Publications

Biometry publications

Publications are no more updated here. See home pages of members.

2009

• J Pitkäniemi, S Varvio, J Corander, N Lehti, J Partanen, E Tuomilehto-Wolf, J Tuomilehto, A Thomas, E Arjas. Analysis of genetic risk with variable age at onset disease - combing population-based registry data and demographic information.  PLoS One Aug 31;4(8):e6836.(2009).
• S Varvio, K Auranen, E Arjas, PH Mäkelä. Evolution of the capsular regulatory genes in Streptococcus pneumoniae.  J Infect Dis 200:1144-51. (2009).
• D Gasbarra, M Pirinen, MJ Sillanpää, E Arjas. Bayesian quantitative trait locus mapping based on reconstruction of recent genetic histories. Genetics , published ahead of print on July 20, 2009 as doi: 10.1534/genetics.109.104190
• L Holmstrom, P Koistinen. Pattern recognition. Wiley Interdisciplinary Reviews: Computational Statristics (in press) (2009).
• MJ Sillanpää. Detecting interactions in association studies by using simple allele recoding. Human Heredity 67:69-75.(2009).

2008

• O Ovaskainen, H Rekola, Meyke, E Arjas. Bayesian methods for analyzing movements in heterogeneous landscapes from mark-recapture data. Ecology 89:542-554.(2008).
• J Corander, J Siren, E Arjas. Bayesian spatial modelling of genetic population structure. Computational Statistics 23:111-129.(2008).
• R Gupta, E Arjas, S Kulathinal, P.Auvinen. Bayesian hierarchical model for estimating gene expression intensity. EURASIP Journal on Bioinformatics and Systems Biology, vol. 2008, Article ID 231950.(2008).
• O Saarela, S Kulathinal, E Arjas, E Läärä. Nested case-control data utilised for multiple outcomes: a likelihood approach and alternatives. Statistics in Medicine 27:5991-6008.(2008).
• S Varvio, T Iso-Touru, J Kantanen, S Viitala, I Tapio, A Mäki-Tanila, M Zerabruk, J Vilkki. Molecular anatomy of the cytoplasmic domain of bovine growth hormone receptor, a quantitative trait locus, Proceedings of the Royal Society of London 275:1525-1534.(2008).
• S Kulathinal, D Gasbarra, S Kinra, S Ebrahim, MJ Sillanpää. Estimation of additive genetic and environmental sources of quantitative trait variation using data on married couples and their siblings. Genetics Research 90:269-279.(2008).
• P Waldmann, J Hallander, F Hoti, MJ Sillanpää. Efficient MCMC implementation of Bayesian analysis of additive and dominance genetic variances in non-inbred pedigrees. Genetics 179:1101-1112.(2008).
• MJ Sillanpää, N Noykova. Hierarchical modeling of clinical and expression quantitative trait loci. Heredity 101:271-284.(2008).
• M Bhattacharjee, CH Botting, MJ Sillanpää. Bayesian biomarker identification based on marker-expression-proteomics data. Genomics 92: 384-392.(2008).
• A Kuparinen, FM Schurr. Assessing the risk of gene flow from genetically modified trees carrying mitigation transgenes. Biological Invasions 10:281-290.(2008).
• A Kuparinen, RB O'Hara, J Merilä. The role of growth history in determining age and size at maturation in exploited fish populations. Fish & Fisheries 9:201-207.(2008)
• T Leinonen, RB O'Hara, JM Cano, J Merilä. Comparative studies of quantitative trait and neutral marker divergence: A meta-analysis. Journal of Evolutionary Biology 21:1-17.(2008)
• CM Mutshinda, RB O'Hara, I.P.Woiwod. Species abundance dynamics under neutral assumptions: a Bayesian approach to the controversy. Functional Ecology 22:340-347.(2008).
• CM Mutshinda, I Antai, RB O'Hara. A probabilistic approach to exposure risk assessment. Stochastic Environmental Research & Risk Assessment 22:441-449.(2008).
• RB O'Hara. Double-blind review: let diversity reign. (Correspondence) Nature 452:28.(2008).
• RB O'Hara. Journal club Nature 452:785.(2008).
• RB O'Hara. European grants: a different view puts rich countries ahead. (Correspondence) Nature 455:285.(2008).
• RB O'Hara, JM Cano, O Ovaskainen, JS Alho, C Teplitsky, C. Bayesian Approaches in Evolutionary Quantitative Genetics. Journal of Evolutionary Biology. 21:949-957.(2008).
• S Ortega-Garcia, G Ponce-Diaz, RB O'Hara, J Merilä. The relative importance of lunar phase and weather conditions on Striped Marlin (Tetrapturus audax) catches in sport fishing. Fisheries Research 93:190-194.(2008).
• A Pagano, D Lesbarreres, RB O'Hara, A Crivelli, M Veith, T Lode, DS Schmeller. Geographical and ecological distributions of frog hemiclones suggest occurrence of both 'General-Purpose Genotype' and 'Frozen Niche Variation' clones. Journal of Zoological Systematics and Evolutionary Research 46:162-168.(2008).
• T Snäll, RB O'Hara, C Ray, SK Collinge. Climate-driven spatial dynamics of plague among prairie dog colonies. American Naturalist 171: 238-248.(2008).
• TJ Webb, RB O'Hara, RP Freckleton. Does double-blind review benefit female authors? Trends in Ecology & Evolution 23:351-353. (2008).
• J Kohonen, S Talikota, J Corander, P Auvinen, E Arjas. A naive Bayes classifier for protein function prediction. In Silico Biology 9, article 0003 (2008).
• M Pirinen, S Kulathinal, D Gasbarra, MJ Sillanpää. Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithm. Genetics Research (accepted).

