"I think John will come to school today."
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Placing 「今日」at the beginning of the sentence means that on this day you have the thought that John will come to school as opposed to having that thought yesterday.
It's a bit nuanced but it becomes clear once you use two temporal adverbs in the same sentence: Today I think that Jon will come to school tomorrow.
You can put any plain form of a verb or adjective before と思います.
For verbs, that includes the dictionary form (such as いく or みる), ない negative form, plain past tense affirmative that usually ends in -た, or plain negative past tense なかった.
ジョンは今日学校に来ると思います。= I think that John will come to school today.
ジョンは今日学校に来たと思います。= I think that John came to school today.
ジョンは今日学校に来ないと思います。= I think that John didn't come to school today.