# Journal Articles

2011, 2010, 2009, 2008, 2007, 2006, 2005, 2004, 2003, 2002, <=2001
## 2017

Z. Woodhead, J Crinion, S Teki, W. Penny, C. Price and A. Leff (2017).
** Auditory training changes temporal lobe connectivity in "Wernicke's aphasia": a randomised trial. **
*Journal of Neurology, Neurosurgery and Psychiatry. * Published Online First: 04 March 2017.
See also the editorial .

G. Ziegler, G Ridgway, S Blakemore, J Ashburner and W. Penny (2017).
** Multivariate dynamical modelling of structural change during development.**
* Neuroimage. * 147:746-762.

R Kaplan, J King, R Koster, W. Penny, N Burgess and K Friston (2017).
** The Neural Representation of Prospective Choice during Spatial Planning and Decisions.**
* PLoS Biology. * 15(1):e1002588.

## 2016

W. Penny and B Sengupta (2016).
** Annealed Importance Sampling for Neural Mass Models.**
* PLoS Computational Biology. * 12(3): e1004797.
Supplementary notes on
Importance Sampling
,
Fisher Information
,
Neural Mass Models
,
Variational Laplace
,
Chib's Estimate of Model Evidence
.

S Tak, M Uga, G Flandin, I Dan and W. Penny (2016).
** Sensor space group analysis for fNIRS data.**
* J Neurosci Methods. * 264: 103-112.

E Aponte, S Raman, B Sengupta, W Penny, K Stephan and J Heinzle (2016).
** mpdcm: A toolbox for massively parallel dynamic causal modelling.**
* J Neurosci Methods. * 257: 7-16.

B Sengupta, K Friston and W. Penny (2016).
** Gradient-based MCMC samplers for dynamic causal modelling.**
* Neuroimage. * 125: 1107-1118.

V Romei, M Bauer, J Brooks, M Economides, W Penny, G Thut, J Driver and S Bestmann (2016).
** Causal evidence that intrinsic beta-frequency is relevant for enhanced signal propagation in the motor
system as shown through rhythmic TMS.**
* Neuroimage. * 126:120-130.

## 2015

G Ziegler, W. Penny, G Ridgway, S Ourselin, K Friston and ADNI (2015).
** Estimating anatomical trajectories with Bayesian mixed-effects modeling.**
* Neuroimage. * 121: 51-68.

J Magerkurth, L Mancini, W. Penny, G Flandin, J Ashburner, C Micallef, E DeVita, P Daga, M White, C Buckley
, A Yamamoto, S Ourselin, T Yousry, J Thornton (2015).
** Objective Bayesian fMRI analysis - a pilot study in different clinical environments.**
* Frontiers in Neuroscience. * 9: 168.

A Tomassini, D Ruge, J Galea, W Penny and S Bestmann (2015).
** The role of dopamine in temporal uncertainty.**
* Journal of Cognitive Neuroscience. * 28:96-110.

B Sengupta, K Friston and W. Penny (2015).
** Gradient-free MCMC methods for dynamic causal modelling.**
* Neuroimage. * 112: 375-381.

S Tak, A Kempny, K Friston, A Leff and W. Penny (2015).
** Dynamic causal modelling for functional near-infrared spectroscopy.**
* Neuroimage. * 111: 338-349.

M Klein-Flugge, S Kennerley, A Saraiva, W. Penny and S Bestmann (2015).
** Behavioural modeling of human choices reveals dissociable effects of physical effort and temporal delay
on reward devaluation.**
* PLoS Computational Biology. * 11(3): e1004116.

