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What to do with threats of blacklisting?
To be brief, I am a PhD student in the UK, and I have recently had some disagreement with the way my advisor handled our collaboration on research. This was initially a fairly minor thing. Not in the sense of what has happened, but minor in the sense that I only wanted to move past it, and to continue productively, but unfortunately he appeared to be too preoccupied, or for whatever reason, unable or unwilling to work together on correcting our results. Frustrating and not good for me, but ok, fine. At the time, no harsh words were exchanged at all, and there was some degree of understanding, although I was not happy with the mistake.
This has escalated beyond belief as soon as I relayed this problem to an administrative person, to explain there was a mutual mistake and I needed more time to submit. I explained the situation briefly to the person responsible for these things, made it clear I held no animosity or any interest in dwelling on it, and just needed some recovery time to move forwards. This was made totally clear to him and he was fine to shift the submission date and funding termination back slightly and he had agreed with me that there should be no blame here.
This has resulted in my advisor going on a furious rant at me in public, saying he refuses to work with me anymore. In private, the advisors have said that my 'complaints' have made the group look bad (no complaint was ever made, only a request for further time), and that they have now lodged some files or something on me with people at the university marking me as problematic. I have also been told that my complaints will make it difficult for me to get a job even after graduation, if I get to that point, because my advisor has no intention of giving me a reference, much less a positive one, and that they can make finding a job very difficult.
What on earth can I do? It seems that my career is now in ruins before it even started.
This whole situation has made me disgusted since it appears to have come almost out of nowhere, based on one conversation with an admin person. But I cannot work elsewhere if they follow through on their threats. How can I salvage my potential career?
Edit: There are just too many details I left out to edit down to size, and I would like to simply close this question or delete it if possible, due to confusion. I would prefer this to editing a popular question with too many specifics.

(1) please edit this down to the question you want us to ask. (2) Is this in the Anglosphere + Western Europe or somewhere else? That matters greatly as to how things work for this.

"I have also been told that my complaints etc." - told by whom?

Apologies for too much information. I have removed some things. My advisors have told me that due to my mentioning of these problems that they can make me unappealing to other staff/academics due to making them look bad.

You haven't yet provided an important piece of information: in which country is this happening? The answer can vary a lot from one country to another.

This is a UK system.

Did you consult with your advisor on whether to ask for extra time, and if so how it should be done?

What was a fairly minor thing? What did the advisor say has upset him? Also, careful about talking about "shared blame" (see below comments). This is a codeword for "actually it's you, but I want to be so generous to take part of it.", similar to the infamous politician's apology, "if I have offended somebody", which is not really one. Maybe indeed it is your adviser, but for you to be helped, please let us understand the complete picture. BTW, once realising one's mistake, heartfelt and unconditional apologies may work wonders, although it might be too late now in the present case.

I did request extra time from the advisor, considering the project had to be cancelled, but did not receive advice, unfortunately. @CaptainEmacs I did not say 'shared blame' in reality; I said why we were changing topic so close to an important date and mentioned that I must take blame myself for also not noticing the paper in my own reading. Again, maybe I removed too much information after being asked to edit things down, so sorry if this question is no good, maybe it should be removed.

I am not sure I fully grasp the situation. In the very beginning of your PhD, you were asked to verify the results you will be building on, which is a completely legitimate task. In some area (Computer Science, for example), it is almost necessary to have a working model of competing techniques to be able to compare fairly on your data. But then you say "I was not happy with the mistake". Following that, from what I understand, you went over your advisor head, and talked to the administrative person saying (basically) that he has been advising you wrongly and you need to recover from that.

Sorry for being blunt, but I am currently in the UK system, and while I absolutely do not condone a furious rant in public, if I was supervising a student who acted like that, I would be very offended. And while I might be able to admit that part of it comes from mistakes in advising and leading the student (and that, as a consequence, I might need to work on those skills as an advisor), I would take such a behaviour of the student as a big breach of trust, possibly big enough that I could not work with, advise or lead such a student any more.

@penelope Apologies, it appears I have made this question confusing but cannot close it since the first answer came so soon. It was not verification of results but that the problem had been already solved by a prior PhD student and was mistakenly brought up again, this was the problem. I tried to request more work but was told thanks but no, and after a month or so of this I was advised that I must say something to deal with this, but did not make any form of complaint.

Yes, it seems like you have indeed made the question confusing, as I am still not following your clarification. Not results verification, sure. But, you then say "work on a problem that has been solved", and besides the mathematical _prove property X", I don't see many problems in science "truly solved". Somebody proposes a good approach for problem X, and a year or two later, somebody working on the same problem proposes a different approach. But, you said you were told "thanks no" when asking for more work, and then advised to say something to deal - who told you and advised you that?

Who is "the person responsible for these things" (in your edit)? Your advisor, the admin person, or did you involve yet a third person in all of this? How is your advisor not the person responsible for your project and work?

This is in mathematics, yes. The result in question had been proved by the previous PhD student in his thesis. He apologised to me but then seemed to just withdraw and avoid advising me for a month or so. The admin person was responsible for my funding, and they contacted me about my intent to submit as this relates to funding, and they probably noticed some delay since I know the guy casually as well.

I have a friend who is a professor in a UK university and he always rants (privately to me) how sensitive the environment is about complaints of any kind. Next time think twice before bringing stuff up to anyone. If you want a friendly and quick resolution go the private route. The moment you bring anything to any kind of authority, apparently, it's a huge issue in the UK independently of how small the initial fact is. And other answers below seem to corroborate all the examples I've heard from this friend of mine.

Luckily, the kind of person ranting about how they'll destroy your career and how many contacts they have etc. in almost all cases is just vastly overestimating their impact.

You can always threaten to run away. Learn some Russian just in case? :)

You went to the administrative person. That was your error and the core issue.
Allow me to give an example from the other side in which this happened:
While I was at another institute, I was asked to take over a lab for another person. The lab hosted a guest cohort from another country so the university needed someone with content knowledge and dual language fluency on short notice. So I was asked if I could take over the lab for a week.
Suffice to say, I did not know that there were particular rules for this lab. Some were obvious (like not leaving equipment plugged in) but I was a little overwhelmed with taking over a course last minute. Further, my work is primarily computational rather than lab focused so the reflex nature of lab rules was not there for me.
After a few nights, the lab manager came in and saw the lab after I had left it. Equipment was left out and plugged in. All a very big mistake on my part. The way she responded was where things got messy.
In hindsight, a more measured response would have been talking to me or even the lab's PI to find out what was going; even going to the department head. Instead she went to the Dean. She did not know the situation with the lab and the dean didnt, but as soon as it went to the dean, the situation became "administrative". Funds were threatened and it ended with me having to write a formal apology to the department head and the lab manager with everyone CCed on the email.  Everyone was aware the situation and most parties were mainly pleased that I was willing to write the apology so the "administrative" side of the situation could go away and we could fix things in house. (I ended up just getting an assistant who was a little more lab savvy). The department head came by and gave me a sympathetic pat on the back.
Was I wrong, certainly. But it was likely an issue that could have been dealt with "in house".
So, what was the end result of going to the administration rather than keeping things in house?  At one end, awkward elevator rides when the lab manager and I crossed paths. She found out the situation, and to find out, she didnt even know I was in the lab. I heard she thought it was an undergraduate group. On the other end, it did leave some lasting trust issues and undermined what had been before a very good working relationship between two labs. But I think that things have smoothed out since that happened.
In other words, once you go to the administration, the situation becomes administrative.

Would you mind expanding on 'You went to the administrative person. That was your error and the core issue.'? I am not asking in a confrontational way - just genuinely a bit lost. I also cannot figure out the 'scale' of OP's situation, but let's assume that the situation was as OP describes it ('a fairly minor thing') and simply needed more time. If the administrator approves, OP did nothing wrong by being granted more time from higher authorities? Would love for some others to chime in!

