetics},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Models, Molecular},
+ keywords = {Monte Carlo Method},
+ keywords = {Protein Unfolding},
+ keywords = {Stochastic Processes},
+ abstract = {We introduce and discuss a novel approach called
+ back-calculation for analyzing force spectroscopy experiments on
+ multimodular proteins. The relationship between the histograms of
+ the unfolding forces for different peaks, corresponding to a
+ different number of not-yet-unfolded protein modules, is exploited
+ in such a manner that the sole distribution of the forces for one
+ unfolding peak can be used to predict the unfolding forces for
+ other peaks. The scheme is based on a bootstrap prediction method
+ and does not rely on any specific kinetic model for multimodular
+ unfolding. It is tested and validated in both
+ theoretical/computational contexts (based on stochastic
+ simulations) and atomic force microscopy experiments on (GB1)(8)
+ multimodular protein constructs. The prediction accuracy is so
+ high that the predicted average unfolding forces corresponding to
+ each peak for the GB1 construct are within only 5 pN of the
+ averaged directly-measured values. Experimental data are also used
+ to illustrate how the limitations of standard kinetic models can
+ be aptly circumvented by the proposed approach.},
+}
+
@article{ kempe85,
author = TKempe #" and "# SBHKent #" and "# FChow #" and "# SMPeterson
#" and "# WSundquist #" and "# JLItalien #" and "# DHarbrecht
projects / thesis.git / commitdiff