From this Daily Times report:
HEC [the Higher Education Commissioin] has compiled a report by taking into account publications by Pakistani universities, which appeared in peer-reviewed journals indexed by Thomson-Reuter, ISI Web of Knowledge during the years 2007 and 2008.
The databases used for this analysis were Science Citation Index, Social Science Citation Index, and Art and Humanities Citation Index.
According to the report, the Quaid-e-Azam University tops the list with 544 publications in 2008 and 409 publications in 2007. University of Karachi comes in second position with 419 publications in 2008 and 276 publications in 2007. Aga Khan University is the only private university that comes in the top five universities on the basis of research publications. The university is third in the list with 311 publications in 2008 and 186 publications in 2007. The University of the Punjab is the only university from Lahore that comes in the top five universities. The university is fifth with 278 publications in 2008 and 162 publications in 2007.