You have not quite told us what happened with you, your advisor and your research group. But even your vague description betrays what I believe to be a lack of awareness to certain aspects of professional/interpersonal interaction which is now biting you in the ass.

This was initially a fairly minor thing. I just needed to explain to others that there was some confusion which my advisor admitted to me privately

This was not a minor, thing - it was a major thing. A huge thing probably. Why?

You repeated something told to you in confidence, to outsiders, and made it (somewhat) generally known.
You assigned blame to your advisor while (seemingly) hinting he was incapable/unwilling to take on the blame, thus slighting his character as a person and as a manager.

... and this was even before any official complaints were lodged about anything and anyone.
Now, maybe that's not the only way to look at what happened, but it could very well be the way that your advisor and many others - in and out of your research group - see things. It's possible that, on the merit of the original matter, what you said was true - but that doesn't help with how you conducted yourself.

This whole situation has made me disgusted.

You must realize that the feeling may be mutual. Try to look at things from the other person's perspective - what do they expect and believe - and be aware that they will judge you from that perspective, not on the basis of the facts, or what you consider to be the facts and circumstances.

What on earth can I do?

Unless it jeopardizes the integrity of yours and others research - swallow your pride/disgust, stash your ego somewhat, and apologize to your advisor for your conduct. Be, or pretend to be, penitent.
Does this mean that he's not really to blame for anything? Not really. Maybe most of the blame is with him. But - that doesn't really matter. You have to be generous with taking blame and cutting people slack (whether they deserve it in your opinion or not), as long as others/society/science don't suffer as a consequence. That's an important salve to apply to situations of people being offended.

Thank you for your advice, but I should make it clear I did not blame him, in fact I made it very clear I was not complaining about anything, only requesting more time due to a shared mistake. I took every step to say that the relationship was good. There was in fact no complaint lodged by me at all. I was requested to edit things down so I removed some clarifying information, perhaps. But there was no complaint ever lodged, informally or formally.

@user41208: This may be clear to you, but reading your question - the opposite was clear to me. I mean, you don't have to say "I'm blaming him" for another party to construe what you've said as an assignment of blaim to him.

Thanks for your perspective. I'm just wondering how this is interpreted as a complaint when the advisor is aware of me not actually making any complaint at all, only a request for further time, and how that escalates so rapidly to "I can make it very hard for you to find work." As for my comment about disgust, this related to further information I edited out after being asked to cut it down. The question is possibly a bit of a mess, I now realise.

@user41208, there is something missing in your story, if I understood, you only asked for extra time due to a shared mistake, I would like to know how you delivered this request to make this situation escalated to that point. The best thing you can do is to go and speak with a good professor who can smoothen the waters with your supervisor, maybe there is misunderstanding or gossiping.

It seems from your story, that your relationship with your supervisor was good, but I do think he got offended that you mentioned " you request further time for this mistake" which is obvious what made him furious, if I were in your shoes, you have to apologize.

@user41208, dont do it again and mention mistakes, I was been forced to quit from my position although doing well, because I found mistake and illustrated to my ex-PI, which made him hate me and forcing me to leave. Unfortunately, some professor get offended when their students correct them. It is supposed that the supervisor humbly learn from their mentee, but this is rare to happen, I wish he can forgive you as soon as possible.

I am also quite confused how (especially from the perspective of the UK system, in which I currently work) it was even possible for an administrative person to grant you more time (once you asked), rather than your advisor. How is an admin person even aware of your schedule in such a manner, or responsible for it? I mean, it is my advisor that is expecting updates from me on a regular basis, if I went to an admin person and said "I didn't have time to implement this as my work station was broken" they would not be able to do anything with the information.

You were new, you did not realize the trouble you would be causing your P.I. Now you need to profusely apologize and eat crow. This is unfortunate because in some sense you were not made aware of the “way these things work.” In the end, that does not save you from having to give a humble and sincere apology.

Seriously?  He makes an innocent comment to the administrator that ended up embarrassing the adviser, and the adviser flies completely off the handle and begins trashing his reputation and threatening to abuse his power to cause future harm to the student's reputation and employability, and you say the student is the one who needs to apologize?!? That's insane!  Right now the student needs to file a massive ethics complaint about this adviser. This is blatant retaliatory behavior, and it should never be tolerated.  Seeing people take the abuser's side on here is disgusting!

@MasonWheeler: It was the opposite of an innocrent comment. It comes off as intentionally badmouthing the adviser. It's not even (or not just) about the embarrassment. Granted, the advisor has over-reacted, and been somewhat irresponsible and quite vindictive, but it's not the way you're describing it.

@MasonWheeler You have to understand that the organizational structure in academia is very flat, relative to companies. The chain of command essentially goes student, PI, department chair, school dean, president. There's no levels like "regional manager", "business sector head". It sounds to me that the OP has brought the issue up to a school-level admin, which is one step away from the "CEO" so to speak. If your lowest-level employee brought an issue about you up to such a high level in a company, you would be very upset as well.

@user71659 Perhaps I would be upset, but I would not retaliate with threats and abuse. That's a thing that should never happen, and regardless of whether or not the student was in the wrong, the teacher was definitely in the wrong in his response, and needs to be smacked down for it.

@MasonWheeler The only person who can possibly be fired here is the student, professors are tenured. Having actually dealt with students, that's not a bad thing. You have to understand that the vast majority of grad students have never worked a paid job, let alone a corporate job with a hierarchy and politics. The nearly all of cases I've seen are definitely originate with the student and are an issue of immaturity, and it's only been getting worse with entitlement. Personally, no sympathies from me, especially not based on a one-sided anonymous Internet story.

@user71659 Once again, regardless of whether or not the student was in the wrong, the teacher was definitely in the wrong in his response. It's quite possible for both sides to have made a mistake, and the teacher's behavior here is inexcusable. Please stop trying to excuse it.

@MasonWheeler Once again, one sided Internet story. Having seen these in person, I wouldn't trust the story even if I heard it in person. Students make things up. Entitlement and immaturity. Professors have years of experience, and in order to even half-succeed, you need to be decent at politics. I trust a professor's actions and judgement far more than a grad student. What's a normal grad student have? 4 years out of high school. That's it. In academia, you need to recognize that fact.

I can't believe people are blaming the student here. If what OP says is true, which I don't see any reason to doubt, the advisor didn't show OP a way forward at all, and OP needed more time to submit. What on earth could he have done except talk to the person responsible for deadlines if the advisor wasn't willing to do anything themselves?

@user71659 This isn't a matter of statistics, how often on average is a professor right, how often on average the student. This is a matter of one occurrence, for which we have nothing to go on except what OP told us. And there's certainly no lack of abusive professors out there, or professors who should never have got into a management situation, professors who feel out of their depth and go into fits if they think they're status is threatened...

The damage has been made. The question is not who to blame, but how to reduce the damage.
Your best option is to do what @einpoklum suggested:

Unless it jeopardizes the integrity of yours and others research -
  swallow your pride/disgust, stash your ego somewhat, and apologize to
  your advisor for your conduct. Be, or pretend to be, penitent.

I would also suggest to read the book "How to Win Friends and Influence People"
by Dale Carnegie. In summary, you need to ask yourself

What do you want the other person to do?
How can you influence them to do what you want?

Looking back:

I have recently had some disagreement with the way my advisor handled
  our collaboration on research. This was initially a fairly minor
  thing. Not in the sense of what has happened, but minor in the sense
  that I only wanted to move past it, and to continue productively, but
  unfortunately he appeared to be too preoccupied, or for whatever
  reason, unable or unwilling to work together on correcting our
  results.

You want your advisor to work with you to correct the results.
What you did: you ignored him when he disagreed.

