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Top Ten Peer-Reviewed Articles

08/01/2014

From NGS library construction to optimal sorting of mitotic cells, BioTechniques has presented you with ample new methods to improve your research this year. Here we list our ten most popular peer-reviewed papers, based on downloads, from the first half of 2014.

1. Library construction for next-generation sequencing: Overviews and challenges
In our first Practical Guide article of 2014, Head et al. review the critical role of the sequencing library and assess the challenges that may arise during its creation. And of course, they also recommend options for troubleshooting and resolving these problems.

2. TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences
The microbiome is a hot topic these days, and taxonomic classification is an important step in these studies. Here, Tuzhikov et al. present an open source command line tool for microbial taxonomy analysis that returns results even for sequences as short as 125 bp.

3. Sensitive ligand-based protein quantification using immuno-PCR: A critical review of single-probe and proximity ligation assays
qPCR has revolutionized gene expression analysis, but many researchers also want to address protein translational patterns in their studies. In this Practical Guide, Hansen et al. review a method that meets this need: PCR-coupled protein quantification, often denoted as immuno-PCR (iPCR), which targets soluble proteins.

4. Linear amplification of target prior to PCR for improved low template DNA results
Forensic DNA studies are often hampered by low quantities of poor quality DNA. Here, Grisedale et al. present an amplification method for target DNA prior to short tandem repeat (STR) analysis without introducing amplification bias.

5. Chromatin in situ proximity (ChrISP): Single-cell analysis of chromatin proximities at a high resolution
To overcome poor resolution or the need for a large number of cells, Chen et al. combined the in situ proximity ligation technique with conventional DNA FISH/immunostaining to create a new method for looking at the proximity of different regions within chromatin.

6. Inactivation of an integrated antibiotic resistance gene in mammalian cells to re-enable antibiotic selection
2014 has brought several new uses for the CRISPR/Cas9 system. Here, Ni et al. used the endonuclease to disrupt antibiotic resistance genes in mammalian cells, enabling researchers to perform additional rounds of genetic manipulation with selection using the same antibiotic.

7. Quantitative analysis of colony morphology in yeast
The structures of biofilms and microbial colonies can influence an organism's phenotype. Here Ruusuvuori et al. present a new automated platform for analyzing yeast colony morphology, offering an alternative to subjective scoring of colonies and facilitating high-throughput experiments.

8. Systematic selection of modified aptamer pairs for diagnostic sandwich assays
Many techniques require pairs of analyte specific reagents for detection and capture. Here, Ochsner et al. present a new method for isolating aptamers and a screening method for determining the best pairs for experimental use.

9. Advantages of using the QIAshredder instead of restriction digestion to prepare DNA for droplet digital PCR
Genomic DNA can be difficult to partition into droplets or wells for digital PCR. To overcome this, researchers use restriction enzymes to cut the DNA into more manageable fragments. But here, Yukl et al. show that using a QIAshredder spin column is quicker and easier. Not only that, but it produces much more uniform fragments and avoids using digestion buffers that can inhibit PCR.

10. Comparative analysis of mitosis-specific antibodies for bulk purification of mitotic populations by fluorescence-activated cell sorting
Chromatin changes during mitosis have caught the attention of many biologists, but to study these cells, it is necessary to first collect a lot of them. Here, Campbell et al. present an optimized FACS-based method for isolating fixed mitotic cells at virtually 100% mitotic purity.

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