Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data

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

[2]  Steven J. M. Jones,et al.  De novo assembly and analysis of RNA-seq data , 2010, Nature Methods.

[3]  N. Friedman,et al.  Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species , 2010, Genome Biology.

[4]  N. Friedman,et al.  Comprehensive comparative analysis of strand-specific RNA sequencing methods , 2010, Nature Methods.

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

[6]  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.

[7]  Miriah D. Meyer,et al.  Genome-wide synteny through highly sensitive sequence alignment: Satsuma , 2010, Bioinform..

[8]  B. Haas,et al.  Advancing RNA-Seq analysis , 2010, Nature Biotechnology.

[9]  Chuan-Xi Zhang,et al.  De novo characterization of a whitefly transcriptome and analysis of its gene expression during development , 2010, BMC Genomics.

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

[11]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[12]  T. Borodina,et al.  Transcriptome analysis by strand-specific sequencing of complementary DNA , 2009, Nucleic acids research.

[13]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[14]  Hunter B. Fraser,et al.  Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing , 2009, Proceedings of the National Academy of Sciences.

[15]  L. Steinmetz,et al.  Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.

[16]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[17]  I. Goodhead,et al.  Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution , 2008, Nature.

[18]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[19]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[20]  N. Friedman,et al.  Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.

[21]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[22]  Steven Salzberg,et al.  Beware of mis-assembled genomes , 2005, Bioinform..

[23]  F. Clark,et al.  Understanding alternative splicing: towards a cellular code , 2005, Nature Reviews Molecular Cell Biology.

[24]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[25]  Pavel A. Pevzner,et al.  De novo identification of repeat families in large genomes , 2005, ISMB.

[26]  Matthew Berriman,et al.  GeneDB: a resource for prokaryotic and eukaryotic organisms , 2004, Nucleic Acids Res..

[27]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[28]  P. Pevzner,et al.  An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[29]  H. Nojima,et al.  Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe. , 2001, Nucleic acids research.

[30]  B. Graveley Alternative splicing: increasing diversity in the proteomic world. , 2001, Trends in genetics : TIG.

[31]  Y. Hiraoka,et al.  Characterization of rec7, an early meiotic recombination gene in Schizosaccharomyces pombe. , 2001, Genetics.

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

[33]  C. Shimoda,et al.  The Schizosaccharomyces pombe spo6+ gene encoding a nuclear protein with sequence similarity to budding yeast Dbf4 is required for meiotic second division and sporulation , 2000, Genes to cells : devoted to molecular & cellular mechanisms.

[34]  Aaron D. Wyner,et al.  Prediction and Entropy of Printed English , 1993 .

[35]  C. Hyltén-Cavallius On a combinatorical problem , 1958 .

[36]  Claude E. Shannon,et al.  Prediction and Entropy of Printed English , 1951 .

[37]  I. Good Normal Recurring Decimals , 1946 .