Does this action likely lead to the desired result? Is it a surprise that your advisor appeared not to have time to work with you?
Regardless of who to blame, whether you did was right or wrong, your action did cause trouble to your advisor, and you turned him into an enemy.
Having an enemy is never a good thing, in particular if you want to work in academia and they work in the same field.

What you want your advisor to do: help with your research, or at least provide a strong reference for you to find another lab.
How can you  achieve this?

Hint: you can't force anybody to help you, they only do it when they really want.
Note: it is your advisor's best interest to have successful students. Failing a student affects his performance and reputation too.

This is the best answer because it is the only one that addresses the question - which was not "what went wrong", but "what can I do going forward?". Don't understand why this was downvoted.


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Can you switch from a non-competitive program to a more competitive program easily in university?
I don't really know how to properly phrase this question but can you transfer from any program, maybe one that's not as competitive, to a more competitive program in university?
I've always been curious: for example, let's say I'm applying for Harvard, a super competitive school. I understand that they don't require you to choose a major until second year. If I were to indicate my interest of a less competitive program, like gender studies or african dance choreography, would I be able to transfer/select a biology program 2nd year? Surely it's much easier to be accepted into one of those programs than a competitive science program, so wouldn't people try to cheat the admissions system by applying for a non-competitive program and then end up choosing a competitive program?
I don't really see what would prevent someone from doing this, as the schools all allow you to choose whatever program you want regardless of your indicated interest.
Question doesn't really make sense but I wanna see what yall say regardless.

"Surely it's much easier to be accepted into one of those programs than a competitive science program" - Citation needed.

Every university is so different in how they handle major selection that your question is off-topic. It took me a few reads to understand your question because it barely makes sense for my school does it.

I'll assume that you really do mean "competitive" and not just "difficult to master". (Otherwise you've stepped into a minefield with your examples, which can be astoundingly difficult). I'll also take "competitive" to mean that there are lots and lots of students wanting to major in those things.
A priori, there is no reason for the university to care a lot which major you choose provided that it has the resources to accommodate you. But some programs that might be competitive (by the above definition) require small classes (and therefore more faculty) or laboratories with a limited number of seats available. Other majors have very deep prerequisite requirements for the upper level courses, requiring that you select those majors early if at all.
So, there are a lot of considerations. Each university will have its own constraints and those constraints will impose rules that don't seem valid until you look at the constraints that led to the rules.
Biology is a lab science, generally speaking, which imposes limits. Computer science may or may not require equipment, depending on how the program is built.
But your expressed interest on entry isn't really a constraint most places. If you want to choose a major, you will be admitted or not based on your current record and any constraints in place at that moment. (caveat: MOST PLACES)

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Blacklisted and cannot do the work I am interested in before, What I should do?
As you may know, I have been working on a specific point of research during one year of my PhD. I am extremely passionate about that topic, because I found problems that can be solved and improvements for the system. For this reason, they did not like me. In particular, one collaborator always underestimated me and later persuaded my ex-PI that my work is doubtful.
Now, I am a research assistant in another distant country. The current PI knows my situation and takes advantage of me. They forced me to work on a topic way off from my background. Moreover, I was shocked to see that they don't have any experience and that there are hostile vibes between senior researchers, which bazzled me, besides the very low payment I receive.
Now, I am trying to apply for other projects, more similar to what I have been working on before. The dilemma is the collaborator is mainly involved in different projects by different research institutes. I have to confess they are the most dominant collaborator, and it is a very small circle. I am literally expelled and a pariah. Even if I tried to find funding for the project, I am afraid they will not approve of my work. I feel in a dead end. I tried to apply for other research topics too, but I failed. I am really passionate and see the potential behind continuing in this research line, it feels like I'm fighting against the Gods of this research line. I am totally hopeless. What I can do in that case?

When you accepted the job offer, were you aware of the topic you have to research in your current lab?

No, they take advantage of my situation! upon arrival, they told me we can kick you outside, they pay me 350 Euro and giving me a room to live in and I didn't have any options after what happened to me.

Have you signed a contract with them?

@DmitrySavostyanov, yes, I was kind of forced, they wrote horribles clauses which I argue with them politely that this is illogical, I was under test for two months and then renew the contract. I do that because I was in a need for financial support, and of course, I didn't get any favoured reply from other potential PIs.

I strongly agree with Dmitry's answer - but you don't seem to. So let me ask a couple of more pragmatic questions about your career. What is your short-term career plan for after your sabbatical ends? (For example, do you intend to apply for more PhD programmes?) What benefits are you getting from this sabbatical that will help you to achieve that plan? (Is it allowing you to pursue your desired research? Are you getting publications from it? Will you get a good reference from your PI and/or collaborators?)

Your current situation is troubling primarily due to non-academic aspects of your employment. You seem to be concerned mostly about academic factors, but let me try to refocus you on what is in my opinion more important: your safety and security.
You are in a foreign country (I presume), and you were forced into your current contract. You were in need of money and you signed an agreement which you find unfair and abusive. You feel insecure, you are not properly payed, and you are provided housing by your employer, whom you fully depend upon. This situation is short of what is known as modern slavery.
Academic aspects of your current situation are irrelevant and academic nature of your work is irrelevant too. Your current working arrangement falls short of basic requirements. While 350 EUR + housing may be appropriate level of pay in some third-world countries, the lack of security and forced nature of this arrangement are not acceptable.
My advice would be to get out as soon as possible. Ask for help in the consulate of your own country, if you need money or legal protection to get out.
When you are safe, please reflect on your experience and ask yourself a question: why do you want an academic work so much, that you agree to work in conditions which are worse compared to what you can get by doing a non-skilled work in your own country? What other (non-academic) career directions you can imagine for yourself and how could you learn more about these opportunities?

Firstly, this is in European country! second, I am basically an assistant lecturer at my home country and take sabbatical leave for sake of doing good research as I lack from supervision. I doubt my country can do something to help me.

Of course, I had the question, and I am not materialistic and accept to live with this small amount, of course, I didnot eat well, but I was doing that because this only place accepted me, of course, I cry sometimes because I didnot find a solution yet, I dont want to fail. Going out now without any money is my biggest fear! Unfortunately, my family cannot support me financially.

I am planning everyday how to get from her asap, but I need to find another good lab to host me as a student again, and thats why I feel I am trapped.

@Monkia You said, they pay you 350 EUR + provide a room. What other money do you expect? Can't you end your sabbatical and go back to your assistant lecturer post in your home country?

I cannot! I escaped from my home university because of corruption and lack of good science, I am sorry but I dont want to fail or give up my dream! I just dont know how to smooth the waters to get in the loop again

Another point, I have to get a PhD to be promoted a lecturer instead of that I will work administrative work, it is like you killed my passion! I cannot explain, but I just need to breathe again and do my work again, but I am stuck.

@Monkia You sound very emotionally involved, and your situation is clearly very stressful to you. I think you need to separate your academic dream from your objective situation including professional and personal aspects. Do you think a discussion with a professional may help you with it?

Yes, I am emotionally involved due to many personal occasions losing my mom and grandma later affected hugely on my mental and physical and by being forced to leave my PhD was the last straw! I am just trying to understand how to get out and be again on the track. Of course, discussion with a professional would help, but I don't know how as long as I see people become non-compassionate, I cried and begged my ex-PI don't get me out, he was smiling and happy and I am always respecting people,  it is odd and awful.

To clarify, by professional I mean a healthcare professional such as a therapist or psychiatrist, not your former PI. A job search coach or employment advisor could also help.

Yes, I have sent a request to have a psychotherapy session, but still didn't get a reply yet.

"Firstly, this is in European country" - @Monkia Some European countries have a lot of protections for students/employees. Others don't. That said, I strongly agree with Dmitry here, you've had seemingly constant issues in more than one lab. Address your mental health first.

