Here a complete list of publications (since 2010) by the researchers affiliated with the OSE group is given. The publication list can also be downloaded as a PDF-file here.

The publications in the list are categorized according to the following classes:

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Monographies

Högnäs, G. and A. Mukherjea. Probability Measures on Semigroups. Convolution Products, Random Walks and Random Matrices. 2nd ed. Springer Science+Business Media, New York, 2011, p. 430.

Book chapters

Arov, D., M. Kurula, and O. Staffans. Boundary control state/signal systems and boundary triplets. In: Boundary Relations, Extension Theory, and Applications. Cambridge University Press, 2012.

Arov, D., M. Kurula, and O. Staffans. Passive state/signal system and conservative boundary relations. In: Boundary Relations, Extension Theory, and Applications. Cambridge University Press, 2012.

Budzban, G. and G. Högnäs. Convolution products of probability measures on a compact semigroup with applications to random measures. In: Algebraic Methods in Statistics and Probability II. Ed. by M. A. G. Viana and H. P. Wynn. American Mathematical Society, 2010, pp. 9398.

Lundell, A. and T. Westerlund. Global optimization of mixed-integer signomial programming problems. In: Mixed Integer Nonlinear Programming. Ed. by Jon Lee and Sven Leyffer. Vol. 154. The IMA Volumes in Mathematics and its Applications. Springer New York, 2012, pp. 349369. ISBN: 978-1-4614-1927-3. DOI: 10.1007/978-1-4614-1927-3_12.

Refereed journal papers

Arov, D. Z. and O. J. Staffans. Symmetries in special classes of passive state/signal systems. In: Journal of Functional Analysis 262 (2012), pp. 50215097.

Arov, D., M. Kurula, and O. Staffans. Canonical state/signal shift realizations of passive continuous time behaviors. In: Complex Analysis and Operator Theory 5 (2 2011), pp. 331402. ISSN: 1661-8254. DOI: 10.1007/s11785-010-0128-8.

Arov, D. and O. Staffans. Canonical conservative state/signal shift realizations of passive discrete time behaviors. In: Journal of Functional Analysis 259.12 (2010), pp. 32653327. ISSN: 0022-1236. DOI: 10.1016/j.jfa.2010.05.019.

Beaumont, M. A., R. Nielsen, C. Robert, J. Hey, O. Gaggiotti, L. Knowles, A. Estoup, M. Panchal, J. Corander, M. Hickerson, S. A. Sisson, N. Fagundes, L. Chikhi, P. Beerli, R. Vitalis, J.-M. Cornuet, J. Huelsenbeck, M. Foll, Z. Yang, F. Rousset, D. Balding, and L. Excoffier. In defence of model-based inference in phylogeography. In: Molecular Ecology 19.3 (2010), pp. 436446. ISSN: 1365-294X. DOI: 10.1111/j.1365-294X.2009.04515.x.

Been, M. de, W. van Schaik, L. Cheng, J. Corander, and R. J. Willems. Draft genome sequence of Enterococcus faecium PC4.1, a Clade B strain isolated from human feces. In: Genome Biology and Evolution Available online (2013). DOI: 10.1093/gbe/evt111.

Blomstedt, P., R. Gauriot, N. Viitala, T. Reinikainen, and J. Corander. Bayesian predictive modeling and comparison of oil samples. In: Journal of Chemometrics 28.1 (2014), pp. 5259. ISSN: 1099-128X. DOI: 10.1002/cem.2566.

Brännback, M., R. Östermark, J. Aaltonen, A. Carsrud, and M. Renko. The fragile link between growth and profitability in small biotech firms: an exploratory study. In: Academy of Management (forthcoming) ().

Cheng, L., T. R. Connor, J. Sirén, D. M. Aanensen, and J. Corander. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. In: Molecular Biology and Evolution Available online (2013). DOI: 10.1093/molbev/mst028. eprint: http://mbe.oxfordjournals.org/content/early/2013/02/13/molbev.mst028.full.pdf+html.

Cheng, L., T. Connor, D. Aanensen, B. Spratt, and J. Corander. Bayesian semi-supervised classification of bacterial samples using MLST databases. In: BMC Bioinformatics 12.1 (2011). ISSN: 1471-2105. DOI: 10.1186/1471-2105-12-302.

Cheng, L., A. Walker, and J. Corander. Bayesian estimation of bacterial community composition from 454 sequencing data. In: Nucleic Acids Research 40.12 (2012), pp. 52405249. DOI: 10.1093/nar/gks227.

Christensen, S., P. Salminen, and B. Q. Ta. Optimal stopping of strong Markov processes. In: Stochastic Processes and their Applications 123 (2013), pp. 11361159.

Connor, T. R., J. Corander, and W. P. Hanage. Population subdivision and the detection of recombination in non-typable Haemophilus influenzae. In: Microbiology (2012). DOI: 10.1099/mic.0.063073-0.

Corander, J., T. R. Connor, C. A. ODwyer, J. S. Kroll, and W. P. Hanage. Population structure in the Neisseria, and the biological significance of fuzzy species. In: Journal of The Royal Society Interface (2011). DOI: 10.1098/rsif.2011.0601.

Corander, J., Y. Cui, T. Koski, and J. Sirén. Have I seen you before? Principles of Bayesian predictive classification revisited. In: Statistics and Computing (), pp. 115. ISSN: 0960-3174. DOI: 10.1007/s11222-011-_9291-7.

Corander, J., Y. Cui, T. Koski, and J. Sirén. Have I seen you before? Principles of Bayesian predictive classification revisited. In: Statistics and Computing (2012). Available online, pp. 115. ISSN: 0960-3174. DOI: 10.1007/s11222-011-9291-7.

Corander, J., M. Gyllenberg, and T. Koski. Learning genetic population structures using minimization of stochastic complexity. In: Entropy 12.5 (2010), pp. 11021124. ISSN: 1099-4300. DOI: 10.3390/e12051102.