2007

• D Gasbarra, M Pirinen, MJ Sillanpää, E Salmela, E Arjas. Estimating genealogies from unlinked marker data: a Bayesian approach. Theoretical Population Biology 72:305-322. (2007).
• D Gasbarra, M Pirinen, MJ Sillanpää, E Arjas. Estimating genealogies from linked marker data: a Bayesian approach. BMC Bioinformatics 8:411-    . (2007).
• T Snäll, RB O´Hara, E Arjas. A mathematical and statistical framework for modeling dispersal. Oikos 116:1036-1050. (2007).
• I Herzon, RB O'Hara. Effects of spatial complexity of farmland within different landscape types on farmland bird communities in the Baltic States. Agriculture, Ecosystems and Environment 118:297-306. (2007).
• M Saastamoinen, M Nieminen, S van Nouhuys, RB O'Hara, J Suomi. Development and survival of a specialist herbivore, Melitaea cinxia, on host plants producing high and low concentrations of iridoid glycosides. Annales Zoologici Fennici 44:70-80. (2007).
• C Mutshinda, I Antai, RB O´Hara. A probabilistic approach to exposure risk assessment. Stochastic Environmental Research & Risk Assessment (in press)
• I Herzon, RB O'Hara. Effects of spatial complexity of farmland within different landscape types on farmland bird communities in the Baltic States. Agriculture, Ecosystems and Environment 118: 297-306. (2007).
• RB O'Hara. Human Expression patterns: Genetic differences between populations. Heredity 98:245-246. (2007).
• Saastamoinen, M., Nieminen, M., van Nouhuys, S., O'Hara, R.B., Suomi, J. Development and survival of a specialist herbivore, Melitaea cinxia, on host plants producing high and low concentrations of iridoid glycosides. Ann. Zool. Fennici 44: 70-80.
• A Kuparinen, FM Schurr. A flexible modelling framework linking the spatio-temporal dynamics of plant genotypes and populations: application to gene flow from transgenic forests. Ecological Modelling 202:476-486.(2007).
• A Kuparinen, F Schurr, O Tackenberg, RB O'Hara. Air-mediated pollen flow from genetically modified to conventional crops -risk assessment with a mechanistic model. Ecological Applications 17:431-440. (2007).
• A Kuparinen, T Snäll, S Vänskä, RB O'Hara. The role of modeling selection in describing stochastic ecological processes. Oikos 116:966-974. (2007).
• A Kuparinen, T Markkanen, H Riikonen, T Vesala. Modeling air-mediated plant diaspore dispersion in forested areas. Ecological Modelling 208:177-188. (2007).
• T Huurre, M Eerola, O Rahkonen, H Aro. Does social support affect the relationship between socio-economic status and depression? A longitudinal study from adolescent until adulthood. Journal of Affective Disorders 100:55-64. (2007).
• M Antila, T Kieseppä, M Eerola, T Partonen, J Lönnqvist, A Tuulio-Henriksson. Cognitive functions in bipolar I disorder patients and their unaffected first-degree relatives. Psycological Medicine 37:679-687. (2007).
• A Kuha, A Tuulio-Henriksson, M Eerola, J Perälä, J Suvisaari, T Partonen, J Lönnqvist. Impaired executive performance of healthy siblings of schizophrenia patients in a population based study. Schizophrenia research 92:142-150 (2007).
• A Ocampo, C Biltoft, M Lucero, RM Ölander, J Ugpo, K Auranen, A Soininen, H Nohynek, H Käyhty. Response and persistence of antibodies to PRP-T and DTwP vaccines with concomitant administration of conjugate vaccines. Vaccine 24:605-611 (2007).
• S Granat, M Zakaria, J Ollgren, E Herva, M Das, L Piirainen, K Auranen, PH Mäkelä. Pneumococcal carriage during the first year of life: a longitudinal study in a semi-rural setting in Bangladesh. Pediatric Infectious Disease Journal 26:319-324. (2007).
• MJ Sillanpää, F Hoti. Mapping quantitative trait loci from a single tail sample of the phenotype distribution. Genetics 177:2361-2377. (2007).
• A Kassinen, L Krogius-Kurikka, H Mäkivuokko, L Paulin, T Rinttilä, J Corander, E Malinen, J Apajalahti and A Palva.The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology, 133:24-33.(2007).
• JM Sistonen, AJ Sajantila, O Lao, J Corander, G Barbujani S Fuselli, S.  CYP2D6 worldwide genetic variation shows high frequency of altered activity variants and no continental structure. Pharmacogenetics and Genomics: 17:93-101. (2007)
• J Corander, M Gyllenberg, T Koski. Random Partition models and Exchangeability for Bayesian Identification of Population Structure. Bulletin of Mathematical Biology, 69:797-815. (2007)
• J Corander, J Tang. Bayesian analysis of population structure based on linked molecular information. Mathematical Biosciences, 205:19-31. (2007).
• H Mäki-Petäys, J Corander, J Aalto, T Liukkonen, P Helle, M Orell, M.  No genetic evidence of sex-biased effective dispersal in a lekking bird, the capercaillie (Tetrao urogallus). Journal of Evolutionary Biology 20:865-873. (2007).
• J Tang, J Tao, H Urakawa, J Corander. T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data. Statistical Applications in Genetics and Molecular Biology, 6.            (2007)