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How important is trendiness of the research one works on?
I used to think that for research postdocs, faculty evaluate things like research potential. Now I think they still do, but they look a lot at whether the research topic interests the faculty. For example I have had a senior faculty member in some field (call it field A) tell me directly: "Field B is much sexier now than field A. Field A was very popular when I was doing my postdoc. Look at this researcher who did outstanding work in field A! Universities wouldn't hire him. He ended up getting something, but if he had worked in field B he would have done much better on the job market."
The lesson I took from this was: to succeed in academia it is not sufficient to do amazing research. It has to be amazing research in an area that interests people on the faculty of the universities you're applying to. For example, if University X has no homotopy theorists, but two representation theorists, then good results in representation theory would trump outstanding results in homotopy theory.
When applying for postdocs, there is sometimes a question asking if applicants have "faculty contacts." I am also taking this as another piece of evidence. My impression is that a blank response looks worse than being able to say: "Professor Y is a potential collaborator." It seems pretty much necessary, to get any position at a given university, to do work in an area that interests some faculty members, so that they can be enthusiastic about an applicant.
A last example. When looking at MathJobs.org you can find postdocs in Europe for working in certain research groups. To get such a position, you need to fit your research into those areas. Suppose professor X is looking for a postdoc who works on problem 1. If two strong applicants apply, but another, by chance, does work more directly related to problem 1, then that applicant would be preferred.
Looking back at my time in grad school I think this is what I should have done: Make a list of all the academics in a given field and see what work they do. Look at who gets the big grants, and what topics the big conferences are in. Based on those criteria, determine who you want to do a postdoc under. Then decide who you want for a thesis adviser. Then steer your research to be interesting to those faculty members at the universities you would like to work in for your postdoc. In other words, direct your entire academic trajectory for a postdoc position. This way, five years later when it's time to apply for jobs, you'll find faculty members interested in your work, because your entire trajectory throughout grad school was towards that goal. This seems to be the best way to get postdoc offers.
In other words, I feel that there are many traps in academia that unsuspecting grad students or junior faculty can fall into and not get out of. Is my impression accurate?
On a more personal note: I have applied for a lot of postdocs and have gotten shortlisted a few times. But I have received zero offers. I suspect that other applicants fit the position better, not because my work wasn't good work (whatever that means), or any deficiencies in my application (though I could be wrong). I have no idea how to avoid these issues in the future besides the (admittedly rather extreme) plan I had proposed.

I don't  understand how the second paragraph relates to the rest. Can you pull it together?

There is no real question stated in the body, just the title.

on average, a nobel laureate made his discoveries 20 years before...

if there would be given a nobel prize for CS, you could probably drop the zero :-)

@Buffy: Hello. I have revised my question. I hope it is clearer.

In other words, direct your entire academic trajectory for a postdoc position. Well, you do at least need to direct each step to increase your chances of making it to the next step. This is true for any career.

" Look at who gets the big grants," do you want to be a researcher or a research manager?  The skills to be a good researcher are not the same as those required to be a good research manager/leader.

Let me give a contrary "strategy". Do the work that you are interested in rather than try to game out a path to success. Background:
There are two advantages of working in "trendy fields". One is that journals probably want to publish more in that area. The other is that, if students are also interested, then universities will probably want to hire teaching faculty in those areas. But, I suspect that universities are happy that you are productive in publication no matter what your research interest.
There is a downside to working in a "trendy field". There will be a lot of competition. There is likely to be more parallel research on the topic that interests you. You may well get "scooped" more often.
There is a risk factor in trying to game out your career: things change. What is trendy today might not be in a couple of years. The academic market may just fall apart when you enter it of course. But it will probably return in a few years and the "once trendy but no more" field may have a resurgence. There is no sure path.
Much better, IMO, is to find something that interests you and makes it possible for you to make a solid contribution and then follow that. You don't have to commit your entire life to it, and can change course as you go, but build a life, not just a career.
I'll make a wild arse guess that you are more likely to be a success in research if you focus more on the research and less on the success. You will probably be less angry at any setbacks, also. Work on interesting problems, collaborate with good people, bring along a lot of students. But make it satisfying.
Five years is a bit less than eternity in any job market, but not a lot less.
I'll also note, for completeness, that universities may specialize in some research areas that may be unrelated to trendiness, but only to history. It is hard to say whether they, at any given moment, want to add more faculty to that concentration or to, instead, hire someone who will bring a broader perspective to a department. Hard to game. There is an advantage, of course, for a young faculty member to join an established working group (easy collaboration) but also a disadvantage. The old codgers might just want all the credit. You don't need physical presence these days for collaboration in most fields.

I feel as if this response is premised on the notion that on-trend and personally interesting research is mutually exclusive.

@Dawn, not at all. But what is more important?

My field (machine learning) has had several boom and bust cycles while I have been part of it.  I suspect that happens in most subject-areas.  Being in anti-phase is the most interesting and likely to produce the most impactful research (if you are actually right).

At least focus on your interests versus your advisors.  We get a lot of questions from weak reeds who just bend with the wind.  But at the end of the day, there's a huge investment of years by junior researchers in these projects.  Need to do something you want to do.  Exercise choice during advisor and project selection, stick up for yourself, etc.
Obviously it's a multivariable function (not just x and y, but some z's and w's floating in there).  So, you should look for something both marketable AND interesting.  While, it is unlikely that optimizing for one variable will optimize for the other, there likely are several areas where you can be both interested/skillful AND that are marketable.  Yes, absolutely you have to use your noggin when deciding this...and your advice to a younger you is relevant.
I would be wary of something that is trendy now if it has the seeds of changing soon.  String theory, nanoscience, machine learning, etc.  At least don't get involved in one of these rush areas if you aren't super interested in it (I don't believe the students who all come here and say they have a "passion" for machine learning--they have a passion for getting hired by Google.)
I think often there is a lot of opportunity at field boundaries (and has been for decades).  "Material science" is the classic example.  If you can collaborate, it opens up possibilities and often you find others can't really compete as well in the border areas (are only able to work in the core). Personally I find that a lot of fun (and also doing applied work)...so it's not even a sales BS job for grants, like with some researchers.  I really like it.
It's probably good if you can package yourself as both a specialist and a fundamentalist.  I.e. I'm the math expert in some bizarre shale oil krieging junk.  But I also can find a home as a graph theory math person (I'm making this up...not sure if those are real things...but you get the idea).  Have some sexy thing like that specialty...but also make a department feel comfortable that you can teach basic classes and fit in with the core math department.
This is not to say there is no demand for people drilling down the center of the field.  But you better plan on being the best, then.  Really top notch.


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Why do some professors not post their long list of publications?
I notice that some professors -- some are now professor emeritus and aren't active in research anymore -- have an essentially blank faculty webpage, only listing their phone number and school address and office location.  What would be typical reasons for professors to leave their webpage blank instead of listing their publications?
Is it a desire for privacy?  An indication that one is no longer active in research?  Disgruntled feelings about academia?

It's a lot of work to dig up references to every single one of one's papers and then code them into the same citation style ...

Maybe you should start from the opposite viewpoint: what use is a long list of publications on my home page, when Google Scholar and Scopus already do a better job?

What use is a list of publications for a professor emeritus? They're not looking for a new job. They don't need to impress a tenure committee. They aren't applying for grants. They're not looking for new graduate students. It's useless to the professor. It might be a tiny help to a third party, but the third party can do exactly what the professor would do to find publications - search Google Scholar or some other database. Why should the professor take time to help someone they don't know, for something that has no value to them?

