Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm

Tracy L. Weissgerber TL, et al., Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm, PLoS Biol 13(4), 2015

Our systematic review of research articles published in top physiology journals (n = 703) suggests that, as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies. Papers rarely included scatter- plots, box plots, and histograms that allow readers to critically evaluate continuous data. Most papers presented continuous data in bar and line graphs. This is problematic, as many different data distributions can lead to the same bar or line graph.

Advertisements

TelomereHunter: telomere content estimation and characterization from whole genome sequencing data

Lars Feuerbach, et al., TelomereHunter: telomere content estimation and characterization from whole genome sequencing data, bioRxiv, 2016

Here, we present TelomereHunter, a new computational tool for determining telomere content that is specifically designed for matched tumor and control pairs. In contrast to existing tools, TelomereHunter takes alignment information into account and reports the abundance of variant repeats in telomeric sequences.

 

The criterion of searching for six non-consecutive repeats in 100bp long reads has been proposed previously (Lee, et al., 2014) and was also found suitable for the data presented in the present study.

Estimating telomere length from whole genome sequence data

Zhihao Ding, et al., Estimating telomere length from whole genome sequence data, Nucleic Acids Research 42(9), 2014

Here, we report a novel method, TelSeq, to measure average telomere length from whole genome or exome shotgun sequence data.

 

We defined reads as telomeric if they contained k or more TTAGGG repeats, with a default threshold value of k = 7.

 

However, in practice with current technology, a typical exome sequencing output contains some fraction (typically 10-50%) of sequence that is off-target, i.e. not exonic. This fraction represents information on the rest of the genome and can be used to estimate relative telomere length by our method.

DNA fingerprinting in botany: past, present, future

Hilde Nybom, et al., DNA fingerprinting in botany: past, present, future, Investigative Genetics 5:1, 2014

In the 1980s, the REFP methodology was also first applied to the chloroplast DNA (cpDNA) molecule.

Since the cp DNA molecule is highly conserved, there is very little intra-specific variation, and cpDNA-based RELP studies have therefore mostly been conducted on an inter-specific level.

While the plant mitochondrial DNA (mtDNA) sequence is usually highly conserved, the size and structure of mtDNA molecules may vary widely even within individual plants. Moreover, recent studies indicated that substitution rates of mtDNA genes can vary enormously even among closely related plant species.

A special situation is encountered when products from protected trees are involved since  woody tissues usually yields heavily degraded DNA. Nevertheless, a set of SNP markers derived from cpDNA intergenic spacers have proven useful for identification of tropical tree species using wood-derived DNA samples.

Evolution of the Vertebrate Gene Regulatory Network Controlled by the Transcriptional Repressor REST

Rory Johnson, et al., Evolution of the Vertebrate Gene Regulatory Network Controlled by the Transcriptional Repressor REST, Mol Biol Evol (2009) 26 (7): 1491-1507

We show that one-third of human RE1s are unique to primates: These sites recruit REST in vivo, target neural genes, and are under purifying evolutionary selection We observe a consistent and significant trend for more ancient RE1s to have higher affinity for REST than lineage-specific sites and to be more proximal to garget genes. Our results lead us to propose a model where new transcription factor binding sites are constantly generated throughout the genome; thereafter refinement of their sequence and location consolidates this remodeling of networks governing neural gene regulation.