Should recruitment committee give lesser weight to Interdisciplinary Publications? I am a Computer Science graduate (presently, working towards Ph.D.). I have been working in the field of Computational Biology/Chemistry, Bioinformatics which involves many different computational approaches. I am rather working towards the development of new computational methods.

However, we report our results in interdisciplinary journals or pure biology/chemistry journals.

Question: I have often heard that -- in my country, many organizations are giving lesser weight to such interdisciplinary publications. But, while I started Ph.D., I used to think that it does not matter much. Even, the recruitment committee does ask questions like Why did you publish in J. Computational X or J. Theoretical X ? How one should respond to such questions being an applicant for a position in Computer Science department?

I did find it funny, though. Either the recruitment committee is not suitable or such candidates are not preferable.  

I came a not-so-similar question on SE: When should I publish in interdisciplinary versus subject-specific scientific journals?
Your key statement is "Either the recruitment committee is not suitable or such candidates are not preferable." But this starts from the wrong point -- you complain that the recruitment committee is unqualified or has the wrong metrics, but this complaint will not help you get a job. You need to accept the fact that they have their criteria and that you won't be able to change them. It is an entirely irrelevant question (for your purposes) whether these criteria are useful in advancing the stature of that organization, the community of computer scientists, or the state of science altogether.

In other words, you need to dissociate yourself from your philosophical objections to the questions they ask, and just come up with a good, even-keeled answer that goes back to the core mission of computer science as understand by the hiring organization. For example, if they ask you why you published in the Journal of Computational X, then you should say "During our research, we did some fundamental development of algorithms and data structures and evaluated how best to map them to the currently existing programming languages. This was core computer science work, but we wanted to show that what we did was also applicable to a broader range of sciences, and so we took our work and mapped it to some problems in X. It was important to us to demonstrate our CS work to other disciplines, and so published it in JCompX."