Your question contain several implicit assumptions that make the question difficult to make a generalised answer.
Firstly, the use of web pages for university faculty varies from country to country and institution to institution. There is no generalised understanding of what a university or faculty members web page should contain, and this is often influenced by cultural norms. Further, this can vary from discipline to discipline. Some academic areas value public lists more than others - academia is such a broad church.
Secondly, you seem to be assuming that professors may have any control over the content of their web pages or published academic profiles. In some places they do, and they may be free to edit them themselves. In some places these are centrally controlled and populated from some form of content management system database. In some places these are managed by a marketing department as part of the institutions advertising and public relations; further some places might use an external public relations agent to populate the pages.
Thirdly, you underestimate the amount of internal politicking and petty squabbles that go on inside large institutions like universities. Professors, particularly senior ones, go in and out of favour like pop chart hits. It is not beyond the bounds of pettiness for someones entries to be deleted out of spite and recognition of their unfavoured status. Their existence cannot be expunged, but their bibliography can be.
Fourthly, you assume that universities have a degree of capability or competence. In my experience there are plenty of incidents university staff (support or academic) being incapable of rendering edits to obviously incorrect profiles.
Fifthly, you assume that perhaps everyone there actually cares about it. Perhaps the professor or the support staff don't really care about this particular part of the profile and have no plans to change it.
Sixthly, you assume the professor or the faculty actually know that the list of publications is missing. In a large institution with many many faculty; even in a caring place, it is possible for errors to slip through unnoticed. Not every faculty member would be egotistical enough  to regularly read their own personal profile.
There may be more reasons, but that list should do for starters.

And 7, even if they know 6, do they care? Few faculty I know care about even having a web page much less keeping it up to date. They’d rather do other things.


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About to submit my PhD thesis in 4 months, feeling lost about my future and inadequate for any job. What should I do?
I am about to submit my PhD thesis in 4 months and have to move on from being a student. I am already 30 (so a sort of mid-life crisis catching up). I feel that I made a really big mistake in entering academia and should have not gone into masters 7 years ago. I feel incompetent with no area of expertise. I am a mathematically and technically weak PhD student in a field of research where being proficient in analytical and theoretical analysis is the only required skill for research. I think I am technically screwed up.
My question is just vague. What should I do, and are my future prospects as limited as I foresee them to be?
Thanks.

Your future prospects are not nearly as limited as you perceive them to be. Right now, you are trapped in the cult-like thinking of academia, which causes you to believe that the only measures of life success are high-octane research output and grant dollars. But these beliefs are false.
If things really are as you have described, then it may be true that you won't be competitive for academic jobs and postdocs. That's fine. Your training will make you an attractive candidate for other jobs in other fields. My guess is that you have a lot of coding skills, and perhaps a lot of experience in data analysis. These abilities are in high demand, and with time, you will be able to position yourself to compete for them.
My suggestion is to take some time away from your PhD studies, if this is possible, before you submit your dissertation. You need to get away from the cult and the patterns of thinking which are currently suffocating you. Visit family or friends, take time alone, play video games for a few weeks straight--whatever you do, clear your head. You will gain the perspective you need in order to identify goals you feel comfortable with and excited about, and once you understand what those are, you will be able to develop a plan to reach them.


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Do journals allow authors to bring their own reviewers
Some papers are published under category "communicated by ...". Do this mean the author contact this person to review the paper instead of editorial board? My question is: do journals generally allow authors to bring their own reviewers for evaluating the papers? It seems that some journals allow that.

Some journals published by societies either require (for all papers) or allow (for some papers) a member to "sponsor" a paper if it was written by a non-member.  For example, in the US, the Proceedings of the National Academy of Sciences used to use this system (although they stopped in 2010.)

There are some journals that ask authors to suggest reviewers. There is no expectation that these people will necessarily be asked, but it gives the editor a backup at least. There are some journals that ask authors to suggest people who should not be reviewers, though I think that is a bit less common.
Most journals, however, have their own pool of reviewers and the author has no input at all into who will review the paper. Most of those use blind reviewing in which you never learn who reviewed your paper.
But in the case you mention, it is likely that someone other than the author sent the paper to the editor. That may actually be required in some situations. There is no expectation that review is then suspended.


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Post-doc wants to break his promise of including me on author list
I am a master student, working for X lab of Y university as a research assistant.
3 months ago, a post-doc(my direct supervisor) recruited me into a project when he wanted to submit his paper within a month, telling me "You can coauthor if you join." Since then I worked overtime to finish exactly what he told me to do, implementing all his new ideas (but none of them worked).
Later he gave up previous submission, had the project updated a bit and now preparing submission to another conference in a month. Last week I asked "Am I on your author list?", only to get "Let me think about that." Project is almost finished currently, in terms of both experiments and writing.
Now I have no idea what to do, his reply sounds like a NO to me. To fight for that, I don't have any strong argument other than his vocal promise. My contribution is not direct, but a part of code he used was written by me (for another project), and I successfully implemented his new ideas.
Given such situation, should I ask him again for this authorship?
Or should I explain everything to PI? If then, how to?

"falsified"? or "finalised"?

@Gimelist I implemented his new ideas and proved they didn't work.

this does not necessarily mean the results are "falsified" - meaning, faked on purpose.

@Gimelist Yes, you are right. I didn't explain clearly.

This is an unfortunate situation. If your results invalidate the post-doc's idea, then most likely they will not be included in the paper, unless one can put a positive spin on it (e.g., "an obvious explanation for the observation is Z, but here we show that Z cannot be right and instead we propose that W is the true underlying mechanism"). In this case you have no claim to authorship, despite the work you've put in. In other words, the promise of authorship was implicitly contingent on the experiments yielding positive results supporting the hypotheses advanced in the paper.
If the current manuscript is based in part on the code you wrote, then there is a case to be made that you should be an author. But I'm always of the opinion that writing some code is a weak argument for being an author, unless there is some novelty or substantial effort on your part.
Note that the post-doc said that they will consider your authorship request. You interpreted that as a no, but that seems to me an unwarranted and premature conclusion. You should have a constructive conversation with them to try to resolve the issue collegially. This kind of situations will pop up in the future, and it is a good skill to learn how to address them. Even if you get nothing out of it in the end, just remember that in the grand scheme of things it's not really a big deal and you'll forget it in (hopefully) a couple of months.

Yes, I believe such situation would pop up in the future.
But right now there isn't much I can do regarding "have a constructive conversation with them to try to resolve the issue collegially" or "address them".
I guess the best timing is 2 months ago or even earlier.

"I'm always of the opinion that writing some code is a weak argument for being an author" - it is OK if, and only if, person writing code knows that before she touches keyboard.

Why should you be included as an author when you, by your own admission, have not made a direct contribution?
Yes, you helped him with the previous version of the paper, but that won't make it into the current version, so naturally, you are not to be listed as an author. How is this not obvious? It is also unfair of you to hold him to his past promise of including you as a co-author: obviously that promise was made under the assumption that your contributions would actually make it into the paper. Since that is not the case, you are, by definition, not an author.
However, you have contributed still, in the sense that your work was helpful and important to the authors. Therefore, you might (and should) be honorably mentioned in the acknowledgement section of the paper.
However, I stress that if you have not directly contributed to the content of a paper, you are not an author.

I think you have a pretty strong case to be on the author's list. First of all, this postdoc actually promised you you could be on the author's list if you helped him out and he should keep his word. Also, helping him implement his ideas, whether this leads to showing the ideas are correct or not, is something that can be credited with co-authorship.
Talk to him and if he's hesitant or negative, use the above arguments to make your case. You can also go to the PI directly and ask whether this situation, in their eyes, would warrant co-authorship.

I think he should try to get you onto the paper.  And you should push for it.  First by telling him how you feel (you think you made a contribution and should be on there).  Second by threatening to escalate things.  Third by actually escalating things (make a stink: complaining to his boss, file a grievance with department and university, write to journal he submits to, etc.)
[Note that the third case, can reverberate against you, but there is a game theoretical aspect to this...people need to realize they can't step on a bee or they will get stung...you need to show you are not a pushover.  Plus it will eat at you if you don't fight.  Possibly the tangible threat is enough to avert these cars crashing and you get your satisfaction before needing to "go nuclear".  But if you threaten something, do it.]

