Thesis archive

​A printed copy of each thesis is available in Quantum Library.
The abstract of each thesis can be read by clicking the author's name.

Deuja Sangam: In silico metabolic modelling of Saccharomyces cerevisiae for the overproduction of succinate using OptKnock and OptGene
Hanif Tanzeela: Annotation of Gyrodactylus salaris transcriptome
Imran Mohsin: Structure determination and analysis of a Beta-Glucosidase from Chaetomium thremophilum
Legehar Ashenafi: ADMET and adverse effects predictive modeling based on FDA-approved drugs Data
Mehryary Farrokh: Optimization and Applications of Large-Scale Biomedical Event Networks
Rauniyar Akash: Computational inference of functional relationships from multiple genomes - Drosophila carbonic anhydrases
Seid Amin: Analysis of Alpha CA Genes in Early Vertebrates and High-Invertebrates
Selvarajan Ilakya: Human Ezrin: Prediction of the 3D structure and interactions with mTOR
Seymen Nogayhan: Prediction of Phosphorylation Sites from Protein Sequences
Tamirat Mahlet Zerihun: Probing MST1 Kinase Sequence ans Structure for Rational Drug Discovery
Välikangas Tommi: Comparison of five popular normalization methods using a spike-in proteomics data set
Yamada Keith: De novo transcriptome assembly and annotation of the isopod Idotea balthica
Yao Tianran: Molecular modeling studies of Escherichia coli MurA: towards novel Mur enzyme inhibitors against resistant bacterial strains

Ahmad Freed: Bioinformatic analysis of Double Restriction Associated DNA (dRAD) sequencing of Eurasian perch using Ion Torrent sequencing platform
Alfredo Santos Rafael: Biclustering analysis on longitudinal microarray expression data
Ali Fawad: Structural and Mechanistic Studies of Phosphoserine Aminotransferase
Ibssa Nebiat: Implementation of Quantitative Reaction-based Model Refinement
Mahmoudian Mehrad: Prediction Model and Feature Selection for Survival Analysis on Lung Adenocarcinoma
Sanghvi Chamundeeswari:  Adopting the Vaadin Java framework to rebuild VTT's Web Interfaces and Database Applications
Tiwari Avlokita: Phylogenetic Analysis of Avidins and Expression of Novel Avidins from Lactrodectus hesperus and Hoeflea phototrophica

Chakroborty Deepankar: Gene expression analysis in cancer microarray datasets, investigating the role of an Embryonic Stem Cell Factor in prognosis
Dandapani Hariharan: Insights into the repair mechanism of iron-sulfur clusters in Escherichia coli
Dimitriou Polytimi: Polyvertaa: A Method for Multiple Alignment of Protein Structures
Koskinen Satu: Genome Assembly and Genomic Analysis of Coxsackievirus A6 Strain Isolated During HFMD Outbreak with Onychomadesis in Finland 2008
Luo Zheyi: The Creation and Annotation of Mention Level Gene Normalization Lists and the Challenges of the Work
Mishra Mrinal: Analysis of the Morphological Heterogeneity and Dynamics of Cancer Cells in Organotypic 3D Culture
Poudel Nirmal: Crystal structure determination and functional prediction of AtuE
Ralph Eliza: Variant calling from next generation sequencing data and information management
Schukov Hannu-Pekka: rAMIDA: R-Based Automated Cell Morphology Analysis
Seyednasrollah Fatemeh: Comparison of tools to detect differential expression in RNA-seq studies
Shokry Hussein: Analysis of the Moose Microbiome

