| 1. |
- Barrio, Alvaro Martínez, et al.
(författare)
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Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX
- 2009
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Ingår i: BMC Bioinformatics. - : BioMed Central. - 1471-2105. ; 10 Suppl. 6, s. S18-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user. RESULTS: An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized in silico tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations. CONCLUSION: The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, http://www.dasregistry.org, or at http://loka.bmc.uu.se/das/sources.
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| 2. |
- Gloriam, David E., et al.
(författare)
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A Community Standard Format for the Representation of Protein Affinity Reagents
- 2010
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 9:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one online warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site. Molecular & Cellular Proteomics 9: 1-10, 2010.
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| 3. |
- Klingström, Tomas, et al.
(författare)
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Workshop on laboratory protocol standards for the molecular methods database
- 2013
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Ingår i: New Biotechnology. - : Elsevier BV. - 1871-6784 .- 1876-4347. ; 30:2, s. 109-113
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Tidskriftsartikel (refereegranskat)abstract
- Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
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| 4. |
- Loftsdottir, Heidur, et al.
(författare)
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Dynamics of insertion sequence element IS629 inactivation of verotoxin 2 genes in Escherichia coli O157:H7
- 2017
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press. - 0378-1097 .- 1574-6968. ; 364:8
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Tidskriftsartikel (refereegranskat)abstract
- There are several anecdotal reports of insertion sequence (IS) element inactivation of verotoxin genes among enterohaemorrhagic Escherichia coli of the serotype O157:H7, a pathogen causing severe gastrointestinal disease in infected humans. These insertions can be expected to drastically reduce the virulence of the bacteria. IS element inactivation has been shown to be reversible in model systems, suggesting the possibility of spontaneous restoration of virulence. In this study, traditional and high-throughput sequencing was used to characterise three patterns of IS629 inactivation of verotoxin 2 genes in EHEC O157:H7, caused by insertion or insertion followed by partial deletion. At least one of the patterns of inactivation appears to have persisted several years among cattle O157:H7, indicating it has no major effect on fitness in the animal reservoir. Digital PCR was used to directly quantify the reversal rates of the insertional inactivation of a selected isolate under laboratory conditions. Inserts were found to be absent from in the order of 1/10(5) of individual genomes, with significantly higher loss frequencies observed in cultures under nutrient-poor conditions. We conclude that strains with this type of inactivation found in food or animal samples should be considered a threat to human health, and may pose a challenge for PCR-based detection methods.
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| 5. |
- Martinez Barrio, Alvaro, 1977-, et al.
(författare)
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GeneFinder: "in silico" positional cloning of trait genes
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Annan publikation (populärvet., debatt m.m.)abstract
- Motivation: Positional cloning of trait genes is extremely laborious and the amount of information available on gene function in different organisms is increasing so rapidly that it is hard for a research group to collect all the relevant information from a number of data sources without performing a large number of manual and time consuming searches. Results: A web service application named GeneFinder was designed and implemented. It collects selected available information related to trait loci within a given chromosomal region that control a specific phenotype. The information contains details on gene function, disease conditions, tissue expression as well as predicted gene homologies in several other species. The information gathered is further ordered by a special-purpose ranking algorithm. A web interface to the GeneFinder web service was also developed where the results are presented in a ranked list easing its interpretation. We explain the design of the architecture, show how our web interface works, and finally test a candidate region. Availability: GeneFinder is publicly available and free to use. The web interface is available at http://www.genefinder.org/.
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| 6. |
- Zubair, Saima, et al.
(författare)
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Genome sequence of Streptococcus agalactiae strain 09mas018883, isolated from a Swedish cow
- 2013
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Ingår i: Genome Announcements. - 2169-8287. ; 1, s. 1-2
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Tidskriftsartikel (refereegranskat)abstract
- We announce the complete genome sequence of Streptococcus agalactiae strain 09mas018883, isolated from the milk of a cow with clinical mastitis. The availability of this genome may allow identification of candidate genes, leading to discovery of antigens that might form the basis for development of a vaccine as an alternative means of mastitis control.
