which = the team's first paper?

I believe they are referring to their research method.

(I googled the text and read the original article; the first paragraph indicates that the research method itself was created through NIST.)

I agree with DD, but it doesn't really matter very much because the antecedent referents are really one and the same thing.

Nanda describes the team's first paper*, which was a joint effort between NIST, the National Cancer Institute and Carnegie-Mellon University.

Nanda describes their observational method, which was a joint effort between NIST, the National Cancer Institute and Carnegie-Mellon University.

Had I read this not as a question from an ESL/EFL, it would have given me no pause whatsoever and I expect the same would run true for pretty much every native speaker.

Thank you.

And thanks to DD.