B. Van Wijk, A. Jha, W. Penny and V Litvak (2015).
** Parametric estimation of cross-frequency coupling.**
* Journal of Neuroscience Methods. * In Press, http://dx.doi.org/10.1016/j.jneumeth.2015.01.032

## 2014

A Javadi, I Brunec, V Walsh W. Penny and H Spiers(2014).
** Transcranial electrical brain stimulation modulates neuronal tuning
curves in perception of numerosity and duration.**
* Neuroimage 102, 451-457. *

S. Kumar and W. Penny (2014).
** Estimating Neural Response Functions from fMRI.**
* Frontiers in Neuroinformatics, 8:48. *

B. Sengupta, K. Friston and W. Penny (2014).
** Efficient Gradient Computation for Dynamical Models.**
* Neuroimage, 98:521-527. *

C Stevenson, M Brookes, J López, L Troebinger, J Mattout , W Penny, P Morris, A Hillebrand, R Henson, G Barnes (2014).
** Does function fit structure? A ground truth for non-invasive neuroimaging.**
* Neuroimage, 94:89-95 *,

A. Jafarpour, L. Fuentemilla, A Horner, W. Penny and E. Duzel (2014).
** Replay of very early encoding representations during recollection.**
* Journal of Neuroscience, 34(1), 242-248 *,

K. Brodersen, L. Deserno, F. Schlagenhauf, Z. Lin, W. Penny, J. Buhmann and K. Stephan (2014).
** Dissecting psychiatric spectrum disorders by generative embedding.**
* Neuroimage: Clinical, 4, 98-111 *,

## 2013

W. Penny, P. Zeidman and N. Burgess (2013).
** Forward and backward inference in spatial cognition.**
* PLoS Computational Biology, 9(12) e1003383 *,

A. Appelgren, W. Penny and S. Bengtsson (2013).
** Impact of feedback on three phases of performance monitoring.** * Experimental Psychology * doi:10.1027/1618-3169/a000242,

S. Bengtsson and W. Penny (2013).
** Self-associations influence task-performance through Bayesian inference. **
*Frontiers in Human Neuroscience. * Volume 7, Article 490.

A. Jafarpour, G. Barnes, L. Fuentemilla, E. Duzel and W. Penny (2013).
** Population level inference for multivariate MEG analysis. **
*PLoS One. * 8(8), e71305.

Z. Woodhead, W. Penny, G. Barnes, H. Crewes, R. Wise, C. Price and A. Leff (2013).
** Reading therapy strengthens top-down connectivity in patients with pure alexia. **
*Brain. * 136, 2579-2591.

S. Teki, G. Barnes, W. Penny, P. Iverson, Z. Woodhead, T. Griffiths and A. Leff (2013).
** The right hemisphere supports but does not replace left hemisphere auditory function in patients with persisting aphasia. **
*Brain. * 136, 1901-12.

W. Penny and G. Ridgway (2013).
** Efficient Posterior Probability Mapping using Savage-Dickey Ratios. **
*PLoS One * 8(3), e59655

## 2012

W. Penny (2012).
** Bayesian models of Brain and Behaviour. **
*ISRN Biomathematics * Volume 2012, Article ID 785791, doi:10.5402/2012/785791

Z. Woodhead, G. Barnes, W. Penny, R. Moran, S. Teki, C. Price and A. Leff (2012).
** Reading front to back: MEG evidence for early feedback effects during word recognition. **
*Cerebral Cortex * 24:817-825.

T. Schofield and W. Penny and K. Stephan and J. Crinion and A. Thompson and C. Price and A. Leff (2012).
** Changes in auditory feedback connections determine the severity of speech processing deficits after stroke. **
*Journal of Neuroscience * 32(12):4260-4270.

M. Rosa and K. Friston and W. Penny (2012).
** Post-hoc selection of dynamic causal models. **
*Journal of Neuroscience Methods. * 208(1):66-78.

A. Jafarpour and A. Horner and L. Fuentemilla and W. Penny and E. Duzel (2012).
** Decoding oscillatory representations and mechanisms in memory. **
*Neuropsychologia* 51(4): 772-80.

J.D. Lopez and W. Penny and J. Espinosa and G. Barnes (2012).
** A general Bayesian treatment for MEG source reconstruction incorporating lead field uncertainty. **
*Neuroimage* 60:1194-1204.

M Zavaglia and R Canolty and T Schofield and A Leff and M Ursino and R Knight and W. Penny (2012).
** A dynamical pattern recognition model of gamma activity in auditory cortex. **
*Neural Networks* 28:1-14.