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| 7. |
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| 8. |
- Andrae, Johanna, et al.
(författare)
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A 1.8kb GFAP-promoter fragment is active in specific regions of theembryonic CNS
- 2001
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Ingår i: Mechanisms of Development. - 0925-4773 .- 1872-6356. ; 107:1-2, s. 181-5
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Tidskriftsartikel (refereegranskat)abstract
- The intermediate filament glial fibrillary acidic protein (GFAP) constitutes the major cytoskeletal protein in astrocytes (J. Neuroimmunol. 8 (1985) 203) and is traditionally referred to as a specific marker for astrocytes. To identify early glial precursors, we created GFAPpromoter-lacZ transgenic mice, using a 1.8kb 5' fragment of human GFAP. The expression of the transgene was first detected in the neuroepithelium at embryonic day 9.5. It was further found in the ventricular zone of the developing telencephalon, in the cerebellar primordium, trigeminal ganglia, and radial glia. Later, scattered beta-gal+ cells were seen in pons, brain stem and glia limitans. The results indicate that GFAP activity is regulated in a region-specific manner during central nervous system (CNS) development and that the gene is turned on in different cell types independently.
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| 9. |
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| 10. |
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| 11. |
- Bannasch, Danika, et al.
(författare)
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Localization of canine brachycephaly using an across breed mapping approach
- 2010
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:3, s. e9632-
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Tidskriftsartikel (refereegranskat)abstract
- The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10-30) and control (20-60) samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.
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| 12. |
- Barrio, Alvaro Martinez, et al.
(författare)
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Targeted Resequencing and Analysis of the Diamond-Blackfan Anemia Disease Locus RPS19
- 2009
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 4:7, s. e6172-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The Ribosomal protein S19 gene locus (RPS19) has been linked to two kinds of red cell aplasia, Diamond-Blackfan Anemia (DBA) and Transient Erythroblastopenia in Childhood (TEC). Mutations in RPS19 coding sequences have been found in 25% of DBA patients, but not in TEC patients. It has been suggested that non-coding RPS19 sequence variants contribute to the considerable clinical variability in red cell aplasia. We therefore aimed at identifying non-coding variations associated with DBA or TEC phenotypes. METHODOLOGY/PRINCIPAL FINDINGS: We targeted a region of 19'980 bp encompassing the RPS19 gene in a cohort of 89 DBA and TEC patients for resequencing. We provide here a catalog of the considerable, previously unrecognized degree of variation in this region. We identified 73 variations (65 SNPs, 8 indels) that all are located outside of the RPS19 open reading frame, and of which 67.1% are classified as novel. We hypothesize that specific alleles in non-coding regions of RPS19 could alter the binding of regulatory proteins or transcription factors. Therefore, we carried out an extensive analysis to identify transcription factor binding sites (TFBS). A series of putative interaction sites coincide with detected variants. Sixteen of the corresponding transcription factors are of particular interest, as they are housekeeping genes or show a direct link to hematopoiesis, tumorigenesis or leukemia (e.g. GATA-1/2, PU.1, MZF-1). CONCLUSIONS: Specific alleles at predicted TFBSs may alter the expression of RPS19, modify an important interaction between transcription factors with overlapping TFBS or remove an important stimulus for hematopoiesis. We suggest that the detected interactions are of importance for hematopoiesis and could provide new insights into individual response to treatment.
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| 13. |
- Barrio, Alvaro Martinez, et al.
