While being stuck in traffic at the Golden Gate bridge during my last San Francisco trip, an idea occurred to me. How about I do some research work to benchmark all suspension bridges in the world?
A quick check at Wikipedia gave me over one hundred candidates, leading me to restrict my ambitious plan [...]
Posted on 20 August 2014 | 1:17 pm
The problem of assembling a large number of noisy long reads is expected to show up, no matter whether one uses Pacbio or nanopore long read technology. The good news is that it is possible to do the assembly and the quality is a lot better than what can be achieved with short reads or [...]
Posted on 20 August 2014 | 12:39 pm
Remember TPP? Here is a good example of what ‘free trade’ will look like after all countries adopt the rules written by multinational corporations.
A Colombian biology student is facing up to 8 years in jail and a fine for sharing a thesis by another scientist on a social network.
Diego Gómez Hoyos posted the [...]
Posted on 19 August 2014 | 8:44 am
We came across this BMC Genomics paper in twitter, but did not get time to read yet. Hopefully, the readers will find it useful.
Background Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA [...]
Posted on 12 August 2014 | 9:49 am
In the past, we talked about ‘short read noise’, which is the noise introduced by clean short reads due to being short. Readers may take at these two of our earlier commentaries for details.
End of Short-Read Era? – (Part I)
End of Short-Read Era? – (Part II)
An excellent biorxiv paper analyzing RNA-seq assemblies [...]
Posted on 16 July 2014 | 3:14 am
Richard Smith-Una, whose work was covered in our blog, releases a new quality assessment program (transrate) that we surely like to check out.
Transcriptome assembly is hard. The algorithms are complex, the data are messy, and it’s often not clear how to determine whether an assembly is suitable for answering a biological question.
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Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed “reads” are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA [...]
Posted on 10 June 2014 | 6:08 am
We had been pondering about those cryptic terms and found by asking some people around that the P stands for polymerase and C stands for chemistry. Therefore, P4-C2 means polymerase of fourth generation and chemistry of second generation.
That got us curious about what the actual DNA polymerase sequences are for 2nd, 3rd or [...]
Posted on 4 April 2014 | 4:58 am
Changing genome in plants used to be incredibly difficult, but not any more. Here is an excellent review -
Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system
Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) [...]
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