Not exactly. You cannot tell MATLAB to skip the first line of a file during run(). However, you can read the content of the file, remove the first line, and execute that content.
temporary_string = fileread(filename);
temporary_string = regexprep(temporary_string, '^[^\n]*\n', '');
Strictly speaking, this is not equivalent to run(), in that run cd's to the directory the file is in but this code does not do that. That makes a difference in search paths -- for example if there was a private/ directory in the folder the file is stored in, then run() would use the functions in the private/ folder, but the above code will not.