Corander, J., J. Xiong, Y. Cui, and T. Koski. Optimal Viterbi Bayesian predictive classification for data from finite alphabets. In: Journal of Statistical Planning and Inference (2012). ISSN: 0378-3758. DOI: 10.1016/j.jspi.2012.07.013.

Eronen, V.-P., M. M. Mäkelä, and T. Westerlund. Extended cutting plane method for a class of nonsmooth nonconvex MINLP problems. In: Optimization Available online (2013a). DOI: 10.1080/02331934.2013.796473.

Eronen, V.-P., M. M. Mäkelä, and T. Westerlund. On the generalization of ECP and OA methods to nonsmooth convex MINLP problems. In: Optimization (2013). Available online iFirst June 6th 2013. DOI: 10.1080/02331934.2012.712118.

Gauriot, R., L. Gunaratnam, R. Moroni, T. Reinikainen, and J. Corander. Statistical Challenges in the Quantification of Gunshot Residue Evidence. In: Journal of Forensic Sciences (in press) (2012).

Haan, C. de, R. Kivistö, M. Hakkinen, J. Corander, and M.-L. Hänninen. Multilocus sequence types of Finnish bovine Campylobacter jejuni isolates and their attribution to human infections. In: BMC Microbiology 10.1 (2010), p. 200. ISSN: 1471-2180. DOI: 10.1186/1471-2180-10-200.

Haan, C. de, K. Lampén, J. Corander, and M.-L. Hänninen. Multilocus sequence types of environmental Campylobacter jejuni isolates and their similarities to those of human, poultry and bovine C. jejuni isolates. In: Zoonoses and Public Health (in press) (2012).

Hakulinen, R., J. S. Puranen, J. V. Lehtonen, M. S. Johnson, and J. Corander. Probabilistic Prediction of Contacts in Protein-Ligand Complexes. In: PLoS ONE submitted (2012).

Högnäs, G. and L. Allen. Special issue on Stochastic Difference Equations. In: Journal of Difference Equations and Applications (2012). (Editors).

Högnäs, G. and B. Jung. Analysis of a stochastic difference equation: Exit times and invariant distributions. In: Fasciculi Mathematici 44 (2010), pp. 6974.

Jääskinen, V., V. Parkkinen, L. Cheng, and J. Corander. Bayesian clustering of DNA sequences using Markov chains. In: Statistical Applications in Genetics and Molecular Biology Available online (2013). DOI: 10.1515/sagmb-2013-0031.

Jääskinen, V., J. Xiong, J. Corander, and T. Koski. Sparse Markov chains for sequence data. In: Scandinavian Journal of Statistics Available online (2013). ISSN: 1467-9469. DOI: 10.1111/sjos.12053.

Jenkins, H. E., R. B. Aylward, A. Gasasira, C. Donnelly, M. Mwanza, J. Corander, S. Garnier, C. Chauvin, E. Abanida, M. A. Pate, F. Adu, M. Baba, and N. Grassly. Implications of a circulating vaccine-derived poliovirus in Nigeria. In: New England Journal of Medicine 362.25 (2010), pp. 23602369. DOI: 10.1056/NEJMoa0910074.

Jern, P., L. Westberg, A. Johansson, L. Jonsson, J. Corander, N.K. Sandnabba, and P. Santtila. Are single nucleotide polymorphisms in the oxytocin and vasopressin 1A/1B receptor genes likely candidates for variation in ejaculatory function? In: British Journal of Urology International (in press) (2012). DOI: 10.1111/j.1464-410X.2012.11419.x.

Johansson, A., P. Jern, P. Santtila, B. von der Pahlen, E. Eriksson, L. Westberg, H. Nyman, J. Pensar, J. Corander, and N. K. Sandnabba. The genetics of sexuality and aggression (GSA) twin samples in Finland. In: Twin Research and Human Genetics FirstView (Oct. 2012), pp. 17. ISSN: 1839-2628. DOI: 10.1017/thg.2012.108.

Johansson, A., P. Santtila, J. Corander, K. Alanko, P. Jern, B. von der Pahlen, and N. K. Sandnabba. Genetic effects on anger control and their interaction with alcohol intoxication: A self-report study. In: Biological Psychology 85.2 (2010), pp. 291298. ISSN: 0301-0511. DOI: 10.1016/j.biopsycho.2010.07.016.

Johansson, A., P. Santtila, J. Corander, P. Jern, B. von der Pahlen, M. Varjonen, and K. Sandnabba. Controlling anger in self-reported sober and alcohol intoxicated states: Moderating effects of trait anger and alcohol consumption. In: Scandinavian Journal of Psychology 52.4 (2011), pp. 382388. ISSN: 1467-9450. DOI: 10.1111/j.1467-9450.2011.00880.x.

Kaarakka, T. and P. Salminen. On fractional Ornstein-Uhlenbeck processes. In: Communications on Stochastic Analysis 5.1 (2011), pp. 121133.

Karelahti, J., P. Vainiomäki, and T. Westerlund. Large scale production planning in the stainless steel industry. In: Industrial and Engineering Chemistry Research 50.9 (2011), pp. 48934906. DOI: 10.1021/ie101376b.

Konstantopoulus, T., A. Kyprianou, and P. Salminen. On the excursions of reflected local time processes and stochastic fluid queues. In: Journal of Applied Probability Spec. Vol. 48A, to appear (2011).

Kuikka, S., J. Vanhatalo, H. Pulkkinen, S. Mäntyniemi, and J. Corander. Experiences in Bayesian inference in Baltic Sea management. In: Statistical Science In press (2013).

Kurula, M. On passive and conservative state/signal systems. In: Integral Equations and Operator Theory 67 (3 2010), pp. 377424. ISSN: 0378-620X. DOI: 10.1007/s00020-010-1787-6.

