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Last modified by varvio@helsinki_fi on 2024/02/14 06:57

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 learningas 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

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

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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

 

 

 

 





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