subject:(Differential Exon Usage DEU )

Brno University of Technology

1. Abo Khayal, Layal. Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis.

Degree: 2019, Brno University of Technology

URL: http://hdl.handle.net/11012/70129

► The high-throughputs sequence technologies produce a massive amount of data, that can reveal new genes, identify splice variants, and quantify gene expression genome-wide. However, the… (more)

Subjects/Keywords: RNA-Seq; diferenciální genová exprese (DGE); alternativní splicing; diferenciální použití exonů (DEU); dlouhá nekódující RNA (lncRNA); RNA-Seq; Differential Gene Expression (DGE); Alternative splicing; Differential Exon Usage (DEU); long non-coding RNA (lncRNA).

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Abo Khayal, L. (2019). Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/70129

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Abo Khayal, Layal. “Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis.” 2019. Thesis, Brno University of Technology. Accessed March 05, 2021. http://hdl.handle.net/11012/70129.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Abo Khayal, Layal. “Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis.” 2019. Web. 05 Mar 2021.

Vancouver:

Abo Khayal L. Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis. [Internet] [Thesis]. Brno University of Technology; 2019. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/11012/70129.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Abo Khayal L. Transkriptomická charakterizace pomocí analýzy RNA-Seq dat: Transcriptomic Characterization Using RNA-Seq Data Analysis. [Thesis]. Brno University of Technology; 2019. Available from: http://hdl.handle.net/11012/70129

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – Berkeley

2. Ruddy, Sean. Shrinkage of dispersion parameters in the double exponential family of distributions, with applications to genomic sequencing.

Degree: Statistics, 2014, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/3rv7g03q

► The prevalence of sequencing experiments in genomics has led to an increased use of methods for count data in analyzing high-throughput genomic data to perform… (more)

▼ The prevalence of sequencing experiments in genomics has led to an increased use of methods for count data in analyzing high-throughput genomic data to perform analyses. The importance of shrinkage methods in improving the performance of statistical methods remains. A common example is that of gene expression data, where the counts per gene are often modeled as some form of an overdispersed Poisson. In this case, shrinkage estimates of the per-gene dispersion parameter have lead to improved estimation of dispersion in the case of a small number of samples. We address a different count setting introduced by the use of sequencing data: comparing differential proportional usage via an overdispersed binomial model. Such a model can be useful for testing differential exon inclusion in mRNA-Seq experiments in addition to the typical differential gene expression analysis. In this setting, there are fewer such shrinkage methods for the dispersion parameter. We introduce a novel method that is developed by modeling the dispersion based on the double exponential family of distributions proposed by Efron (1986), also known as the exponential dispersion model (Jorgensen, 1987). Our methods (WEB-Seq and DEB-Seq) are empirical bayes strategies for producing a shrunken estimate of dispersion that can be applied to any double exponential dispersion family, though we focus on the binomial and poisson. These methods effectively detect differential proportional usage, and have close ties to the weighted likelihood strategy of edgeR developed for gene expression data (Robinson and Smyth, 2007; Robinson et al., 2010). We analyze their behavior on simulated data sets as well as real data for both differential exon usage and differential gene expression. In the exon usage case, we will demonstrate our methods' superior ability to control the FDR and detect truly different features compared to existing methods. In the gene expression setting, our methods fail to control the FDR; however, the rankings of the genes by p-value is among the top performers and proves to be robust to both changes in the probability distribution used to generate the counts and in low sample size situations. We provide implementation of our methods in the R package DoubleExpSeq available from the Comprehensive R Archive Network (CRAN).

Subjects/Keywords: Statistics; Genetics; Biology; Differential Expression; Empirical Bayes; Exon Usage; Overdispersion; RNA-Seq; Shrinkage

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ruddy, S. (2014). Shrinkage of dispersion parameters in the double exponential family of distributions, with applications to genomic sequencing. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/3rv7g03q

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ruddy, Sean. “Shrinkage of dispersion parameters in the double exponential family of distributions, with applications to genomic sequencing.” 2014. Thesis, University of California – Berkeley. Accessed March 05, 2021. http://www.escholarship.org/uc/item/3rv7g03q.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ruddy, Sean. “Shrinkage of dispersion parameters in the double exponential family of distributions, with applications to genomic sequencing.” 2014. Web. 05 Mar 2021.

Vancouver:

Ruddy S. Shrinkage of dispersion parameters in the double exponential family of distributions, with applications to genomic sequencing. [Internet] [Thesis]. University of California – Berkeley; 2014. [cited 2021 Mar 05]. Available from: http://www.escholarship.org/uc/item/3rv7g03q.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ruddy S. Shrinkage of dispersion parameters in the double exponential family of distributions, with applications to genomic sequencing. [Thesis]. University of California – Berkeley; 2014. Available from: http://www.escholarship.org/uc/item/3rv7g03q

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Urbana-Champaign

3. Sadeque, Ahmed. Identification of alternative exon usage in cancer survival using hierarchical modeling.

Degree: MS, 4026, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/34549

► Background Alternative exon usage (AEU) is an important component of gene expression regulation. Exon expression platforms allow the detection of associations between AEU and phenotypes… (more)

▼ Background Alternative exon usage (AEU) is an important component of gene expression regulation. Exon expression platforms allow the detection of associations between AEU and phenotypes such as cancer. Numerous studies have identified associations between gene expression and the brain cancer glioblastoma multiforme (GBM). The few consistent gene expression biomarkers of GBM that have been reported may be due to the limited consideration of AEU and the analytical approaches used. The objectives of this study were to develop a model that accounts for the variations in expression present between the exons within a gene and to identify AEU biomarkers of GBM survival. Methods The expression of exons corresponding to 25,403 genes was related to the survival of 250 individuals diagnosed with GBM in a training data set. Genes exhibiting AEU in the training data set were confirmed in an independent validation data set of 78 patients. A hierarchical model allows the consideration of covariation between exons within a gene and of the effect of the epidemiological characteristics of the patients was developed to identify associations between exon expression and patient survival. The same model serves multi-exon models with and without AEU and single-exon models. Results AEU associated with GBM survival was identified on 2477 genes (P-value < 5.0E-04 (FDR adjusted P-value < 5.0E-04). G-protein coupled receptor 98 (Gpr98) and epidermal growth factor (Egf) were among the genes exhibiting AEU with 30 and 9 exons associated with GBM survival, respectively. Pathways enriched among the AEU genes included focal adhesion, ECM-receptor interaction, ABC transporters and pathways in cancer. In addition, 24 multi-exon genes without AEU and 8 single-exon genes were associated with GBM survival (P-value < 0.0005). Conclusions The inferred patterns of AEU were consistent with in silico AS models. The hierarchical model used offered a flexible and simple way to interpret and identify associations between survival that accommodates multi-exon genes with or without AEU and single exon genes. Advisors/Committee Members: Rodriguez-Zas, Sandra L. (advisor).

Subjects/Keywords: Alternative Splicing (AS); Alternative Exon Usage (AEU); Glioblastoma (GBM)

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sadeque, A. (2012). Identification of alternative exon usage in cancer survival using hierarchical modeling. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/34549

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sadeque, Ahmed. “Identification of alternative exon usage in cancer survival using hierarchical modeling.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/34549.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sadeque, Ahmed. “Identification of alternative exon usage in cancer survival using hierarchical modeling.” 2012. Web. 05 Mar 2021.

Vancouver:

Sadeque A. Identification of alternative exon usage in cancer survival using hierarchical modeling. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/34549.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sadeque A. Identification of alternative exon usage in cancer survival using hierarchical modeling. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/34549

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

4. Wolfe, Sarah Anne. Molecular mechanisms underlying alcohol use disorder and major depressive disorder comorbidity.

Degree: PhD, Cellular and Molecular Biology, 2017, University of Texas – Austin

URL: http://dx.doi.org/10.26153/tsw/2231

► Alcohol Use Disorder (AUD) and Major Depressive Disorder (MDD) are two widespread and debilitating disorders that share a high rate of comorbidity with the presence… (more)

▼ Alcohol Use Disorder (AUD) and Major Depressive Disorder (MDD) are two widespread and debilitating disorders that share a high rate of comorbidity with the presence of either disorder doubling the risk of developing the other. Despite their prevalence, few treatments are available to individuals with comorbid AUD and MDD. Both alcohol and antidepressants promote lasting neuroadaptive changes in synapses and dendrites. With alcohol these changes may provide relief from depressive symptoms, and the initial use of alcohol may be a form of self-medication for individuals with MDD, suggesting ethanol may have antidepressant properties underlying similarities in neurobiological abnormalities. However, the synaptic pathways that are shared by alcohol and antidepressants are unknown. This study aims to identify why acute exposure to ethanol produced lasting antidepressant and anxiolytic behaviors. To understand the functional basis of these behaviors, a molecular pathway activated by rapid antidepressants was investigated. Here ethanol, like rapid antidepressants, altered γ-aminobutyric acid type B receptor (GABA [subscript B] R) expression and signaling, to increase dendritic calcium. New GABA [subscript B] Rs were synthesized in response to ethanol treatment, requiring fragile-X mental retardation protein (FMRP). Ethanol-dependent changes in GABA [subscript B] R expression, dendritic signaling, and antidepressant efficacy were absent in Fmr1-knockout (KO) mice. These findings indicate that FMRP is an important regulator of protein synthesis following acute alcohol exposure, and provided a molecular basis for the antidepressant efficacy of acute ethanol exposure. We identify alterations on a global scale with acute alcohol and antidepressant by sequencing the synaptic transcriptome. We identified parallel alterations in exon usage with acute alcohol and antidepressant treatment. These shared differentially expressed exons may give rise to isoforms and proteins with altered function or localization in the synapse. Some of these differentially expressed exons were identified in genes known to have alternative isoforms with AUD and MDD. These data implicate alternative splicing and isoform expression in the acute antidepressant-like effects of ethanol and the development of comorbid alcohol and depression. Understanding the molecular basis for comorbidity may aid in development of treatment options for afflicted individuals with dual disorders, as well as explore the mechanism for the initiation of addiction with acute exposure to alcohol Advisors/Committee Members: Harris, R. Adron (advisor), Raab-Graham, Kimberly F. (advisor), Golding, Nace (committee member), Morrisett, Richard (committee member), Macdonald, Paul (committee member).

Subjects/Keywords: Alcohol use disorder; Major depressive disorder; Ethanol; Rapid antidepressants; FMRP; GABABR; Ro 25-6981; RNA-sequencing; Synaptoneurosomes; Exon usage

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wolfe, S. A. (2017). Molecular mechanisms underlying alcohol use disorder and major depressive disorder comorbidity. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://dx.doi.org/10.26153/tsw/2231

Chicago Manual of Style (16^th Edition):

Wolfe, Sarah Anne. “Molecular mechanisms underlying alcohol use disorder and major depressive disorder comorbidity.” 2017. Doctoral Dissertation, University of Texas – Austin. Accessed March 05, 2021. http://dx.doi.org/10.26153/tsw/2231.

MLA Handbook (7^th Edition):

Wolfe, Sarah Anne. “Molecular mechanisms underlying alcohol use disorder and major depressive disorder comorbidity.” 2017. Web. 05 Mar 2021.

Vancouver:

Wolfe SA. Molecular mechanisms underlying alcohol use disorder and major depressive disorder comorbidity. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2017. [cited 2021 Mar 05]. Available from: http://dx.doi.org/10.26153/tsw/2231.