Kurula, M. and O. Staffans. Connections between classical and generalised trajectories of a state/signal system. In: Complex Analysis and Operator Theory 5 (2 2011), pp. 403422. ISSN: 1661-8254. DOI: 10.1007/s11785-_010-0129-7.

Kurula, M. and O. Staffans. Well-posed state/signal systems in continuous time. In: Complex Analysis and Operator Theory 4 (2 2010), pp. 319390. ISSN: 1661-8254. DOI: 10.1007/s11785-009-0021-5.

Kurula, M., H. J. Zwart, A. J. van der Schaft, and J. Behrndt. Dirac structures and their composition on Hilbert spaces. In: Journal of Mathematical Analysis and Applications 372.2 (2010), pp. 402422. ISSN: 0022-247X. DOI: 10.1016/j.jmaa.2010.07.004.

Laajala, T. D., J. Corander, N.M. Saarinen, K. Mäkelä, S. Savolainen, M.I. Suominen, E. Alhoniemi, S. Mäkelä, M. Poutanen, and T. Aittokallio. Improved statistical modeling of tumor growth and treatment effect in pre-clinical animal studies with highly heterogeneous responses in vivo. In: Clinical Cancer Research (in press) (2012).

Lastusilta, T., L. G. Papageorgiou, and T. Westerlund. A comparative study of solving the problem of module identification in a complex network. In: Chemical Engineering Transactions 24 (2011), pp. 319324. DOI: 10.3303/CET1124054.

Lebreton, F., W. van Schaik, A. Manson McGuire, P. Godfrey, A. Griggs, V. Mazumdar, J. Corander, L. Cheng, S. Saif, S. Young, Q. Zeng, J. Wortman, B. Birren, R. J.L. Willems, A. M. Earl, and M. S. Gilmore. Emergence of epidemic multi-drug resistant Enterococcus faecium from animal and commensal strains. In: mBio 4 (2013). DOI: 10.1128/mBio.00534-13.

Lundell, A. and K.-M. Björk. Global optimization of a portfolio adjustment problem under credibility measures. In: International Journal of Operational Research (accepted) (2014).

Lundell, A., A. Skjäl, and T. Westerlund. A reformulation framework for global optimization. In: Journal of Global Optimization 57.1 (2013), pp. 115141. ISSN: 0925-5001. DOI: 10.1007/s10898-012-9877-4.

Lundell, A. and T. Westerlund. The reformulation-based ±GO algorithm for solving nonconvex MINLP problems some improvements. In: Chemical Engineering Transactions 32 (2013), pp. 13211326. DOI: 13 . 3303 /CET1332221.

Lundell, A. and T. Westerlund. The reformulation-based ±SGO algorithm for solving nonconvex MINLP problems some improvements. In: AIDIC Conference Series 11 (2013), pp. 211220. DOI: 10.3303/ACOS1311022.

Marttinen, P. and J. Corander. Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. In: BMC Bioinformatics 11.1 (2010). ISSN: 1471-2105. DOI: 10.1186/1471-2105-_11-443.

Marttinen, P., J. Gillberg, A. Havulinna, J. Corander, and S. Kaski. Genome-wide association studies with high-dimensional phenotypes. In: Statistical Applications in Genetics and Molecular Biology In press (2013).

Marttinen, P., W. P. Hanage, N. J. Croucher, T. R. Connor, S. R. Harris, S. D. Bentley, and J. Corander. Detection of recombination events in bacterial genomes from large population samples. In: Nucleic Acids Research 40.1 (2012), e6. DOI: 10.1093/nar/gkr928.

McNally, A., L. Cheng, S. R. Harris, and J. Corander. The evolutionary path to extra intestinal pathogenic, drug resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome. In: Genome Biology and Evolution (2013). DOI: 10.1093/gbe/evt038.

Medvedev, A. and H. T. Toivonen. Directional sensitivity of continuous least-squares state estimators. In: Systems and Control Letters 59.9 (2010), pp. 571577. ISSN: 0167-6911. DOI: 10.1016/j.sysconle.2010.07.001.

Mølgaard, B., W. Birmili, S. Clifford, A. Massling, K. Eleftheriadis, M. Norman, S. Vratolis, B. Wehner, J. Corander, K. Hämeri, and T. Hussein. Evaluation of a statistical forecast model for size-fractionated urban particle number concentrations using data from five European cities. In: Journal of Aerosol Science 66 (2013), pp. 96110. ISSN: 0021-8502. DOI: 10.1016/j.jaerosci.2013.08.012.

Mølgaard, B., T. Hussein, J. Corander, and K. Hämeri. Forecasting size-fractionated particle number concentrations in the urban atmosphere. In: Atmospheric Environment 46 (2012), pp. 155163. ISSN: 1352-2310. DOI: 10.1016/j.atmosenv.2011.10.004.

Moroni, R., L. Aalberg, T. Reinikainen, and J. Corander. Bayesian adaptive approach to estimating sample sizes for seizures of illicit drugs. In: Journal of Forensic Sciences accepted (2010). ISSN: 0379-0738.

Moroni, R., P. Blomstedt, L. Wilhelm, T. Reinikainen, E. Sippola, and J. Corander. Statistical modelling of measurement errors in gas chromatographic analyses of blood alcohol content. In: Forensic Science International 202.1-3 (2010), pp. 7174. ISSN: 0379-0738. DOI: 10.1016/j.forsciint.2010.04.029.

Nasution, D. and R. Östermark. Auditor fee dependence, auditor tenure, and auditor independence: the case of Finland. In: International Journal of Accounting, Auditing and Performance Evaluation 9.3 (), pp. 224246. DOI: 10.1504/IJAAPE.2013.055895.

Nasution, D. and R. Östermark. The impact of social pressures, locus of control, and professional commitment on auditors judgment: Indonesian evidence. In: Asian Review of Accounting 20 (2012), pp. 163178.

Numminen, E., L. Cheng, M. Gyllenberg, and J. Corander. Estimating the Transmission Dynamics of Streptococcus pneumoniae from Strain Prevalence Data. In: Biometrics 69.3 (2013), pp. 748757. ISSN: 1541-0420. DOI: 10.1111/biom.12040.