M-H Boudrias and C. Goncalves and W. Penny and C-H Park and H. Rossiter and P. Talleli and N. Ward(2011).
** Age-related changes in causal interactions between cortical motor regions during hand grip. **
*Neuroimage* 59(4):3398-3405.

G. Ridgway and V. Litvak and G. Flandn and K. Friston and W. Penny (2011).
** The problem of low variance voxels in statistical parametric mapping: a new hat avoids a haircut. **
*Neuroimage* 59(3):2131-2141.

W. Penny (2011).
**Comparing Dynamic Causal Models using AIC, BIC and Free Energy. **
*Neuroimage* 59(1):319-330.

M. Rosa, J Kilner and W. Penny (2011).
**Bayesian comparison of neurovascular coupling models using EEG-fMRI. **
*PLoS Computational Biology* 7(6) e1002070.

L. Harrison, S Bestmann, M. Rosa, W. Penny and G. Green (2011).
**Time scales of representation in the human brain: weighing past information to predict future events. **
* Frontiers in Human Neuroscience*, 5, 00037.

Friston K, Penny W. (2011)
**Post hoc Bayesian model selection. **
*Neuroimage.* 56(4), 2089-2099.

Bach DR, Hulme O, Penny WD, Dolan RJ. (2011)
**The known unknowns: neural representation of second-order uncertainty, and ambiguity. **
*J Neurosci.* 2011 Mar 30;31(13):4811-20.

Litvak V, Mattout J, Kiebel S, Phillips C, Henson R, Kilner J, Barnes G, Oost-
enveld R, Daunizeau J, Flandin G, Penny W, Friston K. (2011)
**EEG and MEG data
analysis in SPM8. **
Comput Intell Neurosci:852961.

L. Fuentemilla, W Penny, N Cashdollar, N Bunzeck and E. Duzel.
**Theta-Coupled Periodic Replay in Working Memory**.
*Current Biology*,
April 13 2010, 20, 1-7.
Supplementary
Material:

W Penny, K Stephan, J. Daunizeau, M. Rosa, K. Frsiton, T. Schofield and
A Leff.
**Comparing Families of Dynamic Causal Models**.
*PLoS Computational Biology*,
Mar 2010, 6(3), e1000709.

E Duzel,
W Penny and
N Burgess.
**Brain oscillations and memory**.
*Curent Opin Neurobiol*,
Feb 22 2010, Epub ahead of print.

K Stephan,
W Penny,
R Moran,
H den Ouden,
J Daunizeau and
K Friston.
**Ten simple rules for dynamic causal modeling**.
*Neuroimage*,
Feb 15 2010, 49(4):3099-109.

M Rosa,
J. Kilner,
F. Blankenburg,
O. Josephs and
W. Penny.
**Estimating the transfer function from neuronal activity to BOLD using simultaneous EEG-fMRI**.
*Neuroimage*,
Jan 15, 2010; 49(4):1496-509.

M Rosa,
S.Bestmann,
L. Harrison, and
W Penny.
**Bayesian model selection maps for group studies**.
*Neuroimage*,
Jan 1 2010; 49(1):217-24.

V Litvak, A Eusebio, A Jha, R Oostenveld, G Barnes, W Penny, L Zrinzo, M Hariz, P Limousin, K Friston, P Brown.
**Optimized beamforming for simultaneous MEG and intracranial local field potential recordings in deep brain stimulation patients**.
*Neuroimage*,
Jan 4 2010; Epub ahead of print.

K Stephan,
W Penny,
J Daunizeau,
R Moran and
K Friston.
**Bayesian model selection for group studies**.
*Neuroimage*,
46(4):1004-17.

W Penny,
V Litvak,
L Fuentemilla,
E Duzel,
and K Friston.
**Dynamic Causal Models for Phase Coupling**.
*J Neurosci Methods*,
183(1):19-30,
2009.

A G Androulidakis,
P Mazzone,
V Litvak,
W Penny,
M Dileone,
L M F Doyle Gaynor,
S Tisch,
V Di Lazzaro,
and P Brown.
**Oscillatory activity in the pedunculopontine area of patients with Parkinson's disease**.
*Exp Neurol*,
211(1):59-66,
2008.

