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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. DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the...

    Authors: Lucian Ilie, Silvana Ilie, Shima Khoshraftar and Anahita Mansouri Bigvand

    Citation: BMC Genomics 2011 12:280

    Content type: Research article

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  2. The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correc...

    Authors: André Gilles, Emese Meglécz, Nicolas Pech, Stéphanie Ferreira, Thibaut Malausa and Jean-François Martin

    Citation: BMC Genomics 2011 12:245

    Content type: Research article

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  3. The transcriptional regulatory network is considered to be built from a set of circuit patterns called network motifs. Experimental studies have provided instances where a feedforward circuit (FFC) appears wit...

    Authors: Hisakazu Iwama, Koji Murao, Hitomi Imachi and Toshihiko Ishida

    Citation: BMC Genomics 2011 12:228

    Content type: Research article

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  4. Parasite-vector interactions are fundamental in the transmission of vector-borne diseases such as leishmaniasis. Leishmania development in the vector sand fly is confined to the digestive tract, where sand fly mi...

    Authors: Anna Dostálová, Jan Votýpka, Amanda J Favreau, Kent D Barbian, Petr Volf, Jesus G Valenzuela and Ryan C Jochim

    Citation: BMC Genomics 2011 12:223

    Content type: Research article

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  5. Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a var...

    Authors: Troy Ketela, Lawrence E Heisler, Kevin R Brown, Ron Ammar, Dahlia Kasimer, Anuradha Surendra, Elke Ericson, Kim Blakely, Dina Karamboulas, Andrew M Smith, Tanja Durbic, Anthony Arnoldo, Kahlin Cheung-Ong, Judice LY Koh, Shuba Gopal, Glenn S Cowley…

    Citation: BMC Genomics 2011 12:213

    Content type: Methodology article

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  6. Hibernation is an adaptive strategy to survive in highly seasonal or unpredictable environments. The molecular and genetic basis of hibernation physiology in mammals has only recently been studied using large ...

    Authors: Vadim B Fedorov, Anna V Goropashnaya, Øivind Tøien, Nathan C Stewart, Celia Chang, Haifang Wang, Jun Yan, Louise C Showe, Michael K Showe and Brian M Barnes

    Citation: BMC Genomics 2011 12:171

    Content type: Research article

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  7. Transcripts can exhibit significant variation in tissue samples from inbred laboratory mice. We have designed and carried out a microarray experiment to examine transcript variation across samples from adipose...

    Authors: Peter T Vedell, Karen L Svenson and Gary A Churchill

    Citation: BMC Genomics 2011 12:167

    Content type: Research article

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  8. High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible.

    Authors: Juha K Rantala, Rami Mäkelä, Anna-Riina Aaltola, Petra Laasola, John-Patrick Mpindi, Matthias Nees, Petri Saviranta and Olli Kallioniemi

    Citation: BMC Genomics 2011 12:162

    Content type: Methodology article

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  9. The β-amyloid precursor protein (APP) and the related β-amyloid precursor-like proteins (APLPs) undergo complex proteolytic processing giving rise to several fragments. Whereas it is well established that Aβ a...

    Authors: Dorothee Aydin, Mikhail A Filippov, Jakob-Andreas Tschäpe, Norbert Gretz, Marco Prinz, Roland Eils, Benedikt Brors and Ulrike C Müller

    Citation: BMC Genomics 2011 12:160

    Content type: Research article

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  10. RT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls....

    Authors: Tomas Hruz, Markus Wyss, Mylene Docquier, Michael W Pfaffl, Sabine Masanetz, Lorenzo Borghi, Phebe Verbrugghe, Luba Kalaydjieva, Stefan Bleuler, Oliver Laule, Patrick Descombes, Wilhelm Gruissem and Philip Zimmermann

    Citation: BMC Genomics 2011 12:156

    Content type: Methodology article

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  11. Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofue...

    Authors: Hamid Rismani-Yazdi, Berat Z Haznedaroglu, Kyle Bibby and Jordan Peccia

    Citation: BMC Genomics 2011 12:148

    Content type: Research article

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  12. MicroRNAs (miRNAs) represent a growing class of small non-coding RNAs that are important regulators of gene expression in both plants and animals. Studies have shown that miRNAs play a critical role in human c...

    Authors: Jin Sung Jang, Vernadette A Simon, Rod M Feddersen, Fariborz Rakhshan, Debra A Schultz, Michael A Zschunke, Wilma L Lingle, Christopher P Kolbert and Jin Jen

    Citation: BMC Genomics 2011 12:144

    Content type: Methodology article

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  13. Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription fac...

    Authors: Joshua WK Ho, Eric Bishop, Peter V Karchenko, Nicolas Nègre, Kevin P White and Peter J Park

    Citation: BMC Genomics 2011 12:134

    Content type: Research article

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  14. We have previously demonstrated that alcohol exposure at early neurulation induces growth retardation, neural tube abnormalities, and alteration of DNA methylation. To explore the global gene expression change...

    Authors: Feng C Zhou, Qianqian Zhao, Yunlong Liu, Charles R Goodlett, Tiebing Liang, Jeanette N McClintick, Howard J Edenberg and Lang Li

    Citation: BMC Genomics 2011 12:124

    Content type: Research article

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  15. Mucosal infections elicit inflammatory responses via regulated signaling pathways. Infection outcome depends strongly on early events occurring immediately when bacteria start interacting with cells in the muc...

    Authors: Jorrit Boekel, Örjan Källskog, Monica Rydén-Aulin, Mikael Rhen and Agneta Richter-Dahlfors

    Citation: BMC Genomics 2011 12:123

    Content type: Research article

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  16. Current methods of measuring transcription in high-throughput have led to significant improvements in our knowledge of transcriptional regulation and Systems Biology. However, endpoint measurements obtained fr...