Nyberg, A., I. E. Grossmann, and T. Westerlund. An efficient reformulation of the multiechelon stochastic inventory system with uncertain demands. In: AIChE Journal 59.1 (2013), pp. 2328. ISSN: 1547-5905. DOI: 10.1002/aic.13977.

Nyberg, A. and T. Westerlund. A new exact discrete linear reformulation of the quadratic assignment problem. In: European Journal of Operational Research 220.2 (2012), pp. 314319. ISSN: 0377-2217. DOI: 10.1016/j.ejor.2012.02.010.

Nyberg, A. and T. Westerlund. Tightening a discrete formulation of the quadratic assignment problem. In: Chemical Engineering Transactions 32 (2013), pp. 13091314.

Nyberg, A., T. Westerlund, and A. Lundell. Improved discrete reformulations for the quadratic assignment problem. In: Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems. Ed. by C. Gomes and M. Sellmann. Vol. 7874. Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2013, pp. 193203. ISBN: 978-3-642-38170-6. DOI: 10.1007/978-3-642-38171-_3_13.

Nyberg, M. and K.-M. Björk. Improving convergence in a complex production planning problem with two hybrid methods. In: Journal of Information, Intelligence and Knowledge 3 (2012).

Nyman, H., T. Talonen, A. Roine, M. Hupa, and J. Corander. Statistical Approach to Quality Control of Large Thermodynamic Databases. In: Metallurgical and Materials Transactions B 43 (5 2012), pp. 11131118. ISSN: 1073-5615. DOI: 10.1007/s11663-012-9679-6.

Opmeer, M. R. and O. J. Staffans. Coprime factorization and optimal control on the doubly infinite discrete time axis. In: SIAM Journal of Control Optimization 50 (2012), pp. 266285. DOI: 10.1137/110823742.

Opmeer, M. R. and O. J. Staffans. Optimal control on the doubly infinite continuous-time axis and coprime factorizations. In: Journal Name Here ? (2011), ??

Opmeer, M. and O. Staffans. Optimal input-output stabilization of infinite-dimensional discrete time-invariant linear systems by output injection. In: SIAM Journal on Control and Optimization 48.8 (2010), pp. 50845107. DOI: 10.1137/090762233.

Orozco-terWengel, P., J. Corander, and C. Schlötterer. Genealogical lineage sorting leads to significant, but incorrect Bayesian multilocus inference of population structure. In: Molecular Ecology 6 (2011), pp. 11081021. ISSN: 1365-294X. DOI: 10.1111/j.1365-294X.2010.04990.x.

Östermark, R. A short note on the Growth Potential of risky fund investments. In: Journal of Derivatives & Hedge Funds 17 (2011), pp. 281290. DOI: 10.1057/jdhf.2011.22.

Östermark, R. Concurrent processing of heteroskedastic vector-valued mixture density models. In: Journal of Applied Statistics 37.10 (2010), pp. 16371659. DOI: 10.1080/02664760903121236.

Östermark, R. Genetic hybrid tuning of VARMAX and state space algorithms. In: Soft Computing A Fusion of Foundations, Methodologies and Applications 14 (1 2010), pp. 9199. ISSN: 1432-7643. DOI: 10.1007/s00500-008-0393-x.

Östermark, R. Hedging with options and cardinality constraints in multi-period portfolio management systems. In: Kybernetes 40.5 (2011), pp. 703718. DOI: 10.1108/03684921111142269.

Östermark, R. Incorporating asset growth potential and bear market safety switches in international portfolio decisions. In: Applied Soft Computing 12.8 (2012), pp. 25382549. ISSN: 1568-4946. DOI: 10.1016/j.asoc.2012.03.052.

Östman, F. and H. T. Toivonen. Adaptive cylinder balancing of internal combustion engines. In: Control Systems Technology, IEEE Transactions on 19.4 (2011), pp. 782791. ISSN: 1063-6536. DOI: 10.1109/TCST.2010.2052925.

Östman, F. and H. T. Toivonen. Torsional system parameter identification of internal combustion engines under normal operation. In: Mechanical Systems and Signal Processing 25.4 (2011), pp. 11461158. ISSN: 0888-3270. DOI: 10.1016/j.ymssp.2010.11.001.

Pitkänen, L.K., M. Tamminen, A. Hynninen, A. Karkman, J. Corander, A. Kotilainen, and M. Virta. Fish farming affects the abundance and diversity of the mercury resistance gene mera in marine sediments. In: Microbes and Environments 26.3 (2011), pp. 205211. DOI: 10.1264/jsme2.ME11119.

Robb-Post, C., J. Stamp, M. Brännback, A. Carsrud, and R. Östermark. Do gooders versus good doers: an empirical examination of growth versus efficiency in social entrepreneurship. In: Frontiers of Entrepreneurship Research 31 (2011). URL: http://digitalknowledge.babson.edu/fer/vol31/iss19/5.

Salminen, P. Optimal stopping, Appell polynomials, and Wiener-Hopf factorization. In: Stochastics An International Journal of Probability and Stochastic Processes 83.46 (2011), pp. 611622. DOI: 10.1080/17442508.2011.552722.

Salminen, P. and M. Yor. On hitting times of affine boundaries by reflecting Brownian motion and Bessel processes. In: Periodica Mathematica Hungarica 62(1) (2011), pp. 75101.

Shepheard, M. A., V. M. Fleming, T. R. Connor, J. Corander, E. J. Feil, C. Fraser, and W. P. Hanage. Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset. In: PLoS ONE 8.5 (2013). DOI: 10.1371/journal.pone.0062369.

Sihvonen, L.M., K. Jalkanen, E. Huovinen, S. Toivonen, J. Corander, M. Kuusi, M. Skurnik, A. Siitonen, and K. Haukka. Clinical isolates of Yersinia enterocolitica Biotype 1A represent two phylogenetic lineages with differing pathogenicity-related properties. In: BMC Microbiology (in press) (2012).

