Conjugation: Do we cite authors or papers?

I would say that it depends of the citation format, and the point is to look what is the subject of the sentence. In the examples you present, the conjugacy would be with the authors and the parenthesis only provides a precision about which paper is concerned.

In math we usually cite like that:

It is proved in [Doe15] that ...

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References

[Doe15] Jane Doe, "paper name" Journal name, 2015

Therefore, we tend to cite the papers. However I often write

In [Doe15], Jane Doe proves that...

where the conjugacy is obvious.