Council of Science Editors:

Wolfe SA. Molecular mechanisms underlying alcohol use disorder and major depressive disorder comorbidity. [Doctoral Dissertation]. University of Texas – Austin; 2017. Available from: http://dx.doi.org/10.26153/tsw/2231

IUPUI

5. Pochareddy, Sirisha. Transcriptional regulation of the human alcohol dehydrogenases and alcoholism.

Degree: 2011, IUPUI

URL: http://hdl.handle.net/1805/2463

►

Indiana University-Purdue University Indianapolis (IUPUI)

Alcohol dehydrogenase (ADH) genes encode proteins that metabolize ethanol to acetaldehyde. Humans have seven ADH genes in a cluster. The… (more)

▼

Indiana University-Purdue University Indianapolis (IUPUI)

Alcohol dehydrogenase (ADH) genes encode proteins that metabolize ethanol to acetaldehyde. Humans have seven ADH genes in a cluster. The hypothesis of this study was that by controlling the levels of ADH enzymes, cis-regulatory regions could affect the risk for alcoholism. The goal was thus to identify distal regulatory regions of ADHs. To achieve this, sequence conservation across 220 kb of the ADH cluster was examined. An enhancer (4E) was identified upstream of ADH4. In HepG2 human hepatoma cells, 4E increased the activity of an ADH4 basal promoter by 50-fold. 4E was cell specific, as no enhancer activity was detected in a human lung cell line, H1299. The enhancer activity was located in a 565 bp region (4E3). Four FOXA and one HNF-1A protein binding sites were shown to be functional in the 4E3 region. To test if this region could affect the risk for alcoholism, the effect of variations in 4E3 on enhancer activity was tested. Two variations had a significant effect on enhancer activity, decreasing the activity to 0.6-fold. A third variation had a small but significant effect. The effect of variations in the ADH1B proximal promoter was also tested. At SNP rs1229982, the C allele had 30% lower activity than the A allele. In addition to studying the regulatory regions of ADH genes, the effects of alcohol on liver-derived cells (HepG2) were also explored. Liver is the primary site of alcohol metabolism, and is highly vulnerable to injuries due to chronic alcohol abuse. To identify the effects of long term ethanol exposure on global gene expression and alternative splicing, HepG2 cells were cultured in 75 mM ethanol for nine days. Global gene expression changes and alternative splicing were measured using Affymetrix GeneChip® Human Exon 1.0 ST Arrays. At the level of gene expression, genes involved in stress response pathways, metabolic pathways (including carbohydrate and lipid metabolism) and chromatin regulation were affected. Alcohol effects were also observed on alternative transcript isoforms of some genes.

Advisors/Committee Members: Edenberg, Howard J., Harrington, Maureen A., Skalnik, David Gordon, Roman, Ann.

Subjects/Keywords: ADH, alcoholism, variations, microarray, exon arrays, differential gene expression, alternative splicing; Alcohol dehydrogenase – Regulation; Gene expression; Alcoholism – Research

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Pochareddy, S. (2011). Transcriptional regulation of the human alcohol dehydrogenases and alcoholism. (Thesis). IUPUI. Retrieved from http://hdl.handle.net/1805/2463

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Pochareddy, Sirisha. “Transcriptional regulation of the human alcohol dehydrogenases and alcoholism.” 2011. Thesis, IUPUI. Accessed March 05, 2021. http://hdl.handle.net/1805/2463.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Pochareddy, Sirisha. “Transcriptional regulation of the human alcohol dehydrogenases and alcoholism.” 2011. Web. 05 Mar 2021.

Vancouver:

Pochareddy S. Transcriptional regulation of the human alcohol dehydrogenases and alcoholism. [Internet] [Thesis]. IUPUI; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1805/2463.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Pochareddy S. Transcriptional regulation of the human alcohol dehydrogenases and alcoholism. [Thesis]. IUPUI; 2011. Available from: http://hdl.handle.net/1805/2463

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Cambridge

6. Cardoso Marcelino dos Santos, Sérgio Miguel. Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data.

Degree: PhD, 2019, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/293475

► Alternative splicing is an important step in gene expression regulation in eukaryotes, through which a single gene can express different transcript isoforms. We can now… (more)

▼ Alternative splicing is an important step in gene expression regulation in eukaryotes, through which a single gene can express different transcript isoforms. We can now use RNA sequencing (RNA-seq) data to identify which isoforms of each gene are being expressed in a specific condition, by quantifying the expression level of each isoform of a gene, even though quantification of isoforms remains a difficult task. In this way, we can better understand how prevalent this process is and how often a gene expresses different isoforms. It can also be evaluated if all isoforms of a gene are about equally expressed or if there is one dominant isoform that is significantly more expressed than the others. Moreover, by applying this analysis to different tissues, it can be assessed if there are changes in splicing between different conditions and if such a change has a biological role. A dataset of 32 normal human tissues was used in this study. The results show that, although alternative splicing can lead to the expression of different transcripts of a gene, many genes have an n-fold dominant transcript – a transcript that is expressed at n times higher level than the second most expressed one. On average, 68% of protein-coding genes expressed in a given tissue have a 2-fold dominant transcript and 47% have a 5-fold dominant transcript. It was observed that the dominant transcript of a gene tends to be the same across tissues, but there are cases where the dominant isoform switches between tissues, these cases are designated switch events. For a given pair of tissues, there are on average around thirty 2-fold switch events and just below four 5-fold switch events. The switching exons often significantly overlap and the most common types of alternative splicing are alternative 3’ selection (24% of the cases) and alternative 5’ selection (21%). To evaluate the conservation of the transcripts, the dominant transcripts were compared to APPRIS principal isoforms. These isoforms are annotated based on their function, protein structure, and cross-species conservation. 69.2% of the 2-fold dominant transcripts and 81.1% of the 5-fold dominant transcripts are APPRIS principal isoforms. It was also observed that in 80% of the switches there are no protein domain changes. Similar results were obtained when the same analysis was done using the GTEx dataset, which has a much higher number of samples, containing data from 54 conditions. In this case, on average 59% of expressed genes in a given condition had a 2-fold dominant transcript and 31% had a 5-fold dominant transcript. The number of switch events was again low, given the number of dominant transcripts, indicating that dominant transcripts tend to be conserved across normal tissues. A comparative analysis of matching tissues common to the two mentioned datasets was also performed and, although the datasets are different, there were switch events in common between both of them. 5 examples of 5-fold switches involving domain swaps were analysed in detail and it was revealed that the…

Subjects/Keywords: alternative splicing; rna-seq; differential transcript usage; switch event; dominant transcript

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cardoso Marcelino dos Santos, S. M. (2019). Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/293475

Chicago Manual of Style (16^th Edition):

Cardoso Marcelino dos Santos, Sérgio Miguel. “Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data.” 2019. Doctoral Dissertation, University of Cambridge. Accessed March 05, 2021. https://www.repository.cam.ac.uk/handle/1810/293475.

MLA Handbook (7^th Edition):

Cardoso Marcelino dos Santos, Sérgio Miguel. “Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data.” 2019. Web. 05 Mar 2021.

Vancouver:

Cardoso Marcelino dos Santos SM. Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Mar 05]. Available from: https://www.repository.cam.ac.uk/handle/1810/293475.

Council of Science Editors:

Cardoso Marcelino dos Santos SM. Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://www.repository.cam.ac.uk/handle/1810/293475

7. Cardoso Marcelino dos Santos, Sérgio Miguel. Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data.

Degree: PhD, 2019, University of Cambridge

URL: https://doi.org/10.17863/CAM.40618 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782794

► Alternative splicing is an important step in gene expression regulation in eukaryotes, through which a single gene can express different transcript isoforms. We can now… (more)

▼ Alternative splicing is an important step in gene expression regulation in eukaryotes, through which a single gene can express different transcript isoforms. We can now use RNA sequencing (RNA-seq) data to identify which isoforms of each gene are being expressed in a specific condition, by quantifying the expression level of each isoform of a gene, even though quantification of isoforms remains a difficult task. In this way, we can better understand how prevalent this process is and how often a gene expresses different isoforms. It can also be evaluated if all isoforms of a gene are about equally expressed or if there is one dominant isoform that is significantly more expressed than the others. Moreover, by applying this analysis to different tissues, it can be assessed if there are changes in splicing between different conditions and if such a change has a biological role. A dataset of 32 normal human tissues was used in this study. The results show that, although alternative splicing can lead to the expression of different transcripts of a gene, many genes have an n-fold dominant transcript - a transcript that is expressed at n times higher level than the second most expressed one. On average, 68% of protein-coding genes expressed in a given tissue have a 2-fold dominant transcript and 47% have a 5-fold dominant transcript. It was observed that the dominant transcript of a gene tends to be the same across tissues, but there are cases where the dominant isoform switches between tissues, these cases are designated switch events. For a given pair of tissues, there are on average around thirty 2-fold switch events and just below four 5-fold switch events. The switching exons often significantly overlap and the most common types of alternative splicing are alternative 3' selection (24% of the cases) and alternative 5' selection (21%). To evaluate the conservation of the transcripts, the dominant transcripts were compared to APPRIS principal isoforms. These isoforms are annotated based on their function, protein structure, and cross-species conservation. 69.2% of the 2-fold dominant transcripts and 81.1% of the 5-fold dominant transcripts are APPRIS principal isoforms. It was also observed that in 80% of the switches there are no protein domain changes. Similar results were obtained when the same analysis was done using the GTEx dataset, which has a much higher number of samples, containing data from 54 conditions. In this case, on average 59% of expressed genes in a given condition had a 2-fold dominant transcript and 31% had a 5-fold dominant transcript. The number of switch events was again low, given the number of dominant transcripts, indicating that dominant transcripts tend to be conserved across normal tissues. A comparative analysis of matching tissues common to the two mentioned datasets was also performed and, although the datasets are different, there were switch events in common between both of them. 5 examples of 5-fold switches involving domain swaps were analysed in detail and it was revealed that the…

Subjects/Keywords: alternative splicing; rna-seq; differential transcript usage; switch event; dominant transcript

10 more images…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cardoso Marcelino dos Santos, S. M. (2019). Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.40618 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782794

Chicago Manual of Style (16^th Edition):

Cardoso Marcelino dos Santos, Sérgio Miguel. “Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data.” 2019. Doctoral Dissertation, University of Cambridge. Accessed March 05, 2021. https://doi.org/10.17863/CAM.40618 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782794.

MLA Handbook (7^th Edition):

Cardoso Marcelino dos Santos, Sérgio Miguel. “Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data.” 2019. Web. 05 Mar 2021.

Vancouver:

Cardoso Marcelino dos Santos SM. Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Mar 05]. Available from: https://doi.org/10.17863/CAM.40618 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782794.

Council of Science Editors:

Cardoso Marcelino dos Santos SM. Assessing the usage of alternative transcripts in human tissues from RNA-seq and proteomics data. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://doi.org/10.17863/CAM.40618 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.782794

Tulane University

8. Zhou, Yu. Gene expression array analysis for female osteoporosis.

Degree: 2018, Tulane University

URL: https://digitallibrary.tulane.edu/islandora/object/tulane:79048

►

Osteoporosis is a prevalent bone metabolic disease characterized by bone fragility. As a key pathophysiological mechanism, the disease is caused by excessive bone resorption (by… (more)

Subjects/Keywords: exon array

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhou, Y. (2018). Gene expression array analysis for female osteoporosis. (Thesis). Tulane University. Retrieved from https://digitallibrary.tulane.edu/islandora/object/tulane:79048

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhou, Yu. “Gene expression array analysis for female osteoporosis.” 2018. Thesis, Tulane University. Accessed March 05, 2021. https://digitallibrary.tulane.edu/islandora/object/tulane:79048.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhou, Yu. “Gene expression array analysis for female osteoporosis.” 2018. Web. 05 Mar 2021.