Sirén, J., W.P. Hanage, and J. Corander. Inference on Population Histories by Approximating Infinite Alleles Diffusion. In: Molecular Biology and Evolution (in press) (2012).

Sirén, J., P. Marttinen, and J. Corander. Reconstructing population histories from single nucleotide polymorphism data. In: Molecular Biology and Evolution 28.1 (2011), pp. 673683. DOI: 10.1093/molbev/msq236.

Skjäl, A., A. Lundell, and T. Westerlund. Global optimization of C2 constraints by convex reformulations. In: Chemical Engineering Transactions 24 (2011), pp. 373378. DOI: 10.3303/CET1124063.

Skjäl, A. and T. Westerlund. New methods for calculating ±BB-type underestimators. In: Journal of Global Optimization 58.3 (2013), pp. 411427. ISSN: 0925-5001. DOI: 10.1007/s10898-013-0057-y.

Skjäl, A., T. Westerlund, R. Misener, and C. Floudas. A generalization of the classical ±BB convex underestimation via diagonal and nondiagonal quadratic terms. In: Journal of Optimization Theory and Applications 154 (2 2012), pp. 462490. ISSN: 0022-3239. DOI: 10.1007/s10957-012-0033-_6.

Smýkal, P., N. Ba ová-Kerteszová, R. Kalendar, J. Corander, A. Schulman, and M. Pavelek. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. In: TAG Theoretical and Applied Genetics (2011), pp. 113. ISSN: 0040-5752. DOI: 10.1007/s00122-011-1539-2.

Smýkal, P., G. Kenicer, A. J. Flavell, J. Corander, O. Kosterin, R. J. Redden, R. Ford, C. J. Coyne, N. Maxted, M. J. Ambrose, and N. T.H. Ellis. Phylogeny, phylogeography and genetic diversity of the Pisum genus. In: Plant Genetic Resources FirstView (2010), pp. 115. DOI: 10.1017/S147926211000033X.

Staffans, O. J. On scattering passive system nodes and maximal scattering dissipative operators. In: Proceedings of the American Mathematical Society 141 (2013), pp. 13771383. DOI: 10.1090/S0002-9939-2012-11887-8.

Staffans, O. and G. Weiss. A physically motivated class of scattering passive linear systems. In: SIAM Journal on Control and Optimization 50.5 (2012), pp. 30833112. DOI: 10.1137/110846403.

Still, C. and T. Westerlund. A linear programming-based optimization algorithm for solving nonlinear programming problems. In: European Journal of Operational Research 200.3 (2010), pp. 658670. ISSN: 0377-2217. DOI: 10.1016/j.ejor.2009.01.033.

Sunnåker, M., A. G. Busetto, E. Numminen, J. Corander, M. Foll, and C. Dessimoz. Approximate Bayesian computation. In: PLoS Computational Biology accepted for publication (2012).

Tamminen, M., A. Karkman, J. Corander, L. Paulin, and M. Virta. Changes in bacterial community composition in Baltic Sea sediment in response to fish farming. In: Aquaculture (2011 (in press)).

Tamminen, M., A. Karkman, J. Corander, L. Paulin, and M. Virta. Differences in bacterial community composition in Baltic Sea sediment in response to fish farming. In: Aquaculture 313.14 (2011), pp. 1523. ISSN: 0044-8486. DOI: 10.1016/j.aquaculture.2011.01.020.

Toivonen, H. T., A. Meinander, T. Asaoka, M. Westerlund, F. Pettersson, A. Mikhailov, J. E. Eriksson, and H. Saxén. Modeling reveals that dynamic regulation of c-FLIP levels determines cell-to-cell distribution of CDd95-mediated apoptosis. In: Journal of Biological Chemistry 286.21 (2011), pp. 1837518382. DOI: 10.1074/jbc.M110.177097.

Tokola, K., A. Lundell, J. Nevalainen, and H. Oja. Design and cost optimization for hierarchical data. In: Biometrical Journal Submitted (2011).

Tokola, K., A. Lundell, J. Nevalainen, and H. Oja. Design and cost optimization for hierarchical data. In: Statistica Neerlandica (accepted) (2014).

Weiss, G. and O. Staffans. Maxwells equations as a scattering passive linear system. In: SIAM Journal on Control and Optimization 51.5 (2013), pp. 37223756. DOI: 10.1137/120869444.

Westerlund, T., A. Lundell, and J. Westerlund. On convex relaxations in nonconvex optimization. In: Chemical Engineering Transactions 24 (2011), pp. 331336. DOI: 10.3303/CET1124056.

Westerlund, T., A. Lundell, and J. Westerlund. Some notes on convex relaxations. In: AIDIC Conference Series. Ed. by S. Pierucci. Vol. 10. Aidic Servizi Srl, 2011, pp. 383392. DOI: 10.3303/ACOS1110042.

Willems, R.J. L., J. Top, W. van Schaik, H. Leavis, M. Bonten, J. Sirén, W. P. Hanage, and J. Corander. Restricted gene flow among hospital subpopulations of Enterococcus faecium. In: mBio 3 (2012).

Preprints

Christensen, S. and P. Salminen. Riesz representation and optimal stopping with two case studies. In: arXiv 1309.2469 (2013), pp. 124. URL: http://arxiv.org/pdf/1309.2469.pdf.

Salminen, P. and B. Q. Ta. Differentiability of excessive functions of one-dimensional diffusions and the principle of smooth fit. In: arXiv 1310.1901 (2013), pp. 122. URL: http://arxiv.org/pdf/1310.1901.pdf.

Proceedings

Arov, D., M. Kurula, and O. Staffans. Continuous-time state/signal systems and boundary relations. In: Leiden 2009 Proceedings. 2010.

