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Publications 2011

• Refereed journals
• Conference proceedings

• A
• Ahveninen, Jyrki; Hämäläinen, Matti; Jääskeläinen, Iiro P.; Ahlfors, Seppo P.; Huang, Samantha; Lin, Fa-Hsuan; Raij, Tommi; Sams, Mikko; Vasios, Christos E.; Belliveau, John W.
  Attention-driven auditory cortex short-term plasticity helps segregate relevant sounds from noise.
  PNAS, 2011. Vol. 108, No. 10, pp. 4182-4187.
• G
• Grabarnik, Pavel; Myllymäki, Mari; Stoyan, Dietrich.
  Correct testing of mark independence for marked point patterns.
  Ecological Modelling, 2011. Vol. 222, pp. 3888-3894.
• H
• Haapalahti, P.; Viitasalo, M.; Perhonen, M.; Väänänen, H.; Mäkijärvi, M.; Swan, H.; Toivonen, L.
  Comparison of QT peak and QT end interval responses to autonomic adaptation in asymptomatic LQT1 mutation carriers.
  Clinical physiology and functional imaging, 2011. Vol. 31, No. 3, pp. 209-214.
• Hekkala, A.M.; Swan, H.; Viitasalo, M.; Väänänen, H.; Toivonen, L.
  Epinephrine bolus test in detecting long QT syndrome mutation carriers with indeterminable electrocardiographic phenotype.
  Annals of noninvasive electrocardiology, 2011. Vol. 16, No. 2, pp. 172-179.
• Heikkilä, Oskari; Oksanen, Jani; Tulkki, Jukka.
  Light extraction limits in textured GaN-InGaN light-emitting diodes: Radiative transfer analysis.
  Applied Physics Letters, 2011. Vol. 99, 161110.
• Heikkinen, Hanna; Vinberg, Frans; Nymark, Soile; Koskelainen, Ari.
  Mesopic background lights enhance dark-adapted cone ERG flash responses in the intact mouse retina: a possible role for gap junctional decoupling.
  Journal of Neurophysiology, 2011. Vol. 105, No. 5, pp. 2309-2318.
• Hietanen, Jari K; Nummenmaa, Lauri.
  The naked truth: The face and body sensitive N170 reponse is enhanced for nude bodies.
  PLOS one, 2011. Vol. 6, No. 11, pp. e24408-e24408.
• Hiltunen, Petri; Särkkä, Simo; Nissilä, Ilkka; Lajunen, Atte; Lampinen, Jouko
  State space regularization in the nonstationary inverse problem for diffuse optical tomography.
  Inverse Problems, 2011. Vol. 27, No. 2, 025009.
• Huber, Reto; Mäki, Hanna; Rosanova, Mario; Casarotto, Silvia; Canali, Paola; Casali, Adenauer; Tononi, Giulio; Massimini, Marcello.
  Human cortical excitability increases with time awake.
  Cerebral Cortex, 2011. pp. 1-5.
• Häme, Yrjö; Pollari, Mika.
  Semi-automatic liver tumor segmentation with hidden Markov measure field model and non-parametric distribution estimation.
  Medical Image Analysis 1361-8415, 2011. pp. 1-10.
• Häyrynen, Teppo; Oksanen, Jani; Tulkki, Jukka.
  Dynamics of cavity fields with dissipative and amplifying couplings through multiple quantum two-state systems.
  Physical Review E, 2011. Vol. 83, No. 1, 013801/1-6.
• I
• Iñiguez, Gerardo; Barrio, Rafael A.; Kertész, János; Kaski, Kimmo K.
  Modelling opinion formation driven communities in social networks.
  Computer Physics Communications, 2011. Vol. 182, No. 9, pp. 1866–1869.
• Iñiguez, Gerardo; Kertész, János; Kaski, Kimmo K.; Barrio, R. A.
  Phase change in an opinion-dynamics model with separation of time scales.
  Physical Review E, 2011. Vol. 83, No. 1, 016111.
• J
• Jo, Hang-Hyun; Pan, Raj Kumar; Kaski, Kimmo.
  Emergence of Bursts and Communities in Evolving Weighted Networks.
  PLoS ONE, 2011. Vol. 6, No. 8, e22687.
• Jylänki, Pasi; Vanhatalo, Jarno; Vehtari, Aki.
  Robust Gaussian Process Regression with a Student-t Likelihood.
  Journal of Machine Learning Research, 2011. Vol. 12, pp. 3227-3257.
• Jääskeläinen, Iiro P. ; Ahveninen, Jyrki; Andermann, Mark L.; Belliveau, John W.; Raij, Tommi; Sams, Mikko.
