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2012


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How the initialization affects the stability of the k-means algorithm

Bubeck, S., Meila, M., von Luxburg, U.

ESAIM: Probability and Statistics, 16, pages: 436-452, January 2012 (article)

ei

Web DOI [BibTex]

2012


Web DOI [BibTex]


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Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

Fusi, N., Stegle, O., Lawrence, ND.

PLoS Computational Biology, 8(1):1-9, January 2012 (article)

Abstract
Expression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or unknown subtle environmental perturbations. These factors can induce a pronounced artifactual correlation structure in the expression profiles, which may create spurious false associations or mask real genetic association signals. Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an eQTL analysis. In contrast to previous methods, PANAMA learns hidden factors jointly with the effect of prominent genetic regulators. As a result, this new model can more accurately distinguish true genetic association signals from confounding variation. We applied our model and compared it to existing methods on different datasets and biological systems. PANAMA consistently performs better than alternative methods, and finds in particular substantially more trans regulators. Importantly, our approach not only identifies a greater number of associations, but also yields hits that are biologically more plausible and can be better reproduced between independent studies. A software implementation of PANAMA is freely available online at http://ml.sheffield.ac.uk/qtl/.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Bayesian flexible fitting of biomolecular structures into EM maps

Habeck, M.

Biophysical journal, 2012 (article) Submitted

ei

[BibTex]

[BibTex]


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Measurement and Calibration of Noise Bias in Weak Lensing Galaxy Shape Estimation

Kacprzak, T., Zuntz, J., Rowe, B., Bridle, S., Refregier, A., Amara, A., Voigt, L., Hirsch, M.

Monthly Notices of the Royal Astronomical Society (MNRAS), 2012 (article)

ei

[BibTex]

[BibTex]


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LMM-Lasso: A Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction

Rakitsch, B., Lippert, C., Stegle, O., Borgwardt, KM.

Bioinformatics, 29(2):206-214, 2012 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Existential neuroscience: a functional magnetic resonance imaging investigation of neural responses to reminders of one’s mortality

Quirin, M., Loktyushin, A., Arndt, J., Küstermann, E., Lo, Y., Kuhl, J., Eggert, L.

Social Cognitive and Affective Neuroscience, 7(2):193-198, 2012 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Active learning for domain adaptation in the supervised classification of remote sensing images

Persello, C., Bruzzone, L.

IEEE Transactions on Geoscience and Remote Sensing, 50(11):4468-4483, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Reinforcement learning to adjust parametrized motor primitives to new situations

Kober, J., Wilhelm, A., Oztop, E., Peters, J.

Autonomous Robots, 33(4):361-379, 2012 (article)

Abstract
Humans manage to adapt learned movements very quickly to new situations by generalizing learned behaviors from similar situations. In contrast, robots currently often need to re-learn the complete movement. In this paper, we propose a method that learns to generalize parametrized motor plans by adapting a small set of global parameters, called meta-parameters. We employ reinforcement learning to learn the required meta-parameters to deal with the current situation, described by states. We introduce an appropriate reinforcement learning algorithm based on a kernelized version of the reward-weighted regression. To show its feasibility, we evaluate this algorithm on a toy example and compare it to several previous approaches. Subsequently, we apply the approach to three robot tasks, i.e., the generalization of throwing movements in darts, of hitting movements in table tennis, and of throwing balls where the tasks are learned on several different real physical robots, i.e., a Barrett WAM, a BioRob, the JST-ICORP/SARCOS CBi and a Kuka KR 6.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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On the Empirical Estimation of Integral Probability Metrics

Sriperumbudur, B., Fukumizu, K., Gretton, A., Schölkopf, B., Lanckriet, G.

Electronic Journal of Statistics, 6, pages: 1550-1599, 2012 (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Effect of MR contrast agents on quantitative accuracy of PET in combined whole-body PET/MR imaging

Lois, C., Bezrukov, I., Schmidt, H., Schwenzer, N., Werner, M., Kupferschläger, J., Beyer, T.

European Journal of Nuclear Medicine and Molecular Imaging, 39(11):1756-1766, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Multitask Learning in Computational Biology

Widmer, C., Rätsch, G.

