Elimba

Well, this is a very delicate situation. On the one hand you are trying to have control over your creation while knowning that the underlying data collected is not the fruit of your labor. On the other hand, your advisor is claiming first authorship of a paper built over data he/she owns. As a new PhD student you should play it cool and accept the rules of the game being played in your lab. for now. By putting his/her name first, your advisor is reminding you who is in control of this yet-to-be-accepted article. If this is a real issue with you, please ask the other graduate students around your adviser what their experience has been with him/her. Personnaly, as a graduate student and then as a Professor, I have run into similar conflicts. For me it wasn't a big deal. In most cases, I would put my students' names first on a paper to make them feel good about themselves (C.V. , travel to conferences) when the content was their work and I did the nice writing (translation, structure, layout, appeal) of the article. When I was a graduate student, I would rather stick to my guns with first authorship when I sweat the data and writing but made sure my adviser was OK with that. It's subtle game of give and take. More than 10 years later, I still have an excellent relationship with my former adviser and Professors. Your ties with your adviser and the Professors of your institution are very important for your future career. Do not sacrifice these ties now and have to regret it later. I hope this helps Mocha. Good luck.

Sorry for the late reply. I am on several fronts at the same time. In principle, any time should be OK. But remember that Professors are human beings, they go on vacation, get very busy with their students at the end of the year, and have mood changes. The first thing you can do is to send a brief introduction of yourself with your research interests. Then, it may be a good idea to propose working with them on an idea that appear on one of their publications (you have to read them before). The purpose of this approach is to create a connection and build mutual interest long before you actually expose your real intentions. In fact, if things go very well between you, the professor may be the one who invites you to join his/her lab. as PhD student. Bingo !

Bones, OK, things are a little clearer now. My advice is that you should go past this incident and move on. As someone said, take the whole thing as a lesson. Your purpose in coming to this institution is not to make money by any means necessary but to acquire knowledge. Well, this is part of it ... Learning about research politics. I hope this helps you.

Hey MKarmooze, You have already a great bunch of advice from the Fuzzy and Dal PhDer. Reading, reading ... you never finish doing that. PhDer told you to pay attention to the discussion section of papers you read. I will add to that, pay even closer attention to the perspective (and conclusion) section of the paper. You can easily hand pick like flowers in a field, nice ideas and suggestions of unfinished business. There are hints in this particular section to help you start off where the other guy left over. But keep in mind that you really need to be grounded in a solid context by following like a curious dog the most important references made at the end of papers. To buid confidence in yourself, find a workshop or an easy conference (generous acceptance rate) in the field, submit a short paper (3 or 6 pages) or at least a poster with one or two ideas. Anything is OK. Think like Tracy Chapman who said in her song Fast Cars "starting from zero and having nothing to loose" . You only need to brush out your ideas. Wait and see what happens. Your paper is accepted, then go and defend your ideas and collect direct feedbacks from peers in the field. Your paper is not accepted, then it's OK too. At least you made an effort to run the Boston marathon (I am in Boston . Then you can read the feedbacks (praises and nasty punches) from the referees in the program committees and reflect on that. My idea here is that you really need to interact with others in your field as soon as possible. Later, you can build on this short experience to climb higher. You do not need to shoot for the stars or aim for a grand prize. You really need to narrow down quickly your research subject around two or three questions stated strongly in the introduction of your papers. Writing a paper in science is no different from story telling in that you are leading your readers on a journey, a wonderful one of discovery and enchantment. The guys in program committees are sensitive to that. I know that for a fact because when I was doing my PhD, I always got a praise about my writing style. Do not forget that side, or your paper may be boring. In spite of its great content, it may not make the cut for publication. Take a look at the Academic Joy site, PhD Candidate section for more detailed resources and tools. I hope this helps you in some way. Stay strong and good luck.

First, let me tell you that your story is not believable. You confuse us with these words: 1. "my manuscript" (title) 2. "our contract with the publisher" 3. "named co-author" 4. "book was written (by me and him)" 5. "advisor published it alone" All these statements cannot be true simultaneously unless the publisher (ex. Springer) is an accomplice of your advisor or you are pretending to be an owner of a work in which you have only a marginal or no contribution. At least, this is the way it appears to us.

Well, you have an entire year to figure out what is best for you. The name and status of the school is not the most important for your PhD project. A PhD is radically different from a Master degree. It is critical that you find an advisor who is expert in the domain of your interest and start communicating with him/her from now. Then you may want to exchange research results with this person and hopefuly write academic paper in a scientific journal with your potential advisor before you come to US. This is an achievement that will surely open the door of a PhD program for you. In the mean time check dedicated Web sites like Academic Joy to get more advice. I wish you success.

Love the idea in the subject of the paper and the paper will love you back. Your grade will congratulate you for your effort and honor you with the highest distinction. It is only when you pour all your attention and love into writing a paper that your reward goes beyond your expectation. Your initial worries then turn into joy and you become one with your paper. It's all about love, love, love ... Look at what these Masters - Marie Curie in particular - did with their PhD dissertations at http://bit.ly/yQegxq (follow the links "PhD Theses" and "Extraordinary Dissertations") . I hope this helps now and in the future. Elimba

I suggest that you talk and get in touch with professors and graduates students active in the field of Bioinformatics. This is a highly demanded expertise on the job market today, specially in top research industrial laboratories. Machine learning (AI) and statistics are the keys to becoming an expert in bioinformatics. This is more about Computational Science than computer science as such. Therefore, you must get advice from your supervisor, choose carefuly your courses (from the palette of courses offered at Stanford) and give the right direction to your research. With the description of your background you gave us here, you are well on your way to mastering bioinformatics. You may also want to read the sound advice on the "PhD Candidate" page of the "Academic Joy" Web site. Good luck.

Typically, every graduate school has a a number of pages of their Web site that explain in details the process of study and getting a PhD degree in their institution. This process is particular to every institution and depends on the nature of the subject and countries . For the detials, you need to speak with the students office and your potential advisor and students who are already in the program. In addition, it is good to read for yourself advice on some Web sites dedicated to PhD students like "Academic Joy".

The magazine "Psychology Today" published an excellent article "Dealing with difficult people" some time ago on this subject.

"publication (from my thesis)" LOL ! I did just the opposite: putting all my publications (journals, conferences) together, linking them, expanding them, clothing them with an introduction and a conclusion and VOILA ! Dissertation done. Take a look at this Web site ( http://bit.ly/yQegxq ) to know how to do this.

You already got great advice above. By the time you see my message, I bet you have already read a bunch of articles and ready to write your review. When I was doing my PhD several years ago, it took me less than 3 months to read and write a pretty good literature review about a particular topic in C.S. It ended up as a "critical review" journal article praised world wide and used as reading material in several graduate courses . How many articles did I read ? Well, something around 150 although I did not make reference to all them in my journal article. I was reading like crazy, 24 / 7 (except when I was sleeping). I was literally breathing articles and became one with them. My best advice is "do by example", read what other students have done and specially reviews that have been published. Good luck to you and other PhD students.

Sorry, but I strongly disagree with this statement. In fact, it is exactly the opposite. You are asking for a grant to conduct future research with the plan described in your proposal. Of course, the applicant needs to give the assurance in his proposal that he/she is in the capacity to do so. This is where the background comes into play. By the way, you do not "write a grant" but you "write a proposal" to "receive a grant" There are a number of excellent articles about writing a winning proposal here: (bottom of right column, blue text): http://bit.ly/IH9Wmn Good luck !