2006

• S Kulathinal, E Arjas. Bayesian inference from case-cohort data with multiple end-points. Scandinavian Journal of Statistics 33:25-36. (2006).
• R Gupta, P Auvinen, A Thomas, E Arjas. Bayesian hierarchical model for correcting signal saturation in microarrays using pixel intensities. Statistical Applications in Genetics and Molecular Biology, Vol.5, No.1, Article 20. (2006).
• P Sokero, M Eerola, T Melartin, H Rytsälä, P Lestelä-Mielonen, E Isometsä. Decline in suicidal ideation is preceded by decline in depression and hopelessness. Journal of Affective Disorders 95:95-102. (2006).
• K Ahonen, ML Hämäläinen, M Eerola, K Hoppu. A randomised trial of rizatriptan in migraine attacks in children. Neurology 67:1135-1143. (2006).
• J Corander. Is there a real Bayesian revolution in pattern recognition for bioinformatics? Current Bioinformatics 1:161-165. (2006)
• J Corander, P Marttinen. Bayesian model learning based on predictive entropy. Journal of Logic, Language and Information, DOI:10.1007/s10849-005-9004-8. (2006)
• J Corander, M Gyllenberg, T Koski. Bayesian model learning based on a parallel MCMC strategy. Statistics and Computing 16:355-362. (2006)
• D Gasbarra, S Kulathinal, I Dewan, A Nissinen. Testing dependence between the failure time and failure models: An application of enlarged filtration. Journal of Statistical Planning and Inference 136:1669-1686. (2006).
• D Gasbarra, E Valkeila, L Vostrikova. Enlargement of filtration and additional information in pricing models: A Bayesian approach. pp. 257-285 in: The Shiryaev Festschrift, from Stochastic Calculus to Mathematical Finance. Edited by: Kabanov Liptser and Stoyanov. Springer, Berlin. (2006).
• M Pirinen, D Gasbarra. Finding consistent gene transmission patterns on large and complex pedigrees. IEEE TCBB 3:252-262. (2006).
• D Gasbarra, MJ Sillanpää. Constructing parental linkage phase and genetic map over distances 1cM using pooled haploid DNA. Genetics 172:1325-1335. (2006).
• F Hoti, MJ Sillanpää. Bayesian mapping of genotype x expression interactions in quantitative and qualitative traits. Heredity 97:4-18. (2006).
• MJ Sillanpää, M Bhattacharjee. Association mapping of complex trait loci with context-dependent effects and unknown context variable. Genetics 174:1597-1611. (2006).
• R Syrjänen, E Herva, PH Mäkelä, H Puhakka, K Auranen, AK Takala, T Kilpi. The value of nasopharyngeal culture in predicting the etiology of acute otitis media in children less than two years of age. Pediatric Infectious Disease Journal 25:1032-1036. (2006).
• H Käyhty, K Auranen, H Nohynek, PH Mäkelä. Nasopharyngeal coloinization: a target for pneumococcal vaccination. Expert Reviews of Vaccines 5:651-667. (2006).
• M Poranen, J Ravantti, A Grahn, R Gupta, P Auvinen, D Bamford. Global changes in cellular gene expression during bacteriophage PRD1 infection. Journal of Virology 80:8081-8088. (2006).
• A Kuparinen. Mechanistic models for wind-dispersal. Trends in Plant Sciences 11:296-301. (2006).
• MS Fred, RB O'Hara, JE Brommer. Consequences of the spatial configuration of resources for the distribution and dynamics of the endangered Parnassius apollo butterfly. Biological Conservation 130:183-192. (2006).
• DJ Golicher, RB O'Hara, L Ruíz-Montoya, L Cayuela. Lifting a veil on diversity: A Bayesian approach to fitting relative abundance models. Ecological Applications 16:202-212. (2006).
• S Lehvävirta, DJ Kotze, J Niemelä, M Mäntysaari, RB O'Hara. Effects of fragmentation and trampling on carabid beetle assemblages in urban woodlands in Helsinki, Finland. Urban Ecosystems 9: 13-26. (2006).
• MS Fred, RB O'Hara, JE Brommer. Consequences of the spatial configuration of resources for the distribution and dynamics of the endangered Parnassius apollo butterfly. Biological Conservation 130:183-192. (2006).
• T Roslin, S Gripenberg, JP Salminen, M Vienola, RB O'Hara, K Pihlaja, P Pulkkinen. Seeing the trees for the leaves - oaks as mosaics for a host-specific moth. Oikos 113:106-120. (2006).
• DJ Golicher, RB O'Hara, L Ruíz-Montoya, L Cayuela. Lifting a veil on diversity: A Bayesian approach to fitting relative abundance models. Ecological Applications 16:202-212. (2006).
• K Matveinen-Huju, J Niemelä, H Rita, RB O'Hara. Retention-tree groups in clear-cuts: do they constitute 'life-boats' for spiders and carabids? Forest Ecology and Management 230:119-135. (2006).
• RB O'Hara. Wholesale analysis of genes, traits and microarrays. Heredity 97:253. (2006).
• RB O'Hara. MS Fowler, CA Johnson. Why negatives should be viewed as positives (Correspondence) Nature 439:782. (2006).
• T Roslin, S Gripenberg, JP Salminen, M Vienola, RB O'Hara, K Pihlaja, P Pulkkinen. Seeing the trees for the leaves - oaks as mosaics for a host-specific moth. Oikos 113:106-120. (2006).
• A Thomas, RB O´Hara, U Ligges, S Sturtz. Making BUGS Open. R News 6:12-17. (2006).

