Rapid technological advances are providing unprecedented insights in the biologicalsciences, with massive amounts of data generated on genomic and protein sequences.These data continue to grow exponentially, and they are extremely valuable for com-putational tools where the effect of genomic variants on human health is predicted.State of the art tools in this field give varying results and only tend to agree in thecase of single variants that are strongly correlated to disease. The aim of this workis to increase the reliability of these methods, as well as our understanding of theunderlying biological mechanisms that lead to disease. We first developed machinelearning (ML) based structural bioinformatics predictors that are able to predictmolecular features of proteins from the sequence alone. We then used these tools forin silico analysis of the molecular effects of known variants on the affected proteins,and integrated these data with other sources heterogenous sources of information,such as the essentiality of a gene, that put the variants into their broader biologicalcontext. With this information we created DEOGEN, a novel predictor in this field,which is able to deal with the two most common forms of genomic variation, namelySingle Nucleotide Variants (SNVs) and short Insertions and DELetions (INDELs).DEOGEN performs at least on par with other state of the art methods in this fieldon different datasets. The method was then extended with additional contextualdata and is now available as DEOGEN2 via a web server, which visualizes the pre-dicted results for all variants in most human proteins through an interactive interfacetargeted to both bioinformaticians and clinicians. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Despite active development during past years, the task of sequencing a genome still remains a challenge. Our current technologies are not able to read the whole genome in one piece. Instead, we shatter the target genome into a large amounts of small pieces that are then sequenced separately. The process of assembling these small pieces together, in order to obtain sequence of the whole genome, is painful and rsource-consuming. Multiple algorithms to solve the assembly problem were developed. This thesis presents yet another assembly algorithm, based on the usage of de Bruijn graphs, and focusing on sequencing short genome regions. The algorithm is compared to well-known solutions in the field. 1

Abstract Stickler and Marshall syndromes are genetic disorders both inherited in an autosomal dominant manner. The genotype-phenotype correlation was performed in ten Stickler/Marshall syndrome patients with mutations in the COL11A1 gene. Four patients had a phenotype classified as Marshall syndrome based on early-onset severe hearing loss and characteristic facial dysmorphism. A splice site mutation in intron 50 of COL11A1 was found in these patients, while the remaining six patients had an overlapping Marshall-Stickler phenotype with a mutation elsewhere in the gene. These results indicate exon 50 as a hot spot for splice site mutations leading to a phenotype of Marshall syndrome rather than Stickler syndrome. Collagen II (COL2A1) precursor mRNA undergoes alternative splicing resulting in two different isoforms, IIA including exon 2 and IIB excluding exon 2. Recent evidence indicates that premature termination codon mutations in exon 2 cause Stickler syndrome with no or minimal extraocular manifestations. Two mutations were observed in this study: Cys64Stop, and a novel structural mutation, Cys57Tyr. Results from the COL2A1 mini-gene studies suggested that both mutations altered positive cis elements for splicing resulting in a lower IIA:IIB ratio. The results further emphasize the importance of exon 2 in the development and normal function of the eye. In addition, patients displaying eye phenotypes in the absence of extraocular manifestations should be analyzed first for exon 2 mutations. Linkage analysis identified a new locus for autosomal recessive nonsyndromic hearing loss (DFNB32) on chromosome 1p13.3-22.1 in a Tunisian family with congenital profound autosomal recessive deafness. The COL11A1 gene is located in this region and was analyzed as a candidate gene. No disease causing sequence variation was observed. The analysis of 85 English and 40 Finnish subjects with high myopia resulted in the identification 23 sequence variations in the SLRP genes LUM, FMOD, PRELP, and OPTC. The two intronic variations and seven amino acid changes, one synonymous and six non-synonymous, were not found in the 308 controls analyzed. Five changes were detected in opticin, and all but one were shown to co-segregate with high myopia in families with incomplete penetrance. The results suggested that sequence variations in the SLRP genes expressed in the eye are genetic risk factors underlying the pathogenesis of high myopia.

