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Genome technology and molecular diagnostics

This section will consider studies that focus on high-throughput approaches, such as sequencing, amplification and microarrays, as well as technologies for molecular diagnostics.This section will consider studies that focus on high-throughput approaches, such as sequencing, amplification and microarrays, as well as technologies for molecular diagnostics.

  1. Quantitative analysis of differential gene expression is of central importance in molecular life sciences. The Gene eXpression Profiling technology (GeXP) relies on multiplex RT-PCR and subsequent capillary el...

    Authors: Pauline Marquardt, Britta Werthmann, Viktoria Rätzel, Markus Haas and Wolfgang Marwan

    Citation: BMC Biotechnology 2021 21:29

    Content type: Methodology article

    Published on:

  2. Elaboration of the epigenetic regulation of chromatin is a long-standing aim in molecular and cellular biology. Hence, there is a great demand for the development of in vitro methods to reconstitute chromatin ...

    Authors: Kei-ichi Okimune, Szilvia K. Nagy, Shogo Hataya, Yaeta Endo and Taichi E. Takasuka

    Citation: BMC Biotechnology 2020 20:62

    Content type: Methodology article

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  3. Few bead-based multiplex assays have been described that detect antibodies against the protozoan parasite Toxoplasma gondii in large-scale seroepidemiological surveys. Moreover, each multiplex assay has specific ...

    Authors: Sandra Klein, Daniel Stern and Frank Seeber

    Citation: BMC Biotechnology 2020 20:53

    Content type: Methodology article

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  4. This study reports the analytical sensitivity and specificity of a Loop-mediated isothermal amplification (LAMP) and compares its amplification performance with conventional PCR, nested PCR (nPCR) and real-tim...

    Authors: Phiaw Chong Foo, A. B. Nurul Najian, Nuramin A. Muhamad, Mariana Ahamad, Maizan Mohamed, Chan Yean Yean and Boon Huat Lim

    Citation: BMC Biotechnology 2020 20:34

    Content type: Research article

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  5. In personalized medicine, companion diagnostic tests provide additional information to help select a treatment option likely to be optimal for a patient. Although such tests include several techniques for dete...

    Authors: Jr-Kai Huang, Ling Fan, Tao-Yeuan Wang and Pao-Shu Wu

    Citation: BMC Biotechnology 2019 19:62

    Content type: Methodology article

    Published on:

    The Correction to this article has been published in BMC Biotechnology 2019 19:77

  7. Long Adapter Single-Stranded Oligonucleotide (LASSO) probes were developed as a novel tool for massively parallel cloning of kilobase-long genomic DNA sequences. LASSO dramatically improves the capture length ...

    Authors: Syukri Shukor, Alfred Tamayo, Lorenzo Tosi, H. Benjamin Larman and Biju Parekkadan

    Citation: BMC Biotechnology 2019 19:50

    Content type: Methodology article

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  8. Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene ...

    Authors: Kateryna Shebanits, Torsten Günther, Anna C. V. Johansson, Khurram Maqbool, Lars Feuk, Mattias Jakobsson and Dan Larhammar

    Citation: BMC Biotechnology 2019 19:31

    Content type: Research article

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  10. With the rapid development of sequencing technologies, increasing amount of genomic information has been accumulated. To clone genes for further functional studies in large scale, a cheap, fast and efficient c...

    Authors: Qin Liu, Hui-Jie Dang, Yuan-Hang Wu, Min Li, Yin-Hua Chen, Xiao-Lei Niu, Kai-Mian Li and Li-Juan Luo

    Citation: BMC Biotechnology 2018 18:44

    Content type: Methodology article

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  11. Recently, an integrated DNA walking strategy has been proposed to prove the presence of GMO via the characterisation of sequences of interest, including their transgene flanking regions and the unnatural assoc...

    Authors: Marie-Alice Fraiture, Julie Vandamme, Philippe Herman and Nancy H. C. Roosens

    Citation: BMC Biotechnology 2018 18:40

    Content type: Research article

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  12. Custom synthesized DNA is in high demand for synthetic biology applications. However, current technologies to produce these sequences using assembly from DNA oligonucleotides are costly and labor-intensive. Th...

    Authors: Yuliya Khilko, Philip D. Weyman, John I. Glass, Mark D. Adams, Melanie A. McNeil and Peter B. Griffin

    Citation: BMC Biotechnology 2018 18:37

    Content type: Methodology article

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  13. We demonstrate the feasibility of creating a pair of reference samples to be used as surrogates for clinical samples measured in either a research or clinical laboratory setting. The reference sample paradigm ...

    Authors: P. Scott Pine, Steven P. Lund, Sanford A. Stass, Debra Kukuruga, Feng Jiang, Lynn Sorbara, Sudhir Srivastava and Marc Salit

    Citation: BMC Biotechnology 2018 18:17

    Content type: Methodology article

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  14. microRNAs (miRNAs) are short non-coding RNAs that fine-tune gene expression. The aberrant expression of miRNAs is associated with many diseases and they have both therapeutic and biomarker potential. However, ...