2005

• S Mäntyniemi, A Romakkaniemi, E Arjas. Bayesian removal estimation of a population size under unequal catchability. Canadian Journal of Fisheries and Aquatic Sciences 62:291-300. (2005).
• D Gasbarra, MJ Sillanpää, E Arjas. Backward simulation of ancestors of sampled individuals. Theoretical Population Biology 67:75-83. (2005).
• V Martinez, G Thorgaard, B Robison, MJ Sillanpää. An application of Bayesian QTL mapping to early development in double haploid lines of rainbow trout including environmental effects. Genetical Research 86:209-221. (2005).
• MJ Sillanpää, M Bhattacharjee. Bayesian association-based fine mapping in small chromosomal segments. Genetics 169:427-439. (2005).
• P Waldmann, MR Garcia-Gi, MJ Sillanpää. Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: an application to Pinus sylvestris. Heredity 94: 623-629. (2005).
• RB O'Hara. Species richness estimates. How many species can dance on the head of a pin? Journal of Animal Ecology 74:375-386. (2005).
• M Pekkinen, S Varvio, KKM Kulju, H Kärkkäinen, S Smolander, A Viherä-Aarnio, V Koski, MJ Sillanpää. Linkage map of birch, Betula pendula Roth, based on microsatellites and AFLP´s. Genome 48:619-625. (2005).
• A Audzijonyte, J Damgaard, S Varvio, JK Vainio, R Väinölä. Phylogeny of Mysis (Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data. Cladistics 21:575-596 (2005).
• S Kühlmann-Berenzon, J Heikkinen, A Särkkä. An additive edge correction for the influence potential of trees. Biometrical Journal 47:517-526. (2005).
• S Smolander, P Stenberg. Simple parametrizations of the radiation budget of uniform broadleaved and coniferous canopies. Remote Sensing of Environment 94:355-363. (2005).
• M. Eerola, T Huurre, H Aro. The problem of attrition in a Finnish longitudinal survey on depression. European Journal of Epidemiology 20:113-120 (2005)
• WP Hanage, TH Kaijalainen, R Syrjänen, K Auranen, M Leinonen, PH Mäkelä, B Spratt. Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland. Infection and Immunity 73:431-435 (2005).
• R Syrjänen, K Auranen, T Leino, T Kilpi, PH Mäkelä. Pneumococcal acute otitis media in relation to pneumococcal nasopharyngeal carriage. Pediatric Infectious Disease Journal 24:801-806 (2005).
• DS Schmeller, RB O'Hara, H Kokko. Male Adaptive Stupidity: Male Maring pattern in hypridogenetic waterfrog. Evolutionary Ecology Research 7:1039-1050 (2005).
• RB O'Hara, J Merilä. Bias and precision in QST estimates: problems and some solutions. Genetics 171:1331-1339 (2005).
• RB O´Hara. Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth. Proceedings of the Royal Society of London,B 272:211-217. (2005).
• M Saastamoinen, M Nieminen, S van Nouhuys, RB O'Hara, J Suomi. Effects of host plant's defensive chemistry on growth, development and survival of the Glanville fritillary (Melitaea cinxia) larvae. .......
• H Mäki-Petäys, A Zakharov, L Viljakainen, J Corander, P Pamilo. Genetic changes associated to declinig populations of Formica ants in fragmented forest landscape. Molecular Ecology 14: 733-742 (2005).
• I Taskinen, J Heikkinen. A nonparametric Bayesian method for assessing uncertainty in thematic maps of forest variables. Journal of Agricultural, Biological and Environmental Statistics. .....

