PLoS computational biology

Seven quick tips for analysis scripts in neuroimaging

van Vliet, M., 26 Aug 2019, (Accepted/In press) In : PLoS computational biology. 13 p.

Research output: Contribution to journal › Article › Scientific › peer-review

Pulse transit time estimation of aortic pulse wave velocity and blood pressure using machine learning and simulated training data

Huttunen, J. M. J., Kärkkäinen, L. & Lindholm, H., 1 Aug 2019, In : PLoS computational biology. 15, 8, p. e1007259

Research output: Contribution to journal › Article › Scientific › peer-review

Modeling enamel matrix secretion in mammalian teeth

Häkkinen, T. J., Sova, S. S., Corfe, I. J., Tjäderhane, L., Hannukainen, A. & Jernvall, J., 1 May 2019, In : PLoS computational biology. 15, 5, p. 1-12 e1007058.

Research output: Contribution to journal › Article › Scientific › peer-review

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

Järvenpää, M., Sater, M. R. A., Lagoudas, G. K., Blainey, P. C., Miller, L. G., McKinnell, J. A., Huang, S. S., Grad, Y. H. & Marttinen, P., 1 Apr 2019, In : PLoS computational biology. 15, 4, p. 1-25 e1006534.

Research output: Contribution to journal › Article › Scientific › peer-review

Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis

Petkoski, S., Palva, J. M. & Jirsa, V. K., 1 Jul 2018, In : PLoS computational biology. 14, 7, e1006160.

Research output: Contribution to journal › Article › Scientific › peer-review

Tracking urban human activity from mobile phone calling patterns

Monsivais, D., Ghosh, A., Bhattacharya, K., Dunbar, R. I. M. & Kaski, K., 1 Nov 2017, In : PLoS computational biology. 13, 11, p. 1-16 e1005824.

Research output: Contribution to journal › Article › Scientific › peer-review

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

Cichonska, A., Ravikumar, B., Parri, E., Timonen, S., Pahikkala, T., Airola, A., Wennerberg, K., Rousu, J. & Aittokallio, T., 1 Aug 2017, In : PLoS computational biology. 13, 8, p. 1-28 e1005678.

Research output: Contribution to journal › Article › Scientific › peer-review

Speciation trajectories in recombining bacterial species

Marttinen, P. & Hanage, W. P., 3 Jul 2017, In : PLoS computational biology. 13, 7, p. 1-15 15 p., e1005640.

Research output: Contribution to journal › Article › Scientific › peer-review

The Maximum Entropy Fallacy Redux?

Aurell, E., 1 May 2016, In : PLoS computational biology. 12, 5, p. 1-7 e1004777.

Research output: Contribution to journal › Article › Scientific › peer-review

Radial Frequency Analysis of Contour Shapes in the Visual Cortex

Salmela, V. R., Henriksson, L. & Vanni, S., 1 Feb 2016, In : PLoS computational biology. 12, 2, p. 1-18 18 p., e1004719.

Research output: Contribution to journal › Article › Scientific › peer-review

Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation

Magarkar, A., Mele, N., Abdel-Rahman, N., Butcher, S., Torkkeli, M., Serimaa, R., Paananen, A., Linder, M. & Bunker, A., 31 Jul 2014, In : PLoS computational biology. 10, 7, p. 1-13 13 p., e1003645.

Research output: Contribution to journal › Article › Scientific › peer-review

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Pitkänen, E., Jouhten, P., Hou, J., Fahad Syed, M., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttilä, M. & Rousu, J., 2014, In : PLoS computational biology. 10, 2, p. 1-12 e1003465.

Research output: Contribution to journal › Article › Scientific › peer-review

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

Skwark, M. J., Raimondi, D., Michel, M. & Elofsson, A., 2014, In : PLoS computational biology. 10, 11, p. 1-14 e1003889.

Research output: Contribution to journal › Article › Scientific › peer-review

Improving Contact Prediction along Three Dimensions

Feinauer, C., Skwark, M. J., Pagnani, A. & Aurell, E., 2014, In : PLoS computational biology. 10, 10, p. 1-13 e1003847.

Research output: Contribution to journal › Article › Scientific › peer-review

Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria

Rousu, J., Agranoff, D. D., Sodeinde, O., Shawe-Taylor, J. & Fernandez-Reyes, D., 2013, In : PLoS computational biology. 9, 4, p. 1-10 1003018.

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Lipid exchange mechanism of the cholesteryl ester transfer protein clarified by atomistic and coarse-grained simulations

Koivuniemi, A., Vuorela, T., Kovanen, P. T., Vattulainen, I. & Hyvönen, M. T., Jan 2012, In : PLoS computational biology. 8, 1, e1002299.

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Metabolic regulation in progression to autoimmune diabetes

Sysi-Aho, M., Ermolov, A., Gopalacharyulu, P. V., Tripathi, A., Seppänen-Laakso, T., Maukonen, J., Mattila, I., Ruohonen, S. T., Vähätalo, L., Yetukuri, L., Härkönen, T., Lindfors, E., Nikkilä, J., Ilonen, J., Simell, O., Saarela, M., Knip, M., Kaski, S., Savontaus, E. & Oresic, M., 2011, In : PLoS computational biology. 7, 10, p. 1-16 e1002257.

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Rolf of lipids in spheroidal high density lipoproteins

Vuorela, T., Catte, A., Niemelä, P. S., Hall, A., Hyvönen, M. T., Marrink, S. J., Karttunen, M. & Vattulainen, I., 2010, In : PLoS computational biology. 6, 10, p. 1-14 e1000964.

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Conformational changes and slow dynamics through microsecond polarized molecular simulation of an integral Kv1.2 ion channel

Bjelkmar, P., Niemela, P., Vattulainen, I. & Lindahl, E., 2009, In : PLoS computational biology. 5, p. e1000289

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Assessing the Nature of Lipid Raft Membranes

Niemelä, P. S., Ollila, S., Hyvönen, M. T., Karttunen, M. & Vattulainen, I., 2007, In : PLoS computational biology. 3, 2, p. 304-312 e34.

Research output: Contribution to journal › Article › Scientific › peer-review

Seriation in Paleontological Data Using Markov Chain Monte Carlo Methods

Puolamäki, K., Fortelius, M. & Mannila, H., 2006, In : PLoS computational biology. 2, 2, p. 62-70 e6.

Research output: Contribution to journal › Article › Scientific › peer-review