La dégénérescence frontotemporale est une pathologie rare, plaçant au premier plan les désordres comportementaux. Après analyse des troubles psycho-comportementaux et de leurs méthodes actuelles d’évaluation, nous avons élaboré et validé un nouvel outil, appelé DAPHNE (pour Desinhibition-Apathie-Persévérations-Hyeroralité-Négligence-Empathie) spécialement conçu pour dépister et quantifier la sévérité et la progression des troubles du comportement dans la variante frontale de dégénérescence frontotemporale (vfDFT), en pratique clinique courante. Cette validation a été effectuée de manière prospective, auprès d’une population de patients présentant une vfDFT suivis pendant 2 ans et également d’une population contrôle afin d’établir sa spécificité. DAPHNE, adaptée des critères révisés de vfDFT, présente d’excellentes caractéristiques psychométriques. Explorant six domaines et dix symptômes comportementaux, avec un système de cotation innovant en 5 points, elle permet à la fois le screening mais également une appréciation quantitative et une aide au diagnostic. Parallèlement à cela, nous avons étudié les liens entre les différents troubles psycho-comportementaux, les fonctions cognitives proprement dites et la cognition sociale chez les patients vfDFT. Plus particulièrement, nous nous sommes intéressés à l’évaluation des troubles émotionnels des patients DFT. À l’aide d’une tâche originale TABEAU, portant sur l’étude de la sensibilité esthétique des patients DFT, nous avons observé des liens entre émotion et troubles du comportement (trouble de l’identification de certaines émotions et émoussement affectif etc.). Si le jugement esthétique est préservé en apparence, le patient est en difficulté sur le plan des processus cognitifs du fait de difficultés d’abstraction et en difficulté sur le plan des processus émotionnels. Ce travail montre quel spectateur est le patient DFT vis à vis de l’art et vient compléter les données de la littérature qui portaient jusque-là sur l’expression artistique. Ce type d’approche cognitive permet donc d’avancer dans la compréhension des interactions entre émotions et troubles du comportement, qui font toute la singularité de cette maladie. Pris dans leur ensemble, nos résultats soulignent l’intérêt majeur de l’étude fine du comportement en pratique quotidienne. À l’ère des biomarqueurs, la clinique garde une place de choix pour le diagnostic et la compréhension des maladies neurodégénératives. / Frontotemporal degeneration is a rare disease with early decline in social behavior and personal conduct. We have first presented behavioral disorders and their current evaluation methods. We developed and validated then a new tool, named DAPHNE (Disinhibition-Apathy-Perseverations-Hyerorality-Neglect-Empathy) specially designed to detect and quantify the severity and the progression of behavioral disorders in the behavioral variant of frontotemporal dementia (bvFTD), in clinical practice. This validation was performed prospectively, in patients with bvFTD with a follow-up of 2 years and also in AD, progressive supranuclear palsy and bipolar patients with cognitive disorders, in order to establish the specificity of this scale. DAPHNE, adapted from revised criteria of bvFTD, has excellent psychometric characteristics. Exploring six areas and ten behavioral symptoms, with an innovative scoring system in 5 points, it enables both the screening but also a quantitative assessment and a diagnostic support.As a second part of our works, we studied the links between the various psycho-behavioral disorders, cognitive functions and social cognition in bvFTD patients. Specifically, we focused on emotion assessment of FTD patients. Using an original task entitled TABEAU, based on the study of aesthetic sensibility of FTD patients, we observed the links between emotions and behavior disorders (such as trouble identifying certain emotions or emotional blunting). The aesthetic judgment seemed preserved. But the patient is in trouble in terms of cognitive processes due to abstraction problems and difficulties with emotional processes. This work shows what type of viewer is the FTD patient in front of a piece of art. It adds to the literature data that were previously based only on artistic expression. This cognitive approach improves the understanding of interactions between emotions and behavior disorders which make the singularity of this disease.Taken together, our results highlight the major interest of the detailed assessment of behavior in daily practice. In biomarkers’ era, clinical practice remains central in diagnosing and understanding of neurodegenerative diseases.