2004

• J Ranta, PH Mäkelä, E Arjas. Predicting meningococcal disease outbreaks in structured populations. Statistics in Medicine 23:927-945. (2004).
• E Arjas, J Parner. Causal reasoning from longitudinal data. Scandinavian Journal of Statistics 31:171-201. (2004).
• MJ Sillanpää, D Gasbarra, E Arjas. Comment on the "On the Metropolis-Hastings acceptance probability to add or drop a quantitative trait locus in Markov Chain Monte Carlo -based Bayesian analyses. Genetics 167: 1037. (2004).
• M Bhattacharjee, CC Pritchard, PS Nelson, E Arjas. Bayesian integrated functional analysis of microarray data. Bioinformatics 20:2943-2953. (2004).
• GA Churchill et 113 authors, incl. MJ Sillanpää. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36:1133-1137. (2004).
• MJ Sillanpää, K Auranen. Replication in genetic studies of complex traits. Annals of Human Genetics 68:646-657. (2004).
• J Corander, P Waldmann, P Marttinen, MJ Sillanpää. BAPS 2: enhanced possibilities for the analysis of the genetic population structure. Bioinformatics 20:2363-2469. (2004).
• KKM Kulju, M Pekkinen, S Varvio. Microsatellite primer pairs for Betula pendula. Molecular Ecology Notes 4:471-473. (2004).
• E Valkeila, D Gasbarra. Initial enlargement: a Bayesian approach. Theory of Probability and Mathematical Statistics 9:26-37. (2004).
• J Karvonen, M Similä, J Haapala, C Haas, M Mäkynen. Comparison of SAR data and operational sea ice products to EM ice thickness measurements in the Baltic Sea. IGARSS´04 (2004).
• J Karvonen, M Similä, M Mäkynen. Open water detection from Baltic Sea ice SAR imagery. IGARSS´04 (2004).
• J Merilä, F Söderman, RB O'Hara, K Räsänen, A Laurila. Local adaptation and genetics of acid-stress tolerance in the moor frog, Rana arvalis. Conservation Genetics, 5:513-527. (2004).
• K Auranen, M Eichner, T Leino, AKT Takala, T Takala, PH Mäkelä. Modelling transmission, immunity and disease of Haemophilus influenzae type b in a structured population. Epidemiology and infection 132:947-957. (2004).
• T Leino, T Takala, K Auranen, PH Mäkelä and AKT Takala. Indirect protection obtained by Haemophilus influenzae type b vaccinations, analysis in a structured population model. Epidemiology and infection 132:959-966 (2004).
• WP Hanage, K Auranen, R Syrjänen, E Herva, PH Mäkelä, T Kilpi, BG Spratt. The ability of pneumococccal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines. Infection and Immunity 72:76-81 (2004).
• Y Zhang, K Auranen, M Eichner. The influence of competition and vaccination on the co-existence of two pneumococcal serotypes. Epidemiology and infection 132:1073-1081. (2004)

2003

• A Ekholm, J Jokinen, JW McDonald, PWF Smith. Joint regression and association modeling of longitudinal ordinal data. Biometrics 59:795-803 (2003).
• T Härkänen, H Hausen, JI Virtanen, E Arjas. A non-parametric frailty model for temporally clustered multivariate failure times. Scandinavian Journal of Statistics 30:523-533 (2003).
• M Eerola, D Gasbarra, P Mäkelä, H Linden, A Adreev. Joint modeling of recurrent infections and antibody response by Bayesian data augmentation. Scandinavian Journal of Statistics 30:677-698 (2003).
• A Ekholm. Comparing the odds and the dependence ratios. In: R.Höglund, M.Jäntti and G.Rosenqvist (eds.) Statistics, Econometrics and Society: Essays in Honour of Leif Nordberg. Statistics, Finland. Pp. 13-25 (2003).
• E Arjas, M Bhattacharjee. Modelling heterogeneity: Hierarchial Bayesian approach. In: T.A.Mazzuchi, N.D.Singpurwalla and R.Soyer (eds.) Mathematical Reliability: An Expository Perspective pp. 71-86. Kluwer Academic (2003).
• M Bhattacharjee, E Arjas. Bayesian modeling of failure prediction using maintenance information. In: T.Bedford and P.H. van Gelden (eds.) Safety and Reliability, Proceedings of ESREL, pp. 151-155. A.A.Balkema Publishers (2003).
• E Arjas, SA Murphy. Discussion on the paper by Murphy. Journal of the Royal Statistical Society, Series B 65:355-356 (2003)
• E Arjas. Causality and statistics. Commentary on the chapter "Causal inference using influence diagrams: the problem of partial compliance" by A.P.Dawid. In: P.Green, N.Hjort and S.Richardson (eds.) Highly Structured Stochastic Systems. Oxford University Press.(2003).
• R Mäkipää, J Heikkinen. Large-scale changes in abundance of terricolous bryophtes and macrolichens in Finland. Journal of Vegetation Science 14:497-508 (2003).
• J Heikkinen. Trans-dimensional Bayesian non-parametrics with spatial point processes. In: S.Richardson, P.J.Green, N.L.Hjort (eds.) Highly structured stochastic systems, pp. 203-206. Oxford University Press (2003).
• S Smolander, P Stenberg. A method to account for shoot scale clumping in coniferous canopy reflectance models. Remote Sensing of Environment 88:363-373 (2003).
• J Karvonen, M Similä, I Heiler. Ice thickness estimation using SAR data and ice thickness history. IGARSS´03 (2003).
• MF Antolin, PJ Ode, GE Heimpel, RB O'Hara, MR Strand. Mating system, population genetics, and sex allele diversity of the parasatoid Bracon hebetor. Heredity 91:373-381. (2003).
• S Pakkasmaa, J Merilä, RB O'Hara. Genetic and maternal effect influences on viability of common frog tadpoles under different environmental conditions. Heredity 91:117-124. (2003).
• M Dreschler, K Frank, I Hanski, RB O'Hara, CWissel. Ranking metapopulation extinction risk for conservation: from patterns in data to management decisions. Ecological Applications 13:990-998. (2003).
• DJ Kotze, J Niemelä, RB O'Hara, H Turin. Testing abundance-range size relationships in European carabid beetles (Coleoptera: Carabidae). Ecography 26:553-566 (2003).
• DJ Kotze, RB O'Hara. Species decline - but why? Explanations of carabid beetle (Coleoptera, Carabidae) declines in Europe. Oecologia 135:138-148. (2003).
• M Straetemans, A Palmu, K Auranen, J Ollgren, GA Zielhuis, T Kilpi. The effect of Pneumococcal conjugate vaccine on the risk of OME at 7 and 24 months of age. International Journal of Pediatric Otorhinolaryngology 67:1235-1242 (2003).
• K Auranen. Towards Bayesian inference in epidemic models: A discussion to "Threshold parameters for epidemics in heterogeneous environments" by Niels Becker. In: P Green, N Hjort and S Richardson (eds.) Highly Structured Stochastic Systems. Oxford University Press (2003).
• M Bhattacharjee, C Pritchard, MJ Sillanpää, E Arjas. Bayesian characterization of natural variation in gene expression. In: KF Johnson and SM Lin (eds.) Methods of Microarray Data Analysis III, Proccedings of the CAMDA02 Conference, pp. 155-172. Kluwer Academic Publishers, Boston (2003).
• J Corander, P Waldmann, MJ Sillanpää. Bayesian analysis of genetic differentiation between populations. Genetics 163:367-374 (2003).
• JU  Palo, RB O'Hara, AT Laugen, A Laurila, CR Primmer, J Merilä. Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data. Molecular Ecology 12:1963-1978 (2003).
• R Kilpikari, MJ Sillanpää. Bayesian analysis of multilocus association in quantitative and qualitative traits. Genetic Epidemiology 25:122-135. (2003).