Vancouver:

Zhou Y. Gene expression array analysis for female osteoporosis. [Internet] [Thesis]. Tulane University; 2018. [cited 2021 Mar 05]. Available from: https://digitallibrary.tulane.edu/islandora/object/tulane:79048.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhou Y. Gene expression array analysis for female osteoporosis. [Thesis]. Tulane University; 2018. Available from: https://digitallibrary.tulane.edu/islandora/object/tulane:79048

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Melbourne

9. Herath Mudiyanselage, Damayanthi Kumari Herath. Methods for profling heterogeneous sequencing data.

Degree: 2019, University of Melbourne

URL: http://hdl.handle.net/11343/233379

► Metagenomics which utilises high throughput DNA sequencing is widely applied to study bacteria and viruses and their effects on their host environments. Metagenomics involves collective… (more)

▼ Metagenomics which utilises high throughput DNA sequencing is widely applied to study bacteria and viruses and their effects on their host environments. Metagenomics involves collective sequencing of genetic material of the species in an environmental sample, subsequently requiring robust methods to elucidate the characteristics of the species in the sample from the heterogeneous data. A key step in learning the taxonomic diversity of a metagenomic sample is binning. Binning refers to grouping the nucleotide sequences belonging to an individual or closely related species. Identification of appropriate features and machine learning methods is essential in binning a metagenome of many unknown genomes. A significant challenge in binning metagenomic sequences is to bin a sample of closely related species. The thesis addresses this challenge and proposes a new two-tiered workflow called Coverage and composition based binning of Metagenomes (CoMet) for binning assembled sequences (contigs) of a metagenomic sample. It is demonstrated that a combination of features coupled with appropriate unsupervised learning methods can improve the precision in binning while enabling characterization of more species in a metagenome of species with similar genetic variants. Species richness is a key species diversity measure which corresponds to the number of species in an environmental sample. Estimating species richness of a metagenome of viruses (i.e. a virome) based on the reference data is challenging because of the limited amount of sequence data of viruses available in reference databases. A limitation identified with the methods that do not rely on reference sequence data in estimating species richness is the assumption of equal genome length for all the species in the sample. The thesis addresses this limitation by proposing a method to estimate species richness from a virome considering the variability of the genome lengths of species in the sample. The proposed method enables inference of genome lengths distribution from the metagenomic sequence data in addition to estimating the species richness. RNA-Seq refers to a set of techniques enabling the effective study of the transcriptome. An application of RNA-Seq is differential transcript usage analysis (DTU) which refers to inferring differences in expressions of multiple transcripts (isoforms) of a gene across different conditions from the sequencing data generated in an experiment. A key step in RNA-Seq data analysis is aligning the sequence reads to a reference sequence. SuperTranscripts is an alternate reference sequence proposed mainly for analyzing organisms with no/incomplete reference sequences. The thesis explores the use of superTranscripts to test for DTU in organisms with good reference sequences and annotations. Three definitions of counting-bins based on superTranscripts which are further used to infer DTU in genes are considered. The results with simulated data of fruit fly and human demonstrate that superTranscripts enable the analysis of DTU in genes with…

Subjects/Keywords: Data Driven; Machine Learning; Highthroughput sequencing; Metagenomics; Transcriptomics; Binning; Species Diversity; Metavirome; Differential Transcript Usage

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APA (6^th Edition):

Herath Mudiyanselage, D. K. H. (2019). Methods for profling heterogeneous sequencing data. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/233379

Chicago Manual of Style (16^th Edition):

Herath Mudiyanselage, Damayanthi Kumari Herath. “Methods for profling heterogeneous sequencing data.” 2019. Doctoral Dissertation, University of Melbourne. Accessed March 05, 2021. http://hdl.handle.net/11343/233379.

MLA Handbook (7^th Edition):

Herath Mudiyanselage, Damayanthi Kumari Herath. “Methods for profling heterogeneous sequencing data.” 2019. Web. 05 Mar 2021.

Vancouver:

Herath Mudiyanselage DKH. Methods for profling heterogeneous sequencing data. [Internet] [Doctoral dissertation]. University of Melbourne; 2019. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/11343/233379.

Council of Science Editors:

Herath Mudiyanselage DKH. Methods for profling heterogeneous sequencing data. [Doctoral Dissertation]. University of Melbourne; 2019. Available from: http://hdl.handle.net/11343/233379

Liberty University

10. Kirby, Melissa Jill. A Qualitative Study On Internal Control Usage And Financial Accountability among Baptist Churches in North Georgia.

Degree: 2020, Liberty University

URL: https://digitalcommons.liberty.edu/doctoral/2719

► This research study addresses the deficiency in knowledge on internal control usage and financial accountability in churches, and the effects they have on losses from… (more)

Subjects/Keywords: Internal Control Usage; Financial Accountability; Baptist Churches; Financial Stewardship; The Differential Association Theory; Accounting; Business

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APA (6^th Edition):

Kirby, M. J. (2020). A Qualitative Study On Internal Control Usage And Financial Accountability among Baptist Churches in North Georgia. (Doctoral Dissertation). Liberty University. Retrieved from https://digitalcommons.liberty.edu/doctoral/2719

Chicago Manual of Style (16^th Edition):

Kirby, Melissa Jill. “A Qualitative Study On Internal Control Usage And Financial Accountability among Baptist Churches in North Georgia.” 2020. Doctoral Dissertation, Liberty University. Accessed March 05, 2021. https://digitalcommons.liberty.edu/doctoral/2719.

MLA Handbook (7^th Edition):

Kirby, Melissa Jill. “A Qualitative Study On Internal Control Usage And Financial Accountability among Baptist Churches in North Georgia.” 2020. Web. 05 Mar 2021.

Vancouver:

Kirby MJ. A Qualitative Study On Internal Control Usage And Financial Accountability among Baptist Churches in North Georgia. [Internet] [Doctoral dissertation]. Liberty University; 2020. [cited 2021 Mar 05]. Available from: https://digitalcommons.liberty.edu/doctoral/2719.

Council of Science Editors:

Kirby MJ. A Qualitative Study On Internal Control Usage And Financial Accountability among Baptist Churches in North Georgia. [Doctoral Dissertation]. Liberty University; 2020. Available from: https://digitalcommons.liberty.edu/doctoral/2719

11. Tessoulin, Benoît. Identification par séquençage de l'exome de la dérégulation des voies de signalisation dans le myélome multiple et leurs conséquences fonctionnelles, notamment sur la voie p53 : Assessment by Whole Exon Sequencing of pathway dysregulations in Multiple Myeloma and their functional impacts, notably on p53 pathway.

Degree: Docteur es, Biologie cellulaire, 2018, Nantes

URL: http://www.theses.fr/2018NANT1027

►

Au sein des hémopathies malignes B, les plasmocytoses malignes (myélome multiple [MM) et leucémie à plasmocyte [PCLI) occupent une place particulière par leur biologie et… (more)

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Au sein des hémopathies malignes B, les plasmocytoses malignes (myélome multiple [MM) et leucémie à plasmocyte [PCLI) occupent une place particulière par leur biologie et leurs aspects cliniques. Biologiquement, elles présentent une forte proportion d’anomalies oncogéniques· (RAS, c-MYC) et de fréquentes altérations de la voie p53 (CDKN2ADel, TP53Del/Mut) qui conduisent, cliniquement, à l’inefficacité des traitements cytostatiques conventionnels. Des lignées cellulaires de MM (HMCls) qui recouvrent en partie la diversité des patients ont été générées depuis 50 ans. Nous avons caractérisé l’exome complet de 33 lignées cellulaires humaines de MM. Les mutations faux-sens sont les plus fréquentes (92%). les HMCLs portent entre 307 et 916 mutant par HMCL, TP53 étant le gène le plus altéré (67%). Des pertes bi-alléliques des voies du cycle cellulaire (CDKN2C, RB1), de la voie NFkB (TRAF3, BIRC2) et de la voie p53 (TP53, CDKN2A) sont fréquentes. La fréquence des mutations/délétion est semblable à celle des patients ( DIS3, PRDM1, KRAS), ou majorée (TP53, CDKN2C, NRAS, PRKD2). la voie MAPK est lá plus altérée (82% des HMCls), principalement par des mutants de RAS: peu décrites, les HMCLs présentent des altérations des voies épigénétiques (73%), de l’ anémie de Fanconi (54%) et très peu d’anonalies directes de la machinerie apoptotique. Nous avons mis en relation les données dexpression, de mutation/délétion et de réponse aux traitements et démontré que l’efficacité de plusieurs traitements est indépendante des mutations. Finalement, le développement de stratégies prenant en compte ces altérations peu décrites dans le MM (Fanconi, Epigenetique) sont nécessaires.

Among B CeH malignancies, plasma-cell the NFKB pathway (TRAF3, BIRC2) and the p53 malignancies (multiple myeloma [MM] and plasma cell pathway (TP53, CDKN2A). Frequency of leukemia [PCL]) harbor particular biological and mutations/deletions in HMCLs were either similar to clinical insights. Biologically, they present with both a that of patients (e.g. DIS3, PRDM1, KRAS), or highly high frequency of oncogenic abnormalities (RAS, e- increased (e.g. TP53, CDKN2C, NRAS, PRKD2). MYC) and a high frequency of p53 pathway MAPK was the most altered pathway (82% of abnormalities (CDKN2Adel, TP53 del/mut). Those two HMCLs), mainly by RAS mutants. Surprisingly, latter leading to chemo-resistance to conventional HMCLs displayed alterations in epigenetic (73%) and cytostatic drugs. Human myeloma cell lines (HMCLs) Fanconi anemia (54%) and few alterations in are widely used for their representation of primary apoptotic machinery. We further identified mutually myeloma cells as they cover patient diversity, exclusive and associated mutations/deletions in afthough not fully. We performed whole-exon genes involved in the MAPK and p53 pathways as sequencing of 33 HMCLs, which were established well as in chromatin regulator/modifier genes. over the last 50 years. Missense mutations were the Finally, by combining the gene expression profile, most frequent mutations {92%). HMCLs harbored…

Advisors/Committee Members: Pellat-Deceunynck, Catherine (thesis director).

Subjects/Keywords: Whole Exon Sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tessoulin, B. (2018). Identification par séquençage de l'exome de la dérégulation des voies de signalisation dans le myélome multiple et leurs conséquences fonctionnelles, notamment sur la voie p53 : Assessment by Whole Exon Sequencing of pathway dysregulations in Multiple Myeloma and their functional impacts, notably on p53 pathway. (Doctoral Dissertation). Nantes. Retrieved from http://www.theses.fr/2018NANT1027

Chicago Manual of Style (16^th Edition):

Tessoulin, Benoît. “Identification par séquençage de l'exome de la dérégulation des voies de signalisation dans le myélome multiple et leurs conséquences fonctionnelles, notamment sur la voie p53 : Assessment by Whole Exon Sequencing of pathway dysregulations in Multiple Myeloma and their functional impacts, notably on p53 pathway.” 2018. Doctoral Dissertation, Nantes. Accessed March 05, 2021. http://www.theses.fr/2018NANT1027.

MLA Handbook (7^th Edition):

Tessoulin, Benoît. “Identification par séquençage de l'exome de la dérégulation des voies de signalisation dans le myélome multiple et leurs conséquences fonctionnelles, notamment sur la voie p53 : Assessment by Whole Exon Sequencing of pathway dysregulations in Multiple Myeloma and their functional impacts, notably on p53 pathway.” 2018. Web. 05 Mar 2021.

Vancouver:

Tessoulin B. Identification par séquençage de l'exome de la dérégulation des voies de signalisation dans le myélome multiple et leurs conséquences fonctionnelles, notamment sur la voie p53 : Assessment by Whole Exon Sequencing of pathway dysregulations in Multiple Myeloma and their functional impacts, notably on p53 pathway. [Internet] [Doctoral dissertation]. Nantes; 2018. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2018NANT1027.

Council of Science Editors:

Tessoulin B. Identification par séquençage de l'exome de la dérégulation des voies de signalisation dans le myélome multiple et leurs conséquences fonctionnelles, notamment sur la voie p53 : Assessment by Whole Exon Sequencing of pathway dysregulations in Multiple Myeloma and their functional impacts, notably on p53 pathway. [Doctoral Dissertation]. Nantes; 2018. Available from: http://www.theses.fr/2018NANT1027

Brno University of Technology

12. Melezinek, František. Výroba spony: Manufacturing of clip.

Degree: 2020, Brno University of Technology

URL: http://hdl.handle.net/11012/192150

► The thesis deals with technology of clip manufacture, used as connecting segment of clip frame. The molding is made out of 0,3 mm metal sheet… (more)

Subjects/Keywords: Střih; ohyb; postupový sdružený nástroj; ocel 51CrV4; lis CUPS 6; 3 DEU; cutting; bending; progressive combined tool; steel 51CrV4; press CUPS 6; 3 DEU

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Melezinek, F. (2020). Výroba spony: Manufacturing of clip. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/192150

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Melezinek, František. “Výroba spony: Manufacturing of clip.” 2020. Thesis, Brno University of Technology. Accessed March 05, 2021. http://hdl.handle.net/11012/192150.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Melezinek, František. “Výroba spony: Manufacturing of clip.” 2020. Web. 05 Mar 2021.

Vancouver:

Melezinek F. Výroba spony: Manufacturing of clip. [Internet] [Thesis]. Brno University of Technology; 2020. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/11012/192150.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Melezinek F. Výroba spony: Manufacturing of clip. [Thesis]. Brno University of Technology; 2020. Available from: http://hdl.handle.net/11012/192150

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Nairobi

13. Obiero, Collins O. The impact of internet usage on newspaper distribution in Kenya .

Degree: 2011, University of Nairobi

URL: http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/12443

► The study set out to discover the impact of the Internet on newspaper sales in Kenya. The research question aimed to seek the answer as… (more)

Subjects/Keywords: Internet usage

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APA (6^th Edition):

Obiero, C. O. (2011). The impact of internet usage on newspaper distribution in Kenya . (Thesis). University of Nairobi. Retrieved from http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/12443

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Obiero, Collins O. “The impact of internet usage on newspaper distribution in Kenya .” 2011. Thesis, University of Nairobi. Accessed March 05, 2021. http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/12443.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Obiero, Collins O. “The impact of internet usage on newspaper distribution in Kenya .” 2011. Web. 05 Mar 2021.

