HughesLab:Academic Analytics: Difference between revisions

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== Academic Analytics==


== Discovery of circadian harmonics ==
== Dynamics of collaborative science in a CTSA ==
[[Image:SciTM_Figure1.jpg|left|thumb|'''Figure 1''': [http://www.ncbi.nlm.nih.gov/pubmed/20944088 Hughes et al. (2011)]<br>Social Networking Analysis of the Institute for Translational Medicine and Therapeutics.]]
[[Image:SciTM_Figure1.jpg|left|thumb|'''Figure 1''': [http://www.ncbi.nlm.nih.gov/pubmed/20944088 Hughes et al. (2011)]<br>Social Networking Analysis of the Institute for Translational Medicine and Therapeutics.]]


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We profiled global gene expression over two full days using Affymetrix microarrays.  We identified rhythmic transcripts in the mouse liver and pituitary, as well as fibroblasts (NIH3T3) and osteosarcoma cells (U2OS).  These data have been made freely available on [http://bioinf.itmat.upenn.edu/circa CircaDB] as a resource to the field. To our surprise, we found several hundred genes cycling with period lengths much shorter than 24 hours (Fig. 1).  These ultradian rhythms had period lengths of ~8 and ~12 hours -- i.e., the second and third harmonics of 24 hour oscillations. </p>
To assess the growth and evolution of a major scientific enterprise, we automatically harvested every paper and grant proposal from the University of Pennsylvania's CTSA, the Institute for Translational Medicine and Therapeutics (ITMAT).  We used these data to construct networks of interacting principal investigators, and measured their dynamics using Social Network Analysis (SNA).   
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Subsequently, we have shown that these rhythms are found in tissues throughout the body.  Moreover, they are found in fruit flies as well, suggesting that circadian harmonics are a common feature of animal transcriptional rhythms.  At a mechanistic level, 12 hour rhythms require both a central and peripheral circadian oscillator, indicating that these rhythms are ultimately downstream of the conventional circadian clock. Typically, they are involved in cellular responses to stress, suggesting that ultradian transcriptional rhythms respond to twice daily stresses.
We found extensive growth in the frequency of collaborations within ITMAT over the course of its tenure.  Most interestingly, this growth exceeded predictions based on the expansion of ITMAT's roster during this time, suggesting that ITMAT membership was itself responsible for the increasing rate of collaborative activity.  This study was highlighted in [http://www.nature.com/news/2010/101013/full/news.2010.538.html Nature News].
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Revision as of 08:17, 6 August 2013

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Dynamics of collaborative science in a CTSA

Figure 1: Hughes et al. (2011)
Social Networking Analysis of the Institute for Translational Medicine and Therapeutics.

To assess the growth and evolution of a major scientific enterprise, we automatically harvested every paper and grant proposal from the University of Pennsylvania's CTSA, the Institute for Translational Medicine and Therapeutics (ITMAT). We used these data to construct networks of interacting principal investigators, and measured their dynamics using Social Network Analysis (SNA).


We found extensive growth in the frequency of collaborations within ITMAT over the course of its tenure. Most interestingly, this growth exceeded predictions based on the expansion of ITMAT's roster during this time, suggesting that ITMAT membership was itself responsible for the increasing rate of collaborative activity. This study was highlighted in Nature News.






Hughes Lab
Department of Biology
University of Missouri, St. Louis

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