    Authors: Rikki A. M. Brown, Michael R. Epis, Jessica L. Horsham, Tasnuva D. Kabir, Kirsty L. Richardson and Peter J. Leedman

    Citation: BMC Biotechnology 2018 18:16

    Content type: Research article

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  15. Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioi...

    Authors: Christoph Geisler

    Citation: BMC Biotechnology 2018 18:8

    Content type: Methodology article

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  16. Detection of DNA methylome at single-base resolution is a significant challenge but promises to shed considerable light on human disease etiology. Current technologies could not detect DNA methylation genome-w...

    Authors: Zhen Jia, Yueyi Shi, Lei Zhang, Yipeng Ren, Tong Wang, Lejun Xing, Baorong Zhang, Guolan Gao and Rongfa Bu

    Citation: BMC Biotechnology 2018 18:7

    Content type: Methodology article

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    The Retraction Note to this article has been published in BMC Biotechnology 2020 20:23

  17. Circulating microRNAs are undergoing exploratory use as safety biomarkers in drug development. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is one common approach used to quantitate l...

    Authors: Russell D. Wolfinger, Sudheer Beedanagari, Eric Boitier, Tao Chen, Philippe Couttet, Heidrun Ellinger-Ziegelbauer, Gregory Guillemain, Claire Mariet, Peter Mouritzen, Raegan O’Lone, P. Scott Pine, Tatiana Sharapova, Jian Yan, Peter S. Yuen and Karol L. Thompson

    Citation: BMC Biotechnology 2018 18:6

    Content type: Methodology article

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  18. Massively parallel genetic sequencing allows rapid testing of known intellectual disability (ID) genes. However, the discovery of novel syndromic ID genes requires molecular confirmation in at least a second o...

    Authors: Tracy Dudding-Byth, Anne Baxter, Elizabeth G. Holliday, Anna Hackett, Sheridan O’Donnell, Susan M. White, John Attia, Han Brunner, Bert de Vries, David Koolen, Tjitske Kleefstra, Seshika Ratwatte, Carlos Riveros, Steve Brain and Brian C. Lovell

    Citation: BMC Biotechnology 2017 17:90

    Content type: Research article

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  19. Next-generation sequencing (NGS) has transformed genomic research by reducing turnaround time and cost. However, no major breakthrough has been made in the upstream library preparation methods until the transp...

    Authors: Amirali Kia, Christian Gloeckner, Trina Osothprarop, Niall Gormley, Erin Bomati, Michelle Stephenson, Igor Goryshin and Molly Min He

    Citation: BMC Biotechnology 2017 17:6

    Content type: Research article

    Published on:

  20. The isolation of unknown DNA sequences flanked by known sequences is an important task in the event-specific detection of GMOs. None of event-specific detection method was developed based on the junction seque...

    Authors: Hongwei Gao, Xiaofan Yu, Tingting Deng, Min Sun, Xizhi Xiao, Xin Huang, Ying Chen and Ronggui Li

    Citation: BMC Biotechnology 2016 16:74

    Content type: Research article

    Published on:

  21. Transcription factors (TFs) are effectors of cell signaling pathways that regulate gene expression. TF networks are highly interconnected; one signal can lead to changes in many TF levels, and one TF level can...

    Authors: Betul Bilgin, Aritro Nath, Christina Chan and S. Patrick Walton

    Citation: BMC Biotechnology 2016 16:62

    Content type: Research article

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  22. Selected microRNAs (miRNAs) that are abnormally expressed in the serum of patients with lung cancer have recently been proposed as biomarkers of this disease. The measurement of circulating miRNAs, however, re...

    Authors: Paola Campomenosi, Elisabetta Gini, Douglas M. Noonan, Albino Poli, Paola D’Antona, Nicola Rotolo, Lorenzo Dominioni and Andrea Imperatori

    Citation: BMC Biotechnology 2016 16:60

    Content type: Methodology article

    Published on:

  23. Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appro...

    Authors: P. Scott Pine, Sarah A. Munro, Jerod R. Parsons, Jennifer McDaniel, Anne Bergstrom Lucas, Jean Lozach, Timothy G. Myers, Qin Su, Sarah M. Jacobs-Helber and Marc Salit

    Citation: BMC Biotechnology 2016 16:54

    Content type: Methodology article

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  24. Research into gene expression enables scientists to decipher the complex regulatory networks that control fundamental biological processes. Quantitative real-time PCR (qPCR) is a powerful and ubiquitous method...

    Authors: Nicky Boulter, Francia Garces Suarez, Stephen Schibeci, Trevor Sunderland, Ornella Tolhurst, Tegan Hunter, George Hodge, David Handelsman, Ulla Simanainen, Edward Hendriks and Karen Duggan

    Citation: BMC Biotechnology 2016 16:27

    Content type: Methodology article

    Published on:

  25. The p53 tumor suppressor protein is mainly regulated by alterations in the half-life of the protein, resulting in significant differences in p53 protein levels in cells. The major regulator of this process is ...