Vancouver:

Obiero CO. The impact of internet usage on newspaper distribution in Kenya . [Internet] [Thesis]. University of Nairobi; 2011. [cited 2021 Mar 05]. Available from: http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/12443.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Obiero CO. The impact of internet usage on newspaper distribution in Kenya . [Thesis]. University of Nairobi; 2011. Available from: http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/12443

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

14. Nassopoulos, Georges. Deducing Basic Graph Patterns from Logs of Linked Data Providers : Déduire des Basic Graph Patterns depuis les Logs des fournisseurs du Linked Data.

Degree: Docteur es, Informatique et applications, 2017, Nantes

URL: http://www.theses.fr/2017NANT4110

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Conformément aux principes de Linked Data, les fournisseurs de données ont publié des milliards de faits en tant que données RDF. Exécuter les requêtes SPARQL… (more)

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Conformément aux principes de Linked Data, les fournisseurs de données ont publié des milliards de faits en tant que données RDF. Exécuter les requêtes SPARQL sur les endpoints SPARQL ou les serveurs Triple Pattern Fragments (TPF) permet de consommer facilement des données du Linked Data. Cependant, le traitement des requêtes SPARQL fédérées, tout comme le traitement des requêtes TPF, décompose la requête initiale en de nombreuses sous-requêtes. Les fournisseurs de données ne voient alors que les sous-requêtes et la requête initiale n’est connue que des utilisateurs finaux. La connaissance des requêtes exécutées est fondamentale pour les fournisseurs, afin d’assurer un contrôle de l’utilisation des données, d’optimiser le coût des réponses aux requêtes, de justifier un retour sur investissements, d’améliorer l’expérience utilisateur ou de créer des modèles commerciaux à partir de tendances d’utilisation. Dans cette thèse, nous nous concentrons sur l’analyse des logs d’exécution des serveurs TPF et des endpoints SPARQL pour extraire les Basic Graph Patterns (BGP) des requêtes SPARQL exécutées. Le principal défi pour l’extraction des BGPs est l’exécution simultanée des requêtes SPARQL. Nous proposons deux algorithmes : LIFT et FETA. Sous certaines conditions, nous constatons que LIFT et FETA sont capables d’extraire des BGPs avec une bonne précision et un bon rappel.

Following the principles of Linked Data, data providers published billions of facts as RDF data. Executing SPARQL queries over SPARQL endpoints or Triple Pattern Fragments (TPF) servers allow to easily consume Linked Data. However, federated SPARQL query processing and TPF query processing decompose the initial query into subqueries. Consequently, the data providers only see subqueries and the initial query is only known by end users. Knowing executed SPARQL queries is fundamental for data providers, to ensure usage control, to optimize costs of query answering, to justify return of investment, to improve the user experience or to create business models of usage trends. In this thesis, we focus on analyzing execution logs of TPF servers and SPARQL endpoints to extract Basic Graph Patterns (BGP) of executed SPARQL queries. The main challenge to extract BGPs is the concurrent execution of SPARQL queries. We propose two algorithms: LIFT and FETA. LIFT extracts BGPs of executed queries from a single TPF server log. FETA extracts BGPs of federated queries from a log of a set of SPARQL endpoints. For experiments, we run LIFT and FETA on synthetic logs and real logs. LIFT and FETA are able to extract BGPs with good precision and recall under certain conditions.

Advisors/Committee Members: Molli, Pascal (thesis director), Serrano Alvarado, Patricia (thesis director), Desmontils, Emmanuel (thesis director).

Subjects/Keywords: Usage Control

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nassopoulos, G. (2017). Deducing Basic Graph Patterns from Logs of Linked Data Providers : Déduire des Basic Graph Patterns depuis les Logs des fournisseurs du Linked Data. (Doctoral Dissertation). Nantes. Retrieved from http://www.theses.fr/2017NANT4110

Chicago Manual of Style (16^th Edition):

Nassopoulos, Georges. “Deducing Basic Graph Patterns from Logs of Linked Data Providers : Déduire des Basic Graph Patterns depuis les Logs des fournisseurs du Linked Data.” 2017. Doctoral Dissertation, Nantes. Accessed March 05, 2021. http://www.theses.fr/2017NANT4110.

MLA Handbook (7^th Edition):

Nassopoulos, Georges. “Deducing Basic Graph Patterns from Logs of Linked Data Providers : Déduire des Basic Graph Patterns depuis les Logs des fournisseurs du Linked Data.” 2017. Web. 05 Mar 2021.

Vancouver:

Nassopoulos G. Deducing Basic Graph Patterns from Logs of Linked Data Providers : Déduire des Basic Graph Patterns depuis les Logs des fournisseurs du Linked Data. [Internet] [Doctoral dissertation]. Nantes; 2017. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2017NANT4110.

Council of Science Editors:

Nassopoulos G. Deducing Basic Graph Patterns from Logs of Linked Data Providers : Déduire des Basic Graph Patterns depuis les Logs des fournisseurs du Linked Data. [Doctoral Dissertation]. Nantes; 2017. Available from: http://www.theses.fr/2017NANT4110

15. Daguenet, Elisabeth. Etude fonctionnelle de la protéine Metastatic lymph node 51 dans le métabolisme des ARN messagers : Functional study of Metastatic lymph node 51 protein in mRNA metabolism.

Degree: Docteur es, Aspects moléculaires et cellulaires de la biologie, 2012, Université de Strasbourg

URL: http://www.theses.fr/2012STRAJ117

►

La protéine MLN51, surexprimée dans environ 30% des cancers du sein, est un facteur clé du métabolisme des ARNm, en tant que membre du complexe… (more)

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La protéine MLN51, surexprimée dans environ 30% des cancers du sein, est un facteur clé du métabolisme des ARNm, en tant que membre du complexe de jonction des exons (EJC). Ce graffiti moléculaire est un régulateur essentiel de l’expression génique de par son implication dans l’épissage, l’export, la traduction, la stabilité et la dégradation des ARNm. A l’échelle structurale, l’EJC est organisé autour d’un coeur protéique avec l’hélicase eIF4A3, MLN51 et l’hétérodimère Magoh/Y14. Ce tétramère sert de plateforme d’ancrage à d’autres facteurs périphériques. Les mécanismes de recrutement du coeur EJC sur l’ARNm ont été élucidés par des approches biochimiques. Dans ce contexte, nous avons initié un travail original destiné à mettre en évidence la localisation cellulaire de l’assemblage du coeur EJC in vivo. L’utilisation de techniques d’imagerie photonique et électronique a permis d’établir un lien véritable entre la localisation du coeur EJC et l’architecture nucléaire. Nous avons montré que la plupart des facteurs EJC sont localisés et interagissent à la périphérie des speckles nucléaires, lieux de stockage des facteurs d’épissage. Ces régions discrètes nucléaires ont été appelées «perispeckles» et sont des entités distinctes des speckles. De manière intéressante, la localisation des protéines coeur coïncide avec celle des ARNm dans les perispeckles et est spatialement reliée aux sites transcriptionnels. Ces données démontrent que l’assemblage du coeur EJC a lieu dans le compartiment nucléaire et définissent le perispeckle comme un territoire intermédiaire entre les speckles nucléaires et sites de transcription où s’opèrent des évènements post-transcriptionnels fondamentaux.

The MLN51 protein, overexpressed in around 30% of breast cancers, is a key factor for mRNA metabolism, as a member of the Exon Junction Complex (EJC). The EJC marks the splicing history of an mRNA and influences many stages of its subsequent metabolism: splicing, dynamic cytoplasmic export, efficient and localized translation, quality-control and stability. Structurally, the EJC is organized around a core complex that is formed by four proteins (eIF4A3, MLN51, Magoh, Y14). The core complex serves as a binding platform for more than a dozen peripheral factors. The EJC is not a pre-assembled complex; however, its assembly mode is well described in vitro using recombinant proteins and splicing extracts. Nevertheless, where this complex assembles in vivo was a matter of debate. By using light and electron microscopy approaches, we established an original link between the cellular distribution of the EJC core factors and the nuclear architecture. The core and most of the peripheral EJC factors are colocalized and interact together in discrete regions of the nucleus, located at the periphery of nuclear speckles. This doughnut-shaped region appears to be a novel nuclear territory that we termed “the perispeckle”. This territory is distinct from nuclear speckles; it contains nascent mRNAs and it is close to active transcription sites. Overall, this…

Advisors/Committee Members: Tomasetto, Catherine-Laure (thesis director).

Subjects/Keywords: MLN51; Exon junction complex; ARN; Épissage; Perispeckle; MLN51; Exon junction complex; RNA; Splicing; Perispeckle; 572.8; 616.99

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Daguenet, E. (2012). Etude fonctionnelle de la protéine Metastatic lymph node 51 dans le métabolisme des ARN messagers : Functional study of Metastatic lymph node 51 protein in mRNA metabolism. (Doctoral Dissertation). Université de Strasbourg. Retrieved from http://www.theses.fr/2012STRAJ117

Chicago Manual of Style (16^th Edition):

Daguenet, Elisabeth. “Etude fonctionnelle de la protéine Metastatic lymph node 51 dans le métabolisme des ARN messagers : Functional study of Metastatic lymph node 51 protein in mRNA metabolism.” 2012. Doctoral Dissertation, Université de Strasbourg. Accessed March 05, 2021. http://www.theses.fr/2012STRAJ117.

MLA Handbook (7^th Edition):

Daguenet, Elisabeth. “Etude fonctionnelle de la protéine Metastatic lymph node 51 dans le métabolisme des ARN messagers : Functional study of Metastatic lymph node 51 protein in mRNA metabolism.” 2012. Web. 05 Mar 2021.

Vancouver:

Daguenet E. Etude fonctionnelle de la protéine Metastatic lymph node 51 dans le métabolisme des ARN messagers : Functional study of Metastatic lymph node 51 protein in mRNA metabolism. [Internet] [Doctoral dissertation]. Université de Strasbourg; 2012. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2012STRAJ117.

Council of Science Editors:

Daguenet E. Etude fonctionnelle de la protéine Metastatic lymph node 51 dans le métabolisme des ARN messagers : Functional study of Metastatic lymph node 51 protein in mRNA metabolism. [Doctoral Dissertation]. Université de Strasbourg; 2012. Available from: http://www.theses.fr/2012STRAJ117

16. França, Gustavo Starvaggi. História evolutiva de exon shuffling em eucariotos.

Degree: Mestrado, Bioquímica, 2010, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/46/46131/tde-26042010-134105/ ;

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Exon shuffling foi primeiramente proposto por Walter Gilbert em 1978 como um mecanismo em que exons de diferentes genes podem ser combinados, levando à formação… (more)

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Exon shuffling foi primeiramente proposto por Walter Gilbert em 1978 como um mecanismo em que exons de diferentes genes podem ser combinados, levando à formação de novos genes. O mecanismo de exon shuffling é favorecido por recombinações intrônicas e está correlacionado com a simetria de exons. Evidências deste mecanismo provém de análises de combinações de fases de introns, correlações entre bordas de exons e de domínios protéicos e da recorrência de domínios em diversas proteínas. Dessa forma, a evolução de proteínas formadas por exon shuffling pode ser inferida considerando a organização exon-intron dos genes, o padrão de combinações de fases de introns e a organização de domínios nas proteínas. Neste sentido, regiões protéicas que possivelmente foram originadas por eventos de exon shuffling foram identificadas através de análises em larga escala em diferentes espécies eucarióticas. A estratégia foi baseada no alinhamento entre todas as proteínas anotadas de uma determinada espécie e a verificação da presença de introns e suas respectivas fases em torno das regiões alinhadas. Nós verificamos que eventos de exon shuffling em eucariotos antigos, de origem anterior aos Metazoa, são predominantemente simétricos 0-0, enquanto nos metazoários a predominância é de unidades simétricas 1-1. Esses dados confirmam idéias anteriores de que a transição para a multicelularidade animal foi marcada pelo embaralhamento extensivo de exons e domínios 1-1. O metazoário basal Trichoplax adhaerens pode ser considerado um representante desta transição, evidenciada pelas freqüências balanceadas de regiões simétricas 0-0 e 1-1. O sinal de flanqueamento por introns em torno das bordas de domínios protéicos confirmou os resultados obtidos através dos alinhamentos, com a prevalência de domínios 0-0 em não metazoários e 1-1 em metazaoários. Um agrupamento hierárquico de domínios flanqueados por introns foi construído, permitindo identificar domínios ou grupos de domínios com evidência de expansões em períodos específicos, como nos vertebrados. Por fim, os genes envolvidos em eventos de exon shuffling foram analisados quanto ao enriquecimento em termos do Gene Ontology. Os resultados indicaram que este mecanismo contribuiu significativamente para a formação de genes relacionados com uma grande diversidade de termos, alguns dos quais envolvidos diretamente com características de metazoários e vertebrados, tais como matriz extracelular, adesão, coagulação sangüínea, processos do sistema imune e sistema nervoso

Exon shuffling was first proposed by Walter Gilbert in 1979 as a mechanism in which exons from different genes could be combined to lead the creation of new genes. The mechanism of exon shuffling is favored by intronic recombinations and it is correlated with symmetry of exons. Evidence of this mechanism come from analyses of intron phase combinations, correlations between the borders of exons and domains and domain recurrence in several proteins. Taking this into account, the evolution of proteins formed by exon shuffling can be…

Advisors/Committee Members: Souza, Sandro José de.

