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At the January of the current year, I have submitted a paper to a high-rank math journal. After around 10 weeks review time and 4 weeks editorial time, a decision of reject-and-resubmit was made (1 minor revise, 2 major revise and one reject-and-resubmit were the decision of reviewers).

I answered the comments, which, in my opinion, significantly improved the paper in a than response letter with more than fifty pages. For example, I proved a set of new interesting theorems and lemmas in the revised version of the paper in answer to some of the comments.

From the submission of the revised paper, nearly 18 weeks have been passed, during which the paper is under the review. I wonder why such a long time is necessary for a journal which gives its reviewers just an 8-week reviewing time.

Does this mean that the probability of acceptance of my paper, is high or low? What is happening in the journal for my paper? I am very much dependent on this paper to finish my Ph.D., and for my job. I worked very very hard but unfortunately at a low-ranking university. Will they judge my paper by the rank of my university or my advisor (co-author)?

My supervisor urges me not to contact the journal editor for the decision about the paper since they may get angry and reject the paper.

My main goal is to sooner defend the thesis as I am under immense pressure. My university needs at least one JCR Q1 or Q2 paper to be able to defend the thesis and graduate.

As this may take more time, my main question is: what is your advice for me, assume rejection of this paper and work on a new paper? Or assume acceptance, or revise and work on writing my Ph.D. thesis? Since the draft of my thesis is dependent on this choice very much, this decision is very crucial for me.

What would you do if you were me? In other words, what is the probability of rejection for a long-time-review in the revised version of a manuscript?

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    I don't think reviewing time is a good predictor of acceptance/rejection. The time depends on too many factors. For example the immense length of your response letter and the scope and depth of your revisions probably affect the turnaround time much more. But the reviewers may also just be busy etc. – henning Dec 22 '18 at 10:22
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In short: We can not tell. There are many influence factors to be considered.

Maybe the following thoughts help a bit:

  • Usually the same reviewer are evaluating a revised version of a paper. If one of those reviewers is late (due to whatever circumstances), one usually waits for them since they are much more competent in reviewing the revised version then a new reviewer would be.

  • If they still do not deliver, the paper might be moved to a new reviewer. They again have 8 weeks of time (even though one usually asks for a rapid response).

This sums up to 8 + ~4 + 8 weeks, which is 5 month. Add one month for the editor and you are at 6 month just for the review. With your 18 weeks I would say the paper is within a time scale in which you don't have to become nervous.

I would recommend writing on your thesis since you did the work and it can be part of the thesis regardless of the acceptance of this specific journal.

If you don't have a response at the end of January (Christmas break for finishing reviews, Jan. for the editor), I would recommend to politely ask the editor about the status.

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