  Short-term plasticity as a neural mechanism supporting memory and attentional functions.
  Brain Research, 2011. Vol. 1422, pp. 66-81.
• K
• Karsai, M.; Kivelä, M.; Pan, R. K.; Kaski, K.; Kertész, J.; Barabási, A.-L.; Saramäki, J.
  Small but slow world: How network topology and burstiness slow down spreading.
  Physical Review E, 2011. Vol. 83, No. 2, 025102.
• Korhonen, R.; Hernandez Pavon, J. C.; Metsomaa, J.; Mäki, H.; Ilmoniemi, R. J.; Sarvas, J.
  Removal of large muscle artifacts from transcranial magnetic stimulation-evoked EEG by independent component analysis.
  Medical and Biological Engineering and Computing, 2011. Vol. 49, pp. 397-407.
• Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari.
  Temporal motifs in time-dependent networks.
  Journal of Statistical Mechanics: Theory and Experiment, 2011. P11005.
• Kovanen, Lauri; Saramäki, Jari; Kaski, Kimmo.
  Reciprocity of mobile phone calls.
  Dynamics of Socio-Economic Systems, 2011. Vol. 2, No. 2, pp. 138-151.
• Kumar, Vibhor; Butcher, Sarah J.; Öörni, Katariina; Engelhardt, Peter; Heikkonen, Jukka; Kaski, Kimmo; Ala-Korpela, Mika; Kovanen, Petri T.
  Three-Dimensional cryoEM Reconstruction of Native LDL Particles to 16Å Resolution at Physiological Body Temperature.
  PLoS One, 2011. Vol. 6, No. 5, e18841.
• L
• Lancichinetti, Andrea; Fortunato, Santo.
  Limits of modularity maximization in community detection.
  Physical Review E, 2011. Vol. 84, 066122.
• Liou, Shr-Tai; Witzel, Thomas; Nummenmaa, Aapo; Chang, Wei-Tang; Tsaic, Kevin Wen-Kai; Kuoe, Wen-Jui; Chunga, Hsiao-Wen; Lin, Fa-Hsuan.
  Functional magnetic resonance inverse imaging of human visuomotor systems using eigenspace linearly constrained minimum amplitude (eLCMA) beamformer.
  NeuroImage, 2011. Vol. 55, No. 1, pp. 87–100.
• Luomahaara, J.; Vesanen, P.T.; Penttilä, J.; Nieminen, J.O.; Dabek, J.; Simola, J.; Kiviranta, M.; Grönberg, L.; Zevenhoven, C.J.; Ilmoniemi, R.J.; Hassel, J.
  All-planar SQUIDs and pickup coils for combined MEG and MRI.
  Superconductor Science and Technology, 2011. Vol. 24, pp. 075020.
• M
• Mahalka A. K., Code C., Rezaijahromi B., Kirkegaard T., Jäättelä M., Kinnunen P. K.
  Activation of phospholipase A2 by Hsp70 in vitro.
  Biochim. Biophys. Acta, 2011. Vol. 1808, No. 10, pp. 2569-2572.
• Mahalka A. K., Maury C. P., Kinnunen P. K.
  1-Palmitoyl-2-(9'-oxononanoyl)-sn-glycero-3-phosphocholine, an oxidized phospholipid, accelerates Finnish type familial gelsolin amyloidosis in vitro.
  Biochemistry, 2011. Vol. 50, No. 22, pp. 4877-4889.
• Marttinen, Pekka; Hanage, William P.; Croucher, Nicholas J.; Connor, Thomas R.; Harris, Simon R.; Bentley, Stephen D.; Corander, Jukka.
  Detection of recombination events in bacterial genomes from large population samples.
  Nucleic Acids Research, 2011. Vol. 40, No. 1, e6.
• Miettinen, Ismo; Alku, Paavo; Salminen, Nelli; May, Patrick; Tiitinen, Hannu.
  Responsiveness of the human auditory cortex to degraded speech sounds: reduction of amplitude resolution vs. additive noise.
  Brain Research, 2011. Vol. 1367, pp. 298-309.
• Mäki, H.; Ilmoniemi, R. J.
  Projecting out muscle artifacts from TMS-evoked EEG.
  NeuroImage, 2011. Vol. 54, pp. 2706–2710.
• N
• Nieminen, Jaakko O.; Vesanen, Panu T.; Zevenhoven, Koos C.J.; Dabek, Juhani; Hassel, Juha; Luomahaara, Juho; Penttilä, Jari S.; Ilmoniemi, Risto J.
  Avoiding eddy-current problems in ultra-low-field MRI with self-shielded polarizing coils.
