There are a number of options open to you.
Speaking as a biologist (PhD) working in industry as a Bioinformatican I would recommend marketing yourself as someone that bridges the two disciplines. You recognise the limitations of both biology and IT, and can translate between the two groups. This is your biggest strength, because you can help companies be more efficient, and bring a different perspective to problems.
Most places in the world industry cant get bioinformaticians. I know companies that have been looking well over a year to find someone suitable. Whilst there are your typical names (Phizer, Bayer, Johnson and Johnson) There are an increasing number of relatively new players investing significant amounts trying to attract new talent. Dow Agro and INVISTA are putting together new bioinformatics teams, Sabic, Heineken, Coke are all looking to use/expand their Bioinformatics. Even Google are trying to attract bioinformaticians at the moment.
You can earn some very good wages in these companies, as your skills are rare. I would not worry too much about papers, as bioinformaticians are often viewed those that provide support.
The reason there is a shortage (besides cross disciplinary nature) is many Bioinformaticians are actually moving to "Big Data" due to the very high pay . This might also suit you. Having done Bioinformatics your in a very good place for "Big data", as nothing has as much information and complexities as Biology. You can do certificate in Big data http://www.tomsitpro.com/articles/big-data-certifications,2-706-2.html
This would allow you to walk into a company like Amazon who are desperate for these type of people (Data mining, databases etc).
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michealsmith
What country are you in? That plays a big role in your options.
Hi mxs, I think this is a good question. As you got, basically we have two main kind of jobs in bioinformatics. 1-Academy, means, research field. 2-Private company. Back 1 year ago, I was making a research inside academy in Canada, and I interviewed some researchers. My question was basically "When you researchers, are developing a financial planning for a project, do you have a specific amount of money, to pay bioinformatics tasks, that you will need?". The answer was, no. Here in Canada, the bioinformatics tasks is a exchange. That means, the bioinformatician will do his job for a little amount of money during 2 or 3 years and at the end will receive a paper - Master degree. The works go on. Now you will receive a new tittle, doctor, then PhD or higher. At the end you will have no enough money, your cv will be powered, and you will have your name in some good publication. The second way is to work in pharmaceutical companies. There they will need you to "create money". There you will have a good salary, based on your project or future drugs you will work on. To be able to work there you must hold at minimal level, doctorate. You can works like a consultant too.