$re = '/\[\d+];(*SKIP)(*F)|(;)/m';
$str = 'Dee, DP(Dee, D. P.)[1];Uppala, SM(Uppala, S. M.);Simmons, AJ(Simmons, A. J.);Kobayashi, S(Kobayashi, S.)[2];Andrae, U(Andrae, U.)[3]';
$subst = "[0]\1";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php