(författare)
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The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:5, s. e19832-
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Tidskriftsartikel (refereegranskat)abstract
- Host-retrovirus interactions influence the genomic landscape and have contributed substantially to mammalian genome evolution. To gain further insights, we analyzed a female boxer (Canis familiaris) genome for complexity and integration pattern of canine endogenous retroviruses (CfERV). Intriguingly, the first such in-depth analysis of a carnivore species identified 407 CfERV proviruses that represent only 0.15% of the dog genome. In comparison, the same detection criteria identified about six times more HERV proviruses in the human genome that has been estimated to contain a total of 8% retroviral DNA including solitary LTRs. These observed differences in man and dog are likely due to different mechanisms to purge, restrict and protect their genomes against retroviruses. A novel group of gammaretrovirus-like CfERV with high similarity to HERV-Fc1 was found to have potential for active retrotransposition and possibly lateral transmissions between dog and human as a result of close interactions during at least 10.000 years. The CfERV integration landscape showed a non-uniform intra-and inter-chromosomal distribution. Like in other species, different densities of ERVs were observed. Some chromosomal regions were essentially devoid of CfERVs whereas other regions had large numbers of integrations in agreement with distinct selective pressures at different loci. Most CfERVs were integrated in antisense orientation within 100 kb from annotated protein-coding genes. This integration pattern provides evidence for selection against CfERVs in sense orientation relative to chromosomal genes. In conclusion, this ERV analysis of the first carnivorous species supports the notion that different mammals interact distinctively with endogenous retroviruses and suggests that retroviral lateral transmissions between dog and human may have occurred.
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| 14. |
- Beisvåg, Vidar, et al.
(författare)
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Contributions of the EMERALD project to assessing and improving microarray data quality
- 2011
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Ingår i: BioTechniques. - : Future Science Ltd. - 0736-6205 .- 1940-9818. ; 50:1, s. 27-31
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Tidskriftsartikel (refereegranskat)abstract
- While minimum information about a microarray experiment (MIAME) standards have helped to increase the value of the microarray data deposited into public databases like ArrayExpress and Gene Expression Omnibus (GEO), limited means have been available to assess the quality of this data or to identify the procedures used to normalize and transform raw data. The EMERALD FP6 Coordination Action was designed to deliver approaches to assess and enhance the overall quality of microarray data and to disseminate these approaches to the microarray community through an extensive series of workshops, tutorials, and symposia. Tools were developed for assessing data quality and used to demonstrate how the removal of poor-quality data could improve the power of statistical analyses and facilitate analysis of multiple joint microarray data sets. These quality metrics tools have been disseminated through publications and through the software package arrayQualityMetrics. Within the framework provided by the Ontology of Biomedical Investigations, ontology was developed to describe data transformations, and software ontology was developed for gene expression analysis software. In addition, the consortium has advocated for the development and use of external reference standards in microarray hybridizations and created the Molecular Methods (MolMeth) database, which provides a central source for methods and protocols focusing on microarray-based technologies.
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| 15. |
- Benachenhou, Farid, et al.
(författare)
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Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
- 2013
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Ingår i: Mobile DNA. - : Springer Science and Business Media LLC. - 1759-8753. ; 4, s. 5-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability. The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible. Results: Hidden Markov models (HMM) were created for 11 clades of LTRs belonging to Retroviridae (class III retroviruses), animal Metaviridae (Gypsy/Ty3) elements and plant Pseudoviridae (Copia/Ty1) elements, complementing our work with Orthoretrovirus HMMs. The great variation in LTR length of plant Metaviridae and the few divergent animal Pseudoviridae prevented building HMMs from both of these groups. Animal Metaviridae LTRs had the same conserved motifs as retroviral LTRs, confirming that the two groups are closely related. The conserved motifs were the short inverted repeats (SIRs), integrase recognition signals (5' TGTTRNR ... YNYAACA 3'); the polyadenylation signal or AATAAA motif; a GT-rich stretch downstream of the polyadenylation signal; and a less conserved AT-rich stretch corresponding to the core promoter element, the TATA box. Plant Pseudoviridae LTRs differed slightly in having a conserved TATA-box, TATATA, but no conserved polyadenylation signal, plus a much shorter R region. The sensitivity of the HMMs for detection in genomic sequences was around 50% for most models, at a relatively high specificity, suitable for genome screening. The HMMs yielded consensus sequences, which were aligned by creating an HMM model (a 'Superviterbi' alignment). This yielded a phylogenetic tree that was compared with a Pol-based tree. Both LTR and Pol trees supported monophyly of retroviruses. In both, Pseudoviridae was ancestral to all other LTR retrotransposons. However, the LTR trees showed the chromovirus portion of Metaviridae clustering together with Pseudoviridae, dividing Metaviridae into two portions with distinct phylogeny. Conclusion: The HMMs clearly demonstrated a unitary conserved structure of LTRs, supporting that they arose once during evolution. We attempted to follow the evolution of LTRs by tracing their functional foundations, that is, acquisition of RNAse H, a combined promoter/polyadenylation site, integrase, hairpin priming and the primer binding site (PBS). Available information did not support a simple evolutionary chain of events.
