Genome technology and molecular diagnostics

Section edited by Mats Nilsson

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.

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  1. Research article

    Improved genome sequencing using an engineered transposase

    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...

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

    BMC Biotechnology 2017 17:6

    Published on: 17 January 2017

  2. Research article

    Characterization of transcription factor response kinetics in parallel

    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...

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

    BMC Biotechnology 2016 16:62

    Published on: 24 August 2016

  3. Methodology article

    A comparison between quantitative PCR and droplet digital PCR technologies for circulating microRNA quantification in human lung cancer

    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...

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

    BMC Biotechnology 2016 16:60

    Published on: 18 August 2016

  4. Methodology article

    Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design

    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...

    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

    BMC Biotechnology 2016 16:54

    Published on: 24 June 2016

  5. Methodology article

    A simple, accurate and universal method for quantification of PCR

    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...

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

    BMC Biotechnology 2016 16:27

    Published on: 9 March 2016

  6. Research article

    Expression screening using a Medaka cDNA library identifies evolutionarily conserved regulators of the p53/Mdm2 pathway

    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 ...

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

    BMC Biotechnology 2015 15:92

    Published on: 8 October 2015

  7. Methodology article

    Establishment of a reborn MMV-microarray technology: realization of microbiome analysis and other hitherto inaccessible technologies

    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...

    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…

    BMC Biotechnology 2014 14:78

    Published on: 21 August 2014

  8. Methodology article

    Optimized DNA extraction from neonatal dried blood spots: application in methylome profiling

    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...

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

    BMC Biotechnology 2014 14:60

    Published on: 1 July 2014

  9. Research article

    Simultaneous multi-analyte urinary protein assay for bladder cancer detection

    The ability to accurately measure multiple proteins simultaneously in a single assay has the potential to markedly improve the efficiency of a myriad of clinical assays. Here, we tested the performance of a ne...

    Charles J Rosser, Yunfeng Dai, Makito Miyake, Ge Zhang and Steve Goodison

    BMC Biotechnology 2014 14:24

    Published on: 1 April 2014

  10. Research article

    DNA polymerase preference determines PCR priming efficiency

    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...

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

    BMC Biotechnology 2014 14:10

    Published on: 30 January 2014

  11. Methodology article

    Rapid and simple detection of methicillin-resistance staphylococcus aureus by orfXloop-mediated isothermal amplification assay

    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...

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

    BMC Biotechnology 2014 14:8

    Published on: 24 January 2014

  12. Methodology article

    Improved workflows for high throughput library preparation using the transposome-based nextera system

    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...

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

    BMC Biotechnology 2013 13:104

    Published on: 20 November 2013

  13. Research article

    Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues

    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....

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

    BMC Biotechnology 2013 13:99

    Published on: 13 November 2013

  14. Research article

    A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations

    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...

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

    BMC Biotechnology 2013 13:80

    Published on: 3 October 2013

  15. Research article

    The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array

    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...

    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

    BMC Biotechnology 2013 13:23

    Published on: 15 March 2013

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