Thesis defended in the Departement of Bioinformatics
PhD thesis
Mikk Puustusmaa - On the origin of papillomavirus proteins (Supervisors: Aare Abroi and M. Remm), 2019
Märt Roosaare - K-mer based methods for the identification of bacteria and plasmids (Supervisor: M. Remm), 2018
Priit Palta - Computational methods for DNA copy number detection. (Supervisor: M. Remm), 2015
Silja Laht - Classification and identification of conopeptides using profile hidden Markov models and position-specific scoring matrices. (Supervisor: M. Remm), 2015
Lauris Kaplinski - The application of oligonucleotidehybridization model for PCR and microarray optimization. (Supervisor: M.Remm) 2013
Tõnu Margus - Distribution and phylogeny of the bacterial translational GTPases and the Mqsr/YgiT regulatory system. (Supervisors: Tanel Tenson and Maido Remm), 2013
Triinu Kõressaar – Improvement of PCR primer design for detection of prokaryotic species. (Supervisor M.Remm) 2012
Age Tats – Sequence motifs influencing the efficiency of translation. (Supervisor: M.Remm and T.Tenson) 2009
Reidar Andreson – Methods and software for predicting PCR failure rate in large genomes. (Supervisor M.Remm) 2008
Reedik Mägi – The linkage disequilibrium and the selection of genetic markers for association studies in European populations. (Supervisor M.Remm) 2007
Master thesis (3+2)
Siimo Kangruoja - Detection of modified organisms from raw sequencing data using k-mers of specific length. (Supervisor: Kairi Raime), 2020
Aneth Lvovs - Detecting endogenous viral elements with parametric methods by example of endogenous bornavirus like elements. Supervisors: Aare Abroi, Heleri Kirsip, 2019
Erki Aun - K-mer-based detection of antibiotic resistance markers in bacteria Pseudomonas aeruginosa. (Supervisor: Age Brauer), 2017
Kaarel Koitne - Choosing a set of stable k-mers for Non-Invasive Prenatal Testing (Supervisor: L. Kaplinski), 2016
Mihkel Vaher - Identifying bacterial strains from unassembled sequencing reads using fixed- length oligomers. (Supervisor: M. Roosaare), 2016
Maarja Lepamets – Integration of PCR primer quality prediction into Primer3 software. (Supervisor: L.Kaplinski), 2015
Fanny-Dhelia Pajuste - A novel method for detecting SNV genotypes from personal genome sequencing data (Supervisor: M.Remm), 2015
Kairi Raime - Development of methodology for taxon-specific primer design and its application for detection of DNA of allergenic plant. (Supervisors: T. Kõressaar and M.Remm), 2015
Mikk Puustusmaa - Detection of E8 protein coding sequence in papillomaviruses in silico. (Supervisors: Aare Abroi, Maido Remm), 2014
Märt Roosaare - Protein domain analysis in the cone snail Conus consors (Supervisor: M. Remm), 2014
Viktorija Kukuškina – Predicting gene number and structure of sea snail Conus Consors with bioinformatic methods. (Supervisor: Lauris Kaplinski), 2013
Andres Veidenberg - DNA Copy Number Assessment and Heritage Analysis of Copy Number Variations from Genotyping Data. (Supervisor: P. Palta), 2009
Master thesis (4+2)
Taavi Võsumaa - Development of a methodology for predicting the quality of resequencing probes. (Supervisor: M. Remm) 2008
Rainis Venta – Uue inimese Sp perekonna geeni (LOC93349) iseloomustamine ja Sp ning AIRE geeniperekonna fülogeneetiline analüüs. (Supervisors: P. Peterson & T. Margus) 2008
Priit Palta – Statistical methods for DNA copy-number detection. (Supervisor: M. Remm) 2007
Kessy Abarenkov – Seeneliikide määramine DNA triipkoodi meetodil ja tulemuste rakendamine biogeograafilises uurimustöös. (Supervisors: U. Kõljalg & M. Remm) 2006
Age Tats – Nukleotiidide, koodonite ja aminohapete sagedused kõrge ekspressioonitasemega geenides. (Supervisor: M. Remm) 2006
Triinu Kõressaar – Polümeraasi ahelreaktsiooni modelleerimine DNA amplifitseerimiseks bakteriaalsetest genoomidest. (Supervisor: M. Remm) 2006
Reidar Andreson – Erinevate in silico meetodite võrdlus PCR praimerite kvaliteedi parandamiseks. (Supervisor: M. Remm) 2002
Bachelor thesis (3+2)
Andrea Jõesaar - Finding specific k-mers to identify animal species which cause food allergy. Supervisor: Reidar Andreson, 2020.
