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Is it necessary to obtain permissions for using figures from my published articles in my dissertation?
How can I ask a journal to use my figures, knowing that the journal is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License?
If it is unnecessary, how can I do it properly?

Not so sure your question aligns well with your title? It seems that the title captures the essence better?

What did you agree to with the publisher when you published the paper?

Is it necessary? No
You can contact the editor. However, in the scenario you painted, that'll be mere formalities.
Your article was published under the CC-SA, the licensor already grants the licensee the right to use and modify.

CC BY-SA 4.0 Attribution-ShareAlike 4.0 International
You are free to:

Share — copy and redistribute the material in any medium or format for any purpose, even commercially.
Adapt — remix, transform, and build upon the material for any purpose, even commercially.

The licensor cannot revoke these freedoms as long as you follow the license terms.
Under the following terms:

Attribution - You must give appropriate credit , provide a link to the license, and indicate if changes were made.

Unless OP also gave away certain rights to the publisher (which they certainly may have), they do not even need to comply with all the CC-BY-SA terms because it's their own content, though academic standards would typically involve citation of published work, even by yourself (and especially when there are coauthors). To know what they can and can't do, we need more information.

@BryanKrause ... Valid point there ... To know what they can and can't do, we need more information

@BryanKrause, ....  My co-author is the supervisor, and I want to translate them from English to French (figure produced by MATLAB).

@semmyk-research My co-author is the supervisor, and I want to translate them from English to French (figure produced by MATLAB).

The general answer to the headline question is yes you need permission from the copyright holder even for your own work if you have given up copyright. But, in almost all cases the original creator will be given a license for certain uses that usually includes such things as reuse in a dissertation. Note, also, that copyright law differs around the world as do the policies of publishers. Again, in the general case, the author should check the license they were given when they signed over copyright.
However, in your case, you already have permission from the CC license you mention (CC-BY-SA), so you don't need to enquire further. But that license remains for your reuse and it should be so stated in your citation.
And, yes, you need to cite the earlier use along with the license.

Thanks, how can i do it properly ???

Do what? The citation?

Yes, what about this for example Figure 1. Simulation results of the proposed controller, reprinted from [author name] ([year]).

Not enough. You need the publication information and the license information. Journals usually have a preferred format for a citation and Creative Commons tells how to list their licenses.

Could you give example?


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How to deal with supervisor's contradictory comments
I'm a PhD student at the end of my 3rd year and I've been working with my supervisor since my BS.c degree. I was diagnosed with clinical anxiety when I turned 18, so when I started my PhD it was important for me to tell my supervisor that I am very anxious and I can get stressed quite eastly.
I am treated by a professional regarding my anxiety, only not as frequently as I probably should at this point. I'll be working on that.
Whenever I have a anxiety/panic crises due to PhD work my supervisor is the first to say that I am doing fine, I got results, my PhD is going fine, I still have time to do what is left, etc. However, when in a more formal meeting it seems like it is the complete opposite. My supervisor tells me that I should have finished that task by now, that I should have already started the next task and bunch of other stuff that in the end makes me feel like I have nothing and I'm not doing enough and fast enough.
I already put a lot of pressure on myself, most of the time is the standards that I set for myself that are the cause of my stress, but I also don't want to disappoint my supervisor who taught me so much and invested a lot of time in me. Even though I know my supervisor cares about my well-being as a student, it feels like they have no idea of how much I actually work, how much effort I put into my work to the point where right now I get home and just sleep.
Depending on the situation I am behind on work or I am doing fine. In the end I just feel even more overwhelmed and stressed and it really messes up my mind.
Any help?

The two comments you give in the second paragraph aren't necessarily contradictory. You have time to finish. You are slow (relative to expectations) on some tasks. That might be true of most of us.

The standards that I set for myself that are the cause of my stress — maybe weigh that against perfect is the enemy of good.

I'm going to against the (subtle?) current here and inquire why you aren't asking your advisor this directly. The phrasing is a bit delicate, sure, but if you're indeed behind, it's only going to get more uncomfortable. And if you're not behind, they need to stop implying the opposite. It's their job to make sure you're getting useful and constructive feedback, and you're ultimately the one responsible for your PhD.

(Warning: subjective answer)
One possible interpretation of your supervisor's "contradictory comments" is that they are trying to juggle multiple roles. As a supportive mentor, they reassure you in a crisis. As a scientific supervisor, they are trying to keep your project on time and on track.
Some of your descriptions (having anxiety/panic crises, feeling overwhelmed and stressed, etc...) sound like you could benefit from more mental health support. If you haven't already, talking to your university's counselling service or another mental health professional might be helpful.
Aside from that, here's some more tangible short-term advice:

(edit: just saw Buffy's post, follow their two steps first)

Is it possible for you to have a different (non-work) support for your anxiety/panic crises? Disentangling your coping strategies for your anxiety from things that trigger your anxiety could help de-escalate these situations. For example, can you call/text a friend or family member instead?

If you feel overwhelmed by your current workload, can you ask your supervisor for more explicit timelines on your immediate tasks? In the long run, I agree with Bryan Krause. For now, given that it's November, can you agree on a list of tasks (with smaller sub-deadlines) until next winter/term/semester break?

