A5010434456- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Epigenetics and DNA Methylation
- Bacillus and Francisella bacterial research
- Genomic variations and chromosomal abnormalities
- Diabetes and associated disorders
- Advanced MEMS and NEMS Technologies
- Acute Lymphoblastic Leukemia research
- Image Processing Techniques and Applications
- Plant Genetic and Mutation Studies
- Photonic and Optical Devices
- Cancer-related molecular mechanisms research
- Viral gastroenteritis research and epidemiology
- Phagocytosis and Immune Regulation
- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Genetic factors in colorectal cancer
- Mitochondrial Function and Pathology
- Bacterial Genetics and Biotechnology
- Gene expression and cancer classification
- Congenital heart defects research
Science for Life Laboratory
2014-2023
Uppsala University
2006-2023
Stockholm University
2014
European Bioinformatics Institute
2010-2013
University of Leicester
2013
Wellcome Trust
2010-2013
Karolinska University Hospital
2013
National Center for Biotechnology Information
2013
Wellcome Sanger Institute
2010-2011
Swedish Defence Research Agency
2001
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human data as well key model organisms such mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) Tasmanian devil (Sarcophilus harrisii) bringing total number of supported to 61 release 64 (September 2011). Of these, 55 appear main website six are provided preview site (Pre!Ensembl; http://pre.ensembl.org)...
The Ensembl project ( http://www.ensembl.org ) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations set of includes additional data focused variation, comparative, evolutionary, functional regulatory annotation. most advanced resources are provided for key including human, mouse, rat zebrafish...
As our knowledge of the complexity gene architecture grows, and we increase understanding subtleties expression, process accurately describing disease-causing variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here Locus Reference Genomic (LRG) format, which been designed for specific purpose variant reporting. The format builds on successful National Center Biotechnology Information (NCBI)...
Locus Reference Genomic (LRG; http://www.lrg-sequence.org/) records contain internationally recognized stable reference sequences designed specifically for reporting clinically relevant sequence variants. Each LRG is contained within a single file consisting of 'fixed' section and regularly updated 'updatable' section. The fixed contains genomic DNA region, essential transcripts proteins variant an exon numbering system. updatable mapping information, annotation all overlapping genes in the...
Massively parallel DNA sequencing (MPS) has the potential to revolutionize diagnostics, in particular for monogenic disorders. Inborn errors of metabolism (IEM) constitute a large group disorders with highly variable clinical presentation, often acute, nonspecific initial symptoms. In many cases irreversible damage can be reduced by initiation specific treatment, provided that correct molecular diagnosis rapidly obtained. MPS thus significantly improve both diagnostics and outcome affected...
Journal Article Preliminary analysis and annotation of the partial genome sequence Francisella tularensis strain Schu 4 Get access R.G. Prior, Prior Defence Evaluation Research Agency, CBD Porton Down, Salisbury, Wilts, UK Search for other works by this author on: Oxford Academic Google Scholar L. Klasson, Klasson Department Molecular Evolution, University Uppsala, Sweden P. Larsson, Larsson National Establishment, Umeå, K. Williams, Williams Infectious Tropical Diseases, London School...
ABSTRACT Most eukaryotic mRNAs depend upon precise removal of introns by the spliceosome, a complex RNAs and proteins. Splicing pre-mRNA is known to take place in Dictyostelium discoideum , we previously isolated U2 spliceosomal RNA experimentally. In this study, identified remaining major bioinformatical approach. Expression was verified from 17 small nuclear (snRNA) genes. All these genes are preceded putative noncoding gene promoter. Immunoprecipitation showed that snRNAs U1, U2, U4, U5,...
Genome data are increasingly important in the computational identification of novel regulatory non-coding RNAs (ncRNAs). However, most ncRNA gene-finders either specialized to well-characterized gene families or require comparisons closely related genomes. We developed a method for de novo screening genes with nucleotide composition that stands out against background genome based on partial sum process. compared performance when assuming independent and first-order Markov-dependent...
Abstract Objectives The aim of this data paper is to describe a collection 33 genomic, transcriptomic and epigenomic sequencing datasets the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH one most frequently used lines for functional studies pediatric ALL, these provide multi-faceted characterization its molecular features. described herein, generated with short- long-read technologies, can both insights into complex aberrant karyotype REH, be as reference quality assessment or...
Abstract Arteria is an automation system aimed at sequencing core facilities. It built on existing open source technologies, with a modular design allowing for community-driven effort to create plug-and-play micro-services. Herein we describe the and elaborate underlying conceptual framework. The breaks down into three levels; orchestration, process execution. At orchestration level it utilizes event-based model of automation. models processes, e.g. steps involved in processing data, as...
In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This led to an explosive growth data produced worldwide. As the amount of increases, so does need for automated solutions processing analysis. The concept workflows gained favour bioinformatics community, but there is little scientific literature describing end-to-end automation systems. Arteria system that aims at providing a solution data-related operational challenges face...
Abstract Objectives The aim of this data paper is to describe a collection 33 genomic, transcriptomic and epigenomic sequencing datasets the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH one most frequently used lines for functional studies pediatric ALL, these provide multi-faceted characterization its molecular features. described herein, generated with short- long-read technologies, can both insights into complex aberrant karyotype REH, be as reference quality assessment or...