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Biostatistics and bioinformatics
Biostatistics and bioinformatics constitute quantitative - predominantly statistical - methodologies for the life sciences. Research focuses on modelling and analysis of biological phenomena and processes, covering a wide spectrum of topics ranging from problems at the molecular level to populations, environments and evolution. Research addresses questions in modelling transcriptional regulation, interface of probabilistic modelling and bio- and environmental sciences, environmental risks, genome-wide association mapping of complex diseases, population genetics, evolution and phylogenetics. Variety of approaches are used, most importantly probabilistic and Bayesian machine learning, as well as computational systems biology. A characteristic feature of the research is a very strong emphasis on collaborative research, carried out jointly with staff members of the sectorial research institutions and other Faculties, especially the Faculty of medicine, the Faculty of biological and environmental sciences, and Aalto University.
People
professor (emeritus) Elja Arjas
professor (part time) Jukka Corander
assistant professor (part time) Antti Honkela
assistant professor (part time) Matti Pirinen
assistant professor Jarno Vanhatalo
university lecturer Sirkka-Liisa Varvio
Studies and teaching
Starting Fall 2017, biostatistics and bioinformatics will be one study strack in the new Life Science Informatics Master´s Programme
Content below not upadated
Master theses
TBA reasearch + thesis collaboration, theses in most cases parts of research projects
| Topic | Faculty / Institute where the thesis has been done and / or research data has been received (translations missing) | Responsible teacher / instructor in the Department of mathematics and statistics |
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1.3.2016 | Ikä-periodi-kohortti-ilmaantuvuusmallin toteutus rinta-ja kivessyövälle upotetulla approksimatiivisella bayesiläisellä menetelmällä | Syöpärekisteri | Corander Jukka |
1.12.2015 | Correcting the Effects of Missing Data in Helsinki Psychotherapy Study using Multiple Imputation | Terveyden ja hyvinvoinnin laitos | Varvio Sirkka-Liisa |
1.12.2015 | U12-type introns and the minor spliceosome in dog | Eläinlääketieteellinen tdk | Varvio Sirkka-Liisa |
3.11.2015 | Linear mixed models for estimating heritability and testing genetic association in family data | FIMM, Lääketieteellinen tdk | Varvio Sirkka-Liisa |
13.10.2015 | Discovering disease trajectories from the Finnish Hospital Discharge Register with the MCL algorithm | FIMM, Lääketieteellinen tdk | Varvio Sirkka-Liisa |
2.6.2015 | Modeling for Mainland-island Metapopulation of Common Shrews (Sore araneus) in Eastern Finland | Biotieteiden laitos, Bio- ja ympäristötieteellinen tdk | Corander Jukka |
14.4.2015 | A Comparison Between Some Discriminative And Generative Classifiers | - | Corander Jukka |
20.1.2015 | A Proteomic Study of Potyviral HC-Pro-interacting Host and Viral Proteins | Elintarvike- ja ympäristötieteiden laitos, Maatalous-metsätieteellinen tdk | Varvio Sirkka-Liisa |
14.10.2014 | Comparative Analysis of Cancer Stem Cell Gene Expressions with respect to Intratumor Heterogenity | - | Varvio Sirkka-Liisa, Corander Jukka |
6.5.2014 | iPRANK: iterative alignment with PRANK | Biotekniikan instituutti | Varvio Sirkka-Liisa |
28.1.2014 | Gene Expression Analysis of Monozygotic Twin Pairs Discordant for Body Mass Index | Kliininen laitos, Lääketieteellinen tdk | Varvio Sirkka-Liisa |
27.5.2013 | Analysing exome variant data for identifying causative SNVs of infantile mitochondrial disorders | Molekyylineurologian tutkimusohjelma, Lääketieteellinen tdk | Varvio, Sirkka-Liisa |
7.5.2013 | A comparison of methods for haplotype inference | - | Koistinen Petri |
5.3.2013 | Bayesian confimatory factor analysis for detection of differential gene expression | Genomibiologian tutkimusohjelma, Lääketieteellinen tdk | Corander Jukka, Koistinen Petri |
27.11.2012 | Correlation analysis for evalution of functional annotation methods of proteins | Biotekniikan instituutti | Corander Jukka |
6.11.2012 | Calculating conservation and predicting hENT1 structure using the amino acid sequence | Farmasian tdk | Varvio Sirkka-Liisa |
9.10.2012 | Linear models with regularization | - | Möttönen Jyrki, Sillanpää Mikko |
18.9.2012 | De-novo assembly and finishing of the genome of neuro-toxin (anatoxin-a) producing cyanobacterium, Anabaena sp. strain 37 | Elintarvike- ja ympäristötieteiden laitos, Maatalous-metsätieteellinen tdk | Varvio Sirkka-Liisa |
14.8.2012 | Differential Methylation Analysis of Monozygotic Twin Pairs Discordant for Body Mass Index | Hjelt-instituutti, Lääketieteellinen tdk | Varvio Sirkka-Liisa |
29.5.2012 | Proteochemometric Modeling of Kinase - Inhibitor Interactions using Field-based Protein Descriptions | ORION / Farmasian tdk | Corander Jukka |
29.5.2012 | Genome-based repositioning of commonly used drugs integrating multi-layer information | Lääketieteellinen tdk | Corander Jukka |