First, let's be honest and admit that the VAST majority (well over 90% in my experience) of experimental science papers are carrying professor advisors who did not make a significant scientific contribution (would not have been included if this were a work supervisor situation or if the amount of work had been another student).  Yes, the culture requires and expects this (even for grants and faculty bonuses).  But let's not ignore them not making contributions and being on the articles.
Second, there are ways the author can take care of you.  Even just a few sentences on scenarios ruled out, with or without details, means that he has included your work into the paper (and you now have a contribution justifying your byline).  A science report is not an organic baby being birthed with an inherent DNA/structure.  There is often some reasonable choice about including or excluding different measurements or experiments into a given report.  As an author who has gotten some work out of a collaborator, I would feel an obligation to try to (if at all feasible) shoehorn some of collaborator work into a general study (even if it did not end up being super important after done) in order to "take care of them", if I had asked them to help me.

P.s.  We hear these sad stories a lot.  You need to try to avoid these situations by nailing down expectations better (ask three times, be very direct).  If you get a brushoff or a "we'll see", DON'T DO THE WORK.  This becomes most important at the start of a collaboration.  Of course you should also use your judgment of who to work with (and while academics are not generally snakes, they're also not generally saints either.)  Penultimately, try to lead collaborations and be the first author, if possible.  Finally, you should make sure to take care of your collaborators when you are the project lead.


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What are my prospects to get a Postdoc position with just 1 publication from PhD?
I am a PhD in Mechanical Engineering. I have already completed my 5 years, am writing my thesis and will be submitting my thesis in 4 months. I have published 1 paper till now. That was 2 years ago. Till then, I have completed 3 more manuscripts, but my supervisor does not have the time to go through them and approve them. As a result, I have manuscripts around 2 years old waiting to get submitted and published.
My supervisor is great with meetings, guidance and advice, but she is frustrating me with her lethargy in correcting my manuscripts. This has made me very anxious about my future. My work is quite different than what is being published at the moment in my field. So, I think my manuscripts would still find a place in a reputed journal in my area of research. However, I can't be very sure of that until I actually submit the drafts. Also, I can't just go behind her back and submit the manuscripts as I don't want to sour my relationship with her.
I am not able to apply for a postdoc position as I am sure that I won't get any response without having any published works. I will be submitting my thesis by end of June. I will defend this fall. But, I don't know what I will do next.
I have applied to various industry positions and have got rejections. I don't think that I will land any position soon.
My question is, what are my career prospects at the moment? And what would the best course of action for me at the moment?
I am almost 30, been in school for Masters and PhD for the past decade. I am feeling quite hopeless. Ideally, I would like to stay in academia as I love doing research and teaching. But, I find that future dissolving away in uncertainty.

"And what would the best course of action for me at the moment?" Have a frank discussion with your supervisor. Basically, you should tell her most of what you write here. Getting these manuscripts published is in her own interest. Maybe she can suggest a post-doc or colleague who helps getting the manuscripts in shape (earning coauthorship as a result) if her workload is too high.

Are you required to include your supervisor as a co-author or can you publish independently? And, are the "manuscripts" your thesis or other work?

Thank you for your response. I have discussed with her. She always says that she will get them done as soon as possible. I don't know if involving another person in getting the manuscripts in shape would be feasible as our papers are all two author papers (Me as the main author, my advisor as the co-author). Also, at the moment our group doesn't have a postdoc. So, can't do much here. @Buffy yes, I am required to put my supervisor as co-author. And yes, the manuscripts are my thesis work. So, technically they have to be brought into shape before submitting.

It seems to me like there are two separate questions here: 1. The title question 2. How can I get my manuscripts submitted when my supervisor and co-author keeps delaying giving feedback? I would suggest asking the two separately - and searching on Academia.SE as I suspect at least q2 will have been asked already.

Except for the difficulties in getting your advisor to respond to you, nothing you say seems unusual. Even that is too common, though. But your age, etc. is pretty typical, or at least not far outside the norm.
But I think that if you can unblock the block that you will be in good shape career wise. Your difficulties with industry could be a lot of unrelated things, and you haven't really tested yourself yet in the academic marketplace.
If you want a career in academia, I suggest you start a search, either as a post-doc or a regular position. You have a lot of work-in-progress to point to which is a point in your favor. I wouldn't wait until you get the block cleared and then something submitted and accepted. It will take to long, but, I suspect, not be judged fundamentally differently than work in progress.
The only issue I see is your "out of the mainstream" research interests. You will need to find a way to present that as an advantage, not a disadvantage. As Apple used to say, Think Different.
There is, I think, no reason to do the two things sequentially: advisor, job-search. Work on both in parallel.
On the advisor front, however, you might want to make it more incremental. Rather than "all these papers", focus on getting just one out the door and then repeat as needed.

You can list the papers as "in preparation" on a pub list.  Not perfect but something.
You need to get those other two papers out.
One, write the version you would submit without any editorial input from your professor.  You should do this regardless.  Always do your best job first, before someone else.  You need to become independent.  Do not just make some graphs and some junky text and expect the professor to rewrite it.  Do the paper you would submit directly to the journal if you were the PI.  Proof the heck out of it.  Read the notice to authors and make a checklist from it.  Etc.
Two, provide the papers are "good to go" (in your estimation), than bust them out.  Tell the advisor you think they are good to go (as is) and you want to submit them. Argue.  Beat on the table.  If needed, get other people involved (but have a tete a tete first).

Putting non-published papers that are "in preparation" into your publication list is bad form on a CV. You can have a separate section for works in progress, but if you put them in the same list it's not going to win you anything but a odour of desperation

[Unnecessary rudeness deleted by moderator.] I have seen a bazillion CVs, including my own that have this. Heck, have seen it for full PIs at R1 (very R1) that have this.

Full PIs at very R1s could write their CVs in crayons or not bother posting them and lose nothing, so that's not really data on what most people should do. / In my field, putting things you haven't published into the published papers section of your CV will only annoy people by demonstrating you are trying to how many publications it looks like you have with things that are not yet publications.


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Is it a bad sign if I do not get anything from problem discussions with professors or fellow students?
This is a question specifically about mathematics.
All math people I've talked with like discussing problems (or math in general) with others, and most people claimed that they learned most from communication rather than from reading textbooks. My situation is, however, different. Most of the time I have math-related conversations, I find that I'm not comprehending what I'm being said, even if it's something not hard (unless I'm familiar with the topic being discussed very well). [In particular, this is true of lectures. However, I am able to understand my notes.] (I'm not sure what the reason is.) In contrast, I learn much more from books and, more importantly, from posting questions on math stackexchange. I was wondering whether this is normal, and whether this will be an obstacle in writing a potential PhD dissertation, since in that case my adviser would probably be the primary source of information, and I wouldn't be able to write a math stack exchange post asking for help.

Everyone has a different way to learn. There is nothing wrong with you, but there is something wrong with an educational system that over relies on lectures. Lectures work for some, but not all. If you have found an effective way to learn, then use that and forget (for the most part) the other. I recommend the answer of Allure, here, especially looking at the learning model suggested.

And, in fact, the "problem" discussed goes beyond mathematics. It is a feature of human differences - learning modalities.

@Buffy to describe our education system as simply lectures is a bit unfair, as it implies only passive listening by students. When it comes to mathematics, the tradition is to 1. hear the instructor explain, 2. see them work the problems, 3. write it down for yourself, 4. get prompted for questions if you failed to follow the derivation or proof. This may not be the best teaching method but it isn't chopped liver. Many do certainly execute poorly, or unwisely try to use slides in math classes in recent years.

I'm actually a mathematician @ASimpleAlgorithm, I didn't say "simply lectures", but over-reliance. But the four points you make are still incomplete. People learn from practice and reinforcement. Only point 3 really starts to achieve that.

