We have yet to fully comprehend the consequences of the Administration’s Anti-French policies carried out between 2003 and 2007, but careful research has been conducted in certain fields, including the effect of French Bashing on the publishing of French papers in American journals following the events of 2003.
Professors Bernard Bégaud, (pharmacology) and Hélène Verdoux (psychiatry) published their findings in late 2004 and revealed a marked decrease in articles from French authors. Many researchers were convinced there was an unofficial boycott of French manuscripts in peer-reviewed journals, but beyond suspicion nothing had yet been proven. The work of Bégaud and Verdoux was to confirm this suspicion through careful analysis of publications in leading American medical journals.
Bégaud and Verdoux discovered that following the threat of a French veto in 2003, the number of French papers published in American journals decreased by the same factor of increase in British journals.
Source :British Medical Journal via Pub Med Central
Working in another field of academic research, I must say that I did not notice such a bias. It may have been there at the margin, but I suspect it was more than compensated for by the extra recruiting opportunities that ambitious French institutions had as a result of the U.S. becoming less hospitable and attractive to non-American researchers after 9/11. In the long term, any bias by American journals will only contribute to the decline of these journals as well as the U.S. as a relative research power.