  Journal of Magnetic Resonance, 2011, Vol. 212, pp. 154-160.
• Noseworthy, P. A.; Tikkanen, J. T.; Porthan, K.; Oikarinen, L.; Pietilä, A.; Harald, K.; Peloso, G.M.; Merchant, F. M.; Jula, A.; Väänänen, H.; Hwang, S.J.; O'Donnell, C.J.; Salomaa, V.; Newton-Cheh, C.; Huikuri, H.V.
  The early repolarization pattern in the general population: clinical correlates and heritability.
  Journal of the American College of Cardiology, 2011. Vol. 57, No. 22, pp. 2284-2289.
• Näsi T.; Mäki H.; Kotilahti K.; Nissilä I.; Haapalahti P.; Ilmoniemi R.J.
  Magnetic-Stimulation-Related Physiological Artifacts in Hemodynamic Near-Infrared Spectroscopy Signals.
  PLoS ONE, 2011. Vol. 6, No. 8, e24002.
• Näsi T.; Virtanen J.; Noponen T.; Toppila J.; Salmi T.; Ilmoniemi R. J.
  Spontaneous Hemodynamic Oscillations during Human Sleep and Sleep Stage Transitions Characterized with Near-Infrared Spectroscopy.
  PLoS ONE, 2011. Vol. 6, No. 10, e25415.
• P
• Pan, Raj Kumar; Saramäki, Jari.
  Path lengths, correlations, and centrality in temporal networks.
  Phys. Rev. E, 2011. Vol. 84, 016105.
• Pan, Raj Kumar; Kivelä, Mikko; Saramäki, Jari; Kaski, Kimmo; Kertész, János.
  Using explosive percolation in analysis of real-world networks.
  Phys. Rev. E, 2011. Vol. 83, 046112.
• Payne, Stephen; Flanagan, Ronan; Pollari, Mika; Alhonnoro, Tuomas; Bost, Claire; O'Neill, David; Peng, Tingying; Stiegler, Philipp.
  Image-based multi-scale modelling and validation of radio-frequency ablation in liver tumours.
  Philosophical transactions of the royal society a-mathematical physical and engineering sciences, 2011. Vol. 369, No. 1954, pp. 4233-4254.
• R
• Rahko, J.; Paakki, J-J.; Starck, T.; Nikkinen, J.; Pauls, D.; Kätsyri, J.; Jansson-Verkasalo, E.; Carter, A.; Hurtig, T.; Mattila, M.-L.; Jussila, K.; Remes, J.; Kuusikko-Gauffin, S.; Sams, M.; Bölte, S.; Ebeling, H.; Moilanen, I.; Tervonen, O.; Kiviniemi, V.
  Valence scaling of dynamic facial expressions is altered in high-functioning subjects with autism spectrum disorders: an fMRI study.
  Journal of Autism and Developmental Disorders, 2011.
• Rantonen, Jorma; Luoto, Satu; Vehtari, Aki; Hupli, Markku; Karppinen, Jaro; Malmivaara, Antti; Taimela, Simo.
  The effectiveness of two active interventions compared to self-care advice in employees with non-acute low back symptoms. A randomised, controlled trial with a 4-year follow-up in the occupational health setting.
  Occupational and Environmental Medicine, 2011.
• Rauschecker, Josef.
  An expanded role for the dorsal auditory pathway in sensorimotor control and integration.
  Hearing Research, 2011. Vol. 271, No. 1-2, pp. 16–25.
• Ruspantini, I.; Mäki, H.; Korhonen, R.; D’Ausilio A.; Ilmoniemi, R. J.
  The functional role of the ventral premotor cortex in a visually paced finger tapping task: A TMS study.
  Behavioural Brain Research, 2011. Vol. 220, pp. 325–330.
• Ruspantini, I.; D’Ausilio A.; Mäki, H.; Ilmoniemi, R. J.
  Some considerations about the biological appearance of pacing stimuli in visuomotor finger tapping tasks.
  Cognitive Processing, 2011. pp. 1-4 (In Press).
• S
• Saalasti,Satu; Kätsyri, Jari; Tiippana, Kaisa; Laine-Hernandez, Mari; von Wendt, Lennart; Sams, Mikko.
  Audiovisual Speech Perception and Eye Gaze Behavior of Adults with Asperger Syndrome.
  Journal of Autism and Developmental Disorders, 2011. pp. 1-10.
• Saalasti, Satu; Tiippana, Kaisa; Kätsyri, Jari; Sams, Mikko.
  The effect of visual spatial attention on audiovisual speech perception in adults with Asperger Syndrome.
  Experimental Brain Research, 2011. Vol. 213, pp. 283-290.