Afzal Saira: Structural and functional studies of Integrin α2β1I-domain
Battula Pradeep: Crystal Structure Determination of Phosphoserine Aminotransferase from Bacillus alcalophilus in the Free and Phosphoserine-Bound Forms
Carvalho Leonor: Slr0006 and Related Proteins: Phylogeny, Structure and Function
Ezu Shedrack Uzochukwu: Phylogenetic inference of prokaryotic organisms using RNA polymerase, Ribosomal RNA and Elongation factor G (ef-g) as genetic markers
Heininen-Brown Mari: Homology modeling of a structural complex including a novel human embryonic stem cell protein L1TD1
Mishra Pashupati: Biclustering of human gut microbial data
Mohammadi Omid: Study of complex structure and interaction of EibD with IgG's FC region
Murukesan Gayathri: Microarray analysis of the transcriptome of Tobacco Mosaic Virus (TMV) - infected Tobacco plants
Sazzad Mohammed Abdullah Al: Identification of Genomic Structure Variation of Synechocystis sp. pcc 6803 Mutants through Next Generation Sequencing
Solis Mezarino Victor: Identification of nuclear envelope proteins by differential abundance analysis and prediction of their translocation mechanisms to the inner nuclear membrane
Thapa Keshav Kumar: The pseudouridine glycosidase enzyme family: Docking studies, comparative phylogenetic analysis and genome mining

Agrawal Nitin:  Folding of Aquaporin 1: Simulating Helix 3 insertion
Chand Thaman: A database approach to proteomics experimental data
Ghimire Bishwa Raj: Parallelization of two-locus epistasis detection in a High Performance Computing (HPC) system
Hasan Shihab: CEPiNS: Conserved Exon Prediction in Novel Species
Isojärvi Janne: Exploration of the chemical space occupied by a unique library of natural and naturally derived compounds with a focus on the investigation of the space occupied by butyrylcholinesterase inhibitors
Kaewphan Suwisa: Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP(H) Metabolism in E. coli with Event Extraction
Kinaret Pia: Astman, allergisen nuhan ja ei-allergisen nuhan proteomin muutosten karakterisointi ylähengitysteistä
Mekuria Gashaw: Estimation of Missing Values in Genetic Interaction Data
Weldenegodguad Melak: A computational meta-analysis search for metabolic components of Alkane biosynthesis
Yadav Avinash: PepRecon: A software tool for visualization and evaluation ofliquid chromatography-mass spectrometry data

Muleta Abdi: Crystal Structure Determination of a Tau Class Glutathione Transferase Isoenzyme from Glycine max
Peltonen Sanna: Regulatory networks of NADP(H)-metabolism
Pokharel Kisun: 3D modeling and structural analysis of GT4 family Yersinia enterocolitica 0:3 Wbc proteins
Saeidi Firouz: Investigation, Extension and Implementation of the Proteios system
Subedi Bishwa Prakash:  Comparative structural studies of wild-type PhaZ7 and Tyr105 mutants
Sundström Robin: Structural studies of class 1 non-symbiotic hemoglobin in Populus tremula x tremuloides

Bhattachariya Anirban: Screening platform for butyrylcholinesterase inhibitors: from in vitro data generation to in silico quantative data structure-activity analysis
Dawoudi Mohammad Reza: DNA Modelization in Biomedical Image Matching
Okser Sebastian: A machine learning approach to determining carotid atherosclerosis predisposition based on genotypes
Syed Muhammad Fahad: Matching of Proteomics and Microarray Data

Hammais Anna: Evaluating the combination of ChIP-chip data and promoter sequence analysis for the detection of binding sites of the human transcription factor ATF-2
Heinonen Tiia: Functional analysis tools for microarray gene expression data
Mpindi John Patrick: Gene Tissue outlier Index (GTI): a novel method for differential gene expression analysis
Suni Veronika: Towards a Synthetic Spectral Library of Phosphopeptides

Chouhan Bhanupratap Singh: Bioinformatics analysis of PhaZ7
Heimonen Juho: Evaluation of biological relationships as information extraction target through complex-to-binary mapping
Terho Perttu: Moniparametrisen virtaussytometriadatan analyysimenetelmän kehitys ja käytettävyysarviointi