De novo assembly of bacterial transcriptomes from RNA-seq data

[1]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[2]  B. Tjaden,et al.  Computational analysis of bacterial RNA-Seq data , 2013, Nucleic acids research.

[3]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[4]  Martin Vingron,et al.  Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..

[5]  Xuan Li,et al.  Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study , 2011, BMC Bioinformatics.

[6]  Pavel A Pevzner,et al.  How to apply de Bruijn graphs to genome assembly. , 2011, Nature biotechnology.

[7]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[8]  Zhong Wang,et al.  Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.

[9]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[10]  Cole Trapnell,et al.  Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.

[11]  Manolis Kellis,et al.  Comparative Functional Genomics of the Fission Yeasts , 2011, Science.

[12]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[13]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.

[14]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.

[15]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[16]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[17]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[18]  Inanç Birol,et al.  De novo transcriptome assembly with ABySS , 2009, Bioinform..

[19]  Paul Flicek,et al.  Sense from sequence reads: methods for alignment and assembly , 2009, Nature Methods.

[20]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[21]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[22]  Giovanni Manzini,et al.  Opportunistic data structures with applications , 2000, Proceedings 41st Annual Symposium on Foundations of Computer Science.

[23]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[24]  Akademie van Wetenschappen,et al.  Koninklijke Nederlandse Akademie Van Wetenschappen , 2001 .

[25]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[26]  D. J. Wheeler,et al.  A Block-sorting Lossless Data Compression Algorithm , 1994 .

[27]  de Ng Dick Bruijn A combinatorial problem , 1946 .