JMLR W\&CP. ICML 2011 Unsupervised and Transfer Learning Workshop, 27, pages: 207-216, 2012 (article)

Abstract
Computational Biology provides a wide range of applications for Multitask Learning (MTL) methods. As the generation of labels often is very costly in the biomedical domain, combining data from different related problems or tasks is a promising strategy to reduce label cost. In this paper, we present two problems from sequence biology, where MTL was successfully applied. For this, we use regularization-based MTL methods, with a special focus on the case of a hierarchical relationship between tasks. Furthermore, we propose strategies to refine the measure of task relatedness, which is of central importance in MTL and finally give some practical guidelines, when MTL strategies are likely to pay off.

ei

PDF [BibTex]

PDF [BibTex]


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Machine Learning and Interpretation in Neuroimaging - Revised Selected and Invited Contributions

Langs, G., Rish, I., Grosse-Wentrup, M., Murphy, B.

pages: 266, Springer, Heidelberg, Germany, International Workshop, MLINI, Held at NIPS, 2012, Lecture Notes in Computer Science, Vol. 7263 (proceedings)

ei

DOI [BibTex]

DOI [BibTex]


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MICCAI, Workshop on Computational Diffusion MRI, 2012 (electronic publication)

Panagiotaki, E., O’Donnell, L., Schultz, T., Zhang, G.

15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Workshop on Computational Diffusion MRI , 2012 (proceedings)

ei

PDF [BibTex]

PDF [BibTex]


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Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

Windram, O., Madhou, P., McHattie, S., Hill, C., Hickman, R., Cooke, E., Jenkins, DJ., Penfold, CA., Baxter, Ll., Breeze, E., Kiddle, SJ., Rhodes, J., Atwell, S., Kliebenstein, D., Kim, Y-S., Stegle, O., Borgwardt, KM., others

The Plant Cell Online, 24(9):3530-3557, 2012, all authors: Oliver Windram,Priyadharshini Madhou,Stuart McHattie,Claire Hill,Richard Hickman,Emma Cooke,Dafyd J. Jenkins,Christopher A. Penfold,Laura Baxter,Emily Breeze,Steven J. Kiddle,Johanna Rhodes,Susanna Atwell,Daniel J. (article)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Improved Linear Mixed Models for Genome-Wide Association Studies

Listgarten, J., Lippert, C., Kadie, CM., Davidson, RI., Eskin, E., Heckerman, D.

Nature Methods, 9, pages: 525–526, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Calibration of Boltzmann distribution priors in Bayesian data analysis

Mechelke, M., Habeck, M.

Physical Review E, 86(6):066705, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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CSB: A Python framework for computational structural biology

Kalev, I., Mechelke, M., Kopec, K., Holder, T., Carstens, S., Habeck, M.

Bioinformatics, 28(22):2996-2997, 2012 (article)

Abstract
Summary: Computational Structural Biology Toolbox (CSB) is a cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice. Availability: Stable release packages are available for download from the Python Package Index (PyPI), as well as from the project’s web site http://csb.codeplex.com.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Design of a Haptic Interface for a Gastrointestinal Endoscopy Simulation

Yu, S., Woo, H. S., Son, H. I., Ahn, W., Jung, H., Lee, D. Y., Yi, S. Y.

Advanced Robotics, 26(18):2115-2143, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Significant global reduction of carbon uptake by water-cycle driven extreme vegetation anomalies

Zscheischler, J., Mahecha, M., von Buttlar, J., Harmeling, S., Jung, M., Randerson, J., Reichstein, M.

Nature Geoscience, 2012 (article) In revision

ei

[BibTex]

[BibTex]


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Emotionally Assisted Human-Robot Interaction Using a Wearable Device for Reading Facial Expressions

Gruebler, A., Berenz, V., Suzuki, K.

Advanced Robotics, 26(10):1143-1159, 2012 (article)

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link (url) DOI [BibTex]


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Measurement and calibration of noise bias in weak lensing galaxy shape estimation

Kacprzak, T., Zuntz, J., Rowe, B., Bridle, S., Refregier, A., Amara, A., Voigt, L., Hirsch, M.

Monthly Notices of the Royal Astronomical Society, 427(4):2711-2722, Oxford University Press, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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From Dynamic Movement Primitives to Associative Skill Memories

Pastor, P., Kalakrishnan, M., Meier, F., Stulp, F., Buchli, J., Theodorou, E., Schaal, S.

Robotics and Autonomous Systems, 2012 (article)

am

Project Page [BibTex]

Project Page [BibTex]


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A new seam-tracking algorithm through characteristic-point detection for a portable welding robot

Chang, D., Son, D., Lee, J., Lee, D., Kim, T., Lee, K., Kim, J.

Robotics and Computer-Integrated Manufacturing, 28, 2012 (article)

pi

[BibTex]

[BibTex]


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A Well-posed Kelvin-Helmholtz Instability Test and Comparison

McNally, C., Lyra, W., Passy, J.

