With grep:

grep -vwf file matrix > matrix.new
mv matrix.new matrix

• option -f FILE use FILE as pattern input file
• option -w select only those lines containing matches that form whole words
• option -v select non-matching lines

Note that file must not contain any empty lines.

With grep:

grep -vwf file matrix > matrix.new
mv matrix.new matrix

• option -f FILE use FILE as pattern input file
• option -w select only those lines containing matches that form whole words
• option -v select non-matching lines

Note that file must not contain any empty lines.

Or if you create your identifier file manually with an anchor ^ to match the start of the line and a space character after each identifier to mark the end of the pattern:

printf '^%s \n' denovo{1,100,1000,100000} > file
grep -vf file matrix > matrix.new
mv matrix.new matrix