Popular Genes

Nature recently had a news feature documenting the most popular genes in the human genome by Elie Doglin.  In addition to a list of the most popular genes and their location in the human genome, the article discusses the history of popular genes.  Genes that became popular signaled new scientific discoveries at the time.  This was a fun read.


Source: Peter Kerpedjiev/NCBI-NLM (from The most popular genes in the human genome)



Ruth Simmons, President of PVAMU

I was excited to see that Ruth Simmons, former president of Smith College (1995-2000) and Brown University (2002-2012), has been named as the permanent president of Prairie View A&M University.

via Now in Her 70s, First Black Ivy-League President Finds a Third Act – The Chronicle of Higher Education

While I never met Ruth Simmons while I was at Brown, I saw images of her frequently on the Brown CS0931 page in 2012:

Screen Shot 2017-10-24 at 11.03.03 AM

The course, Introduction to Computation for the Humanities & Social Sciences, taught computational thinking to non-computational undergraduate majors.  Each year, the undergraduate TAs design the course page around a theme.  I was an instructor for CS0931 in the spring of 2012, when students created the page as an homage to Dr. Simmons in her last year as president of the university.  The Staff page is particularly fun.   Dr. Simmons clearly left an impression on the undergraduates at Brown University, and I bet she’ll do the same at Prairie View A&M.



Breakdown of CS faculty hires in 2017

Craig E. Wills of WPI recently wrote a report that describes the outcomes of advertised CS faculty positions across institutions in 2017. It was a follow-up to a previous report on the CS positions advertised in 2017.  The report contains a wealth of information about the number of faculty positions filled at different institutions.

In summary, 244 of the 323 advertised positions were fulfilled, giving an aggregate 75% success rate.  Not surprisingly, this success varied by institution type: 90% of the positions advertised by the top 100 graduate schools according to U.S. News Rankings were filled, whereas other PhD-granting institutions, Masters-granting institutions, and Bachelors-granting institutions had 67%, 66%, and 69% success rates, respectively.

Wills also looked at the faculty positions by research area.  I’ll focus on three:

  • AI/DM/ML: artificial intelligence, computational linguistics, data mining, machine learning, natural language processing, text analytics
  • CompSci: computational biology, computational life science, computational medicine, computational neuroscience (you get the picture…)
  • Security: cryptography, forensics, information assurance, privacy, security

The figure below shows the percent of faculty positions sought for each field on the x-axis and the percent of faculty positions filled for each field on the y-axis:


Points that lie on the red x=y line indicate that the percent of faculty positions filled exactly matched the percent of faculty positions sought.  Let’s look at the three largest outliers:

  • AI/DM/ML was sought for 11% of the positions by area, but ended up filling 21% of the positions.
  • DataSci was sought for 16% of the positions by area, but ended up filling only 7% of the positions.
  • Security was sought for 23% of the positions, but ended up filling only 12% of the positions.

Wills cited many factors associated with these discrepancies, including the fact that nearly a quarter of the positions did not specify an area of interest in their ad.  Additionally, institutions simply did not end up hiring in the areas of interest, either because they could not find candidates in that area or they found better candidates in other areas.  Areas could also be satisfied with multiple fields (for example AI/DM/ML or DataSci accounted for 27% of the positions sought and ended up filling 28% of the positions when combined).

Another factor that Wills considered was the number of Ph.D.s produced by area (based on Taulbee Survey results):


It’s good to be in Security, since only 6% of the Ph.D.s produced are in this area compared to the demand of 23% of the positions sought in this area.  It’s also good to be in AI/DM/ML because over 20% of the faculty positions were filled in this area, even if the job ads didn’t specify it.

Overall, the report was an interesting read – I’m looking forward to seeing these trends over time.

Female Code Breakers

Here’s a fascinating story about the women who helped break codes during WWII.  The article appeared as part of ACM TechNews, and is excerpted from the book Code Girls: The Untold Story of the American Women Code Breakers of World War II by Liza Mundy.

via The Secret History of the Female Code Breakers Who Helped Defeat the Nazis – POLITICO Magazine

(Thanks to Barbara Ryder, emeritus professor and former chair of Computer Science at Virginia Tech, for the pointer)

New Reed CompBio Blog

As part of a recently-funded collaborative REU (generously supported by the CRA-W), my colleague Derek Applewhite and I are working with undergraduates to study machine learning methods to predict genes that regulate cell movement patterns in schizophrenia.  The team will post their work on new a Reed College blog, The Pathway Not Taken, and I may re-post selected pieces here.  The first post gives a general idea of the problem we will work on, and how biology and computer science are intertwined in the project.