Subjects/Keywords: Domains; Domínios; Evolução; Evolution; Exon shuffling; Exon shuffling; Extracellular matrix; Genoma; Genome; Introns; Introns; Matriz extracelular; Metazoans; Metazoários

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

França, G. S. (2010). História evolutiva de exon shuffling em eucariotos. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/46/46131/tde-26042010-134105/ ;

Chicago Manual of Style (16^th Edition):

França, Gustavo Starvaggi. “História evolutiva de exon shuffling em eucariotos.” 2010. Masters Thesis, University of São Paulo. Accessed March 05, 2021. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-26042010-134105/ ;.

MLA Handbook (7^th Edition):

França, Gustavo Starvaggi. “História evolutiva de exon shuffling em eucariotos.” 2010. Web. 05 Mar 2021.

Vancouver:

França GS. História evolutiva de exon shuffling em eucariotos. [Internet] [Masters thesis]. University of São Paulo; 2010. [cited 2021 Mar 05]. Available from: http://www.teses.usp.br/teses/disponiveis/46/46131/tde-26042010-134105/ ;.

Council of Science Editors:

França GS. História evolutiva de exon shuffling em eucariotos. [Masters Thesis]. University of São Paulo; 2010. Available from: http://www.teses.usp.br/teses/disponiveis/46/46131/tde-26042010-134105/ ;

Tampere University

17. Isokangas, Lydia. Development of CAbase and an Exon Analysis Pipeline for Visual Assessment of Predicted Genes for the Carbonic Anhydrases .

Degree: 2016, Tampere University

URL: https://trepo.tuni.fi/handle/10024/99277

► Background and Aims Humans are able to quickly recognize and evaluate visual patterns, thus this thesis aims to apply this feature to the analysis of… (more)

▼ Background and Aims Humans are able to quickly recognize and evaluate visual patterns, thus this thesis aims to apply this feature to the analysis of aspects of the conservation of carbonic anhydrase proteins. This was facilitated through the creation of two pipelines: * One to create a publically available specialized database to service the CA research world named CAbase, and, * One to create a visual display of the aligned exons of the cDNA transcripts contained within CAbase with indicators to show the positions of start and stop codons along with the locations of the predicted signal and mitochondrial targeting peptides. This pipeline was named Exon_Analysis. Carbonic anhydrases (CAs) are ubiquitous proteins that reversibly catalyse carbon dioxide into carbonic acid. Through the events of duplication, the CAs exist in at least 16 different isoforms and potentially up to 17 different isoforms. Methods The pipelines were created using freely available tools that included python, MySQL, various bioinformatic tools such as Clustal Omega, PRANK, BLAST and Pal2Nal. The data for CAbase was extracted from Ensembl, NCBI, UniProt, RSCB PDB, UniGene and FlyBase. Additionally, calculated data from using SignalP and TargetP was also included. CAbase is hosted on the Amazon Web Server and can be accessed using any computer that has access to the Internet and has MySQL installed. Exon_Analysis draws a scaled exon MSA schematic based on a PRANK MSA of the cDNA transcripts for a CA isoform. The exons and other indicators such as the start and stop codon, and the signal and target peptides are all drawn in different colours and in their scaled locations. Thus it is possible to see the conserved nature of the exons within the coding regions and the aligned start and stop codons and the peptides for each CA isoform. Results CAbase is now publically available for anyone to use. However, it is still somewhat user unfriendly due to the requirement that user be familiar with SQL. CAbase facilitated the use of Exon_Analysis. This pipeline has enabled the quality control of the predicted genes one exon at a time. Evolutionary events such as the conservation of short exons within CAs VI, IX, XII, XIV, X and XI has been shown in the exon MSA schematics. Both tools could be adapted for use with other proteins. Conclusion CAbase is a specialized database for CA researchers that can continue to be adapted to their needs. It allows researchers to create specific queries without having to filter for unwanted proteins. Exon_Analysis creates an exon MSA schematic to visualise the relationship between the exons and other features of interest. This facilitates the quality control of predicted genes one exon at a time.

Subjects/Keywords: carbonic anhydrases; specialised database; exon; ca; predicted genes quality check; signal peptide; mitochondrial targeting; exon analysis pipeline; visual assessment

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Isokangas, L. (2016). Development of CAbase and an Exon Analysis Pipeline for Visual Assessment of Predicted Genes for the Carbonic Anhydrases . (Masters Thesis). Tampere University. Retrieved from https://trepo.tuni.fi/handle/10024/99277

Chicago Manual of Style (16^th Edition):

Isokangas, Lydia. “Development of CAbase and an Exon Analysis Pipeline for Visual Assessment of Predicted Genes for the Carbonic Anhydrases .” 2016. Masters Thesis, Tampere University. Accessed March 05, 2021. https://trepo.tuni.fi/handle/10024/99277.

MLA Handbook (7^th Edition):

Isokangas, Lydia. “Development of CAbase and an Exon Analysis Pipeline for Visual Assessment of Predicted Genes for the Carbonic Anhydrases .” 2016. Web. 05 Mar 2021.

Vancouver:

Isokangas L. Development of CAbase and an Exon Analysis Pipeline for Visual Assessment of Predicted Genes for the Carbonic Anhydrases . [Internet] [Masters thesis]. Tampere University; 2016. [cited 2021 Mar 05]. Available from: https://trepo.tuni.fi/handle/10024/99277.

Council of Science Editors:

Isokangas L. Development of CAbase and an Exon Analysis Pipeline for Visual Assessment of Predicted Genes for the Carbonic Anhydrases . [Masters Thesis]. Tampere University; 2016. Available from: https://trepo.tuni.fi/handle/10024/99277

18. Busetto, Virginia. Study of the splicing factor CWC27 and its link to genetic diseases and EJC assembly : Étude du facteur d'épissage CWC27 et de son lien avec les maladies génétiques et l'assemblage de l'EJC.

Degree: Docteur es, Biologie moléculaire, 2019, Paris Sciences et Lettres (ComUE)

URL: http://www.theses.fr/2019PSLEE037

► Chez les métazoaires, la majorité des gènes codant des protéines contiennent des introns qui sont excisés par la machinerie d’épissage ou « spliceosome » pendant… (more)

▼ Chez les métazoaires, la majorité des gènes codant des protéines contiennent des introns qui sont excisés par la machinerie d’épissage ou « spliceosome » pendant leur transcription. En plus d’enlever les introns, l'étape d'épissage habille les ARNm naissants avec des protéines de liaison à l'ARN (RBPs) qui modulent les étapes suivantes du cycle de vie des ARNm. Le complexe EJC (Exon Junction Complex) déposé par le spliceosome sur les ARNm est un composant majeur de l’ensemble des protéines couvrant les ARNm (particules mRNP). L'EJC est structurellement organisé autour de l'ARN hélicase eIF4A3 qui sert de plate-forme de liaison pour de multiples facteurs annexes. EIF4A3 est spécifiquement recrutée par la machinerie d’épissage par le facteur d’épissage CWC22 avant l'excision des introns. L’EJC joue un rôle central dans le devenir des ARNm en contribuant à la régulation de l’épissage alternatif ainsi que de la localization, la traduction et la dégradation des ARNm. De multiples interrogations subsistent quant au mécanisme par lequel les EJCs sont assemblés par le spliceosome ainsi que le lien existant entre l'expression altérée de protéines de l’EJC et des défauts de développement ou des pathologies humaines. L’objectif de mon doctorat est de caractériser le facteur d'épissage CWC27 dont la fonction précise est inconnue. La première partie de mon travail de recherche consiste en la caractérisation de mutations pathogènes identifiées dans le gène humain CWC27 en collaboration avec des généticiens humains. Cette étude a révélé que des mutations tronquantes de CWC27 sont associées à un phénotype de Rétinite pigmentaire (RP) avec parfois des défauts de développement. J'ai notamment montré que la mutation homozygote c.599+1G>A de CWC27 conduit à l'expression de deux nouveaux transcrits alternatifs contenant un codon de terminaison précoce (PTC). Dans un deuxième temps, j’ai caractérisé biochimiquement et fonctionnellement la protéine CWC27. Afin de purifier efficacement CWC27, j’ai fusionné la protéine endogène avec une étiquette d'affinité FLAG introduite dans le génome des cellules HeLa par la méthode CRISPR-Cas9. La précipitation de FLAG-CWC27 couplée à la spectrométrie de masse quantitative a identifié CWC22 et eIF4A3 comme des partenaires majeurs de CWC27. En exprimant des versions sauvages ou tronquées de CWC22 et CWC27, nous montrons que le domaine C-terminal de CWC27 est médiateur de l'interaction avec CWC22 et eIF4A3. Les mutations correspondant à celles observées chez les patients entraînent la perte des interactions avec CWC22 et eIF4A3. Puis, en utilisant des protéines recombinantes, nous avons reconstitué in vitro le complexe trimérique CWC27/CWC22/eIF4A3 et montré que CWC27 stabilise la liaison de eIF4A3 à CWC22. En collaboration avec des biologistes structuraux, nous avons résolu la structure 3D du complexe CWC27/CWC22/eIF4A3. Cette structure éclaire les premiers contacts de eIF4A3 avec les facteurs d’épissage. Puis, nous avons étudié par RNA-seq, l'impact de la perte de CWC27 sur le transcriptome de cellules… Advisors/Committee Members: Le Hir, Hervé (thesis director).

Subjects/Keywords: Épissage; Cwc27; Maladies génétiques; Exon junction complex (EJC); Splicing; Cwc27; Genetic diseases; Exon junction complex (EJC); 572.8

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Busetto, V. (2019). Study of the splicing factor CWC27 and its link to genetic diseases and EJC assembly : Étude du facteur d'épissage CWC27 et de son lien avec les maladies génétiques et l'assemblage de l'EJC. (Doctoral Dissertation). Paris Sciences et Lettres (ComUE). Retrieved from http://www.theses.fr/2019PSLEE037

Chicago Manual of Style (16^th Edition):

Busetto, Virginia. “Study of the splicing factor CWC27 and its link to genetic diseases and EJC assembly : Étude du facteur d'épissage CWC27 et de son lien avec les maladies génétiques et l'assemblage de l'EJC.” 2019. Doctoral Dissertation, Paris Sciences et Lettres (ComUE). Accessed March 05, 2021. http://www.theses.fr/2019PSLEE037.

MLA Handbook (7^th Edition):

Busetto, Virginia. “Study of the splicing factor CWC27 and its link to genetic diseases and EJC assembly : Étude du facteur d'épissage CWC27 et de son lien avec les maladies génétiques et l'assemblage de l'EJC.” 2019. Web. 05 Mar 2021.

Vancouver:

Busetto V. Study of the splicing factor CWC27 and its link to genetic diseases and EJC assembly : Étude du facteur d'épissage CWC27 et de son lien avec les maladies génétiques et l'assemblage de l'EJC. [Internet] [Doctoral dissertation]. Paris Sciences et Lettres (ComUE); 2019. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2019PSLEE037.