Arov, D., M. Kurula, and O. Staffans. Passive behaviors and their passive state/signal realizations in continuous time. In: Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems MTNS 2010. 2010.

Corander, J., Y. Cui, and Koski T. Inductive inference and partition exchangeability in classification. In: Springer Lecture Notes in Artificial Intelligence (LNAI). 2011.

Corander, J., T. Janhunen, J. Rintanen, H. Nyman, and J. Pensar. Learning chordal markov networks by constraint satisfaction. In: Advances in Neural Information Processing Systems. Ed. by C. J. C. Burges, L. Bottou, M. Welling, Z. Ghahramani, and K. Q. Weinberger. Vol. 26. 2013, pp. 13491357.

Corander, J., T. Koski, T. Pavlenko, and A. Tillander. Bayesian Block-diagonal Predictive Classifier for Gaussian data. In: Advances in Intelligent and Soft Computing. 2012.

Hietarinta, L. and H. T. Toivonen. Least-squares support vector regression for identification of periodic systems. In: Proceedings IFAC Workshop on Periodic Control Systems (PSYCO 2010). 2010.

Kian, Q., A. Di Lieto, J. Corander, P. Auvinen, and D. Greco. Reanalysis of bipolar disorder and schizophrenia gene expression complements the Kraepelian dichotomy. In: Proceedings of the 11th International Conference on Systems Biology, ICSB 2010. 2011.

Lastusilta, T. and T. Westerlund. A comparative study of solving Quadratic Assignment Problems using some standard MINLP solvers. In: SIMULTECH 2011 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications. 2011, pp. 409412.

Lundell, A. and T. Westerlund. Finding an optimized set of transformations for convexifying nonconvex MINLP problems. In: Proceedings of the 11th International Symposium on Process Systems Engineering 15-19 July 2012, Singapore. Ed. by I.A. Karimi and R. Srinivasan. 2012.

Lundell, A. and T. Westerlund. Refinement strategies for piecewise linear functions utilized by reformulation-based techniques for global optimization. In: 23rd European Symposium on Computer Aided Process Engineering. Ed. by A. Kraslawski and I. Turunen. Vol. 32. Computer Aided Chemical Engineering. Elsevier, 2013, pp. 529534. DOI: 10.1016/B978-0-444-_63234-0.50089-0.

Mølgaard, B., T. Hussein, J. Corander, and K. Hämäri. Bayesian forecast model for size-fractionated urban particle number concentrations. In: Proceedings of the Finnish Center of Excellence and Graduate School in Physics, Chemistry, Biology and Meteorology of Atmospheric Composition and Climate Change´. Ed. by M. Kulmala, J. Bäck, H. K. Lappalainen, and T. Nieminen. Report series in aerosol science 126. 2011, pp. 270271.

Nissfolk, O., R. Pörn, T. Westerlund, and F. Jansson. A mixed integer quadratic reformulation of the quadratic assignment problem with rank-1 matrix. In: Proceedings of the 11th International Symposium on Process Systems Engineering 15-19 July 2012, Singapore. Ed. by I.A. Karimi and R. Srinivasan. 2012.

Nissfolk, O. and T. Westerlund. A metaheuristic optimization algorithm for binary quadratic problems. In: 23rd European Symposium on Computer Aided Process Engineering. Ed. by A. Kraslawski and I. Turunen. Vol. 32. Computer Aided Chemical Engineering. Elsevier, 2013, pp. 469474. DOI: 10.1016/B978-0-444-63234-0.50079-8.

Nyberg, M. and K.-M. Björk. Solving a complex production planning problem with mathematical programming techniques. In: Proceedings of ICAOR 10 (2010).

Pörn, R., O. Nissfolk, F. Jansson, and T. Westerlund. The Coulomb glass modeling and computational experience with a large scale 0-1 QP problem. In: 21st European Symposium on Computer Aided Process Engineering. Ed. by E.N. Pistikopoulos, M.C. Georgiadis, and A.C. Kokossis. Vol. 29. Computer Aided Chemical Engineering. Elsevier, 2011, pp. 658662. DOI: 10.1016/B978-0-444-53711-9.50132-2.

Shirdel, A. H., K.-M. Björk, and Toivonen H. T. Identification of linear switching system with unknown dimensions. In: Proceedings of the 47th Annual Hawaii International Conference on System Sciences (HICSS). Ed. by R. H. Sprague. 2014, pp. 13441352.

Skjäl, A., R. Misener, T. Westerlund, and C. A. Floudas. A generalization of the classical ±BB underestimation to include bilinear terms. In: 22nd European Symposium on Computer Aided Process Engineering. Ed. by D. Bogle and M. Fairweather. Vol. 30. Computer Aided Chemical Engineering. Elsevier, 2012, pp. 12021206.

Skjäl, A. and T. Westerlund. Comparison of two convex underestimation methods for quadratic functions. In: 23rd European Symposium on Computer Aided Process Engineering. Ed. by A. Kraslawski and I. Turunen. Vol. 32. Computer Aided Chemical Engineering. Elsevier, 2013, pp. 535540. DOI: 10.1016/B978-0-444-63234-0.50090-7.

Staffans, O. The Reciprocal Symmetry in State/Signal Systems in Continuous Time. In: Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems MTNS 2010. 2010.

Toivonen, H. T. and L. Hietarinta. Floquet-type representations of linear periodic systems general case. In: Proceedings of the 18th IFAC World Congress, 2011. Ed. by S. Bittanti, A. Cenedese, and S. Zampieri. Vol. 18. 2011. DOI: 10.3182/20110828-6-IT-1002.02385.

Westerlund, T. and A. Lundell. Global optimization of signomial programming problems. In: Proceedings of the European Workshop on Mixed Integer Nonlinear Programming. 2010.

PhD theses

Blomstedt, P. On Bayesian predictive modeling: With applications on the analysis of chromatography data in forensic investigations. PhD thesis. Åbo Akademi University, 2013. ISBN: 978-952-12-2965-7.