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| 16. |
- Bongcam Rudloff, Erik
(författare)
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2013 Annual General Meeting: Executive Board Report
- 2013
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Ingår i: EMBnet.journal. - 2226-6089. ; 19.1, s. 24-25
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- During the past year, the Executive Board (EB) met regularly and held frequent meetings with the Operational Board via Skype. These meetings allowed discussion of a range of issues relating to the Project Committees (PCs), to EMBnet.journal, to the website, the Stichting accounts, membership, etc. In alternate months, we also endeavoured to convene Skype meetings open to the full EMBnet constituency; however, for larger numbers of attendees, technical issues continued to cause problems. Attempting to address these issues, we took the first steps towards evaluating the various tools and technologies available for online meetings, by creating a list of existing tools, and a protocol on how to test them. The test will be realised in the same spirit as the ‘ping project1' of the ‘80s. The 2013 AGM allowed us to convene a working group to discuss the issues in more detail, and to initiate a common experiment with different software and different Nodes. The ultimate goal is to write a white paper and to publish the results in EMBnet.journal. The last year has been both busy and productive, building substantially on the programme of work we outlined in 2010. In particular, working closely with Itico2 to improve the EMBnet ‘brand', we finally launched the new website, which now includes a new online fee-payment module for individual members. We call on all members to help augment the content of the new site and to help keep it up-to-date. Since the 2012 AGM in Uppsala, EMBnet's training strategy has been dominated by our leadership of GOBLET3 (the Global Organisation for Bioinformatics Learning, Education and Training), which has been established as a Stichting, registered in the Netherlands, following the successful model of EMBnet. Working through GOBLET has significantly increased our level of interaction and cooperation with a range of major international societies and networks (including ISCB4, ASBCB5,ISB6, APBioNet7, SoIBio8, ABN9 and so on) - from the original 10 members who signed the Memorandum of Understanding to establish GOBLET, a further 16 organisations and several individuals have committed to join the Foundation. Another profound advance for EMBnet this year has been the final ratification of the new statutes, which were voted in during the Uppsala 2012 AGM - these statutes became legally binding in April 2013. The most significant result of the change is that we are now able formally to accept individual members (this allows, say, former Node managers to join, or any individual to participate in EMBnet's activities but whose organisation is not a member). Since ratification of the statutes, we have already had several membership applications, and welcomed one new organisation; new memberships will be processed without delay via the online payment system. The new statutes also ushered in changes to the internal structure of the organisation, obliging the PC Chairs and the EB to work together much more closely than they have done in the past; it has also allowed us to streamline the way in which EMBnet's activities
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| 17. |
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| 18. |
- Bongcam Rudloff, Erik
(författare)
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2016 EMBnet Annual General Meeting – Executive Board Report
- 2017
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Ingår i: EMBnet.journal. - : EMBnet Stichting. - 2226-6089. ; 22
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- During the past year, the Executive Board (EB) held regular monthly meetings either via Skype or using Adobe Connect. These meetings were carried out with the Interim Board (IB), comprising members of the EB and Teresa Attwood and Etienne de Villiers. The IB was established during the 2015 Annual General Meeting (AGM) both to support the new EB in its first steps forward (as three of its members were new), and to help oversee implementation and delivery of the investment strategy. The EB also regularly invited Special Interest Group (SIG) Chairs to participate at EB-IB meetings. Additional monthly meetings open to the full EMBnet constituency were also convened. In this report, we provide a brief overview of activities and achievements from June 2015 to October 2016.