15.5.2012 | Phylogenic Profiling of Streptomyces Species Associated with Potato Scab | Maataloustieteiden laitos, Maatalous-metsätieteellinen tdk | Varvio Sirkka-Liisa |
29.11.2011 | Measurements of Relative Hazards Without Active Follow-up of a Cohort - Applications to Vaccine Efficacy | - | Koistinen Petri, Auranen Kari |
29.11.2011 | Bayesian Clustering of DNA Sequences Using Markov Chains and a Partition Model | - | Corander Jukka, Koistinen Petri |
29.11.2011 | Spatial Interpolation of Atmospheric Remote Sensing Observations | Ilmatieteen laitos | Corander Jukka |
11.10.2011 | Stochastic genotype imputation in Finnish population based cohorts | FIMM, Lääketieteellinen tdk | Corander Jukka |
6.9.2011 | Apple cultivar identification using automated shape analysis | Maataloustieteiden laitos, Maatalous-metsätieteellinen tdk | Koistinen Petri |
6.9.2011 | Case-control haplotype inference for HLA-genes in coronar artery disease | Haartman-instituutti, Lääketieteellinen tdk | Varvio Sirkka-Liisa |
30.5.2011 | Analysing the Course of the A(H1N1) Influenza Epidemic of 2009 in Finland | THL | Varvio Sirkka-Liisa, Koistinen Petri |
30.5.2011 | Large-scale Genotyping Pipe-line for Non-model organisms | Biotieteiden laitos, Bio- ja ympäristötieteellinen tdk | Varvio Sirkka-Liisa |
25.5.2011 | Poisson-malli ilmaantuvuudelle. Altistus Tsernobylin radioaktiivisille päästöille ja kilpirauhassyövän ilmaantuvuus Suomessa | STUK | Corander Jukka, Koistinen Petri |
5.4.2011 | Bayesian association analysis using RJMCMC applied to drug responses | ORION | Corander Jukka, Varvio Sirkka-Liisa |
5.4.2011 | Computational Methods for Pathway Analysis of Genome-Wide Association Study Results | FIMM, Lääketieteellinen tdk | Sillanpää Mikko, Varvio Sirkka-Liisa |
1.3.2011 | Approximating Posterior Distrubutions over Dendrogram Spaces with an Application to Population Genetics | - | Corander Jukka, Koistinen Petri |
1.2.2011 | Finding Enriched Gene Sets by Confirmatory Factor Analysis | - | Corander Jukka, Varvio Sirkka-Liisa |
7.12.2010 | Genetic risk prediction of coronary heart disease. Prospective study of Finnish and Swedish cohorts | FIMM, Lääketieteellinen tdk | Varvio Sirkka-Liisa |
8.6.2010 | Shrinkage variable selection methods for linear regression models with application to QTL mapping | - | Sillanpää Mikko, Varvio Sirkka-Liisa |
4.5.2010 | Kampylobakteeritartuntojen lähteiden selvittäminen ja mallintaminen | EVIRA | Auranen Kari, Corander Jukka |
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Biometrian ja bioinformatiikan gradut
Many theses have been done in collaboration with research groups in Viikki and Meilahti campuses and sectorial research institutions (EVIRA, METLA, THL), as indicated in brackets:
Gradu tehdään usein tutkimusryhmässä Viikin tai Meilahden kampuksella, tai THL:ssä, EVIRA:ssa, METLA:ssa.
- Tuontieläinten BSE-riskinarviointiin kehitetty tilastollinen Bayes-malli (2009, EVIRA)
- Markov Random Fields and Spatial Smoothing in Improving of Forest Inventory Estimates (2010, METLA)
- Luokitusmenetelmien vertailua maastotyypin luokituksessa satelliittikuvaperusteisesti (2008, METLA)
- Lineaarisen rakenteellisen keskiarvo-mallin laajennus useaan käsittelyryhmään ja soveltaminen kliiniseen tutkimusaineistoon (2008, KTL)
- Ekologisen vasteen mallit (2008, METLA)
- Case definition of pneumococcal pneumonia: a latent class analysis approach (2007, KTL)
- Tilastollinen analyysi masennuslääkkeiden käytön yleisyydelle ja hoitosuosituksen toteutumiselle (KTL)
- Examining equity in access to health care using register data - Pathways to coronary revascularisations in Finland 1995-1998 (2007, KTL)
- Bayesläiset menetelmät diskriminatiivisessa ja generatiivisessa luokittelussa (2007)
- Spatiaaliset pisteprosessit levinneisyysmuutosten tarkastelussa (2005)
- Sarjatuhopolttajan asuinpaikan ennustaminen etäisyyskäyttäytymistiedon perusteella (2005)
- Verivalmisteiden hepatiitti C-tartuntariski (2005)
Courses:
57795 Biometry and bioinformatics I, 2-5 cr
57796 Biometry and bioinformatics II, 5-10 cr
57797 Biometry and bioinformatics III, 5-10 cr
57744 Bayesian theory with applications, 5 cr
57733 Computational statistics, 8 cr
57741 Event-history analysis, 6-8 cr
57748 Genetic analysis and molecular evolution, 4-6 cr
57756 Genome-wide association studies, GWAS-minicourse, 2 cr
57742 Hierarchical models, 6-8 cr
57746 Longitudinal data-analysis, 5-10 cr
57059 Markovian modelling and Bayesian learning, 5 cr
57734 Modelling inheritance in pedigrees and populations, 4-6 cr
57780 Molecular genetics reading group, 2 cr
57740 Nonparametric statistics, 6 cr
57729 Phylogeny inference and data analysis, 4-10 cr
57729 Phylogeny inference, seminar, 3-5 cr
57730 Sequence evolution from molecules to genomes, 4-6 cr
57710 Software tools for statisticians, 5-10 cr
57734 Statistical genetics, 4-10 cr
57755 Statistical methods in gene mapping, 4-6 cr
57739 Statistical methods in medicine and epidemiology, 5-10 cr
57745 WinBUGS/OpenBUGS with applications, 5-10 cr