Kurula, M. Towards input/output-free modelling of linear infinite-dimensional systems in continuous time. PhD thesis. Åbo Akademi University, 2010. ISBN: 978-952-12-2410-2.

Lastusilta, T. GAMS MINLP solver comparisons and some improvements to the AlphaECP algorithm. PhD thesis. Åbo Akademi University, 2011. ISBN: 978-952-12-2653-3.

Lindberg, P. The knapsack problem approach in solving partial hedging problems of options. PhD thesis. Åbo Akademi University, 2012. ISBN: 978-952-12-2773-8.

Nyberg, A. Some reformulations for the quadratic assignment problem. PhD thesis. Åbo Akademi University, 2014. ISBN: 978-952-12-3019-6.

Skjäl, A. On the Use of Convex Underestimators in Global Optimization. PhD thesis. Åbo Akademi University, 2014. ISBN: 978-952-12-3018-9.

Ta, B. Q. Excessive functions, Appell polynomials and optimal stopping. PhD thesis. Åbo Akademi University, 2014. ISBN: 978-952-12-3045-5.

Masters theses

Anckar, A. Hausdorffdimensionen av mått. MSc. thesis. Åbo Akademi University, 2011.

Eklund, T. Ett stokastiskt dynamiskt system med tillämpning på datorgrafik. MSc. thesis. Åbo Akademi University, 2013.

Kronqvist, J. Development of measurements and control algorithms with industrial applications. MSc. thesis. Åbo Akademi University, 2013.

Neovius, J. A two-tier optimization model for a production-distribution network, a case study. MSc. thesis. Åbo Akademi University, 2010.

Niemelä, M. En komparativ studie om binärklassificerare med tillämpning inom kriminologi. PhD thesis. Åbo Akademi University, 2012.

Nissfolk, O. Minimering av totalenergin för elektronkonfigurationen i oordnade material. MSc. thesis. Åbo Akademi University, 2010.

Nyberg, A. En modifikation av extended cutting plane algoritmen för lösandet av kvadratiska tilldelningsproblem. MSc. thesis. Åbo Akademi University, 2010.

Øvergaard, J. Elbalans-, risk- och informationshantering i Katternögruppens elhandel. MSc. thesis. Åbo Akademi University, 2010.

Pensar, J. Labeled Directed Acyclic Graphs. MSc. thesis. Åbo Akademi University, 2011.

Rosama, N. Design of radial flow reactors. MSc. thesis. Åbo Akademi University, 2011.

Storbjörk, J. Modelling and simulation of power plant generators. MSc. thesis. Åbo Akademi University, 2012.

Sundqvist, D. Mapping of heat streams and heat pumps in heat recovery systems for paper machines. MSc. thesis. Åbo Akademi University, 2010.

Reports

Eronen, V.-P., M. Mäkelä, and T. Westerlund. Nonsmooth Extended Cutting Plane Method for Generally Convex MINLP Problems. In: TUCS Technical Report 1055 (2012). ISSN: 1239-1891.

Eronen, V.-P., M. Mäkelä, and T. Westerlund. On convex nonsmooth MINLP. In: TUCS Technical Report 988 (Nov. 2010). ISSN: 1239-1891.

Högnäs, G. On a stochastic Ricker competition model. Report. Cornell University Library, 2013. URL: http://arxiv.org/pdf/1302.3147v1.pdf.

Kurula, M. and H.J. Zwart. The duality between the gradient and divergence operators on bounded Lipschitz domains. In: Internal report, University of Twente Memorandum 1994 (2012). ISSN: 1239-1891. URL: http://eprints.eemcs.utwente.nl/22373/.

Presentations

Corander, J. Bayesian inference about evolution of recombinogenic bacteria. Lecture at University of Utrecht. Apr. 2010.

Corander, J. Bayesian machine learning using non-reversible MCMC. Pacific Symposium on Biocomputing 2010. Jan. 2010.

Corander, J. Bayesian population genetic modelling using BAPS. Lecture at University College London. Feb. 2010.

Corander, J. Bayesian population genetic modelling using BAPS. Lecture at Uppsala University. Apr. 2010.

Corander, J. Bayesian reconstruction of population genealogies. Valencia meeting on Bayesian statistics 9. June 2010.

Corander, J. Bayesian reconstruction of population genealogies from molecular marker data. Vienna Graduate School of Population Genetics. Mar. 2011.

Corander, J. Going BANANAS Bayesian reconstruction of population genealogies. Lecture at Harvard University. Nov. 2010.

Corander, J. Have I seen you before? Theory of predictive classification revisited. AI and Statistics 2010. May 2010.

Corander, J. Have I seen you before? Theory of predictive classification revisited. Lecture at Bocconi University. Oct. 2010.

Corander, J. Reconstructing population histories from molecular marker data. Zürich Colloquium for Computational Molecular Evolution (ZC-CME). May 2011.

Glader, C. On the construction of finite Blaschke products with preassigned critical points. Invited lecture at: Workshop on Riemann-Hilbert problems, circle packing and conformal geometry. Freiberg, Germany. Sept. 2013.

Högnäs, G. A stochastic competition model. 17th International Conference on Difference Equations and Applications ICDEA 2011, Trois-Rivières, Qué. July 2011.

Högnäs, G. Competition models with demographic stochasticity. The Fourth Conference on Computational and Mathematical Population Dynamics CMPD4, Taiyuan, China. May 2013.

Högnäs, G. On some stochastic competition models. ICDEA 2012 18th International Conference on Difference Equations and Applications. July 2012.

Högnäs, G. Stochastic difference equations. PODE 2010, Xanthi, Greece. May 2010.

Högnäs, G. Stochastically perturbed Ricker equations. ICDEA 2010, Riga, Latvia. July 2010.

Kurula, M. Conservative state/signal systems and interconnection. Seminar at University of Twente, Enschede. Mar. 2011.