The ability of Next-Generation Sequencing (NGS) to produce massive quantities of genomic data inexpensively has allowed to study the structure of viral populations from an infected host at an unprecedented resolution. As a result of a high rate of mutation and recombination events, an RNA virus exists as a heterogeneous "swarm". Virologists and computational epidemiologists are widely using NGS data to study viral populations. However, discerning rare variants is muddled by the presence of errors introduced by the sequencing technology. We develop and implement time- and cost-efficient strategy for NGS of multiple viral samples, and computational methods to analyze large quantities of NGS data and to handle sequencing errors. In particular, we present: (i) combinatorial pooling strategy for massive NGS of viral samples; (ii) kGEM and 2SNV — methods for viral population haplotyping; (iii) ShotMCF — a Multicommodity Flow (MCF) based method for frequency estimation of viral haplotypes; (iv) QUASIM — an agent-based simulator of viral evolution taking in account viral variants and immune response.

Adenovirus (Ad) is a widely studied DNA virus, but the nucleoprotein structure of the viral genome in the cell is poorly characterized. Our objective is to study Ad DNA-protein associations and how these affect the viral life cycle. Most of the viral DNA condensing protein, protein VII, is lost within a few hours of infection and this loss is independent of transcription. Cellular histones associate with the viral DNA after removal of protein VII, with a preferential deposition of H3.3. Micrococcal nuclease accessibility assays at 6 hpi showed laddering of the viral DNA, suggesting the genome is wrapped in physiologically spaced nucleosomes. Although viral DNA continues to associate with H3.3 at late times of infection, the overall level of association with histones is greatly reduced. Knockdown of the H3.3 chaperone HIRA had no effect on the viral life cycle suggesting that other H3.3 chaperones are involved. Our studies have begun to elucidate the nucleoprotein structure of Ad DNA in the infected cell nucleus.

Cílem práce byla analýza studentských bankovních účtů v České republice. Její součástí byl podrobný popis situace a následné srovnání studentských účtů přítomných na našem trhu. Vytvořil jsem srovnávací model, pomocí kterého jsem identifikoval nejlepší nabídku. Dále jsem provedl dotazníkové šetření majitelů studentských bankovních účtů. Výsledky jednotlivých odpovědí byly zobrazeny ve formě grafického přehledu i s uvedením případného ověření platnosti statistických hypotéz. Na základě takto získaných dat jsem vytvořil soubor doporučení pro marketing studentských bankovních účtů.

The theme of the graduation thesis is the process of public procurement in the state-established organization. Since the sphere of public procurement is very extensive the thesis focus on possibilities of use of multiple criteria decision making methods for the selection of the optimal offer. In addition to multicriterial decision making methods the thesis deals with preparative phase of the whole process especially with the statement of the evaluative criteria and determination of their weights. The thesis refers to the deficiencies of the process of public procurement that we can see in practice and tries to propose the possibilities how to avoid these deficiencies.

Cílem práce byla analýza studentských bankovních účtů v České republice. Její součástí byl podrobný popis situace a následné srovnání studentských účtů přítomných na našem trhu. Vytvořil jsem srovnávací model, pomocí kterého jsem identifikoval nejlepší nabídku. Dále jsem provedl dotazníkové šetření majitelů studentských bankovních účtů. Výsledky jednotlivých odpovědí byly zobrazeny ve formě grafického přehledu i s uvedením případného ověření platnosti statistických hypotéz. Na základě takto získaných dat jsem vytvořil soubor doporučení pro marketing studentských bankovních účtů.

The main goal of diploma thesis is the evaluation of the position of Všeobecná zdravotní pojišťovna in the system of czech health insurance companies by application of multiple criteria decision making methods. Health insurance companies are compared by provided benefits. Analysis is concentrated on three groups : the general public, women and men.