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Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
Article
Article
Davis J. McCarthy; Yunshun Chen; Gordon K. Smyth · Nucleic Acids Research · 2012
A flexible statistical framework is developed for the analysis of read counts from RNA-Seq gene expression studies. It provides the ability to analyse complex experiments involving multiple treatment conditions and block...
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Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
Article
Article
Anna Klindworth; Elmar Pruesse; Timmy Schweer; Jörg Peplies; Christian Quast; Matthias Horn; Frank Oliver Glöckner · Nucleic Acids Research · 2012
16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers...
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Article
Article
Anton Bankevich; Sergey Nurk; Dmitry Antipov; Alexey Gurevich; Mikhail Dvorkin; Alexander S. Kulikov; Valery M. Lesin; Sergey Nikolenko · Journal of Computational Biology · 2012
The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagen...
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The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data
Article
Article
Ethan Cerami; Jianjiong Gao; Uğur Doğrusöz; Benjamin Groß; S. Onur Sumer; Bülent Arman Aksoy; Anders J. Skanderup; Caitlin J. Byrne · Cancer Discovery · 2012
The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor ...
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