Kristina Kasvandik - K-mer based methods and their usage for masking repeat sequences. Supervisor: Reidar Andreson, 2019.
Carmen Oroperv - Evaluation of the parameters affecting sequencing coverage. Supervisor: Fanny-Dhelia Pajuste, 2019.
Marlen Timm - Calling known protein sequence altering SNVs and genotypes from human exome sequencing data by using k-mers. Supervisor: Age Brauer, 2018.
Sylvia Krupp - Human genome size evaluation with k-mer method. Supervisor: Tarmo Puurand, 2018.
Brigitta-Robin Raudne - Various pipeline analysis for virus detection. Supervisors: M.Puustusmaa and M.Vaher, 2018.
Karl Erss - Estimation of telomere length from next generation sequencing data. Supervisor: T.Puurand, 2017.
Anna Smertina - Annotation of single nucleotide variants in human genome: an overview and annotation of artefact SNVs from NGS. Supervisor: U.Gerst Talas, 2016
Madis Sarapuu - Determing the number of tandem repeats in the human Per3 gene from next generation sequencing data. Supervisors: T. Puurand, M.Teder-Laving, 2016
Triin Edula - The comparison of scaffolding programs using previously assembled genome sequences. Supervisor: Reidar Andreson, 2014
Maarja Lepamets - Oligomer-based bioinformatic methods for identifying bacteria from sequencing reads. Supervisor: Lauris Kaplinski, 2014
Maarja Lepamets - Statistical analysis of Conus consors’ conotoxin genes flanking regions. Supervisors: M. Remm, M. Möls, 2013
Kairit Kolsar – Sequencing angiosperms and whole genome duplications in plant evolution. Supervisor: T. Puurand, 2011
Signe Kalamees – Searching for the male infertility genetic markers. Supervisor: T. Puurand, 2007
Priit Tomson – DNA mikrokiipidel kasutatavate oligote kvaliteeti mõjutavad parameetrid ja meetodid nende disainiks. Supervisor: R. Anderson, 2005
Heiko Kase – Marker selection methods for association studies. Supervisor: R.Mägi, 2005
Taavi Võsumaa – Mikroorganismide identifitseerimine keskkonaproovides nukleiinhapete hübridiseerimise teel mikrokiipidel. Supervisor M. Remm, 2004
Bachelor thesis (4+2)
Aleksander Sudakov - Implementation of genomic signature method for detection of horizontal gene transfer. (Supervisor T. Margus) 2006.a.
Mikk Eelmets – Geenide ja eksonite piirie ja haplotüübi bloki piiride korrelatsioon. (Supervisor M. Remm) 2006.a.
Meelis Olev – Grouping efficiency of different PCR primers. (Supervisor L. Kaplinski) 2005.a.
Helle Uibokand – Automated PCR primer design for bacterial genes – genome based approach. (Supervisor T. Margus) 2005.a.
Priit Palta – Hübridiseerimisproovide disaini metoodika geeni koopiaarvu määramiseks. (Supervisor M. Remm) 2005.a.
Kadi-Liina Kuusik – Automaatne PCR-i praimerite disain kõikidele inimese genoomi SNP-dele. (Supervisor M. Remm) 2004.a.
Age Tats – Valkude translatsiooni mõjutavate mRNA motiivide bioinformaatiline analüüs. (Supervisors T. Tenson & M. Remm) 2004.a.
Kessy Abarenkov – Liigispetsiifilised oligonukleotiidid resupinaatsete lehternahkiseliste ITS järjestuste põhjal. (Supervisors U. Kõljalg & M.Remm) 2004.a.
Triinu Kõressaar – Praimerite automaatne disain eukarüootide geenidele ja veebiinfosüsteemi loomine automaatseks online praimerite kättesaamiseks. (Supervisor M. Remm) 2004.a.