2013 Runners-Up. Genetic microsurgery for the masses

Scientific Value Weights more than Being Open or Toll Access: An analysis of the OA advantage in Nature and Science

Purpose

We attempt to find out whether OA or TA really affects the dissemination of scientific discoveries.

Design/methodology/approach

We design the indicators, hot-degree, and R-index to indicate a topic OA or TA advantages. First, according to the OA classification of the Web of Science (WoS), we collect data from the WoS by downloading OA and TA articles, letters, and reviews published in Nature and Science during 2010–2019. These papers are divided into three broad disciplines, namely biomedicine, physics, and others. Then, taking a discipline in a journal and using the classical Latent Dirichlet Allocation (LDA) to cluster 100 topics of OA and TA papers respectively, we apply the Pearson correlation coefficient to match the topics of OA and TA, and calculate the hot-degree and R-index of every OA-TA topic pair. Finally, characteristics of the discipline can be presented. In qualitative comparison, we choose some high-quality papers which belong to Nature remarkable papers or Science breakthroughs, and analyze the relations between OA/TA and citation numbers.

Findings

The result shows that OA hot-degree in biomedicine is significantly greater than that of TA, but significantly less than that of TA in physics. Based on the R-index, it is found that OA advantages exist in biomedicine and TA advantages do in physics. Therefore, the dissemination of average scientific discoveries in all fields is not necessarily affected by OA or TA. However, OA promotes the spread of important scientific discoveries in high-quality papers.

Research limitations

We lost some citations by ignoring other open sources such as arXiv and bioArxiv. Another limitation came from that Nature employs some strong measures for access-promoting subscription-based articles, on which the boundary between OA and TA became fuzzy.

Practical implications

It is useful to select hot topics in a set of publications by the hot-degree index. The finding comprehensively reflects the differences of OA and TA in different disciplines, which is a useful reference when researchers choose the publishing way as OA or TA.

Originality/value

We propose a new method, including two indicators, to explore and measure OA or TA advantages.

Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)

SUMMARY

Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have revolutionized human genome engineering and opened countless possibilities to basic science, synthetic biology and gene therapy. Albeit the enormous potential of these tools, their performance is far from perfect. It is essential to perform a posterior careful analysis of the gene editing experiment. However, there are no computational tools for genome editing assessment yet, and current experimental tools lack sensitivity and flexibility. We present a platform to assess the quality of a genome editing experiment only with three mouse clicks. The method evaluates next-generation data to quantify and characterize insertions, deletions and homologous recombination. CRISPR Genome Analyzer provides a report for the locus selected, which includes a quantification of the edited site and the analysis of the different alterations detected. The platform maps the reads, estimates and locates insertions and deletions, computes the allele replacement efficiency and provides a report integrating all the information.

AVAILABILITY AND IMPLEMENTATION

CRISPR-GA Web is available at http://crispr-ga.net. Documentation on CRISPR-GA instructions can be found at http://crispr-ga.net/documentation.html

CONTACT

mguell@genetics.med.harvard.edu.

Unlocking the treasure trove: from genes to schizophrenia biology

Significant progress is being made in defining the genetic etiology of schizophrenia. As the list of implicated genes grows, parallel developments in gene editing technology provide new methods to investigate gene function in model systems. The confluence of these two research fields--gene discovery and functional biology--may offer novel insights into schizophrenia etiology. We review recent advances in these fields, consider the likely obstacles to progress, and consider strategies as to how these can be overcome.