K H Brodersen,
W D Penny,
L M Harrison,
J Daunizeau,
C C Ruff,
E Duzel,
K J Friston,
and K E Stephan.
**Integrated Bayesian models of learning and decision making for saccadic eye movements**.
*Neural Netw*,
21(9):1247-60,
2008.

K Friston,
C Chu,
J Mourao-Miranda,
O Hulme,
G Rees,
W Penny,
and J Ashburner.
**Bayesian decoding of brain images**.
*Neuroimage*,
39(1):181-205,
2008.

L M Harrison,
W Penny,
J Daunizeau,
and K J Friston.
**Diffusion-based spatial priors for functional magnetic resonance images.
**.
*Neuroimage*,
41(2):408-23,
2008.

L M Harrison,
W Penny,
G Flandin,
C C Ruff,
N Weiskopf,
and K J Friston.
**Graph-partitioned spatial priors for functional magnetic resonance images.
**.
*Neuroimage*,
43(4):694-707,
2008.

W D Penny,
E Duzel,
K J Miller,
and J G Ojemann.
**Testing for nested oscillation.
**.
*J Neurosci Methods*,
174(1):50-61,
2008.

N Trujillo-Barreto,
E Aubert-Vazquez,
and W Penny.
**Bayesian M/EEG source reconstruction with spatio-temporal priors.
**.
*Neuroimage*,
39(1):318-35,
2008.

G. Flandin and W.D. Penny.
**Bayesian fMRI data analysis with sparse spatial basis function priors**.
*NeuroImage*,
34(3):1108-1125,
2007.

L. Harrison,
W.D. Penny,
J. Ashburner,
N. Trujillo-Bareto,
and K.J. Friston.
**Diffusion-based spatial priors for imaging**.
*NeuroImage*,
38:677-695,
2007.

K.Friston,
J. Mattout,
N. Trujillo-Barreto,
J. Ashburner,
and W. Penny.
**Variational free energy and the Laplace approximation**.
*Neuroimage*,
34(1):220-234,
2007.

W. D. Penny,
G. Flandin,
and N. Trujillo-Barreto.
**Bayesian comparison of spatially regularised general linear models**.
*Human Brain Mapping*,
28(4):275-293,
2007.

W. D. Penny and K.J. Friston.
**Functional Imaging**.
*Scholarpedia*,
2(5):1478,
2007.

W. D. Penny,
J. Kilner,
and F. Blankenburg.
**Robust Bayesian General Linear Models**.
*Neuroimage*,
36(3):661-671,
2007.

K.E. Stephan,
L.M. Harrison,
S.J. Kiebel,
O. David,
W.D. Penny,
and K.J. Friston.
**Dynamic causal models of neural system dynamics: current state and future extensions**.
*Journal of Biosciences*,
32:411-416,
2007.

K.E. Stephan,
J.C. Marshall,
W.D. Penny,
K.J. Friston,
and G.R. Fink.
**Interhemispheric integration of visual processing during task-driven lateralization**.
*Journal of Neuroscience*,
27:3512-3522,
2007.

J. Mattout,
C. Phillips,
W.D. Penny,
M. Rugg,
and K.J. Friston.
**MEG source localization under multiple constraints: an extended Bayesian framework**.
*NeuroImage*,
30(3):753-767,
2006.

U. Noppeney and W. D. Penny.
**Two approaches to repetition suppression**.
*Human Brain Mapping*,
27:411-416,
2006.

U. Noppeney,
W. D. Penny,
C. J. Price,
G. Flandin,
and K. J. Friston.
**Identification of degenerate neuronal systems based on intersubject variability**.
*Neuroimage*,
30:885-890,
2006.

U.Noppeney,
C.Price,
W.Penny,
and K.Friston.
**Two distinct neural mechanisms for category selective responses**.
*Cerebral Cortex*,
16(3):437-445,2006.

