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Transcriptomic methods

This section covers novel experimental and analytical approaches for transcriptomic, epigenetic, and related high-throughput genomic studies. Studies which use transcriptomic and high-throughput genomic methods, but which do not present a novel methodological approach, should be submitted to the section in the journal relating to the organism studied.

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  1. Gene expression profiling is an important approach for detecting diagnostic and prognostic biomarkers, and predicting drug safety. The development of a wide range of technologies and platforms for measuring mR...

    Authors: Alison S Devonshire, Ramnath Elaswarapu and Carole A Foy

    Citation: BMC Genomics 2010 11:662

    Content type: Research article

    Published on:

  2. We evaluated (a) the feasibility of whole genome cDNA-mediated Annealing, Selection, extension and Ligation (DASL) assay on formalin-fixed paraffin-embedded (FFPE) tissue and (b) whether similar conclusions ca...

    Authors: Muhammad G Kibriya, Farzana Jasmine, Shantanu Roy, Rachelle M Paul-Brutus, Maria Argos and Habibul Ahsan

    Citation: BMC Genomics 2010 11:622

    Content type: Research article

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  3. Since human brain tissue is often unavailable for transcriptional profiling studies, blood expression data is frequently used as a substitute. The underlying hypothesis in such studies is that genes expressed ...

    Authors: Chaochao Cai, Peter Langfelder, Tova F Fuller, Michael C Oldham, Rui Luo, Leonard H van den Berg, Roel A Ophoff and Steve Horvath

    Citation: BMC Genomics 2010 11:589

    Content type: Research article

    Published on:

  4. All crustaceans periodically moult to renew their exoskeleton. In krill this involves partial digestion and resorption of the old exoskeleton and synthesis of new cuticle. Molecular events that underlie the mo...

    Authors: Paul J Seear, Geraint A Tarling, Gavin Burns, William P Goodall-Copestake, Edward Gaten, Özge Özkaya and Ezio Rosato

    Citation: BMC Genomics 2010 11:582

    Content type: Research article

    Published on:

  5. Analysis of microarray experiments often involves testing for the overrepresentation of pre-defined sets of genes among lists of genes deemed individually significant. Most popular gene set testing methods ass...

    Authors: Daniel M Gatti, William T Barry, Andrew B Nobel, Ivan Rusyn and Fred A Wright

    Citation: BMC Genomics 2010 11:574

    Content type: Research article

    Published on:

  6. Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is...

    Authors: Sujai Kumar and Mark L Blaxter

    Citation: BMC Genomics 2010 11:571

    Content type: Research article

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  7. Physiological left ventricular hypertrophy (LVH) involves complex cardiac remodeling that occurs as an adaptive response to chronic exercise. A stark clinical contrast exists between physiological LVH and path...

    Authors: Ignat Drozdov, Sophia Tsoka, Christos A Ouzounis and Ajay M Shah

    Citation: BMC Genomics 2010 11:557

    Content type: Research article

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  8. The demands of microarray expression technologies for quantities of RNA place a limit on the questions they can address. As a consequence, the RNA requirements have reduced over time as technologies have impro...

    Authors: Andy G Lynch, James Hadfield, Mark J Dunning, Michelle Osborne, Natalie P Thorne and Simon Tavaré

    Citation: BMC Genomics 2010 11:540

    Content type: Research article

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  9. The Limbal epithelial crypt (LEC) is a solid cord of cells, approximately 120 microns long. It arises from the undersurface of interpalisade rete ridges of the limbal palisades of Vogt and extends deeper into ...

    Authors: Bina B Kulkarni, Patrick J Tighe, Imran Mohammed, Aaron M Yeung, Desmond G Powe, Andrew Hopkinson, Vijay A Shanmuganathan and Harminder S Dua

    Citation: BMC Genomics 2010 11:526

    Content type: Research article

    Published on:

  10. The contribution of alternative splicing and isoform expression to cellular response is emerging as an area of considerable interest, and the newly developed exon arrays allow for systematic study of these pro...

    Authors: Toni Whistler, Cheng-Feng Chiang, William Lonergan, Mark Hollier and Elizabeth R Unger

    Citation: BMC Genomics 2010 11:496

    Content type: Research article

    Published on:

  11. Identifying associations between genotypes and gene expression levels using microarrays has enabled systematic interrogation of regulatory variation underlying complex phenotypes. This approach has vast potent...

    Authors: Tomas Babak, Philip Garrett-Engele, Christopher D Armour, Christopher K Raymond, Mark P Keller, Ronghua Chen, Carol A Rohl, Jason M Johnson, Alan D Attie, Hunter B Fraser and Eric E Schadt

    Citation: BMC Genomics 2010 11:473

    Content type: Methodology article

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Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.