• Sinha, Sitabhra; Izhara, Ashraf; Pan, Raj Kumar; Wells, Bryan Kenneth.
  Network analysis of a corpus of undeciphered Indus civilization inscriptions indicates syntactic organization.
  Computer Speech & Language, 2011. Vol. 25, No. 3, pp. 639–654.
• Susac, A.; Ilmoniemi, R. J.; Ranken, D.; Supek, S.
  Face activated neurodynamic cortical networks.
  Medical and biological engineering and computing 0140-0118, 2011. Vol. 49, No. 5, pp. 531-543.
• Särkkä, S.; Huovilainen, A.
  Accurate Discretization of Analog Audio Filters with Application to Parametric Equalizer Design.
  IEEE Transactions on Audio, Speech, and Language Processing, 2011. Volume 19(8), pp. 2486-2493.
• T
• Tejera-Garcia R., Ranjan S., Zamotin V., Sood R., Kinnunen P. K.
  Making unilamellar liposomes using focused ultrasound.
  Langmuir, 2011. Vol. 27, No. 16, pp. 10088-10097.
• Tibély, Gergely; Karsai, Márton; Kovanen, Lauri; Kaski, Kimmo; Kertész, János; Saramäki, Jari.
  Communities and beyond: Mesoscopic analysis of a large social network with complementary methods.
  Phys. Rev. E, 2011. Vol. 83, 056125.
• Tiippana, K.; Puharinen, H.; Möttönen, R; Sams, M.
  Sound location can influence audiovisual speech perception when attention is manipulated.
  NeuroImage, 2011. Vol. 55, pp. 1252-1259.
• Toivanen, Miika; Lampinen, Jouko.
  Incremental object matching and detection with Bayesian methods and particle filters.
  IET Computer Vision, 2011. Vol. 5, No. 4, pp. 201–210.
• V
• Vehtari, Aki; Vanhatalo, Jarno.
  Discussion to 'Riemann manifold Langevin and Hamiltonian Monte Carlo methods'.
  Journal of the Royal Statistical Society, Series B (Statistical Methodology), 2011. p. 201.
• Viinikainen, M.; Kätsyri, J.; Sams, M.
  Representation of perceived sound valence in the human brain.
  Human Brain Mapping, 2011. DOI: 10.1002/hbm.21362.
• Virtanen J.; Noponen T.; Kotilahti K.; Virtanen J.; Ilmoniemi R. J.
  Accelerometer-based method for correcting signal baseline changes caused by motion artifacts in medical near-infrared spectroscopy.
  Journal of Biomedical Optics, 2011. Vol. 16, No. 8, 087005. DOI: 10.1117/1.3606576
• Virtanen J.; Noponen T.; Toppila J.; Salmi T.; Meriläinen P.
  Impaired cerebral vasoreactivity may cause cerebral blood volume dip following obstructive sleep apnea termination.
  Sleep and Breathing, 2011. DOI: 10.1007/s11325-011-0526-9 (In Press)
• Volinsky R., Cwiklik L., Jurkiewicz P., Hof M., Jungwirth P., Kinnunen P. K.
  Oxidized phosphatidylcholines facilitate phospholipid flip-flop in liposomes.
  Biophysical Journal, 2011. Vol. 101, No. 6, pp. 1376-1384.
• W
• Waller, L.A.; Särkkä, A.; Olsbo, V.; Myllymäki, M.; Panoutsopoulou, I.G.; Kennedy, W.R.; Wendelschafer-Crabb, G.
  Second-order spatial analysis of epidermal nerve fibres.
  Statistics in Medicine, 2011. Vol. 30, No. 23, pp. 2827-2841.
• Y
• Yrttiaho, Santeri; May, Patrick; Tiitinen, Hannu; Alku, Paavo
  Cortical encoding of aperiodic and periodic speech sounds: evidence for distinct neural populations.
  NeuroImage, 2011. Vol. 55, No. 3, pp. 1252-1259.
• Z
• Zhang, W.; Zhang. Y.; Sood, R.; Ranjan, S.; Surovtseva, E.; Ahmad, A.; Kinnunen, P. K.; Pyykkö, I.; Zou J.
  Visualization of intracellular trafficking of Math1 protein in different cell types with a newly-constructed nonviral gene delivery plasmid.
  J. Gene Med., 2011. Vol. 13, No. 2, pp. 134-144. doi: 10.1002/jgm.1537.
• Zhao, Kun; Karsai, Márton; Bianconi, Ginestra.
  Entropy of Dynamical Social Networks.
  PLoS One, 2011. Vol. 6, No. 12, e28116.

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