I am applying for tenure track position. In application form, we are asked to upload several publications. Some of my works are with experimentalists (I am more in theory side myself) and have been published in very prestigious journals. But I am 2nd author in some of them. Can I use them or I should be 1st author? What about papers which I am 2nd name but with same contribution?
You absolutely can. In your research statement you should devote some space to explaining your contribution and degree of involvement. I would imagine that, being part of a multi-disciplinary team, you may well have played some critical role. If you and your adviser find the story compelling, chances are they will, too.