K.J. Friston,
W.D. Penny,
and O. David.
**Modelling brain responses**.
In M.F. Glabus, editor, *International Review of Neurobiology, Neuroimaging, Part A*.
Elsevier,
2005.

K.J. Friston,
W.D. Penny,
and D.E. Glaser.
**Conjunction revisited**.
*NeuroImage*,
25(3):661-667,
2005.

W.D. Penny,
Z. Ghahramani,
and K.J. Friston.
**Bilinear Dynamical Systems**.
*Phil Trans R Soc B*,
360(1457):983-993,
2005.

W.D. Penny,
N. Trujillo-Bareto,
and K.J. Friston.
**Bayesian fMRI time series analysis with spatial priors**.
*NeuroImage*,
24(2):350-362,
2005.

K.E. Stephan,
W.D. Penny,
J.C. Marshall,
G.R. Fink,
and K.J. Friston.
**Investigating the functional role of Callosal connections with Dynamic Causal Models**.
*Ann. N.Y. Acad. Sci.*,
1064:16-36,
2005.

B. Strange,
A. Duggins,
W. Penny,
R. Dolan,
and K. Friston.
**Information theory, novelty and hippocampal responses: unpredicted or unpredictable ?**.
*Neural Networks*,
18:225-230,
2005.

E. Curran,
P. Sykacek,
M.Stokes,
S.J. Roberts,
W. Penny,
I. Johnsrude,
and A.M. Owen.
**Cognitive Tasks for Driving a Brain Computer Interfacing System: A Pilot Study**.
*IEEE Transactions on Neural Systems and Rehabilitation Engineering*,
12(1):48-54,
2004.

W.D. Penny,
K.E. Stephan,
A. Mechelli,
and K.J. Friston.
**Comparing Dynamic Causal Models**.
*NeuroImage*,
22(3):1157-1172,
2004.

W.D. Penny,
K.E. Stephan,
A. Mechelli,
and K.J. Friston.
**Modelling Functional Integration: A Comparison of Structural Equation and Dynamic Causal and Models**.
*NeuroImage*,
23:264-274,
2004.
Note: Supplement 1.

N. Ramnani,
T.E.J. Behrens,
W.D. Penny,
and P.M. Matthews.
**New approaches for exploring anatomic and functional connectivity in the human brain**.
*Biological Psychiatry*,
2004, 56(9), 613-619.

K.E. Stephan,
L. Harrison,
W.D. Penny,
and K.J. Friston.
**Biophysical models of fMRI responses**.
*Current Opinion in Neurobiology*,
14(5):629-635,
2004.

K.J. Friston,
L. Harrison,
and W.D. Penny.
**Dynamic Causal Modelling**.
*NeuroImage*,
19(4):1273-1302,
2003.

K.J. Friston and W.D. Penny.
**Posterior probability maps and SPMs**.
*NeuroImage*,
19(3):1240-1249,
2003.

D.R. Gitelman,
W.D. Penny,
J. Ashburner,
and K.J. Friston.
**Modeling regional and psychophysiologic interactions in fMRI: the importance of hemodynamic deconvolution**.
*NeuroImage*,
19:200-207,
2003.

L. Harrison,
W.D. Penny,
and K.J. Friston.
**Multivariate Autoregressive Modelling of fMRI time series**.
*NeuroImage*,
19(4):1477-1491,
2003.

W.D. Penny and K.J. Friston.
**Mixtures of General Linear Models for Functional Neuroimaging**.
*IEEE Transactions on Medical Imaging*,
22(4):504-514,
2003.

W.D. Penny,
S.J. Kiebel,
and K.J. Friston.
**Variational Bayesian Inference for fMRI time series**.
*NeuroImage*,
19(3):727-741,
2003.

M.J. Cassidy and W.Penny.
**Bayesian nonstationary autogregressive models for biomedical signal analysis**.
*IEEE Transactions on Biomedical Engineering*,
49(10):1142-1152,
2002.

K.J. Friston,
W.D. Penny,
C. Phillips,
S.J. Kiebel,
G. Hinton,
and J. Ashburner.
**Classical and Bayesian Inference in Neuroimaging: Theory**.
*NeuroImage*,
16:465-483,
2002.

