How can I search a column in MySQL containing unix timestamps with a query referencing a different format?
Try this:

SQL code:

SELECT COUNT(FOO1)
FROM footable
WHERE FOOTIME &gt;= UNIX_TIMESTAMP('2012-01-01');


SELECT COUNT(FOO1)
FROM footable
WHERE FROM_UNIXTIME(FOOTIME)&gt;='2012-01-01'; 


Sample data:

CREATE TABLE footable (
  FOO1 varchar(30) primary key,
  FOOTIME int(11)
  );

INSERT INTO footable (FOO1, FOOTIME)
VALUES ('blah', UNIX_TIMESTAMP(now() - INTERVAL 1 YEAR)),
('Blahblah', UNIX_TIMESTAMP(now() - INTERVAL 2 YEAR)),
('BLablahblah', UNIX_TIMESTAMP(NOW() - INTERVAL 5 YEAR));


SQLFiddle demo