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My official passport name is very long Mukhammadyusuf Fakhriddinov that's why I use Yusuf Fakhriddinov on my publications, also on most websites I use shorter name. Will it cause any confusion in the future and what should I do if someone asks to prove that publication is mine. Thank you for answers!

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Can you use a shorter name. Yes, you can.

Try to be 'unique' within your organisation. Obviously, if you move to other organisations (change job), you cannot guarantee uniqueness.

Will it cause any confusion in the future and what should I do if someone asks to prove that publication is mine

Given that the uniqueness of your 'known' name might not be unique at all material time over your career, what you can do is to register an identity on ORCID with your name and include the shorter one as also known as.

Try to be consistent in your research engagements (journal, conf, grant, reports ...).
Within your field, put a face to your known name (in networking , conferences...).

If for any reasons you're ask to prove identity (your publication),

  • show your ORCID, and
  • (relevant) correspondence for the publication. This might just be email or if need be, extracts from journal or conf submission process.
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Yes, it's okay to use a shorter name.

But make sure that:

  1. Your Department is aware of your assumed name for publications so that calls can be redirected to you.

  2. That no one else in your Department has a name (or assumed name) close to your assumed name at the time of publication.

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