A. Mechelli,
W.D. Penny,
C.J. Price,
D.R. Gitelman,
and K.J. Friston.
**Effective connectivity and intersubject variability: using a multisubject network to test differences and commonalities**.
*NeuroImage*,
17(3):1459-1469,
2002.

W.D. Penny,
S.J. Kiebel,
J.M. Kilner,
and M.D. Rugg.
**Event-related brain dynamics**.
*Trends in Neuroscience*,
25(8):387-389,
2002.

W.D. Penny and S.J. Roberts.
**Bayesian Multivariate Autoregresive Models with structured priors**.
*IEE Proceedings on Vision, Image and Signal Processing*,
149(1):33-41,
2002.

S.J. Roberts and W.D. Penny.
**Variational Bayes for Generalised Autoregressive models**.
*IEEE Transactions on Signal Processing*,
50(9):2245-2257,
2002.

P.R.J. Barnes M.R. Johnson, C.D. Good, W.D. Penny and J.W. Scadding.
**Playing the odds in clinical decision making: lessons from berry aneuryisms undetected by magnetic resonance angiography**.
*British Medical Journal*,
322:1347-1349,
2001.

S.J. Roberts and W.D. Penny.
**Real-Time Brain-Computer Interfacing: A Preliminary Study Using Bayesian Learning**.
*Medical and Biological Engineering and Computing*,
38(1):56-61,
2000.

D. Husmeier,
W.D. Penny,
and S.J. Roberts.
**An empirical evaluation of Bayesian sampling with hybrid Monte Carlo for training neural network classifiers**.
*Neural Networks*,
12:677-705,
1999.

W.D. Penny and S.J. Roberts.
**Dynamic models for nonstationary signal segmentation**.
*Computers and Biomedical Research*,
32(6):483-502,
1999.

W.D. Penny,
E. Curran S.J. Roberts,
and M. Stokes.
**EEG-based communication: a pattern recognition approach**.
*IEEE Transactions on Rehabilitation Engineering*,
8(2),
1999.

W.D. Penny and S.J. Roberts.
**Bayesian neural networks for classification: how useful is the evidence framework ?**
*Neural Networks*,
12:877-892,
1998.

S. J. Roberts,
D. Husmeier,
W. Penny,
and I. Rezek.
**Bayesian Approaches to Gaussian Mixture Modelling**.
*IEEE Transactions on Pattern Analysis and Machine Intelligence*,
20(11):1133-1142,
1998.

S.J. Roberts,
W. Penny,
and I. Rezek.
**Temporal and spatial complexity measures for EEG-based brain-computer interfacing**.
*Medical and Biological Engineering and Computing*,
37(1):93-99,
1998.

W.D. Penny and D. Frost.
**Neural network modelling of the level of observation decision in an acute psychiatric ward**.
*Computers and Biomedical Research*,
30:1-17,
1997.

W.D. Penny and D. Frost.
**Neural networks in clinical medicine**.
*Medical Decision Making*,
16(4):386-398,
1996.

S. J. Roberts and W. D. Penny.
**A maximum certainty approach to feedforward neural networks**.
*Electronics Letters*,
33(4):306-307,
1996.

S.J. Roberts and W.D. Penny.
**Neural networks: friends or foes ?**.
*Sensor Review*,
17(1):64-70,
1996.

W.D. Penny and T.J. Stonham.
**Generalisation in multilayer sigma-pi networks**.
*IEEE Transactions on Neural Networks*,
6(2):506-508,
1995.

W.D. Penny and T.J.Stonham.
**Storage capacity of multilayer boolean neural networks**.
*Electronics Letters*,
29(15):1340-1341,
1993.

**Disclaimer:**

*
This material is presented to ensure timely dissemination of
scholarly and technical work. Copyright and all rights therein
are retained by authors or by other copyright holders.
All person copying this information are expected to adhere to
the terms and constraints invoked by each author's copyright.
In most cases, these works may not be reposted
without the explicit permission of the copyright holder.
*