Council of Science Editors:

Busetto V. Study of the splicing factor CWC27 and its link to genetic diseases and EJC assembly : Étude du facteur d'épissage CWC27 et de son lien avec les maladies génétiques et l'assemblage de l'EJC. [Doctoral Dissertation]. Paris Sciences et Lettres (ComUE); 2019. Available from: http://www.theses.fr/2019PSLEE037

19. S. Vashisht. COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY.

Degree: 2017, Università degli Studi di Milano

URL: http://hdl.handle.net/2434/470076

► Spinal Muscular Atrophy (SMA) is among the most common genetic neurological diseases that cause infant mortality. SMA is caused by deletion or mutations in the… (more)

▼ Spinal Muscular Atrophy (SMA) is among the most common genetic neurological diseases that cause infant mortality. SMA is caused by deletion or mutations in the survival motor neuron 1 gene (SMN1), which are expected to generate alterations in RNA transcription, or splicing and most importantly reductions in mRNA transport within the axons of motor neurons (MNs). SMA ultimately results in the selective degeneration of MNs in spinal cord, but the underlying reason is still not clear entirely. The aim of this study is to investigate splicing abnormalities in SMA, and to identify genes presenting differential splicing possibly involved in the pathogenesis of SMA at genome-wide level. We performed RNA-Sequencing data analysis on 2 SMA patients and 2 controls, with 2 biological replicates each sample, derived from their induced Pluripotent Stem Cells-differentiated-MNs. Three types of analyses were executed. Firstly, differential expression analysis was performed to identify possibly mis-regulated genes using Cufflinks. Secondly, alternative splicing analysis was conducted to find differentially-used exons (DUEs; using DEXSeq) as splicing patterns are known to be altered in MNs by the suboptimal levels of SMN protein. Thirdly, we did RNA-binding protein (RBP) - motif discovery for the set of identified alternative cassette-DUEs, to pinpoint possible mechanisms of such alterations, specific to MNs. The gene ontology enrichment analysis of significant DEGs and alternative cassette-DUEs revealed various interesting terms including axon-guidance, muscle-contraction, microtubule-based transport, axon-cargo transport, synapse etc. which suggests their involvement in SMA. Further, promising results were obtained from motif analysis which has identified 22 RBPs out of which 7 RBPs namely, PABPC1, PABPC3, PABPC4, PABPC5, PABPN1, SART3 and KHDRBS1 are known for mRNAs stabilization and mRNA transport across MN-axon. Five RBPs from PABP family are known to interact directly with SMN protein that enhance mRNA transport in MNs. To validate our results specific wet-lab experiments are required, involving precise recognition of RNA-binding sites correspondent with our findings. Our work has provided a promising set of putative targets which might offer potential therapeutic role towards treating SMA. During the course of our study, we have observed that current methods for an effective understanding of differential splicing events within the transcriptomic landscape at high resolution are insufficient. To address this problem, we developed a computational model which has a potential to precisely estimate the “transcript expression levels” within a given gene locus by disentangling mature and nascent transcription contributions for each transcript at per base resolution. We modeled exonic and intronic read coverages by applying a non-linear computational model and estimated expression for each transcript, which best approximated the observed expression in total RNA-Seq data. The performance of our model was good in terms of… Advisors/Committee Members: added supervisor: F. BIANCHI - He has provided very useful suggestions and recommendations to improve my research work that I have presented in the form of yearly reports during my PhD project. In every discussion or during work presentations he appreciated my work and motivated me to keep on going with more good work external supervisor: ULE, JERNEJ - Due to similar area of study, he helped more specifically throughout my PhD project by analyzing my yearly work reports very deeply. Every discussion with him was very fruitful and helped me to draw strong conclusions from my results, supervisor: U. Pozzoli, BIANCHI, FABRIZIO.

Subjects/Keywords: RNA transcription; mRNA splicing; Alternative splicing; Alternative cassette exons; Neurodegenerative genetic disorder; Spinal Muscular Atrophy; Survival Motor Neuron 1 gene; RNA-Sequencing; Biological replicates; induced Pluripotent Stem Cells; Motor neurons; Differentially expressed genes; Differentially-used exon; Differential splicing; Gene Ontology enrichment; Motif; RNA-Binding Proteins; Non-linear computational model; Mature mRNA; Nascent mRNA; Exonic read coverage; Intronic read coverage; Settore MED/04 - Patologia Generale

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Vashisht, S. (2017). COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/470076

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Vashisht, S.. “COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY.” 2017. Thesis, Università degli Studi di Milano. Accessed March 05, 2021. http://hdl.handle.net/2434/470076.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Vashisht, S.. “COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY.” 2017. Web. 05 Mar 2021.

Vancouver:

Vashisht S. COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY. [Internet] [Thesis]. Università degli Studi di Milano; 2017. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2434/470076.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Vashisht S. COMPUTATIONAL APPROACHES IN THE ESTIMATION AND ANALYSIS OF TRANSCRIPTS DIFFERENTIAL EXPRESSION AND SPLICING: APPLICATION TO SPINAL MUSCULAR ATROPHY. [Thesis]. Università degli Studi di Milano; 2017. Available from: http://hdl.handle.net/2434/470076

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universidade do Porto

20. Neves, André Pacheco Pereira. Web usage mining for click fraud detection.

Degree: 2010, Universidade do Porto

URL: http://www.rcaap.pt/detail.jsp?id=oai:repositorio-aberto.up.pt:10216/71308

Estágio realizado na AuditMark e orientado pelo Eng.º Pedro Fortuna

Tese de mestrado integrado. Engenharia Informática e Computação. Faculdade de Engenharia. Universidade do Porto. 2010

Advisors/Committee Members: Borges, José Luís Cabral de Moura, Rossetti, Rosaldo José Fernandes, Universidade do Porto. Faculdade de Engenharia.

Subjects/Keywords: Web usage mining

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Neves, A. P. P. (2010). Web usage mining for click fraud detection. (Thesis). Universidade do Porto. Retrieved from http://www.rcaap.pt/detail.jsp?id=oai:repositorio-aberto.up.pt:10216/71308

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Neves, André Pacheco Pereira. “Web usage mining for click fraud detection.” 2010. Thesis, Universidade do Porto. Accessed March 05, 2021. http://www.rcaap.pt/detail.jsp?id=oai:repositorio-aberto.up.pt:10216/71308.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Neves, André Pacheco Pereira. “Web usage mining for click fraud detection.” 2010. Web. 05 Mar 2021.

Vancouver:

Neves APP. Web usage mining for click fraud detection. [Internet] [Thesis]. Universidade do Porto; 2010. [cited 2021 Mar 05]. Available from: http://www.rcaap.pt/detail.jsp?id=oai:repositorio-aberto.up.pt:10216/71308.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Neves APP. Web usage mining for click fraud detection. [Thesis]. Universidade do Porto; 2010. Available from: http://www.rcaap.pt/detail.jsp?id=oai:repositorio-aberto.up.pt:10216/71308

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Nairobi

21. Ng'ethe, Josephine W. Mobile phones usage in rural Kenya for business a survey study in Machakos district .

Degree: 2010, University of Nairobi

URL: http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/22197

► ICT has been cited as a factor for increased business income among the rural poor. As such it is expected that mobile would increase growth… (more)

Subjects/Keywords: Mobile phones usage

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ng'ethe, J. W. (2010). Mobile phones usage in rural Kenya for business a survey study in Machakos district . (Thesis). University of Nairobi. Retrieved from http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/22197

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ng'ethe, Josephine W. “Mobile phones usage in rural Kenya for business a survey study in Machakos district .” 2010. Thesis, University of Nairobi. Accessed March 05, 2021. http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/22197.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ng'ethe, Josephine W. “Mobile phones usage in rural Kenya for business a survey study in Machakos district .” 2010. Web. 05 Mar 2021.

Vancouver:

Ng'ethe JW. Mobile phones usage in rural Kenya for business a survey study in Machakos district . [Internet] [Thesis]. University of Nairobi; 2010. [cited 2021 Mar 05]. Available from: http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/22197.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ng'ethe JW. Mobile phones usage in rural Kenya for business a survey study in Machakos district . [Thesis]. University of Nairobi; 2010. Available from: http://erepository.uonbi.ac.ke:8080/xmlui/handle/123456789/22197

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Victoria

22. Tongay, Karan Naresh. Privacy preserving software engineering for data driven development.

Degree: Department of Computer Science, 2020, University of Victoria

URL: http://hdl.handle.net/1828/12446

► The exponential rise in the generation of data has introduced many new areas of research including data science, data engineering, machine learning, artificial in- telligence… (more)

▼ The exponential rise in the generation of data has introduced many new areas of research including data science, data engineering, machine learning, artificial in- telligence to name a few. It has become important for any industry or organization to precisely understand and analyze the data in order to extract value out of the data. The value of the data can only be realized when it is put into practice in the real world and the most common approach to do this in the technology industry is through software engineering. This brings into picture the area of privacy oriented software engineering and thus there is a rise of data protection regulation acts such as GDPR (General Data Protection Regulation), PDPA (Personal Data Protection Act), etc. Many organizations, governments and companies who have accumulated huge amounts of data over time may conveniently use the data for increasing business value but at the same time the privacy aspects associated with the sensitivity of data especially in terms of personal information of the people can easily be circumvented while designing a software engineering model for these types of applications. Even before the software engineering phase for any data processing application, often times there can be one or many data sharing agreements or privacy policies in place. Every organization may have their own way of maintaining data privacy practices for data driven development. There is a need to generalize or categorize their approaches into tactics which could be referred by other practitioners who are trying to integrate data privacy practices into their development. This qualitative study provides an understanding of various approaches and tactics that are being practised within the industry for privacy preserving data science in software engineering, and discusses a tool for data usage monitoring to identify unethical data access. Finally, we studied strategies for secure data publishing and conducted experiments using sample data to demonstrate how these techniques can be helpful for securing private data before publishing. Advisors/Committee Members: Ernst, Neil A. (supervisor).

Subjects/Keywords: Data Privacy; Privacy; Data Engineering; Software Engineering; Data Driven Developers; Data Science; Privacy Preserving; Data Driven Development; Machine Learning; One class SVM; Data Usage Monitoring; Health data; k-anonymity; l-diversity; differential privacy; Information management; Secure data sharing; Survey; Audits and access control; Data Privacy Tactics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Tongay, K. N. (2020). Privacy preserving software engineering for data driven development. (Masters Thesis). University of Victoria. Retrieved from http://hdl.handle.net/1828/12446

Chicago Manual of Style (16^th Edition):

Tongay, Karan Naresh. “Privacy preserving software engineering for data driven development.” 2020. Masters Thesis, University of Victoria. Accessed March 05, 2021. http://hdl.handle.net/1828/12446.

MLA Handbook (7^th Edition):

Tongay, Karan Naresh. “Privacy preserving software engineering for data driven development.” 2020. Web. 05 Mar 2021.

Vancouver:

Tongay KN. Privacy preserving software engineering for data driven development. [Internet] [Masters thesis]. University of Victoria; 2020. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1828/12446.

Council of Science Editors:

Tongay KN. Privacy preserving software engineering for data driven development. [Masters Thesis]. University of Victoria; 2020. Available from: http://hdl.handle.net/1828/12446

Vanderbilt University

23. Sexton, Nicole Rose. Murine Hepatitis Virus Regulation of Nucleotide Selectivity and Fidelity by the RNA-dependent RNA Polymerase and the 3’-5’ Exoribonuclease.

