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Yes, Smith's paper is a classic. We are sorry that we thought it is well-known and did not cite it.

I do not feel secure with the tense here. After the verb 'thought', is 'is' okay? Or should it be 'was'?

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    This makes little sense, and there must be more context. In the first place, is the speaker apologizing for thinking that the paper was well known, or for failing to cite it? Also, why would someone fail to cite a paper merely because it is well known—or unknown, for that matter? – P. E. Dant Reinstate Monica Sep 2 '16 at 3:51
  • I did not cite it simply because none will cite newton's paper anymore. – John Sep 2 '16 at 3:55
  • Ah! The first lesson of academe: cite, cite, and cite again. Also, in English we capitalize proper names such as Sir Isaac Newton, and none is not the same as no one or no-one. Is the speaker apologizing for thinking that the paper was well known, for failing to cite it, or for the entire event? – P. E. Dant Reinstate Monica Sep 2 '16 at 3:59
  • As you have phrased the sentence, it sounds as if you are apologizing for thinking that Newton's paper is well known. Is that your intention? This has nothing to do with the tense of to be. – P. E. Dant Reinstate Monica Sep 2 '16 at 4:09
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    What a strange sentence! Still, you asked about the grammar. Since the status of the paper as well-known is still current at the time of the utterance, it is possible to use the present tense. It can, optionally, be backshifted to past tense; it's a free choice really. – BillJ Sep 3 '16 at 8:32
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Yes, Smith's paper is a classic. We are sorry that we thought it is well-known and did not cite it.

You can use either verb. is or was

It depends on what you want to express in the sentence.

You have a Complex Sentence with one main (independent) clause and TWO dependent clauses:

Main: We are sorry and did not cite it.

Dependent one: that we thought [a noun dependent clause]

Dependent two: (that) it is well-known [a noun dependent clause]

The verb that you use in clause two relies on clause one:

“…that we thought” | “(that) it is/was well-known”

I’ll bold the reasons…

thought is past tense, and if you want to show another completed action in the past, use the past tense was [I needed to see a doctor because I felt sick.]

Again,

thought is past tense, and if you want to state a general truth, use the present tense is [Nicolaus Copernicus believed the Sun is the center of our solar system, not the Earth.]

This is based on this chart, of which I used your first dependent clause to fill in for the independent clause in the first column “Sequence of Tense in Independent Clause”

http://grammar.ccc.commnet.edu/grammar/sequence.htm

CORRECT: We are sorry that we thought it is well-known and did not cite it.

CORRECT: We are sorry that we thought it was well-known and did not cite it

Proof that the second dependent clause is relying on the first and can substitute for "Tense In Independent Clause" in the chart:

We are sorry that we thought it is/was well-known and did not cite it.

The main clause uses the noun dependent clause “that we thought” as a predicate nominative (a noun) after the linking verb “are” to explain “We”; the verb “thought” is transitive in the noun clause and therefore, takes an object, a direct object, which is the second noun clause with the understood relative pronoun (that) introducing the clause “(that) it is/was well-known.”

Present Tense:

http://www.englishpage.com/verbpage/simplepresent.html

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