Research article  

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

Zhen Li, Zhonghua Zhang, Pengcheng Yan, Sanwen Huang, Zhangjun Fei, Kui Lin BMC Genomics 2011, 12:540 (2 November 2011)

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Research article  

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazumitsu Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa BMC Genomics 2011, 12:516 (20 October 2011)

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Methodology article  

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

Hyunsoo Kim, Yingtao Bi, Sharmistha Pal, Ravi Gupta, Ramana V Davuluri BMC Bioinformatics 2011, 12:305 (27 July 2011)

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Methodology article  

Querying large read collections in main memory: a versatile data structure

Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, Eric Rivals BMC Bioinformatics 2011, 12:242 (17 June 2011)

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Research article  

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

James R Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D Pepper, Crispin J Miller BMC Genomics 2010, 11:282 (5 May 2010)

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Method  

Global and unbiased detection of splice junctions from RNA-seq data

Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten Genome Biology 2010, 11:R34 (17 March 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

Correction  

Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

Erica Mica, Viviana Piccolo, Massimo Delledonne, Alberto Ferrarini, Mario Pezzotti, Cesare Casati, Cristian Del Fabbro, Giorgio Valle, Alberto Policriti, Michele Morgante, Graziano Pesole, M Enrico Pè, David S Horner BMC Genomics 2010, 11:109 (12 February 2010)

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Research article  

The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines

Courtney Coleman, Dario Copetti, Guido Cipriani, Sarolta Hoffmann, Pál Kozma, László Kovács, Michele Morgante, Raffaele Testolin, Gabriele Di Gaspero BMC Genetics 2009, 10:89 (30 December 2009)

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Research article  

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

Erica Mica, Viviana Piccolo, Massimo Delledonne, Alberto Ferrarini, Mario Pezzotti, Cesare Casati, Cristian Del Fabbro, Giorgio Valle, Alberto Policriti, Michele Morgante, Graziano Pesole, M Enrico Pè, David S Horner BMC Genomics 2009, 10:558 (25 November 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Methodology article  

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species

Diana Bellin, Alberto Ferrarini, Antonio Chimento, Olaf Kaiser, Natasha Levenkova, Pascal Bouffard, Massimo Delledonne BMC Genomics 2009, 10:555 (24 November 2009)

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Research article  

Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray

Ilanit Samolski, Alberto de Luis, Juan Vizcaíno, Enrique Monte, M Belén Suárez BMC Microbiology 2009, 9:217 (13 October 2009)

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Research article  

Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing

Shrinivasrao P Mane, Clive Evans, Kristal L Cooper, Oswald R Crasta, Otto Folkerts, Stephen K Hutchison, Timothy T Harkins, Danielle Thierry-Mieg, Jean Thierry-Mieg, Roderick V Jensen BMC Genomics 2009, 10:264 (12 June 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central