Skip to main content

Advertisement

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.

Page 10 of 11

  1. Euphorbia fischeriana is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbo...

    Authors: Roberto A Barrero, Brett Chapman, Yanfang Yang, Paula Moolhuijzen, Gabriel Keeble-Gagnère, Nan Zhang, Qi Tang, Matthew I Bellgard and Deyou Qiu

    Citation: BMC Genomics 2011 12:600

    Content type: Research article

    Published on:

  2. Sequencing-by-ligation (SBL) is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons). SBL has the adv...

    Authors: Antoine Ho, Maurice Murphy, Susan Wilson, Susan R Atlas and Jeremy S Edwards

    Citation: BMC Genomics 2011 12:598

    Content type: Methodology article

    Published on:

  3. Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised result...

    Authors: Robert R Kitchen, Vicky S Sabine, Arthur A Simen, J Michael Dixon, John MS Bartlett and Andrew H Sims

    Citation: BMC Genomics 2011 12:589

    Content type: Research article

    Published on:

  4. Cellular function is regulated by the balance of stringently regulated amounts of mRNA. Previous reports revealed that RNA polymerase II (RNAPII), which transcribes mRNA, can be classified into the pausing sta...

    Authors: Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazumitsu Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi and Yasuyuki Ohkawa

    Citation: BMC Genomics 2011 12:516

    Content type: Research article

    Published on:

  5. The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pac...

    Authors: M Aleksi Kallio, Jarno T Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, Mikko Koski, Janne Käki and Eija I Korpelainen

    Citation: BMC Genomics 2011 12:507

    Content type: Software

    Published on:

  6. In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modula...

    Authors: Özgen Deniz, Oscar Flores, Federica Battistini, Alberto Pérez, Montserrat Soler-López and Modesto Orozco

    Citation: BMC Genomics 2011 12:489

    Content type: Research article

    Published on:

  7. Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a vari...

    Authors: Luke D Gardner, David Mills, Aaron Wiegand, David Leavesley and Abigail Elizur

    Citation: BMC Genomics 2011 12:455

    Content type: Research article

    Published on:

  8. Gene expression assays have been shown to yield high quality genome-wide data from partially degraded RNA samples. However, these methods have not yet been applied to postmortem human brain tissue, despite the...

    Authors: Maggie L Chow, Hai-Ri Li, Mary E Winn, Craig April, Cynthia C Barnes, Anthony Wynshaw-Boris, Jian-Bing Fan, Xiang-Dong Fu, Eric Courchesne and Nicholas J Schork

    Citation: BMC Genomics 2011 12:449

    Content type: Research article

    Published on:

  9. microRNAs (miRNA) are short, endogenous transcripts that negatively regulate the expression of specific mRNA targets. miRNAs are found both in tissues and body fluids such as plasma. A major perspective for th...

    Authors: Steffen G Jensen, Philippe Lamy, Mads H Rasmussen, Marie S Ostenfeld, Lars Dyrskjøt, Torben F Ørntoft and Claus L Andersen

    Citation: BMC Genomics 2011 12:435

    Content type: Research article

    Published on:

  10. We introduce Glaucoma Discovery Platform (GDP), an online environment for facile visualization and interrogation of complex transcription profiling datasets for glaucoma. We also report the availability of Dat...

    Authors: Gareth R Howell, David O Walton, Benjamin L King, Richard T Libby and Simon WM John

    Citation: BMC Genomics 2011 12:429

    Content type: Database

    Published on:

  11. Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such...

    Authors: Mary E Winn, Marian Shaw, Craig April, Brandy Klotzle, Jian-Bing Fan, Sarah S Murray and Nicholas J Schork

    Citation: BMC Genomics 2011 12:412

    Content type: Research article

    Published on:

  12. Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to ...

    Authors: Massimo Iorizzo, Douglas A Senalik, Dariusz Grzebelus, Megan Bowman, Pablo F Cavagnaro, Marta Matvienko, Hamid Ashrafi, Allen Van Deynze and Philipp W Simon

    Citation: BMC Genomics 2011 12:389

    Content type: Research article

    Published on:

  13. KRAB-ZFPs (Krüppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, K...

    Authors: Sylvain Meylan, Anna C Groner, Giovanna Ambrosini, Nirav Malani, Simon Quenneville, Nadine Zangger, Adamandia Kapopoulou, Annamaria Kauzlaric, Jacques Rougemont, Angela Ciuffi, Frederic D Bushman, Philipp Bucher and Didier Trono

    Citation: BMC Genomics 2011 12:378

    Content type: Research article

    Published on:

  14. Transcription factors in disease-relevant pathways represent potential drug targets, by impacting a distinct set of pathways that may be modulated through gene regulation. The influence of transcription factor...

    Authors: Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi and Eivind Hovig

    Citation: BMC Genomics 2011 12:353

    Content type: Methodology article

    Published on:

  15. Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach ...

    Authors: Franc Llorens, Manuela Hummel, Xavier Pastor, Anna Ferrer, Raquel Pluvinet, Ana Vivancos, Ester Castillo, Susana Iraola, Ana M Mosquera, Eva González, Juanjo Lozano, Matthew Ingham, Juliane C Dohm, Marc Noguera, Robert Kofler, Jose Antonio del Río…

    Citation: BMC Genomics 2011 12:326

    Content type: Research article

    Published on:

  16. Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to ...

    Authors: Barbara Feldmeyer, Christopher W Wheat, Nicolas Krezdorn, Björn Rotter and Markus Pfenninger

    Citation: BMC Genomics 2011 12:317

    Content type: Research article

    Published on:

  17. The recent development of next generation sequencing technologies has made it possible to generate very large amounts of sequence data in species with little or no genome information. Combined with the large p...

    Authors: Anna W Santure, Jake Gratten, Jim A Mossman, Ben C Sheldon and Jon Slate

    Citation: BMC Genomics 2011 12:283

    Content type: Research article

    Published on:

  18. 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

    Published on:

  19. 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

    Published on:

  20. 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

    Published on:

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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

    Published on:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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

    Published on:

  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

  37. 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

    Published on:

  38. 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

    Published on:

  39. 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

    Published on:

  40. 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

    Published on:

  41. 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

    Published on:

  42. 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

    Published on:

  43. 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

    Published on:

2018 Journal Metrics

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.

Advertisement