Degree: PhD, Microbiology and Immunology, 2017, Vanderbilt University

URL: http://hdl.handle.net/1803/11536

► All positive sense (+)RNA viruses encode RNA-dependent RNA polymerases (RdRps), essential for replication and regulation of the fidelity of nucleotide addition to nascent genomes. The… (more)

▼ All positive sense (+)RNA viruses encode RNA-dependent RNA polymerases (RdRps), essential for replication and regulation of the fidelity of nucleotide addition to nascent genomes. The coronavirus (CoV) RdRp is encoded in nonstructural protein 12 (nsp12). CoV replication utilizes a large complex of proteins, many of which may influence replication fidelity. Specifically, nsp14 encodes a proofreading 3'-5' exoribonuclease (ExoN) in nsp14 that when inactivated (nsp14-ExoN(-)) results in decreased replication fidelity with up to a 20-fold increase in mutations across the CoV genome. Nsp12-RdRp and nsp14-ExoN interact during replication; however, the role of nsp12-RdRp in CoV replication fidelity was not known. To test the role of nsp12-RdRp, we identified residues predicted to participate in replication fidelity by homology modeling, minority variants present after treatment with mutagen, and consensus level mutations present after treatment with the mutagen 5-fluorouracil (5-FU). Mutations, at identified residues, were engineered into MHV nsp14-ExoN(+) and nsp14-ExoN(-) isogenic backgrounds. Viable recovered viruses, as well as populations of virus from passage in the presence of mutagen, were tested for sensitivity to the mutagens 5-fluorouracil (5-FU) or 5-azacytidine (5-AZC). Additionally, changes in replication kinetics, RNA synthesis, competitive fitness, reversion, and/or the accumulation of mutations were quantified. These results demonstrate that nsp14-ExoN masks the contributions of nps12-RdRp to the fidelity of genome replication for CoVs. However, fidelity determinants in nsp12-RdRp still affect replication kinetics and fitness. CoVs encode an extensive replication complex with a number of proteins likely involved in fidelity regulation. These results are essential to understanding the core of this fidelity complex. Advisors/Committee Members: David K. Cortez (committee member), Kristen M. Ogden (committee member), H. Earl Ruley (committee member), Mark R. Denison (committee member), Christopher R. Aiken (Committee Chair).

Subjects/Keywords: Coronavirus; RdRp; ExoN; Mutations; Replication-transcription complex; MHV

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APA (6^th Edition):

Sexton, N. R. (2017). Murine Hepatitis Virus Regulation of Nucleotide Selectivity and Fidelity by the RNA-dependent RNA Polymerase and the 3’-5’ Exoribonuclease. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/11536

Chicago Manual of Style (16^th Edition):

Sexton, Nicole Rose. “Murine Hepatitis Virus Regulation of Nucleotide Selectivity and Fidelity by the RNA-dependent RNA Polymerase and the 3’-5’ Exoribonuclease.” 2017. Doctoral Dissertation, Vanderbilt University. Accessed March 05, 2021. http://hdl.handle.net/1803/11536.

MLA Handbook (7^th Edition):

Sexton, Nicole Rose. “Murine Hepatitis Virus Regulation of Nucleotide Selectivity and Fidelity by the RNA-dependent RNA Polymerase and the 3’-5’ Exoribonuclease.” 2017. Web. 05 Mar 2021.

Vancouver:

Sexton NR. Murine Hepatitis Virus Regulation of Nucleotide Selectivity and Fidelity by the RNA-dependent RNA Polymerase and the 3’-5’ Exoribonuclease. [Internet] [Doctoral dissertation]. Vanderbilt University; 2017. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1803/11536.

Council of Science Editors:

Sexton NR. Murine Hepatitis Virus Regulation of Nucleotide Selectivity and Fidelity by the RNA-dependent RNA Polymerase and the 3’-5’ Exoribonuclease. [Doctoral Dissertation]. Vanderbilt University; 2017. Available from: http://hdl.handle.net/1803/11536

Vanderbilt University

24. Case, James Brett. Roles of the Coronavirus 3'-to-5' Exoribonuclease and N7-Methyltransferase in Counteracting Innate Immunity.

Degree: PhD, Microbiology and Immunology, 2018, Vanderbilt University

URL: http://hdl.handle.net/1803/10826

► Coronaviruses (CoVs) are positive-sense RNA viruses that infect numerous mammalian and avian species and are capable of causing severe and lethal disease in humans. CoVs… (more)

▼ Coronaviruses (CoVs) are positive-sense RNA viruses that infect numerous mammalian and avian species and are capable of causing severe and lethal disease in humans. CoVs encode many innate immune antagonists that counteract the host innate immune response to facilitate efficient viral replication. CoV non-structural protein 14 (nsp14) is a multifunctional protein that encodes 3’-to-5’ exoribonuclease (ExoN) and N7-methyltransferase (N7-MTase) activities. CoV ExoN activity performs a proofreading function and is required for high-fidelity replication of the uniquely large CoV RNA genome. Furthermore, eukaryotic mRNAs possess a methylated 5’-guanosine cap that is required for RNA stability, efficient translation, and protection from cell-intrinsic defenses. CoV nsp14 N7-MTase activity is implicated in viral RNA 5’ capping resulting in structures that mimic cellular 5’ caps. In this dissertation research, I tested the hypothesis that nsp14 ExoN and N7-MTase activities function to antagonize the innate immune response. Using site directed mutagenesis to ablate CoV nsp14 ExoN activity, I demonstrate that ExoN activity is required for resistance to the innate immune response and that viruses lacking ExoN activity that were generated during an antiviral state are less viable to establish a subsequent infection. In addition, I demonstrate that CoV nsp14 N7-MTase activity prevents detection of viral RNAs by innate sensors, confers resistance to the IFN-β-mediated innate immune response, and directs efficient translation of viral proteins. Altogether, this dissertation research demonstrates that CoV nsp14 ExoN and N7-MTase activities are required for viral resistance to the effects of the IFN-β-mediated innate immune response and represent highly conserved targets for the attenuation of CoVs. Advisors/Committee Members: Mark R. Denison (committee member), Kristen M. Ogden (committee member), James W. Thomas (committee member), Manuel Ascano Jr. (committee member), Eric P. Skaar (Committee Chair).

Subjects/Keywords: RNA capping; ExoN; Coronvirus; innate immunity; interferon; innate immune antagonism

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APA (6^th Edition):

Case, J. B. (2018). Roles of the Coronavirus 3'-to-5' Exoribonuclease and N7-Methyltransferase in Counteracting Innate Immunity. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10826

Chicago Manual of Style (16^th Edition):

Case, James Brett. “Roles of the Coronavirus 3'-to-5' Exoribonuclease and N7-Methyltransferase in Counteracting Innate Immunity.” 2018. Doctoral Dissertation, Vanderbilt University. Accessed March 05, 2021. http://hdl.handle.net/1803/10826.

MLA Handbook (7^th Edition):

Case, James Brett. “Roles of the Coronavirus 3'-to-5' Exoribonuclease and N7-Methyltransferase in Counteracting Innate Immunity.” 2018. Web. 05 Mar 2021.

Vancouver:

Case JB. Roles of the Coronavirus 3'-to-5' Exoribonuclease and N7-Methyltransferase in Counteracting Innate Immunity. [Internet] [Doctoral dissertation]. Vanderbilt University; 2018. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1803/10826.

Council of Science Editors:

Case JB. Roles of the Coronavirus 3'-to-5' Exoribonuclease and N7-Methyltransferase in Counteracting Innate Immunity. [Doctoral Dissertation]. Vanderbilt University; 2018. Available from: http://hdl.handle.net/1803/10826

25. Boger, Robert Warren. Fission Yeast Exon Junction Complex Orthologs Ensure the Maturation of Meiotic Transcripts During Meiosis.

Degree: 2016, Wake Forest University

URL: http://hdl.handle.net/10339/59308

► Meiosis, requisite for sexual reproduction, encompasses unique processes that do not occur in vegetative cells, including precise expression of specific genes (meiotic genes). During mitotic… (more)

Subjects/Keywords: Exon junction complex

…x29;, the fission yeast ortholog of eIF4AIII, which is a core member of the mammalian exon… …a manner such that 3-7 bases on its 3’ end spanned an exon- 9 exon junction, ensuring… …of total meiotic mRNA, regardless of splice-state. Primers contained within a single exon… …eIF4AIII is a member of the exon junction complex (EJC), and acts as a molecular clamp… …S. pombe ortholog of eIF4aIII, which is a member of the exon junction complex (EJC…

11 more images…

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APA (6^th Edition):

Boger, R. W. (2016). Fission Yeast Exon Junction Complex Orthologs Ensure the Maturation of Meiotic Transcripts During Meiosis. (Thesis). Wake Forest University. Retrieved from http://hdl.handle.net/10339/59308

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Boger, Robert Warren. “Fission Yeast Exon Junction Complex Orthologs Ensure the Maturation of Meiotic Transcripts During Meiosis.” 2016. Thesis, Wake Forest University. Accessed March 05, 2021. http://hdl.handle.net/10339/59308.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Boger, Robert Warren. “Fission Yeast Exon Junction Complex Orthologs Ensure the Maturation of Meiotic Transcripts During Meiosis.” 2016. Web. 05 Mar 2021.

Vancouver:

Boger RW. Fission Yeast Exon Junction Complex Orthologs Ensure the Maturation of Meiotic Transcripts During Meiosis. [Internet] [Thesis]. Wake Forest University; 2016. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10339/59308.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Boger RW. Fission Yeast Exon Junction Complex Orthologs Ensure the Maturation of Meiotic Transcripts During Meiosis. [Thesis]. Wake Forest University; 2016. Available from: http://hdl.handle.net/10339/59308

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Australian National University

26. Blom, Mozes. The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans .

Degree: 2016, Australian National University

URL: http://hdl.handle.net/1885/118217

► Understanding the evolutionary processes that generate and maintain biodiversity is a fundamental objective in ecology and evolution. In this dissertation, I characterize phylogenetic patterns in… (more)

▼ Understanding the evolutionary processes that generate and maintain biodiversity is a fundamental objective in ecology and evolution. In this dissertation, I characterize phylogenetic patterns in a recent radiation of Australian skinks, discuss the ecological context of diversification and how this has translated into macroevolutionary change across the continent. By also reconstructing the evolutionary history of all Cryptoblepharus species globally, I shed further light on the evolutionary and biogeographic processes that have shaped the diversity of the genus. This dissertation project has generated an empirical framework for future studies into the continuous nature between micro- and macroevolutionary change. To infer the phylogeny of Australian Cryptoblepharus, I generated an exon- capture dataset and designed a bioinformatic pipeline to generate quality filtered sequence alignments (Appendix A). Multi-locus datasets are required to confidently infer species trees for rapidly speciating clades due to a high prevalence of gene tree incongruence among loci. In Chapter I, I use the Cryptoblepharus radiation as an empirical example and describe how to account for differences in gene tree resolution when employing summary-coalescent methods for species tree inference. Our study highlights the importance of phylogenetically informative loci but simultaneously demonstrates that the addition of non-informative loci does not introduce phylogenetic noise. In Chapter II, I then use comparative methods and morphological measurements for over 800 individuals, to examine the ecological context of diversification in Australian Cryptoblepharus. Specifically, I focus on whether habitat specialisation can explain current patterns of variation in ecologically relevant traits. I observed significant differences in morphology between species that occur in distinct environments (rock, arboreal and littoral) and species that occur within the same habitat are often cryptic. These findings suggest that isolated analogous habitats have provided ecological opportunity and repeatedly promoted adaptive diversification, while speciation within habitat has accrued without ecomorphological change. In contrast to well known adaptive radiations in insular environments, continental radiations are likely driven by alternative diversification processes that jointly stimulate species proliferation. In Chapter III, I explore patterns of introgression between phylogenetically divergent species. I combine population and phylogenetic tools, to quantify the extent of introgression between ecomorphologically distinct and similar taxa. I describe the frequent occurrence of mitochondrial haplotype sharing across species boundaries and the complete replacement of the mitochondrial genome in one species. Furthermore, non-sister…

Subjects/Keywords: Cryptoblepharus; Scincidae; phylogenomics; introgression; speciation; macroevolution; biogeography; continental radiation; exon capture

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APA (6^th Edition):

Blom, M. (2016). The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans . (Thesis). Australian National University. Retrieved from http://hdl.handle.net/1885/118217

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Blom, Mozes. “The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans .” 2016. Thesis, Australian National University. Accessed March 05, 2021. http://hdl.handle.net/1885/118217.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Blom, Mozes. “The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans .” 2016. Web. 05 Mar 2021.

Vancouver:

Blom M. The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans . [Internet] [Thesis]. Australian National University; 2016. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1885/118217.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Blom M. The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans . [Thesis]. Australian National University; 2016. Available from: http://hdl.handle.net/1885/118217

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

27. 木村,洋平. CD44variant exon 9 plays an important role in colon cancer initiating cells. : CD44 variant exon 9は大腸癌幹細胞において重要な役割を示す.