Astrophysical Journal, Supplement, 201, pages: 18, 2012 (article)

DOI [BibTex]

DOI [BibTex]


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Image analysis for cosmology: results from the GREAT10 Galaxy Challenge

Kitching, T. D., Balan, S. T., Bridle, S., Cantale, N., Courbin, F., Eifler, T., Gentile, M., Gill, M. S. S., Harmeling, S., Heymans, C., others,

Monthly Notices of the Royal Astronomical Society, 423(4):3163-3208, Oxford University Press, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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A new seam-tracking algorithm through characteristic-point detection for a portable welding robot

Doyoung Chang, Donghoon Son, Jungwoo Lee, Donghun Lee, Tae-wan Kim, Kyu-Yeul Lee, Jongwon Kim

Robotics and Computer-Integrated Manufacturing, 28, 2012 (article)

[BibTex]

[BibTex]


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Fourier-transform photocurrent spectroscopy using a supercontinuum light source

Petermann, C., Beigang, R., Fischer, P.

APPLIED PHYSICS LETTERS, 100(6), 2012 (article)

Abstract
We demonstrate an implementation of frequency-encoded photocurrent spectroscopy using a super-continuum light source. The spectrally broad light is spatially dispersed and modulated with a special mechanical chopper design that permits a continuous wavelength-dependent modulation. After recombination, the light beam contains a frequency encoded spectrum which enables us to map the spectral response of a given sample in 60 ms and with a lateral resolution of 10 mu m. (C) 2012 American Institute of Physics.

pf

DOI [BibTex]

DOI [BibTex]


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Tail-assisted pitch control in lizards, robots and dinosaurs

Libby, T., Moore, T., Chang, E., Li, D., Cohen, D., Jusufi, A., Full, R.

Nature, 2012 (article)

bio

link (url) [BibTex]

link (url) [BibTex]


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Eine neue Form von Cavity Enhanced Absorption Spectroscopy

Petermann, C., Fischer, P.

DE Gruyter, 79(1), 2012, Best paper award OPTO 2011 (article)

Abstract
Wir stellen eine Kopplungsmethode für resonatorgestützte Absorptionsmessungen vor, bei der Licht durch einen im Resonator platzierten akustooptischen Modulator aktiv ein- und ausgekoppelt wird. Dies ermöglicht es Cavity-Ring-Down-Spektroskopie (CRDS) mit breitbandigen und zeitlich inkohärenten Lichtquellen niedriger spektraler Leistungsdichte durchzuführen. Das Verfahren wird zum ersten Mal mit einer breitbandigen Superkontinuum-Quelle demonstriert.

___________________________________________________________________________________________

A new coupling scheme for cavity enhanced absorption spectroscopy makes use of an intracavity acousto-optical modulator to actively switch light into (and out of) a resonator. This allows cavity ringdown spectroscopy (CRDS) to be implemented with broadband temporally incoherent light sources with low spectral power densities. The method is demonstrated for the first time using a broadband supercontinuum source. Best paper award OPTO 2011.

pf

link (url) [BibTex]

link (url) [BibTex]


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The Response of Giant Stars to Dynamical-timescale Mass Loss

Passy, J., Herwig, F., Paxton, B.

Astrophysical Journal , 760, pages: 90, 2012 (article)

DOI [BibTex]

DOI [BibTex]


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Simulating the Common Envelope Phase of a Red Giant Using Smoothed-particle Hydrodynamics and Uniform-grid Codes

Passy, J., De Marco, O., Fryer, C., Herwig, F., Diehl, S., Oishi, J., Mac Low, M., Bryan, G., Rockefeller, G.

Astrophysical Journal , 744, pages: 52, 2012 (article)

DOI [BibTex]

DOI [BibTex]


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Rapid Inversion: Running Animals and Robots Swing like a Pendulum under Ledges

Mongeau, J., McRae, B., Jusufi, A., Birkmeyer, P., Hoover, A., Fearing, R.

PLoS One, 2012 (article)

bio

link (url) [BibTex]

link (url) [BibTex]


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First SN Discoveries from the Dark Energy Survey

Abbott, T., Abdalla, F., Achitouv, I., Ahn, E., Aldering, G., Allam, S., Alonso, D., Amara, A., Annis, J., Antonik, M., others,

The Astronomer's Telegram, 4668, pages: 1, 2012 (article)

ei

[BibTex]

[BibTex]


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Autonomous battery management for mobile robots based on risk and gain assessment

Berenz, V., Tanaka, F., Suzuki, K.

Artif. Intell. Rev., 37(3):217-237, 2012 (article)

am

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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On the Survival of Brown Dwarfs and Planets Engulfed by Their Giant Host Star

Passy, J., Mac Low, M., De Marco, O.