@Buffy I don't quite understand what you object to about my statement. Are you "simply" calling those four steps a "lecture" or not? If so that's unfair. If you're only referring to one step and skipping the others that's unfair too. As for the segue into broader criticisms of teaching methods, I was only arguing for fairly describing the classroom portion. Students are also supposed to work homework problems and generally study for tests on their own, and get feedback via those. In my opinion the only real flaw is the over-reliance on student self-motivation.

And by the way I'm also worried that people are being too quick to grab learning styles as an excuse. No one can keep up with a complex math lecture on an area/topic they are unfamiliar with. Imagine we are having a conversation and I defined some new words for you, all using easy definitions ("blark means old tree" then used those definitions to tell you new definitions. Then so on. After a couple iterations you are lost (unless you write it down and keep referring back and translating). Math is the same, you need to be an expert to follow "off-the-cuff" because you need the steps memorized.

I suspect I have similar issues as you: when others talk about complicated subjects, I find they're speaking in English, but they're also not speaking in English (because I don't understand them).
I've thought about this a bit and although I am by no means an expert, I think the cause of the issue can be understood with the VAK learning style model. (Note that this model has been heavily criticized; however my perspective is whether it's correct or not is unimportant if it works for your particular case). Basically, people can be very broadly divided into three groups: those that learn best by doing something, those that learn best by listening, and those that learn best by reading. You are good at learning by reading, but poor at learning by listening. If you go to a lecture where the lecturer does not prepare lecture slides, only stands there and talks, you find you struggle. Comparatively if you do get lecture slides, then everything makes sense and you learn smoothly. If you can have only the lecture slide or the talk, you would much prefer the slides.
The bad news is, being bad at learning by listening is of course detrimental. It's just so much more convenient to explain something instead of get out pen and paper. The good news is, if you know what the issue is, you'll able to compensate for it. You'll need to concentrate on these conversations because if you drift, you won't be able to recover easily. Don't be afraid to say "can you repeat that?", and don't be afraid to ask for clarification if something is not immediately obvious to you either. You can also try bringing around a notebook and immediately writing down something you hear, since you are liable to forget quickly otherwise.
If you are so bad at learning by listening that face-to-face meetings with your supervisor are unproductive, try telling him that and suggesting email instead.

Understanding mathematics is, in general, hard.
For me, some methods of having reliably fruitful mathematical discussions are:

Have someone else explain a problem, an object, an operator, or a proof to you. Ask stupid questions. Have the other person explain. Do not accept anything before it has been clarified to you, unless it is common background knowledge that one should take on faith to get to the main point of discussion. The one explaining will likely benefit, as the discussion forces them to sharpen their understanding and exposes things that they have glossed over as obvious, or simply not noticed.
Explain a specific problem you have to a colleague. Have them act as per point 1.
Try to understand a given operator or object together. Draw pictures, give examples and counter-examples, calculate an easy example explicitly, come up with a physical/biological interpretation. Here, doing the process together reduces the amount of mistakes and thinking time. If one of the people discussing is faster than the other, than this might turn into point 1 or 2.

In general, I would suggest asking more questions, even and especially if they seem simple.
I would also suggest reflecting on what the problem is.

Can you follow up to a point, but then drop? If so, ask more questions.
Do you think the others are following or are they simply nodding along, thinking that everyone else is following and afraid of disturbing the process? Maybe ask them after a discussion with 3+ people.
Are you incapable of concentrating on the mathematics and thus drop from the discussion? If so, I do not have contructive advice. It might or might not be something that can be diagnozed.

I have trouble understanding something said out loud because I need time to process the information. I usually have to have someone write it down. It is usually possible to request that or to bring paper and pen with you. I also learn much better when I have a carefully written textbook, but these become rare after a certain point. I think the best thing to do in this case is to ask for references (if a speaker gives a lot of expository information, ask for where to read about it).

I got an applied math PhD 'without' discussions. Like you, I much prefered reading papers and textbook to lectures, discussions, working together etc. I would skip class to read course material.  I later found out that most people visualize math expressions in their mind's eye (I can't), which seems like a key enabler of discussions. When people 'talk equations' I lose interest pretty quickly. There are a lot of talks which one is  supposed to attend. It was meaningless to me. Bring pen and paper so you can work on something else. I did not benefit much from the advisor-student relationship, which is a pity. If you can, try to find an advisor that will read what you write and give feedback on that.  On the plus side, reading a lot helps you hone your writing skills. There are many routes to the PhD.


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Is being socially reclusive okay for a graduate student?
I am Ph.D student in computer science and mathematics. I have published a few research papers and working on some papers. I am an after mid-stage student and I spend almost 90 percent of my time in my study place. I do exercise for half an hour per day. Before joining the Ph.D I was shy and now I am not shy, but my collegues around me now find me a strange person. This  is due to the following reasons:

Many times I don't talk to the people whom I meet while going back to my room or some other place. This is because I am in a thinking mode, thinking about a research problem.
I don't participate in group activities as the feedback given by my collegues.
I don't congratulate (much) or wish people around me like on occasion like new year, birthday etc., but I congratulate people around me on their research or academic achievements. Let me elaborate more, I do congratulate my friends and family outside academia.

Although I know my behavior, when working I try to avoid distractions. Many people find my avoidance weird. I can't be perfect as I spend most of the time on research problems. How to tell them I am not avoiding them?
Note that I have many friends, but not like hundreds, but some. I usually talk with them every day.
Question: Is being weird okay for a graduate student?

Please can you clarify your exact concern. In what way are you worried that being weird might not be "okay"? E.g. are you worried that it might have negative consequences for your career?

@user2390246 both way as a researcher and in a social life. Although I am much more interested as a researcher.

Why are you not wishing your colleagues Happy Birthday when you could? It is okay to not make a big fuss, but obviously ignoring it would seem strange and almost offensive in many cultures.

In some places conformity is enforced. Sadly. Sadly. In reality everyone is different and some are a bit "more different" than others. Apple Computer once had an advertising campaign "Think Different", celebrating this idea.
On a universal scale, yes, it is fine to be weird so long as it doesn't impact negatively on others. On a universal scale it is fine, even, to celebrate weirdness. But you "gotta do what you gotta do" in the real world.
You say you have overcome shyness. That is an important skill in the academic world, which tends a bit toward introversion. We think deep (we hope) and that takes effort that we don't like to dissipate with relatively meaningless rituals, such as the Friday on the Cricket Pitch.
However, there are some things you can do to blend in a bit so that the question doesn't arise. The easy ones are to find a way to be reminded to give holiday/birthday greetings. This is pretty painless. It might give you a bit of "space" to be weird in more essential ways - spending time in deep thought without communicating, and seeking quiet times for reflection.
If you practice a few things a few times, then you will probably find that they become more natural and more likely to get done without effort. I suspect that you used something like that as a way to overcome shyness earlier.
But if uniformity is truly enforced, then you need to accommodate it just for your own self preservation.

My spouse is from a culture with high expectations of conformity. Luckily she was a bit of a wild child in this regard and was able to reap the benefits of aggressively bucking this expectation when she came to the US for grad school. Unfortunately, however, many other students from her country come to the US and behave like the OP, never building their networks, never experiencing the culture, never making friends, never really broadening their minds outside of some narrow discipline. The OP sounds like he/she is looking for validation rather than critique.

Politeness is not the same as uniformity or conformity. Not going to a non-academic social is unlikely to be an issue (although you're less likely be on the tip of the tongue for collaborations or discussions), but being actively and stubbornly rude will get you noticed for the wrong reasons. (Virtually) No one is good enough to be absorbed fully on their one true project and are almost certainly going around in previously trodden circles.