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| 19. |
- Bongcam Rudloff, Erik
(författare)
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2nd Combined Working Group and Management Committee Meeting of Urine and Kidney Proteomics COST Action 29-30 March 2009, Nafplio, Greece
- 2009
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Ingår i: PROTEOMICS - Clinical Applications. - : Wiley. - 1862-8346 .- 1862-8354. ; 3, s. 1017-1022
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Tidskriftsartikel (refereegranskat)abstract
- EuroKUP (Urine and Kidney Proteomics; www.eurokup.org) is a COST (European Cooperation in the field of Scientific and Technical research: www.cost.esf.org Action fostering amulti-disciplinary network of investigators from 25 countries and focusing on facilitating translational proteomic research in kidney diseases. Four Working Groups focusing respectively on defining clinically important research questions in kidney diseases, kidney tissue proteomics, urine proteomics and bioinformatics have been generated. The EuroKUP members had their second combined Working Group and Management Committee (MC) meeting in Nafplio, Greece from March 29 to 30, 2009. This report summarizes the main presentations, discussions and agreed action points during this meeting. These refer to the design of collaborative projects and clinical center networks for specific kidney diseases; establishment of guidelines for kidney tissue proteomics analysis by laser-based imaging- and laser capture microdissection-MS; development and characterization of a "standard" urine specimen to be used for assessment of platform capability and data comparability in clinical proteomics applications; definition of statistical requirements in biomarker discovery studies; and development of a specialized kidney and urine ontology. Various training activities are planned involving training schools on laser capture microdissection-and imaging-MS, workshops on ontologies as well as short-term travel grants for junior investigators.
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| 20. |
- Bongcam Rudloff, Erik
(författare)
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Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
- 2023
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Ingår i: Frontiers in Microbiology. - 1664-302X. ; 14
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Forskningsöversikt (refereegranskat)abstract
- The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory 'omics' features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.
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| 21. |
- Bongcam Rudloff, Erik
(författare)
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BBMRI : the Pan-European research infrastructure for Biobanking and Biomolecular Resources: managing resources for the future of biomedical research
- 2009
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Ingår i: EMBnet.News. - 1023-4144 .- 1023-4152. ; 15, s. 3-8
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Biobanks are a key resource for unravelling the molecular basis of disease subtypes, identification of new targets for therapy and reduction of attrition in drug discovery and development. The broad spectrum of existing biobanks is considered as a specific strength of European research. Unfortunately the diversity - lack of standardisation - of these biobanks and the differential ethical and legal landscape across Europe have prevented their effective use. Development of common IT infrastructure and sustainable funding schemes are key features for large transnational projects interlinking different national and regional biobanks. Agreement on common standards is equally important for all de novo biobanks. In 2008, a pan-European infrastructure BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) was established to bring cohesion to the European biobanking community and to make the existing and new high quality biological resources available for health research in Europe
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| 22. |
- Bongcam Rudloff, Erik
(författare)
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Capacity building and bioinformatics challenges
- 2014
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Ingår i: The SLU Global Food Security Research and Capacity Development Programme 2012-2014 – A Swedish Government Initiative. ; 2014:6, s. 68-71