    Authors: Saravanan Rajan, Haig Djambazian, Huan Chu Pham Dang, Rob Sladek and Thomas J Hudson

    Citation: BMC Genomics 2011 12:115

    Content type: Methodology article

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  17. Many human diseases and phenotypes are related to RNA expression, levels of which are influenced by a wide spectrum of genetic and exposure-related factors. In a large genome-wide study of muscle tissue expres...

    Authors: Clinton C Mason, Robert L Hanson, Vicky Ossowski, Li Bian, Leslie J Baier, Jonathan Krakoff and Clifton Bogardus

    Citation: BMC Genomics 2011 12:98

    Content type: Research article

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  18. Segmental duplication and deletion were implicated for a region containing the human immunoglobulin heavy chain variable (IGHV) gene segments, 1.9III/hv3005 (possible allelic variants of IGHV3-30) and hv3019b9...

    Authors: Sreemanta Pramanik, Xiangfeng Cui, Hui-Yun Wang, Nyam-Osor Chimge, Guohong Hu, Li Shen, Richeng Gao and Honghua Li

    Citation: BMC Genomics 2011 12:78

    Content type: Research article

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  19. Sessile bivalves of the genus Mytilus are suspension feeders relatively tolerant to a wide range of environmental changes, used as sentinels in ecotoxicological investigations and marketed worldwide as seafood. M...

    Authors: Paola Venier, Laura Varotto, Umberto Rosani, Caterina Millino, Barbara Celegato, Filippo Bernante, Gerolamo Lanfranchi, Beatriz Novoa, Philippe Roch, Antonio Figueras and Alberto Pallavicini

    Citation: BMC Genomics 2011 12:69

    Content type: Research article

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  20. Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression. In this study, we established a robust discovery pipeline to identify epigenetically de...

    Authors: Toby Hulf, Tennille Sibbritt, Erik D Wiklund, Saul Bert, Dario Strbenac, Aaron L Statham, Mark D Robinson and Susan J Clark

    Citation: BMC Genomics 2011 12:54

    Content type: Methodology article

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  21. Estrogen receptors alpha (ERα) and beta (ERβ) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found c...

    Authors: Oli MV Grober, Margherita Mutarelli, Giorgio Giurato, Maria Ravo, Luigi Cicatiello, Maria Rosaria De Filippo, Lorenzo Ferraro, Giovanni Nassa, Maria Francesca Papa, Ornella Paris, Roberta Tarallo, Shujun Luo, Gary P Schroth, Vladimir Benes and Alessandro Weisz

    Citation: BMC Genomics 2011 12:36

    Content type: Research article

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  22. Gaucher disease is caused by defective glucocerebrosidase activity and the consequent accumulation of glucosylceramide. The pathogenic pathways resulting from lipid laden macrophages (Gaucher cells) in viscera...

    Authors: You-Hai Xu, Li Jia, Brian Quinn, Matthew Zamzow, Keith Stringer, Bruce Aronow, Ying Sun, Wujuan Zhang, Kenneth DR Setchell and Gregory A Grabowski

    Citation: BMC Genomics 2011 12:20

    Content type: Research article

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  23. G protein coupled receptors (GPCRs) are one of the most widely studied gene superfamilies. Thousands of GPCR research studies have utilized heterologous expression systems such as human embryonic kidney cells ...

    Authors: Brady K Atwood, Jacqueline Lopez, James Wager-Miller, Ken Mackie and Alex Straiker

    Citation: BMC Genomics 2011 12:14

    Content type: Research article

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  24. Recent progress in high-throughput technologies has greatly contributed to the development of DNA methylation profiling. Although there are several reports that describe methylome detection of whole genome bis...

    Authors: Liu Yang, Kunlin Zhang, Wei Dai, Ximiao He, Qian Zhao, Jing Wang and Zhong Sheng Sun

    Citation: BMC Genomics 2011 12:10

    Content type: Research article

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  25. The radiation bystander effect is an important component of the overall biological response of tissues and organisms to ionizing radiation, but the signaling mechanisms between irradiated and non-irradiated by...

    Authors: Shanaz A Ghandhi, Anshu Sinha, Marianthi Markatou and Sally A Amundson

    Citation: BMC Genomics 2011 12:2

    Content type: Research article

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  26. MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique ...

    Authors: Henk PJ Buermans, Yavuz Ariyurek, Gertjan van Ommen, Johan T den Dunnen and Peter AC 't Hoen

    Citation: BMC Genomics 2010 11:716

    Content type: Methodology article

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  27. Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance...

    Authors: Wolfram Langer, Florian Sohler, Gabriele Leder, Georg Beckmann, Henrik Seidel, Jörn Gröne, Michael Hummel and Anette Sommer

    Citation: BMC Genomics 2010 11:676

    Content type: Research article

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  28. Previously we reported extensive gene expression reprogramming during epithelial to mesenchymal transition (EMT) of primary prostate cells. Here we investigated the hypothesis that specific histone and DNA met...

    Authors: Xi-Song Ke, Yi Qu, Yang Cheng, Wen-Cheng Li, Varda Rotter, Anne Margrete Øyan and Karl-Henning Kalland

    Citation: BMC Genomics 2010 11:669

    Content type: Research article

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  29. 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

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  30. 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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  31. 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

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  32. 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

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  33. 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

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  34. 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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  35. 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

    Published on:

  36. 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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  37. 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

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  38. 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:

  39. 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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