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Svendsen, A.L.; Feychting, M.; Klæboe, L.; Langmark, F.; Schüz, J. |
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Title |
Time Trends in the Incidence of Acute Lymphoblastic Leukemia among Children 1976-2002: A Population-Based Nordic Study |
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Journal Article |
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Year |
2007 |
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The Journal of Pediatrics |
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The Journal of Pediatrics |
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151 |
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5 |
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548-550 |
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0022-3476 |
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WP9 Epidemiology |
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IARC @ ErdmannF @ |
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102 |
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Park, P.J. |
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Title |
ChIP–seq: advantages and challenges of a maturing technology |
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Journal Article |
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2009 |
Publication |
Nature Reviews Genetics |
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Nat Rev Genet |
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10 |
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10 |
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669-680 |
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Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing
technology, ChIP–seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP–chip. With the decreasing cost of sequencing, ChIP–seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP–seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms. |
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1471-0056 |
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Swiss TPH @ christoph.schmid @ |
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112 |
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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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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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Author |
Szalkowski, A.M.; Schmid, C.D. |
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Title |
Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts |
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Journal Article |
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Year |
2011 |
Publication |
Briefings in Bioinformatics |
Abbreviated Journal |
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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