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Moderna biotekniska framgångar bidrar till att skapa nya möjligheter inom den globala jordbrukssektorn och till att på lång sikt minska fattigdom och hunger. Nya växtgenotyper som till exempel är toleranta mot torka eller översvämning eller som klarar av insekt- eller svampangrepp är några exempel. Metodutveckling inom bioinformatik ligger till grund för många av dessa framgångar. Få afrikanska forskare har fått utbildning i hur man använder och drar nytta av dessa verktyg och det saknas en utvecklad infrastruktur inom området bioinformatik i det afrikanska vetenskapssamhället. Projektet syftar till att bygga upp bioinformatikkapacitet inom afrikanska jordbruksuniversitet och institutioner. Detta kommer att bidra till ett förbättrat bioteknikstöd i jordbrukets kamp mot hunger. Forskare från SLU tillsammans med afrikanska partners (från ILRI-BecA (International Livestock Research Institute - Biosciences of Eastern and Central Africa), ICPE (International Center for Insect Physiology and Ecology) and ICRISAT (International Crops Research Institute for the Semi-Arid Tropics)) arbetar för att öka samarbetet mellan svenska och afrikanska forskare inom bioinformatik och för att bygga upp en afrikansk bioinformatikinfrastruktur. Flera workshops och utbildningstillfällen har genomförts i Sverige och Afrika under 2013. I december hålls en bioinformatikkurs vid Mikocheni Agricultural Research Institute (MARI) i Dar es Salaam, Tanzania och vid PWANI University i Kilifi, Kenya. Där har projektet möjliggjort att servrar som är till endast för bioinformatikdata (eBioKit-servrar) installerats. Detta gör att forskare inom olika "Life Sciences"områden får tillgång till "open source" mjukvaror och att alla databaser som behövs finns tillgängliga så att forskare kan bygga sina egna databaser anpassade till egna forskningsområden.
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| 23. |
- Bongcam Rudloff, Erik
(författare)
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Comparison of common adverse neonatal outcomes among preterm and term infants at the National Referral Hospital in Tanzania: a case-control study
- 2022
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Ingår i: Ethiopian journal of pediatrics and child health. - : African Journals Online (AJOL). - 2413-2640 .- 2519-0334. ; 17, s. 93-104
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Tidskriftsartikel (refereegranskat)abstract
- Background: Neonatal period is a critical period in a child’s heath because it is associated with higher risk of adverse health outcomes. The objective of this study was to assess common adverse health outcomes and compare the risk of such outcomes between preterm and term neonates, in Tanzania. Methods: This was a case-control study involving infants admitted at Muhimbili National Hospital between August and October 2020. About 222 pairs of preterm and term infants were followed until discharge. Logistic regression was used to compare risk of health outcomes. Statistical sig-nificance was achieved at p–value < 0.05 and 95% confidence interval. Result: Preterm neonates had increased risk of mortality (OR = 7.2, 95% CI: 3.4----– 15.1), ap-nea (OR = 4.7, 95% CI: 3.4 – 15.1), respiratory distress syndrome (OR = 10.9, 95% CI: 6.1 – 19.6), necrotizing enterocolitis (OR = 5.5, 95% CI: 1.2 – 25.3), anemia (OR = 4.3, 95% CI: 2.8 – 6.6), pneumonia (OR = 2.7, 95% CI: 1.6 – 4.6) and sepsis (OR = 2.6, 95% CI: 1.7 – 3.9). No dif-ference in risk of intraventricular hemorrhage, patent ductus arteriosus and jaundice was ob-served. Conclusion: For promoting neonates' health, prevention and treatment of the higher risk adverse neonatal outcomes should be prioritized.
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| 24. |
- Bongcam Rudloff, Erik, et al.
(författare)
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Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033
- 2014
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Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 9, s. 718-725
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Tidskriftsartikel (refereegranskat)abstract
- Bacillus amyloliquefaciens subsp. plantarum UCMB5033 is of special interest for its ability to promote host plant growth through production of stimulating compounds and suppression of soil borne pathogens by synthesizing antibacterial and antifungal metabolites or priming plant defense as induced systemic resistance. The genome of B. amyloliquefaciens UCMB5033 comprises a 4,071,167 bp long circular chromosome that consists of 3,912 protein-coding genes, 86 tRNA genes and 10 rRNA operons.
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| 25. |
- Bongcam Rudloff, Erik
(författare)
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Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
- 2015
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Ingår i: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 11
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Annan publikation (refereegranskat)abstract
- In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy-paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.
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