Is "OK" good enough?
It's "OK" to be strange and reclusive, but being socially reclusive will stunt your career long term. You will not be considered for projects, not be sought after for collaborations, students who go on to success will not be as likely to reference your papers or publications in informal situations, and you will be less likely to be considered for promotions/tenure/etc. Not maliciously perhaps, but the social recluse just doesn't come to mind as often as more gregarious colleagues do. It essentially closes doors unnecessarily. This isn't to say that you shouldn't be true to your personality, but the fact is that success in any field of endeavor, even academic ones, is as much affected by your social skills as your intellectual skills.
Look at the mid-nineteenth century physician Dr. Ignaz Semmelweis, who identified that hand-washing and sterilization of instruments drastically reduced incidence of death from childbed fever. Because of his poor social skills (note that he was actively abrasive and confrontational rather than merely reclusive), he was unable to gain acceptance for his findings, and unsanitary medical practices continued despite his efforts.

From the article, I am not entirely sure if the rejection was because of Semelweis's lack of social skills. Do you have a better reference for that?

How about this one? It specifically calls out his disregard of the political side of research and his unwillingness to suffer fools. https://www.headstuff.org/culture/history/terrible-people-from-history/ignaz-semmelweis-medical-pioneer/

Nice answer. The book Outliers talks about this point as well. Once a threshold is reached, IQ becomes less important and other skills and traits become more important.

There is no universal answer to this.
If "being weird" is okay varies among all places. In some places, you "being weird" would imply that other people would not give you information, not recommend you, avoid you etc., in other places "being weird" is totally okay.
Definitely, I've seen weirder (and worse) behaviour between grad students and also higher ranked people.
Ask yourself the following questions:

Are you okay with being seen weird by your collegues? Do you face consequences which seem "bad" to you?
Is it possible for you to change some of your behaviour and would you feel okay doing this?
What do people "that matter most" think of you? This definitely includes your supervisor. Who else this involves, depends on your plans.
What is the norm in your place? If your behaviour is far from the norm (e.g. if whenever someone has a birthday, the whole week the person is celebrated and nobody works this week, then not gratulating would be very far from the norm), you might want to reconsider your behaviour.

A personal remark: I find it strange if one generally never congratulates people for birthdays or New Year. It is nice and does not cost you anything - why not do this?
Something I want to add: You might also want to think about what you want to do after your pHd: In my impression, in the non-academic world, social skills count far more than in the academic world. You might want to train your social skills, your abilities to interact etc

+1 for mentioning the world outside academia. I also find academia to much more tolerant of personal quirks than industry.

@DohnJoe: Yes. And sometimes, even more than "quirks" are accepted - there is a famous professor I know who acts like all students are stupid and openly says that women should not study (and treats their female students accordingly) - this is dismissed as "it's a famous guy, he just has some quirks"..

Note that I am not that kind of person. To me researcher from each caste, gender and community are equal. The problem with me to me seems that i ignore people trying hard to focus on research and second thing is I am introvert.

@staff Being in a thinking process is alright, but you should come back to the colleague(s) you ignored earlier for that reason and tell them something along the lines of "Sorry I walked past without saying anything earlier. I was thinking so hard, I barely noticed anyone!". That might help others to understand that you were absent-minded but not oblivious.

Do you plan to stay in academia in the long term?  If yes, then being socially reclusive is going to be a huge handicap.  You really should work on your social skills to succeed.
If you stay in academia, then there is basically one path forward: end up in a position where you are responsible for students and postdocs, and contribute to running your department or institution. People skills are critical.
To make it in academia, collaboration is essential. You must be able to find collaborators and be able to work efficiently with them. You must be able to talk to people at conferences and get them interested in your work. Again, people skills are critical.
The higher the position you apply for, the more you will be judged based on your social skills. It probably won't be hard to find a postdoc position, but when you interview for faculty positions, you will likely meet the entire department and you must appear likeable to a majority of your potential future colleagues to get hired.

Personally, I am a socially reclusive "older" postdoc with people skills that are not excellent. At this point in my career I am finding this to be a significant problem to the point that sometimes I am considering whether academia is suitable for me at all ...
The good news is that with willingness, one can improve. I certainly got much better at this since I started my PhD. However, you can't go in with the attitude that "in academia it's okay to be weird".

I'd also like to comment on this remark by @anewguest:

You might also want to think about what you want to do after your pHd: In my impression, in the non-academic world, social skills count far more than in the academic world.

This might be true, but in the long term, it is going to be very hard to find stable employment in academia that does not require good people skills. You will finish your PhD at some point, and you cannot be a postdoc forever. What then?
Lack of sociability is definitely a handicap in industry as well, but not necessarily a deal-breaker.

While you are right that even in academia you should (!) need social skills (although many don't), I do think in industry it's more extreme. For what it's worth, I never encountered the strange "I won't congratulate you for your birthday even though you would like it, because I think my communication style is superiour than yours and you are only worthy of my praise if you did yome big achievement"-attitude in industry.

You should read Workplace.SE more :-)

Of the 3 points you describe, #2 seems like the most limiting, as you are missing out on academic and professional discussions that are not purely social. Thinking critically about other people's ideas and approaches, and learning to incorporate others' critiques of your own work are very important skills that should be developed during a PhD. If you do not engage your peers academically, you are missing out on an easily-accessible resource for your own development.
Group feedback sessions aren't meant to be social gatherings, so opting out because you don't like to socialize is missing the point of the session. By avoiding these sessions, you are effectively sending the message that "I don't care what you're working on, nor do I care what you think about what I'm working on". That will be widely regarded as a poor attitude for an academic, especially one so early in their career. Not wanting to socialize is acceptable, but be aware of such situations that could stifle your own development.

It depends on what you want to achieve. If your interest in working on your CS/maths topics for the rest of your life, and deeply inside are fine being a recluse; if you only consider the social aspect as a means to further your ability to think about CS/maths, then you might just get away with it. Yes, more open people are more easily visible, but it certainly is possible to create a reputation through skill/achievement, generally speaking.
I'm not in academia myself, but have a lot of experience with knowledge sharing, networking, virtual teams, extro/introversion topics etc. in the workplace. My strong experience is that being visible, agreeable and likeable on a purely human level is incredibly strongly correlated with long-term success/placement in a company. Being visible, aggressive and strong-willed leads to short/mid-term success and also of course helps to make money. Being invisible, reclusive, known only in your immediate surroundings is... well... leading to not so much. And I assume it's pretty much the same in academia. If you don't intend to get much anywhere else, if that doesn't clash with your deeply ingrained life goals, then  that is perfectly fine.

What do you mean OK? You are who you are.
Don't worry so much.
There is plenty of different personalities in academia.
If you are a graduate student you would supposedly already have had at least one such professor or two, no?

Caveat: I'm writing this answer as someone who identifies somewhat with the autism spectrum, so I'm also socially weird and thus may not be fully qualified to answer, though perhaps this perspective can help.  To your question "How to tell them I am not avoiding them?", my experience has been that this is not really possible.  Social rituals are part of human interaction, as you've identified, and if you don't partake in the rituals or inadvertently send confusing signals during those rituals, it can be interpreted as being standoffish.  Not participating is itself sending a signal.
It sounds like you already have a reasonable model for this, so it's a matter of prioritizing.  That said, you've focused on relatively small things like birthdays, holidays, etc, but what I've found to be even more effective at building connections is to express an interest in their interests and listen to how they describe them.  In any case, as others here have pointed out, social interactions (and, by extension, politics) are an important part of a career in academia.  So, if your goal is to further your research opportunities, it's a good idea to devote some energy to this social aspect.  This comes up in most career paths, by the way, though politics might be more acutely present in academia than other technical disciplines (though, I'm only aware of this anecdotally from friends in research, as I'm in industry, personally.)
As an addendum, you've probably found that your friends become more accepting of your quirks as they get to know you, as they are less likely to misinterpret confusing signals or reticence to participate socially at times.  As such, aim to cultivate some friends within the context of your research (which you're likely already doing) and those friends may help open doors for you.