2002

• E Arjas. Predictive inference and discontinuities. Nonparametric Statistics 14:31-42. (2002).
• E Arjas. Contribution (invited) to the discussion on the paper Statistical issues in fisheries' stock assessment by S. Gavaris and J. N. Ianelli. Scandinavian J. of Statistics 29:268-269. (2002).
• M Bhattacharjee, E Arjas, U Pulkkinen. Modelling heterogeneity in nuclear power plant valve failure data. In: Mathematical and Statistical Methods in Reliability (B.H.Lindqvist, K. A.Doksum, Eds.) World Scientific (2002), 341-353.
• J Corander, MJ Sillanpää. A unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. Journal of Theoretical Biology 218:435-446. (2002)
• A Ekholm, J Jokinen, T Kilpi. Combining regression and association modelling for longitudinal data on bacterial carriage. Statistics in Medicine 21:773-791. (2002)
• FJ Hoti, MJ Sillanpää, L Holmström. A note on estimating the posterior density of qualitative trait locus from a Markov chain Monte Carlo sample. Genetic Epidemiology 22:369-376. (2002)
• T Härkänen, MA Larmas, JI Virtanen, E Arjas. Applying modern survival analysis methods to longitudinal dental caries studies. Journal of Dental Research 81:144-148. (2002).
• SB Kulathinal, D Gasbarra. Testing equality of cause-specific hazard rates corresponding to m competing risks among k groups. Lifetime Data Analysis 8:147-161. (2002)
• K Kuulasmaa, SB Kulathinal, D Gasbarra. Estimation of an errors-in-variables regression model when the variances of the measurement errors vary between the observations. Statistics in Medicine 21:1089-1101. (2002)
• T Leino, K Auranen, PH Mäkelä, H Käyhty, M Ramsay, M Slack, AK Takala. Haemophilus influenzae type b and cross-reactive antigens in natural Hib infection dynamics; modelling in two populations. Epidemiology and Infection 129:73-83. (2002)
• S Mäntyniemi, A Romakkaniemi. Bayesian mark-recapture estimation with an application to a salmonid smolt population. Canadian Journal of Fisheries and Aquatic Sciences 59:1748-1758. (2002)
• RB O'Hara, E Arjas, H Toivonen, I Hanski. Bayesian analysis of metapopulation data. Ecology 83:2408-2415. (2002).
• S Palmroth, P Stenberg, S Smolander, P Voipio, H Smolander. Fertilization has little effect on light-interception efficiency of Picea abies shoots. Tree Physiology 22:1185-1192. (2002)
• J Ranta, R Maijala. A probabilistic transmission model of Salmonella in the primary broiler production chain. Risk Analysis 22:47-58. (2002)
• MJ Sillanpää. Mathematics-assisted mapping in analysis of medical disease. Annals of Medicine 34:291-298. (2002)
• MJ Sillanpää, J Corander. Model choice in gene mapping: what and why. Trends in Genetics 18:301-307. (2002).
• MJ Sillanpää. Discussion on the meeting: Statistical modelling and analysis of genetic data. Journal of Royal Statistical Society, Series B 64:758. (2002).