Degree: 博士(医学), 2014, University of Fukui / 福井大学

URL: http://hdl.handle.net/10098/8439

以下に掲載 : Oncotarget 4(5) pp.785-791 2013. Impact Journals. 共著者 : Youhei Kimura, Takanori Goi, Toshiyuki Nakazawa, Hirono Yasuno, Kanji Katayama, Takeshi Urano, Akiko Yamaguchi

Subjects/Keywords: colon cancer; CD44 variant exon; stem cells; Cancer initiating cells

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APA (6^th Edition):

木村,洋平. (2014). CD44variant exon 9 plays an important role in colon cancer initiating cells. : CD44 variant exon 9は大腸癌幹細胞において重要な役割を示す. (Thesis). University of Fukui / 福井大学. Retrieved from http://hdl.handle.net/10098/8439

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

木村,洋平. “CD44variant exon 9 plays an important role in colon cancer initiating cells. : CD44 variant exon 9は大腸癌幹細胞において重要な役割を示す.” 2014. Thesis, University of Fukui / 福井大学. Accessed March 05, 2021. http://hdl.handle.net/10098/8439.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

木村,洋平. “CD44variant exon 9 plays an important role in colon cancer initiating cells. : CD44 variant exon 9は大腸癌幹細胞において重要な役割を示す.” 2014. Web. 05 Mar 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

木村,洋平. CD44variant exon 9 plays an important role in colon cancer initiating cells. : CD44 variant exon 9は大腸癌幹細胞において重要な役割を示す. [Internet] [Thesis]. University of Fukui / 福井大学; 2014. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10098/8439.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

木村,洋平. CD44variant exon 9 plays an important role in colon cancer initiating cells. : CD44 variant exon 9は大腸癌幹細胞において重要な役割を示す. [Thesis]. University of Fukui / 福井大学; 2014. Available from: http://hdl.handle.net/10098/8439

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete
Not specified: Masters Thesis or Doctoral Dissertation

28. 加藤, 成. Cancer Stem Cell Marker in circulating tumor cells of Human Colorectal Cancer:Expression of CD44variant exon9 is Strongly Correlated to Treatment Refractoriness,Recurrence,and Prognosis : ヒト大腸癌症例における循環腫瘍細胞での癌幹細胞マーカー:CD44variant exon9の発現は治療抵抗性、再発、予後との関連性が高い.

Degree: 博士(医学), 2015, University of Fukui / 福井大学

URL: http://hdl.handle.net/10098/8833

以下に掲載 : Anticancer Research 35 pp.239-244 2015. International Institute of Anticancer Research. 共著者 : Shigeru Katoh, Takanori Goi, Takayuki Naruse, Yuki Ueda, Hidetaka Kurebayashi, Toshiyuki Nakazawa, Youhei Kimura, Yasuno Hirono, Akio Yamaguchi

Subjects/Keywords: Colorectal cancer; CD44 variant exon 9; circulating tumor cells

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APA (6^th Edition):

加藤, �. (2015). Cancer Stem Cell Marker in circulating tumor cells of Human Colorectal Cancer:Expression of CD44variant exon9 is Strongly Correlated to Treatment Refractoriness,Recurrence,and Prognosis : ヒト大腸癌症例における循環腫瘍細胞での癌幹細胞マーカー:CD44variant exon9の発現は治療抵抗性、再発、予後との関連性が高い. (Thesis). University of Fukui / 福井大学. Retrieved from http://hdl.handle.net/10098/8833

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

加藤, 成. “Cancer Stem Cell Marker in circulating tumor cells of Human Colorectal Cancer:Expression of CD44variant exon9 is Strongly Correlated to Treatment Refractoriness,Recurrence,and Prognosis : ヒト大腸癌症例における循環腫瘍細胞での癌幹細胞マーカー:CD44variant exon9の発現は治療抵抗性、再発、予後との関連性が高い.” 2015. Thesis, University of Fukui / 福井大学. Accessed March 05, 2021. http://hdl.handle.net/10098/8833.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

加藤, 成. “Cancer Stem Cell Marker in circulating tumor cells of Human Colorectal Cancer:Expression of CD44variant exon9 is Strongly Correlated to Treatment Refractoriness,Recurrence,and Prognosis : ヒト大腸癌症例における循環腫瘍細胞での癌幹細胞マーカー:CD44variant exon9の発現は治療抵抗性、再発、予後との関連性が高い.” 2015. Web. 05 Mar 2021.

Vancouver:

加藤 �. Cancer Stem Cell Marker in circulating tumor cells of Human Colorectal Cancer:Expression of CD44variant exon9 is Strongly Correlated to Treatment Refractoriness,Recurrence,and Prognosis : ヒト大腸癌症例における循環腫瘍細胞での癌幹細胞マーカー:CD44variant exon9の発現は治療抵抗性、再発、予後との関連性が高い. [Internet] [Thesis]. University of Fukui / 福井大学; 2015. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10098/8833.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

加藤 �. Cancer Stem Cell Marker in circulating tumor cells of Human Colorectal Cancer:Expression of CD44variant exon9 is Strongly Correlated to Treatment Refractoriness,Recurrence,and Prognosis : ヒト大腸癌症例における循環腫瘍細胞での癌幹細胞マーカー:CD44variant exon9の発現は治療抵抗性、再発、予後との関連性が高い. [Thesis]. University of Fukui / 福井大学; 2015. Available from: http://hdl.handle.net/10098/8833

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Adelaide

29. Stringer, Danielle Nicole. The systematics and biogeographic history of Australian arid zone oniscidean isopods (Philosciidae).

Degree: 2019, University of Adelaide

URL: http://hdl.handle.net/2440/121597

► Groundwater-dependent ecosystems in the Australian arid zone consist of highly diverse and relictual endemic invertebrates with complex evolutionary histories. Recent molecular phylogenetic studies on Haloniscus… (more)

▼ Groundwater-dependent ecosystems in the Australian arid zone consist of highly diverse and relictual endemic invertebrates with complex evolutionary histories. Recent molecular phylogenetic studies on Haloniscus isopods, in particular, have identified significant levels of short-range endemicity, revealed extensive diversity with 26 new putative species, and have uncovered preliminary findings for a pattern of a shared evolutionary history amongst Haloniscus species from disparate and isolated groundwater regions. However, molecular datasets were restricted to either a single mitochondrial (cytochrome “c” oxidase subunit I (COI)) or two genes (COI and 18S rRNA), which resulted in poor topological resolution for internal branches, and evolutionary connections were not assessed in detail with divergence dating analyses. In this study, we aimed to generate a substantial and informative phylogenomic dataset with a transcriptome-based exon capture approach to examine the evolution and biogeographic history of Haloniscus from three major Australian arid zone groundwater-dependent ecosystems: subterranean calcrete aquifers of the Yilgarn region in Western Australia and Ngalia Basin region, Northern Territory, and surface springs fed by the Great Artesian Basin in South Australia. In Chapter 2, we generated an effective methodological framework to infer an isopod-specific orthologous marker set and bait design targeting 469 single-copy protein-coding genes, provided empirical data and post-processing scripts to improve future exon capture experiments, and produced a well-resolved Haloniscus isopod phylogeny for further phylogenetic and biogeographic inference. In Chapter 3, we implemented this dataset, together with additional phylogenetic analyses, divergence time dating and ancestral area reconstructions, to highlight significant historical connections between Haloniscus from the three groundwater regions and the influence of two major aridification intervals, one in the late Miocene and a second, following a temporary return to warmer and wetter conditions, in the Pliocene, on the isolation and ensuing diversification of the fauna. These findings contribute key insights into the biogeographic history of the Australian continent, and provide support for important hypotheses regarding the aridification of Australia. Lastly, in Chapter 4, we described four new species of Haloniscus, presented a revised generic diagnosis and key to the genus, transferred the genus from Scyphacidae to Philosciidae, and also transferred two species from Andricophiloscia to Haloniscus. The exploitation of groundwater for industrial, agricultural, and domestic uses represents a serious threat to these important taxa, and the formal documentation and naming of species (beyond just molecular results) is critical to the successful conservation management of these climate relicts and their refugial ecosystems. Advisors/Committee Members: Austin, Andrew (advisor), School of Social Sciences (school).

Subjects/Keywords: arid zone; biogeography; exon capture; groundwater; lsopoda; taxonomy

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APA (6^th Edition):

Stringer, D. N. (2019). The systematics and biogeographic history of Australian arid zone oniscidean isopods (Philosciidae). (Thesis). University of Adelaide. Retrieved from http://hdl.handle.net/2440/121597

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Stringer, Danielle Nicole. “The systematics and biogeographic history of Australian arid zone oniscidean isopods (Philosciidae).” 2019. Thesis, University of Adelaide. Accessed March 05, 2021. http://hdl.handle.net/2440/121597.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Stringer, Danielle Nicole. “The systematics and biogeographic history of Australian arid zone oniscidean isopods (Philosciidae).” 2019. Web. 05 Mar 2021.

Vancouver:

Stringer DN. The systematics and biogeographic history of Australian arid zone oniscidean isopods (Philosciidae). [Internet] [Thesis]. University of Adelaide; 2019. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2440/121597.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Stringer DN. The systematics and biogeographic history of Australian arid zone oniscidean isopods (Philosciidae). [Thesis]. University of Adelaide; 2019. Available from: http://hdl.handle.net/2440/121597

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of California – San Francisco

30. Huff, Jason Troy. Genomic studies of mammalian gene regulation.

Degree: Biochemistry and Molecular Biology, 2011, University of California – San Francisco

URL: http://www.escholarship.org/uc/item/0jb6x3mg

► Much of biological complexity is achieved through regulated gene expression. In eukaryotes the rst step of gene expression involves transcription of DNA within chromatin to… (more)

▼ Much of biological complexity is achieved through regulated gene expression. In eukaryotes the rst step of gene expression involves transcription of DNA within chromatin to produce RNA, which often undergoes extensive processing co- and posttranscriptionally. Chromatin can aect one or more steps in gene expression at any number of genomic elements to achieve proper regulation. Furthermore, chromatin itself can be modied as a result of expression, thus bearing an epigenetic mark of gene activity that can be used for further regulation. Here, we used experimental and computational approaches in a variety of mammalian systems to establish how chromatin at various genomic elements is related to gene expression and co-transcriptional steps of RNA processing.First, we used X chromosome-wide chromatin states to elucidate how genes can be expressed from within otherwise silent chromatin in humans. Second, we explored the mechanism of a chromatin-modifying complex in modulating mouse embryonic stem cell behavior. Last, we uncovered a correlation between chromatin structure and human gene architecture and gured out how this relates to RNA processing. The results present a scenario in which transcribed genes contain active chromatin locally restricted to the genes proper, even in the midst of otherwise silent chromatin. The active chromatin in these regions is kept in such a state probably through the action of many factors. A corollary, specically that many factors can subsequently make use of chromatin marks, is also valid and in the case of embryonic stem cells, a chromatin complex makes use of an active mark at promoters to repress transcription for cellular self-renewal. Finally, we identied novel connections between active chromatin marks and introns and exons, which we propose are influenced through a mechanism involving co-transcriptional exon denition, a process previously thought to be important only in RNA processing. Analogously to active marks at promoters, these intronic and exonic chromatin marks could be subsequently used to regulate gene-centered DNA metabolism. In summary, these studies demonstrate the utility of genome-scale approaches in identifying features of gene expression in relationship to chromatin and produce several avenues for future research.

Subjects/Keywords: Molecular Biology; chromatin; exon; human; intron; mammalian; transcription

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APA (6^th Edition):

Huff, J. T. (2011). Genomic studies of mammalian gene regulation. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/0jb6x3mg

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Huff, Jason Troy. “Genomic studies of mammalian gene regulation.” 2011. Thesis, University of California – San Francisco. Accessed March 05, 2021. http://www.escholarship.org/uc/item/0jb6x3mg.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Huff, Jason Troy. “Genomic studies of mammalian gene regulation.” 2011. Web. 05 Mar 2021.

Vancouver:

Huff JT. Genomic studies of mammalian gene regulation. [Internet] [Thesis]. University of California – San Francisco; 2011. [cited 2021 Mar 05]. Available from: http://www.escholarship.org/uc/item/0jb6x3mg.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Huff JT. Genomic studies of mammalian gene regulation. [Thesis]. University of California – San Francisco; 2011. Available from: http://www.escholarship.org/uc/item/0jb6x3mg

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Open Access Theses and Dissertations