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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 02 February 2016, Vol.113(5), pp.E498
    Description: Author contributions: G.D., S.H., and I.I. wrote the paper.
    Keywords: Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Burkitt Lymphoma -- Metabolism ; Lymphoma, B-Cell -- Metabolism ; Proto-Oncogene Proteins C-Myc -- Metabolism ; RNA, Long Noncoding -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States, Feb 2, 2016, Vol.113(5), p.E498
    Keywords: Burkitt Lymphoma – Physiological Aspects ; B Cells – Physiological Aspects
    ISSN: 0027-8424
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Nature, March 11, 2010, Vol.463(7286), p.250(6)
    Description: Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of ~60 small RNAs including the e-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.
    Keywords: Antisense Rna -- Analysis ; Gene Expression -- Analysis ; Transcription (Genetics) -- Analysis ; Helicobacter Pylori -- Genetic Aspects ; Helicobacter Pylori -- Physiological Aspects
    ISSN: 0028-0836
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  • 4
    In: Clinical Infectious Diseases, 2016, Vol. 63(suppl2), pp.S52-S56
    Description: The goal of administering medical interventions is to help patients live longer or live better. In keeping with this goal, there has been increasing interest in taking the “voice” of the patient into account during the development process, specifically in the evaluation of treatment benefits of medical interventions, and use of patient-centered outcome data to justify reimbursement. Patient-reported outcomes (PROs) are outcome assessments (OAs) used to define endpoints that can provide direct evidence of treatment benefit on how patients feel or function. When PROs are appropriately developed, they can increase the efficiency and clinical relevance of clinical trials. Several PROs have been developed for OA in specific infectious diseases indications, and more are under development. PROs also hold promise for use in evaluating adherence, adverse effects, satisfaction with care, and routine clinical practice.
    Keywords: Infectious Diseases ; Clinical Trials ; Patient - Reported Outcomes ; Endpoints ; Clinical Practice
    ISSN: 1058-4838
    E-ISSN: 1537-6591
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  • 5
    Language: English
    In: Clinical Infectious Diseases, August 15, 2016, Vol.63(4), p.S52(5)
    Keywords: Communicable Diseases – Care and Treatment ; Clinical Trials – Usage ; Outcome and Process Assessment (Medical Care) – Analysis
    ISSN: 1058-4838
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  • 6
    Language: English
    In: Nucleic acids research, July 2011, Vol.39(Web Server issue), pp.W112-7
    Description: Small non-coding RNAs (ncRNAs) such as microRNAs, snoRNAs and tRNAs are a diverse collection of molecules with several important biological functions. Current methods for high-throughput sequencing for the first time offer the opportunity to investigate the entire ncRNAome in an essentially unbiased way. However, there is a substantial need for methods that allow a convenient analysis of these overwhelmingly large data sets. Here, we present DARIO, a free web service that allows to study short read data from small RNA-seq experiments. It provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates. The DARIO web site can be accessed at http://dario.bioinf.uni-leipzig.de/.
    Keywords: Sequence Analysis, RNA ; Software ; RNA, Untranslated -- Chemistry
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 7
    Language: English
    In: Methods in molecular biology (Clifton, N.J.), 2011, Vol.719, pp.199-217
    Description: The advent of High Throughput Sequencing (HTS) methods opens new opportunities for the analysis of genomes and transcriptomes. While the sequencing of a whole mammalian genome took several years at the turn of this century, today it is only a matter of weeks. The race towards the thousand-dollar genome is fueled by the - ethically challenging - idea of personalized genomic medicine. However, these methods allow new and interesting insights in many aspects such as the discovery of novel noncoding RNA classes, structural variants, or alternative splice sites to name a few. Meanwhile, several methods for HTS have been introduced to the markets. Here, an overview on the technologies and the bioinformatics analysis of HTS data is given.
    Keywords: Computational Biology -- Methods ; Sequence Analysis, DNA -- Methods
    E-ISSN: 1940-6029
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 8
    Language: English
    In: Algorithms for Molecular Biology, March 18, 2011, Vol.6, p.4
    Description: Background Fast seed-based alignment heuristics such as BLAST and BLAT have become indispensable tools in comparative genomics for all studies aiming at the evolutionary relations of proteins, genes, and non-coding RNAs. This is true in particular for the large mammalian genomes. The sensitivity and specificity of these tools, however, crucially depend on parameters such as seed sizes or maximum expectation values. In settings that require high sensitivity the amount of short local match fragments easily becomes intractable. Then, fragment chaining is a powerful leverage to quickly connect, score, and rank the fragments to improve the specificity. Results Here we present a fast and flexible fragment chainer that for the first time also supports a sum-of-pair gap cost model. This model has proven to achieve a higher accuracy and sensitivity in its own field of application. Due to a highly time-efficient index structure our method outperforms the only existing tool for fragment chaining under the linear gap cost model. It can easily be applied to the output generated by alignment tools such as segemehl or BLAST. As an example we consider homology-based searches for human and mouse snoRNAs demonstrating that a highly sensitive BLAST search with subsequent chaining is an attractive option. The sum-of-pair gap costs provide a substantial advantage is this context. Conclusions Chaining of short match fragments helps to quickly and accurately identify regions of homology that may not be found using local alignment heuristics alone. By providing both the linear and the sum-of-pair gap cost model, a wider range of application can be covered. The software clasp is available at http://www.bioinf.uni-leipzig.de/Software/clasp/.
    Keywords: Genes -- Research ; Genetic Algorithms -- Usage
    ISSN: 1748-7188
    Source: Cengage Learning, Inc.
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  • 9
    Language: English
    In: Algorithms for Molecular Biology, March 18, 2011, Vol.6, p.4
    Description: Background Fast seed-based alignment heuristics such as BLAST and BLAT have become indispensable tools in comparative genomics for all studies aiming at the evolutionary relations of proteins, genes, and non-coding RNAs. This is true in particular for the large mammalian genomes. The sensitivity and specificity of these tools, however, crucially depend on parameters such as seed sizes or maximum expectation values. In settings that require high sensitivity the amount of short local match fragments easily becomes intractable. Then, fragment chaining is a powerful leverage to quickly connect, score, and rank the fragments to improve the specificity. Results Here we present a fast and flexible fragment chainer that for the first time also supports a sum-of-pair gap cost model. This model has proven to achieve a higher accuracy and sensitivity in its own field of application. Due to a highly time-efficient index structure our method outperforms the only existing tool for fragment chaining under the linear gap cost model. It can easily be applied to the output generated by alignment tools such as segemehl or BLAST. As an example we consider homology-based searches for human and mouse snoRNAs demonstrating that a highly sensitive BLAST search with subsequent chaining is an attractive option. The sum-of-pair gap costs provide a substantial advantage is this context. Conclusions Chaining of short match fragments helps to quickly and accurately identify regions of homology that may not be found using local alignment heuristics alone. By providing both the linear and the sum-of-pair gap cost model, a wider range of application can be covered. The software clasp is available at http://www.bioinf.uni-leipzig.de/Software/clasp/.
    Keywords: Genes -- Research ; Genetic Algorithms -- Usage
    ISSN: 1748-7188
    Source: Cengage Learning, Inc.
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  • 10
    In: Nature, 2010, Vol.464(7286), p.250
    Description: Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of approximately 60 small RNAs including the epsilon-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.
    Keywords: Gene Expression Profiling ; Genome, Bacterial -- Genetics ; Helicobacter Infections -- Microbiology ; Helicobacter Pylori -- Genetics ; RNA, Bacterial -- Genetics;
    ISSN: 0028-0836
    E-ISSN: 14764687
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