2001

• E Arjas. Causal analysis and statistics: a social sciences perspective. European Sociological Review 17:59-64. (2001).
• E Arjas. Longitudinal data: Event history analysis in discrete time. Entry, International Encyclopedia of the Social and Behavioral Sciences. Elsevier: 9063-9067. (2001).
• E Kokki, J Ranta, A Penttinen, E Pukkala, J Pekkanen. Small area estimation of incidence of cancer around a known source of exposure with fine resolution data. Occupational & Environmental Medicine 58:315-320. (2001).
• T Leino, K Auranen, J Jokinen, M Leinonen, P Tervonen, AK Takala. Pneumococcal carriage in children during their first two years: Important role of family exposure. Pediatric Infectious Disease Journal 20:1022-1027. (2001).
• C Maliepaard, MJ Sillanpää, J van Ooijen , RC Jansen, E Arjas. Bayesian versus frequentist analysis of multiple quantitative trait loci with an application to an outbred apple cross. Theoretical and Applied Genetics 103:1243-1253. (2001).
• P Onkamo, P Sevon, VV Ollikainen, HTT Toivonen, H Mannila, J Kere. Association analysis of data mining tools. American Journal of Human Genetics 69 (4)Suppl.1:1320. (2001).
• J Ranta, T Hovi, E Arjas. Poliovirus surveillance by examining sewage water specimens; studies on detection probability using simulation models. Risk Analysis 21:1087-1096. (2001).
• M Rytkönen, J Ranta, J Tuomilehto, M Karvonen. Bayesian analysis of geographical variation in the incidence of type I diabetes in Finland. Diabetologia 44 (Suppl 3):B37-B44, (2001).
• P Sevon, V Ollikainen, P Onkamo, HTT Toivonen, H Mannila, J Kere. Mining associations between genetic markers, phenotypes and covarions. Genetic epidemiology 21 Suppl. 1:S588-S593. (2001).
• MJ Sillanpää, R Kilpikari, S Ripatti, P Onkamo, P Uimari. Bayesian association mapping for quantitative traits ina mixture of two populations. Genetic Epidemiology 21 (Suppl 1):S692-S699. (2001).
• MJ Sillanpää, E Arjas. Statistical methods for the genetic mapping of complex traits. In "CSC Report on Scientific Computing 1999-2000". (S. Kotila and J. Haataja, Eds.), Scientific Computing Ltd.
• M Similä, E Arjas, M Mäkynen, M Hallikainen. Bayesian classification model for sea ice roughness from scatterometer data. IEEE Transactions on Geoscience and Remote Sensing 39:1586-1595. (2001).
• S Ripatti, J Pitkäniemi, MJ Sillanpää. Joint modeling of genetic association and population stratification using latent class models. Genetic Epidemiology 21 (suppl. 1):S409-S414. (2001).
• S Smolander, P Stenberg. A method for estimating light interception by a conifer shoot. Tree Physiology 21:1586-1595. (2001).
• P Uimari, MJ Sillanpää. Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genetic Epidemiology 21:224-242. (2001).

2000

• E Arjas, A Andreev. Predictive inference, causal reasoning, and model assessment in nonparametric Bayesian analysis: a case study. Lifetime Data Analysis 6:187-205. (2000).
• K Auranen, E Arjas, T Leino, AK Takala. Transmission of pneumococcal carriage in families: a latent Markov process model for binary longitudinal data. Journal of American Statistical Association 95:1044-1053. (2000).
• K Auranen, Back-calculating the age-specific incidence of recurrent subclinical haemophilus influenzae type b infection. Statistics in Medicine 19:281-296. (2000).
• WJ Edmunds, OG van Heijden, M Eerola, NJ Gay. Modelling rubella in Europe. Epidemiology and Infection 125:617-634. (2000).
• A Ekholm, JW McDonald, PWF Smith. Association models for a multivariate binary response. Biometrics 56:712-617. (2000).
• D Gasbarra, SR Karia. Analysis of competing risks by using Bayesian smoothing. Scandinavian Journal of Statistics 27:605-617. (2000).
• P Hurme, MJ Sillanpää, E Arjas, C Vogl, T Repo, O Savolainen. Adaptation in Scots pine is based on alleles with large effect on bud set date and frost hardiness. Genetics 156:1309-1322. (2000).
• T Härkänen, J Virtanen, E Arjas. Caries on permanent teeth: a nonparametric Bayesian analysis. Scandinavian Journal of Statistics 27:577-588. (2000).
• T Leino, K Auranen, PH Mäkelä, H Käyhty, AK Takala. Dynamics of natural immunity caused by subclinical infections, case study on Haemophilus influenzae type b (Hib). Epidemiology and Infection 125:583-591. (2000).
• J Pitkäniemi, P Onkamo, E Arjas, E Tuomilehto-Wolf, J Tuomilehto. Estimation of transmission probabilities in families ascertained trough a proband with variable age-at-onset disease: application to the HLA A, B and DR loci in Finnish families with type 1 diabetes. Human Heredity 50: 308-317. (2000).
• J Ranta, A Penttinen. Probabilistic small area risk assessment using gis-based data: a case study on Finnish childhood diabetes. Statistics in Medicine 19:2345-2359. (2000).
• HTT Toivonen, P Onkamo, K Vasko, V Ollikainen, P Sevon, H Mannila, M Herr, J Kere. Data mining applied to linkage disequilibrium mapping. American Journal of Human Genetics 67:133-145. (2000).

