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Predrag Radivojac
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Interested in applying to Indiana University and would like to do Bioinformatics research? You can apply to the Computer Science program or Informatics program. Under each of those, you can conduct Bioinformatics research. My recommendation for now is to apply to the Informatics program since Bioinformatics is well integrated there via a Bioinformatics track. If you are interested in conducting research under my direction feel free to contact me. However, it is important to know that students are admitted to the Computer Science and Informatics programs by the graduate admissions committee. Thus, your application material needs to stick out as one of the best. All admitted students have to take several courses upon arrival. In the Informatics program (track Bioinformatics) there are 3 core courses (e.g. I601-Complex Systems; I611-Mathematical and Logical Foundations of Informatics), 4 methodology courses (e.g. I519-Introduction to Bioinformatics; I619-Structural Bioinformatics), I501-Introduction to Informatics and a Pedagogy graduate class. Indiana University also requires that a student completes a minor (e.g. Biology or Statistics are potential choices). You need about 2 years to complete the coursework, though sometimes you may want to take classes even later. After completing the coursework, you need to take the qualifying exam which in the Bioinformatics track involves passing (1) Algorithms or Machine learning; (2) Molecular biology, Evolutionary biology or Structural biology, and (3) one core course of the three you completed. Research is a crucial part of your graduate education and success in receiving a Ph.D. degree, but there are courses you need to take to be ready for research. Our program is designed to combine formal education (courses) and state-of-the-art research. If you are admitted with a stipend, most likely you will have to teach a class in your first two semesters (as a teaching assistant, or as we call it here, associate instructor). That is an additional burden, but is also very useful for you because you need an adjustment period and a salary. Try to avoid pressure of research while adjusting to a new environment. Talk to the students that are ahead of you in the program, they will give you important advice on how to select courses, how to select an advisor (must find one within the first two years), how to work with an advisor, and many other things. For technical details on how to apply, what the requirements are, what the acceptable test scores are, or for various statistics (number of admitted students in past years and the like), feel free to contact our Graduate Studies Administration. You can also send emails to Linda Hostetter or Rachel Lawmaster. They will help you to apply to our program. Good starting points for bioinformatics research If you would like to pursue bioinformatics-related research and have a computer science background I recommend you start with these two papers. They will give you a nice overview of the problems in bioinformatics and should be a must read for any bioinformatics student. Hunter, L. Molecular biology for computer scientists. Artificial Intelligence for Molecular Biology, Ed. L. Hunter, pp. 1-46, AAAI Press, 1993. (pdf) Cohen, J. Bioinformatics-an introduction for computer scientists. ACM Computing Surveys, 36 (2), pp.122-158, June 2004. (pdf) A fairly comprehensive overview paper on the machine learning approaches is by Jain and colleagues. Jain, A. K. et al. Statistical pattern recognition: a review. IEEE Transactions on Pattern Analysis and Machine Intelligence, 22 (1), pp. 4-37, January 2000. (pdf) Check out this excellent set of tutorials on machine learning by Andrew Moore. What programming languages you should know As you could expect, in addition to biology, bioinformatics requires substantial understanding of computer and information sciences. This also includes programming experience. Typically, you will be developing new approaches for which knowledge of script languages is essential. If you are comfortable with Matlab, Perl, Python or Ruby (in alphabetical order) you will be in good shape. You should also have basic familiarity with databases. Every now and then you will want to do things fast, so good knowledge of C/C++ will give you an edge. Funding and expectations Usually, we like to see how well you fare in courses before we consider you for research funding. This may be one semester or two semesters or even more. There is competition out there, so do your best. If you are interested in my research and feel you can contribute to it, feel free to contact me. If you are interested in a research project, my expectations are that your work is of high and publishable quality. I also expect impeccable integrity. Many students are sometimes surprised by how much work has to be put into a research paper. It can go from several months to a year or two of decent work. Rarely will a quickly finished paper be worth something (unless you are really really good and lucky). I'd like you to be open minded and curious. Try always to make things better. Read papers, read books, read articles on the internet. Take initiative, don't wait to get the tasks. Try your own ideas, many may fail but you'll be happy when some work. Make reliable programs, take extra time to debug (before asking me to debug with you!). Always try to understand if the results you obtained make sense. Don't be afraid to ask questions. I guess these pieces of advice are telling you what the expectations are. If you are interested in a non-research related project (e.g. a Capstone project), you will be expected to develop a high quality and professional program. As you could expect, the program should be thoroughly tested and shouldn't break easily. Internship positions We do not have internship positions. Letters of recommendation If you have taken at least one of my courses or if you worked with me on a research project and performed well, I will be more than happy to be your reference. Helping you with accomplishing your career goals accomplishes my career goals too. To perform "well" typically means you got an A in a class, or you completed a solid project or showed curiosity, potential and persistence. Even better if you demonstrated it all. Remember that I need to have enough positive material to write a letter that can help you. Living in Bloomington Here is a link from the Department of Biology. This is a great link from Mookie Baik's web site. Nice pictures, Mookie! Last modified: November 04, 2009 |