| 1. |
- Mannapperuma, Chanaka, 1982-
(författare)
-
Human-computer interaction principles for developing web-based genomics resources
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genomics projects, including genome sequencing, transcriptomics, genome-wide association mapping and epigenetics assays, producevast quantities of data. Extracting the required information from such complex datasets is a significant challenge and even where software tools do exist, these are often not intuitive or designed fornon-specialist users. This dissertation details how I have applied design principles from the field of Human-Computer Interaction (HCI) to the development of intuitive bioinformatics web-based resources for exploring genomics data. In the first part of the thesis I detail the development of a specialised genomics resource that enables non specialists who lack bioinformatics skills to access, explore and extract new knowledge from a variety of genomics data types. These tools were developed in collaboration with wet lab biologists and bioinformaticians who represent typical end-users. The tools developed have been integrated within the PlantGenIE (Plant Genome IntegrativeExplorer) web resource, which has been established as a platform for exploring genomics data for Populus, conifer, Eucalyptus and Arabidopsisgenomics data. Even though the ability to collect, store and manage data is increasing faster due to new technologies and science, our ability to understand it remains constant. To help address this, in the second part of this dissertation I focus on the usability enhancement of tools based on the HCI and User Experience (UX) practices. To achieve this, I utilised visualisation techniques and design principles in the design process for the improvement of the PlantGenIEUser Interface (UI), and applied usability methods to evaluate the UX of PlantGenIE tools. These results were then used to inform adaptations and fine-tuning of those. I show that utilisation of these research methods and practices with the development life cycle represents a framework for designing usable bioinformatics tools. Wider-scale use of these methods by future designers and developers will enable the creation of more usable bioinformatics resources.
|
|
| 2. |
- Schiffthaler, Bastian, 1990-
(författare)
-
Embracing the data flood : integrating diverse data to improve phenotype association discovery in forest trees
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Complex traits represent valuable research targets as many highly desirable properties of plants and animals (such as growth rate and height) fall into this group. However, associating biological markers with these traits is incredibly challenging, in part due to their small effect sizes. For the two species at the core of our research, European aspen (Populus tremula) and Norway spruce (Picea abies), association studies are even more challenging, primarily due to the fragmented state of their genome assemblies. These assemblies represent the gene space well, but poorly represented inter-genic regions hinder variant discovery and large scale association studies.In this thesis, I present my work to improve association discovery of complex traits in forest trees. Firstly, to overcome the issues with assembly fragmentation, I have created an updated version of the P. tremula genome, which is highly contiguous and anchored in full chromosomes. To calculate the dense linkage map required to order and orient the aspen assembly, I developed "BatchMap", a parallel implementation of linkage mapping software. BatchMap has been successfully applied to several dense linkage maps, including aspen and Norway spruce, and was essential to the progress in improving the aspen genome assembly. Further, I developed seidr, which represents a starting point in multi-layer, network-based systems biology, an analysis technique with promising prospects for complex trait association analysis. As a case study, I applied some of the methods developed to the analysis of leaf shape in natural populations of European aspen, a complex, omnigenic trait.The multi-layer model of systems biology and related analysis techniques offer promise in the analysis of complex traits, and this thesis represents a starting point toward an intricate, holistic model of systems biology that may help to unravel the overwhelmingly complicated nature of complex traits.
|
|
| 3. |
- Thelin, Lisa, et al.
(författare)
-
Diverging functions among calreticulin isoforms in higher plants
- 2011
-
Ingår i: Plant Signalling & Behavior. - : Taylor & Francis. - 1559-2316 .- 1559-2324. ; 6:6, s. 905-910
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The ER chaperone calreticulin plays vital roles in numerous cellular processes, including Ca2+-homeostasis, apoptosis and cell adhesion, in animal cells. Although calreticulin has been systematically characterized in animal cells, the focus has been on one of the isoforms. However, recent advances in the plant calreticulin field have revealed functional divergence of calreticulin isoforms. While two of the plant isoforms appear to work within a general ER chaperone framework, the third isoform is associated with folding of receptors for brassinosteroids and bacterial peptides. Hence, the discovery of functional specialization of plant calreticulins opens up new vistas for calreticulins also in the animal field.
|
|