Kurula, M. Functional models for Schur functions on C+. Workshop on System and Operator Realizations of Analytic Functions, the Lorentz Center, Leiden, the Netherlands. Feb. 2013.

Kurula, M. Proving existence of solutions of PDEs using feedback theory. 20th International Symposium on Mathematical Theory of Networks and Systems MTNS2012, Melbourne, Australia. July 2012.

Kurula, M. Proving existence of solutions of PDEs using feedback theory. 26th Nordic and 1st European-Nordic Congress of Mathematicians, Lund, Sweden. June 2013.

Lastusilta, T. A comparative study of solving the problem of module identification in a complex network. 10th International Conference on Chemical and Process Engineering ICheaP-10. May 2011.

Lundell, A. Finding an optimized set of transformations for convexifying nonconvex MINLP problems. International Symposium on Process Systems Engineering PSE12. July 2012.

Lundell, A. Implementation of the ±BB underestimator in a piecewise reformulation framework for global optimization. Second World Congress on Global Optimization WCGO 2, Chania, Greece. July 2011.

Lundell, A. On convex relaxations in nonconvex optimization. 10th International Conference on Chemical and Process Engineering ICheaP-10. May 2011.

Lundell, A. Reformulation based global optimization of nonconvex MINLP problems. INFORMS Annual Meeting 2013, Minneapolis, USA. Oct. 2013.

Lundell, A. The signomial global optimization algorithm some recent advances. 24th European Conference on Operations Research EURO XXIV, Lisbon. July 2010.

Nyberg, A. Improved discrete reformulations for the quadratic assignment problem. The 10th International Conference on Integration of Artificial Intelligence and Operations Research techniques in Constraint Programming. May 2013.

Nyberg, A. Tightening a discrete formulation of the quadratic assignment problem. 11th International Conference on Chemical and Process Engineering ICheaP-11, Milan, Italy. June 2013.

Pörn, R. The Coulomb glass modeling and computational experience with a large scale 0-1 QP problem. 21st European Symposium on Computer Aided Process Engineering, Chalkidiki, Greece. May 2011.

Salminen, P. On optimal stopping of strong Markov processes. The 6th General AMaMeF and Banach Center Conference, Warsawa, Poland. June 2013.

Salminen, P. On the smooth fit principle in optimal stopping. Colloquium lecture on Mathematical Statistics and Stochastic Processes Universität Hamburg, Germany. Dec. 2013.

Staffans, O. Conservative boundary control systems. Lecture at Tel Aviv University. Oct. 2010.

Staffans, O. Frequency domain well-posed linear systems. CDPS, Craiova, Romania. July 2013.

Staffans, O. On the past time final state and initial state future time optimal control problems. CDPS2011, Wuppertal, Germany. July 2011.

Staffans, O. On the past time final state and initial state future time optimal control problems. Plenary speaker at the 14th International Internet Seminar on Infinite dimensional Systems Theory, Blaubeuren, Germany. June 2012.

Staffans, O. Passive and conservative state/signal systems. Seminar lecture at University of Bath, England. May 2010.

Staffans, O. Passive behaviors and their passive state/signal realizations in continuous time. MTNS10, Budapest. July 2010.

Staffans, O. Passive behaviors and their passive state/signal realizations in continuous time. IWOTA 2010, Berlin. July 2010.

Staffans, O. Scattering and impedance passive and conservative systems. Oberwolfach workshop Wellposedness and Controllability of Evolution Equations. Dec. 2010.

Staffans, O. The dynamics induced by a boundary relation. Lecture at the Henk de Snoo Seminar in Groningen. Dec. 2010.

Staffans, O. The reciprocal symmetry in state/signal systems in continuous time. MTNS10, Budapest. July 2010.

Staffans, O. Time versus frequency domain. Lecture at the Workshop on System and Operator Realizations of Analytic Functions, the Lorentz Center, Leiden, the Netherlands. Feb. 2013.

Toivonen, H. T. Floquet-type representations of linear periodic systems general case. 18th IFAC World Congress. Aug. 2011.

Toivonen, H. T. Identification of switching linear systems using self-organizing models. Lecture at Zhejiang University. Sept. 2011.

Westerlund, T. Global optimization of signomial programming problems. European Workshop on Mixed Integer Nonlinear Programming, Marseille. Apr. 2010.

Westerlund, T. The reformulation-based ±GO algorithm for solving nonconvex MINLP problems some improvements. 11th International Conference on Chemical and Process Engineering ICheaP-11, Milan, Italy. June 2013.

Posters

Lundell, A. and T. Westerlund. Refinement strategies for piecewise linear functions utilized by reformulation-based techniques for global optimization. European Symposium on Computer Aided Process Engineering ESCAPE 23, Lappeenranta, Finland. June 2013.

Nissfolk, O. and T. Westerlund. A Metaheuristic Optimization Algorithm for Binary Quadratic Problems. European Symposium on Computer Aided Process Engineering ESCAPE 23, Lappeenranta, Finland. June 2013.

Nyman, H., J. Pensar, and J. Corander. Stratified gaussian graphical models. Fifth IMS-ISBA joint meeting MCMSki IV, Chamonix, France. Jan. 2014.

Pensar, J., H. Nyman, T. Koski, and J. Corander. Bayesian learning of Labeled Directed Acyclic Graphs using non-reversible MCMC. Fifth IMS-ISBA joint meeting MCMSki IV, Chamonix, France. Jan. 2014.

Pensar, J., H. Nyman, T. Koski, and J. Corander. Context specific graphical models. Eleventh World Meeting of ISBA, Kyoto, Japan. June 2012.

Skjäl, A. Global optimization of C2 constraints by convex reformulations. 10th International Conference on Chemical and Process Engineering ICheaP-10. May 2011.

Skjäl, A.. and T. Westerlund. A comparison of two convex underestimation methods for quadratic functions. European Symposium on Computer Aided Process Engineering ESCAPE 23, Lappeenranta, Finland. June 2013.