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Fujita, P.A.; Rhead, B.; Zweig, A.S.; Hinrichs, A.S.; Karolchik, D.; Cline, M.S.; Goldman, M.; Barber, G.P.; Clawson, H.; Coelho, A.; Diekhans, M.; Dreszer, T.R.; Giardine, B.M.; Harte, R.A.; Hillman-Jackson, J.; Hsu, F.; Kirkup, V.; Kuhn, R.M.; Learned, K.; Li, C.H.; Meyer, L.R.; Pohl, A.; Raney, B.J.; Rosenbloom, K.R.; Smith, K.E.; Haussler, D.; Kent, W.J. |
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Title |
The UCSC Genome Browser database: update 2011 |
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Journal Article |
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Year |
2011 |
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Nucleic Acids Research |
Abbreviated Journal |
Nucleic Acids Research |
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39 |
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Database |
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D876-D882 |
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The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a 'mean+whiskers' windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks. |
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0305-1048 |
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Swiss TPH @ christoph.schmid @ |
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113 |
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Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S.L. |
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Title |
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome |
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2009 |
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Genome Biology |
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Genome Biology |
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10 |
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3 |
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R25 |
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Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu. |
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1465-6906 |
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Swiss TPH @ christoph.schmid @ |
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114 |
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Szalkowski, A.M.; Schmid, C.D. |
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Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts |
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2011 |
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Briefings in Bioinformatics |
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Briefings in Bioinformatics |
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12 |
Issue |
6 |
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626-633 |
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1467-5463 |
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Swiss TPH @ christoph.schmid @ |
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115 |
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Paietta, E.; Schwarzmeier, J.D. |
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Differences in beta-adrenergic receptor density and adenylate cyclase activity between normal and leukaemic leukocytes |
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1983 |
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European Journal of Clinical Investigation |
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Eur J Clin Invest |
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13 |
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4 |
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339-346 |
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Adenylate Cyclase/*blood; Adult; Alprostadil; B-Lymphocytes/metabolism; Histamine/pharmacology; Humans; Isoproterenol/pharmacology; Leukemia/*blood; Leukocytes/drug effects/*metabolism; Monocytes/metabolism; Neutrophils/metabolism; Prostaglandins E/pharmacology; Receptors, Adrenergic, beta/*metabolism; T-Lymphocytes/metabolism |
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An identical class of high-affinity binding sites for the 125I-labelled beta-adrenergic antagonist hydroxybenzylpindolol, was identified on intact human normal and leukaemic peripheral blood leukocytes. On normal unfractionated lymphocytes, polymorphonuclear leukocytes, and monocytes, receptor density did not differ significantly (1200-1400 receptors per cell; P greater than 0.3), but it was higher on B- than on T-lymphocytes (P less than 0.05). In leukaemia, monocytic blast cells expressed highest receptor numbers, whereas very low receptor density was seen on the pathologic B-cells from chronic lymphocytic leukaemia. Among normal leukocytes, adenylate cyclase activation by hormones (isoproterenol, prostaglandin E1, histamine) and sodium fluoride was strongest in plasma membranes from monocytes, but very weak in polymorphonuclear leukocytes either due to uncoupling of hormone receptors from adenylate cyclase or to low catalytic activity. In T-cells, enzyme activity was significantly lower than in B-cells. Loss of adenylate cyclase sensitivity to hormones and fluoride occurred in leukaemic cells from chronic and acute lymphocytic leukaemia. |
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English |
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0014-2972 |
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WP6 In vivo |
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PMID:6311563 |
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TIHO @ Maren.Fedrowitz @ |
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127 |
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Gunde Ziegelberger, Anne Dehos, Bernd Grosche, Sabine Hornhardt, Thomas Jung and Wolfgang Weiss |
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Title |
Childhood leukemia – Risk factors and the need for an interdisciplinary research agenda. |
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2011 |
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Prog Biophys Mol Biol |
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107 |
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3 |
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312-314 |
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The International Agency for Research on Cancer (IARC) has classified high as well as low-frequency fields as “possibly carcinogenic to humans” (Group 2B). For high frequency fields the recent assessment is based mainly on weak positive associations described in some epidemiological studies between glioma and acoustic neuroma and the use of mobile and other wireless phones. Also for lowfrequency fields the evidence is based on epidemiological findings revealing a statistic association between childhood leukemia (CL) and low-level magnetic fields. The basic findings are already 10 years old. They have since been supported by further epidemiological studies. However, the knowledge on the main/crucial question of causality has not improved. This fact and in addition the small, but statistically significant increased incidence of CL in the surrounding of German nuclear power plants have motivated the German Office for Radiation Protection (BfS) to work toward a better understanding of the main causes of CL. A long-term strategic research agenda has been developed which builds on an interdisciplinary, international network and aims at clarifying the aetiology of childhood acute lymphoblastic leukemia. |
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CNR-ISIB @ paolo.ravazzani @ |
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142 |
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