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Can I use an -ing clause in this case?
A and B complement each other well, A having an extensive knowledge in the biological side of the project while B being focused on the geographical aspects.
I hope it is clear what I am trying to say. A and B are scientists, one is a biologist and another is a geographer, so their collaboration is beneficial for the project.
While doesn't license participle clauses with explicit subjects, so you can't sustain that particular parallelism. But you're not required to; here are a couple of possible rewrites:
A and B complement each other well, A having an extensive knowledge of the biological side of the project while B focuses on the geographical aspects.
A and B complement each other well: A has an extensive knowledge of the biological side of the project while B focuses on the geographical aspects.
A and B complement each other well: A's extensive knowledge of the biological side of the project is paralleled by B's expertise in the geographical aspects.
