| 1. |
- Aken, Bronwen L., et al.
(författare)
-
The Ensembl gene annotation system
- 2016
-
Ingår i: Database. - : Oxford University Press (OUP). - 1758-0463.
-
Tidskriftsartikel (refereegranskat)abstract
- The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.
|
|
| 2. |
- Ameur, Adam, et al.
(författare)
-
SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
-
Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
-
Tidskriftsartikel (refereegranskat)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
|
|
| 3. |
|
|
| 4. |
|
|
| 5. |
- Ruffier, Magali, et al.
(författare)
-
Ensembl core software resources : storage and programmatic access for DNA sequence and genome annotation
- 2017
-
Ingår i: Database. - : OXFORD UNIV PRESS. - 1758-0463.
-
Tidskriftsartikel (refereegranskat)abstract
- The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list (http://www.ensembl.org/info/about/contact/index.html).
|
|
| 6. |
- Thulin, Andreas, et al.
(författare)
-
The development and evaluation of an online hearing loss prevention program.
- 2023
-
Ingår i: Preventive Medicine Reports. - 2211-3355. ; 35
-
Tidskriftsartikel (refereegranskat)abstract
- Recent studies underline the need for research on approaches to encouraging healthy listening habits. This study aims to develop and evaluate an online hearing loss prevention program; and examine its influence on the participants' use of hearing protection, hearing loss prevention knowledge, attitude towards noise, and program useability and adherence. The study was conducted in the county of Västra Götaland, Sweden, from March through October 2021. The program included four modules focused on hearing and hearing loss prevention and was accessible to the participants for four weeks. In total, 75 participants completed the program which was evaluated using the Youth Attitude to Noise Scale and four additional self-designed questionnaires. The questionnaires were deployed before and immediately after program completion. The findings indicate that the program may influence the participants' attitudes toward noise and the use of hearing protection. The participants who completed the program perceived high useability and increased hearing loss prevention knowledge. This program is most needed to promote healthy hearing. Future studies should target specific groups with this program and evaluate its long-term effects.
|
|