    Authors: Ping Zhang, Anne Sophie Kratz, Mohammed Salama, Seham Elabd, Thorsten Heinrich, Joachim Wittbrodt, Christine Blattner and Gary Davidson

    Citation: BMC Biotechnology 2015 15:92

    Content type: Research article

    Published on:

  27. Immunomagnetic nanobead (IMNB) labeled with specific antibody, has been demonstrated to be useful for the capturing and detection of viruses.

    Authors: Shunli Yang, Shuanghui Yin, Youjun Shang, Di Wang, Weimin Ma, Jijun He, Jianhong Guo, Jianping Cai and Xiangtao Liu

    Citation: BMC Biotechnology 2015 15:83

    Content type: Research article

    Published on:

  28. With the accelerating development of bioscience, the problem of research cost has become important. We previously devised and developed a novel concept microarray with manageable volumes (MMV) using a soft gel...

    Authors: Harshita Sharma, Yasunori Kinoshita, Seiichi Fujiu, Shota Nomura, Mizuho Sawada, Shamim Ahmed, Masaki Shibuya, Kosaku Shirai, Syota Takamatsu, Tsuyoshi Watanabe, Hitoshi Yamazaki, Ryohei Kamiyama, Tetsuya Kobayashi, Hidenao Arai, Miho Suzuki, Naoto Nemoto…

    Citation: BMC Biotechnology 2014 14:78

    Content type: Methodology article

    Published on:

  29. Neonatal dried blood spots (DBS) represent an inexpensive method for long-term biobanking worldwide and are considered gold mines for research for several human diseases, including those of metabolic, infectio...

    Authors: Akram Ghantous, Richard Saffery, Marie-Pierre Cros, Anne-Louise Ponsonby, Steven Hirschfeld, Carol Kasten, Terence Dwyer, Zdenko Herceg and Hector Hernandez-Vargas

    Citation: BMC Biotechnology 2014 14:60

    Content type: Methodology article

    Published on:

  31. Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicat...

    Authors: Wenjing Pan, Miranda Byrne-Steele, Chunlin Wang, Stanley Lu, Scott Clemmons, Robert J Zahorchak and Jian Han

    Citation: BMC Biotechnology 2014 14:10

    Content type: Research article

    Published on:

  32. Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the most prevalent pathogens responsible for nosocomial infections throughout the world. As clinical MRSA diagnosis is concerned, current diagn...

    Authors: Jianyu Su, Xiaochen Liu, Hemiao Cui, Yanyan Li, Dingqiang Chen, Yanmei Li and Guangchao Yu

    Citation: BMC Biotechnology 2014 14:8

    Content type: Methodology article

    Published on:

  33. The Nextera protocol, which utilises a transposome based approach to create libraries for Illumina sequencing, requires pure DNA template, an accurate assessment of input concentration and a column clean-up th...

    Authors: Sarah Lamble, Elizabeth Batty, Moustafa Attar, David Buck, Rory Bowden, Gerton Lunter, Derrick Crook, Bassam El-Fahmawi and Paolo Piazza

    Citation: BMC Biotechnology 2013 13:104

    Content type: Methodology article

    Published on:

  34. The starting material for RNA sequencing (RNA-seq) studies is usually total RNA or polyA+ RNA. Both forms of RNA represent heterogeneous pools of RNA molecules at different levels of maturation and processing....

    Authors: Ammar Zaghlool, Adam Ameur, Linnea Nyberg, Jonatan Halvardson, Manfred Grabherr, Lucia Cavelier and Lars Feuk

    Citation: BMC Biotechnology 2013 13:99

    Content type: Research article

    Published on:

  35. Gene transcripts specifically expressed in a particular cell type (cell-type specific gene markers) are useful for its detection and isolation from a tissue or other cell mixtures. However, finding informative...

    Authors: Miguel A Andrade-Navarro, Femina Kanji, Carmen G Palii, Marjorie Brand, Harold Atkins and Carol Perez-Iratxeta

    Citation: BMC Biotechnology 2013 13:80

    Content type: Research article

    Published on:

  38. Dried blood (Guthrie card) spots provide an efficient way to collect and store blood specimens. DNA from this source has been utilised for a number of molecular analyses including genome-wide association studi...

    Authors: JiHoon E Joo, Ee Ming Wong, Laura Baglietto, Chol-Hee Jung, Helen Tsimiklis, Daniel J Park, Nicholas C Wong, Dallas R English, John L Hopper, Gianluca Severi, Graham G Giles and Melissa C Southey

    Citation: BMC Biotechnology 2013 13:23

    Content type: Research article

    Published on:

  39. In bacterial systems, the sequence congruence of genomic DNA (gDNA) and cDNA obtained following reverse transcription of RNA, makes gDNA an automatic target for qPCR primers. This could lead to aberrant gene e...

    Authors: Vijay J Gadkar and Martin Filion

    Citation: BMC Biotechnology 2013 13:7

    Content type: Research article

    Published on:

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