Astrophysical Journal, Letters , 759, pages: L30, 2012 (article)

DOI [BibTex]

DOI [BibTex]


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RoboCup@Home: Demonstrating Everyday Manipulation Skills in RoboCup@Home

Stueckler, J., Holz, D., Behnke, S.

IEEE Robotics and Automation Magazine (RAM), 19(2):34-42, 2012 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Two-dimensional autonomous microparticle manipulation strategies for magnetic microrobots in fluidic environments

Pawashe, C., Floyd, S., Diller, E., Sitti, M.

IEEE Transactions on Robotics, 28(2):467-477, IEEE, 2012 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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Variants of guided self-organization for robot control

Martius, G., Herrmann, J.

Theory in Biosci., 131(3):129-137, Springer Berlin / Heidelberg, 2012 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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A metric for comparing the anthropomorphic motion capability of artificial hands

Feix, T., Romero, J., Ek, C. H., Schmiedmayer, H., Kragic, D.

IEEE RAS Transactions on Robotics, TRO, pages: 974-980, 2012 (article)

ps

Publisher site Human Grasping Database Project [BibTex]

Publisher site Human Grasping Database Project [BibTex]


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The Ankyrin 3 (ANK3) Bipolar Disorder Gene Regulates Psychiatric-related Behaviors that are Modulated by Lithium and Stress

Leussis, M., Berry-Scott, E., Saito, M., Jhuang, H., Haan, G., Alkan, O., Luce, C., Madison, J., Sklar, P., Serre, T., Root, D., Petryshen, T.

Biological Psychiatry , 2012 (article)

ps

Prepublication Article Abstract [BibTex]

Prepublication Article Abstract [BibTex]


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Vortex dynamics in nonparabolic potentials

Langner, H. H., Kamionka, T., Martens, M., Weigand, M., Adolff, C. F., Merkt, U., Meier, G.

{Physical Review B}, 85(17), 2012 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Micromagnetic simulations on GPU, a case study: Vortex core switcing by high-frequency magnetic fields

Van de Wiele, B, Vansteenkiste, A., Kammerer, M., Van Waeyenberge, B., Dupré, L., De Zutter, D.

{IEEE Transactions on Magnetics}, 48(6):2068-2072, 2012 (article)

mms

DOI [BibTex]

DOI [BibTex]


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On the energetics of transversal and longitudinal fluctuations of atomic magnetic moments

Dietermann, F., Sandratskii, L. M., Fähnle, M.

{Journal of Magnetism and Magnetic Materials}, 324(18):2693-2695, 2012 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Gradual softening of Al-Zn alloys during high-pressure torsion

Mazilkin, A. A., Straumal, B. B., Borodachenkova, M. V., Valiev, R. Z., Kogtenkova, O. A., Baretzky, B.

{Materials Letters}, 84, pages: 63-65, North-Holland, Amsterdam, 2012 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Direct imaging of phase relation in a pair of coupled vortex oscillators

Vogel, A., Drews, A., Weigand, M., Meier, G.

{AIP Advances}, 2, 2012 (article)

mms

DOI [BibTex]

DOI [BibTex]


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A sensorimotor paradigm for Bayesian model selection

Genewein, T, Braun, DA

Frontiers in Human Neuroscience, 6(291):1-16, October 2012 (article)

Abstract
Sensorimotor control is thought to rely on predictive internal models in order to cope efficiently with uncertain environments. Recently, it has been shown that humans not only learn different internal models for different tasks, but that they also extract common structure between tasks. This raises the question of how the motor system selects between different structures or models, when each model can be associated with a range of different task-specific parameters. Here we design a sensorimotor task that requires subjects to compensate visuomotor shifts in a three-dimensional virtual reality setup, where one of the dimensions can be mapped to a model variable and the other dimension to the parameter variable. By introducing probe trials that are neutral in the parameter dimension, we can directly test for model selection. We found that model selection procedures based on Bayesian statistics provided a better explanation for subjects’ choice behavior than simple non-probabilistic heuristics. Our experimental design lends itself to the general study of model selection in a sensorimotor context as it allows to separately query model and parameter variables from subjects.

ei

DOI [BibTex]

DOI [BibTex]


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Three-dimensional microfiber devices that mimic physiological environments to probe cell mechanics and signaling

Ruder, W. C., Pratt, E. D., Bakhru, S., Sitti, M., Zappe, S., Cheng, C., Antaki, J. F., LeDuc, P. R.

Lab on a Chip, 12(10):1775-1779, Royal Society of Chemistry, 2012 (article)

pi

[BibTex]

[BibTex]