1999

• E Arjas. Probabilistic token causation: A Bayesian perspective. In "Applied Probability and Stochastic processes" (J.G. Shanthikumar, U. Sumita, Eds.) Kluwer, Dordrecht: 63-72. (1999).
• E Arjas. Contribution (invited) to the discussion on the paper "Inference tools for complex computer codes" by A. O'Hagan, M.C. Kennedy and J.E. Oakley. In "Bayesian Statistics 6", (J.M. Bernardo, J.O. Berger, A.P. Dawid, A.F.M. Smith, Eds.) Clarendon Press, Oxford: 520. (1999).
• K Auranen, M Eichner, H Käyhty, A K Takala, E Arjas. A hierarchical Bayesian model to predict the duration of immunity to Hib. Biometrics 55:168-174. (1999).
• J Heikkinen, E Arjas. Modeling a Poisson Forest in Variable Elevations: a Nonparametric Bayesian Approach. Biometrics 55:738-745. (1999).
• P Onkamo, S Väänänen, M Karvonen, J Tuomilehto. Worldwide increase in incidence of typeI diabetes - the analysis of the data on published incidence trends. Diabetologia 42:1395-1403. (1999).
• T Podar, P Onkamo, T Forsen, M Karvonen, E Tuomilehto-Wolf, J.Tuomilehto and the DiMe Study Group. Neonatal antropometric measurements and risk of childhood-onset Type I diabetes. Diabetes Care 22:2092-2093. (1999).
• J Ranta, PH Mäkelä, A Takala, E Arjas. Predicting the course of meningococcal disease outbreaks in closed subpopulations. Epidemiology and Infection 123:359-371. (1999).
• MJ Sillanpää, E Arjas. Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151:1605-1619. (1999).
• P Uimari, J Pitkäniemi, P Onkamo. A Bayesian MCMC approach to map disease genes in simulated GAW11 data. Genetic Epidemiology 17:S743-S748. (1999).

1998

• E Arjas. The real time approach. Entry, Encyclopedia in Biostatistics, (P. Armitage, T. Colton, Eds.), Wiley: 3737-3738. (1998).
• A Andreev, E Arjas. Acute middle ear infection in small children: a Bayesian analysis using multiple time scales. Lifetime Data Analysis 4 121-137. (1998).
• J Heikkinen, E Arjas. Nonparametric Bayesian estimation of a spatial Poisson intensity. Scandinavian Journal of Statistics 25:435-450. (1998).
• SR Karia, J Toivonen, E Arjas. Analysis of contraceptive failure data in IUD studies: modern competing risks approach. Contraception 58:361-374. (1998).
• L Liu, E Arjas. A Bayesian model for fatigue crack growth. In "Practical Nonparametric and Semiparametric Bayesian Statistics", (D. Dey, P. Müller, D. Sinha, Eds.) Springer, New York: 339-353. (1998).
• MJ Sillanpää, E Arjas. Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148:1373-1388. (1998).
• P Stenberg, H Smolander, D Sprugel, S Smolander. Shoot structure, light interception and distribution of nitrogen in an Abies amabilis canopy. Tree Physiology 18:759-767. (1998).
• P Uimari, JP Gibson. The value of crossbreeding infromation in selection of poultry under a dominance model. Animal Science 66:519-528. (1998).
• M Virtala, S Kuikka, E Arjas. Stochastic virtual population analysis. ICES Journal of Marine Sciences 55:892-904. (1998).
• Q Zhang, D Boichard, C Hoeschele, A Ernst, B Eggen, M Murkve, L Pfister-Genskov, A Witte, FE Grignola, P Uimari, G Thaller, MD Bishop. Mapping quantitative trait loci for milk production and health of dairy cattle in a large, outbred pedigree. Genetics 149:1959-1573. (1998).

1997

• E Arjas, D Gasbarra. On prequential model assessment in life history analysis. Biometrika 84:505-522. (1997).
• E Arjas, J Heikkinen. An algorithm for nonparametric Bayesian estimation of a Poisson intensity. Computational Statistics 12:385-402. (1997).
• E Arjas, L Liu, N Maglaperidze. Prediction of growth: a hierarchical Bayesian approach. Biometrical Journal 39:741-759. (1997).
• I Hoeschele, P Uimari, F E Grignola, Q Zhang, KM Gage. Advances in statistical methods to map quantitative trait loci in outbred populations. Genetics 147:1445-1457. (1997).
• H Kuittinen, M Sillanpää, O Savolainen. Genetic basis of adaptation: flowering time in Arabidopsis thaliana. Theoretical and Applied Genetics 95:573-583. (1997).
• P Uimari, I Hoeschele. Mapping linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo Algorithms. Genetics 146:735-743. (1997).
• P Uimari, SJ Kemp, J CM Dekkers, AJ Teale, BW Kennedy. Sensitivity of segregation analysis to data structure and transformation: a case study of trypanotolerance in mice. Heredity 78:424-432.(1997).