P.S: If there's a canonical winter break of some sort ahead, I'd really recommend taking a bit of time off. It might seem counter-intuitive, but taking some time to care for your mental health/reduce stress will help give you the stamina to take on the rest of your PhD.

Now that you mentioned, I do believe that my supervisor is trying so be a supportive but also keep my project going and on track.  I'm going to try  and apply all of your advices, thank you a lot.

This is a PhD, the supervisor should guide, but not dictate a schedule.

I agree with you in principle- the explicit timelines supposed to be a stop-gap. Given that OP might have year(s?) left in their degree, I think it's worth asking for extra support for ~1 month to bring the full weight of modern medicine down on those "panic crises". Mental health issues can lead to cognitive distortions (like rejection sensitivity) that make effective planning and communication more difficult: I think it makes sense to try and reduce the influence of this limiting factor first.

Two things. First, I hope you are working with a professional on your clinical anxiety and are finding solutions to that. Some things you say suggest that there is the possibility of some obsessive behavior - not completing because it isn't yet perfect.
Second, you should mention the seeming contradiction to the advisor and ask whether you are actually at risk or if it is just a bit of frustration on their part. Your anxiety may, as I suggested in a comment (copied below), be an interpretation on your part that isn't intended. Your anxiety is, perhaps, stressing any message that seems negative. It isn't impossible that they think they are encouraging you.

The two comments you give in the second paragraph aren't necessarily contradictory. You have time to finish. You are slow (relative to expectations) on some tasks. That might be true of most of us.

Thank you a lot for your insight, I hadn't though about it in that perspective, it is something that I need to keep in mind for sure

What you actually need to know is not where you are at but what you still need to do to accomplish your goals (such as: to graduate).
Rather than asking your advisor about your progress, ask about what you still need to do and work on a timeline for accomplishing those things. If it's too overwhelming to consider all that there is left to do, ask your advisor to help break the task into meaningful chunks with incremental deadlines. You may need to further divide tasks into what you need to do in the next week, next day, next hour, etc, if that fits your working style.

Thank you for this suggestion. I'm going to try the the task division for sure!

I am very sorry to say this, but You are doing OK is trying to contain your anxiety attack and God knows what you might do when in the throes of such an episode (yes, PhD students do commit suicide, and the risk that this might happen weighs heavily on the mind of a supervisor, especially when it's occurred in recent years at the institution).
You should be much further by now. is, I am afraid, the unvarnished truth, that you are behind schedule if the aim is to finish within the nominal time frame.

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The reason to be waitlisted in a PhD position application
What can be the possible reasons to be not accepted to a PhD program if you are a first author in the journal with high impact factor , have a work experience and graduated with honors from the top university.
Some candidates that were accepted don’t have the Master diploma and no publications. My field is bioinformatics, majority of candidates were wet labs.
There were a selection with interviews but there were no problems or questions that were not answered by me.
The committee consisted of people more familiar with the others candidate topics than mine, moreover none of a jury had a computational lab. They came to a conclusion that bioinformatics just analyze the data of a project that the wet lab part designed, which is not true. All of that may be of course because of the my presentation but the point is that they didn’t give a feedback so I cannot improve from that and that’s why I am asking a question here.
Important to note that I had a knowledge of the questions on the wet lab that were asked which out of the bioinformatician scope.
I’ve asked for a feedback and the answer was: everything was good

No way for anyone but them to answer this. Likely there were many qualified candidates. Likely some met certain needs better than others. Good that you were waitlisted, not rejected.

"My field is bioinformatics, majority of candidates were wet labs" - maybe the admissions committee prefers.people with wet lab experience. Is that wrong? Why? You aren't guaranteed a job by meeting all the expectations, you have to be the best (or top N) candidate. It's not their job to help you improve, their job is to pick the candidates they think will be most successful. Perhaps you should have applied to other places that would have a better view of your experience. Some of that is luck of who makes the decisions.

Please do not deface your question, even if it is closed. Rather try to [edit] it to address the issues that led to closure (without invalidating most of the answers). Even if you cannot edit it, others might or the question could still serve as a sign post.

In general waitlists mean they think they have better candidates than you, but you're competitive enough that if one of the other candidates decline, they'll choose you instead. Your application isn't declined, it's just that they don't consider it as strong as the other candidates' application. You might think your application is stronger, but your judgment does not matter here, only theirs does.
(But do keep in mind that lots of things are assessed in a PhD application, beyond publications, work experience, and grades; their relative weights might be different as well.)

Good performance in an interview is more than just "answering all the questions". How you answer matters a lot: do you display intellectual maturity and evidence of deeper understanding? Often, a candidate who doesn't know the answer to a technical question but who is able to give a logically-reasoned suggestion for what the answer might be is more attractive than a candidate who just seems to have memorised a textbook.
Also, it is often difficult to be wholly objective about ranking candidates. Person A has more C++ experience than Person B; but person B has taken more classes on differential equations. Who is 'better'? Eventually it just comes down to a judgement call about who the interviewers feel is best-suited to the position.

So is someone who recognizes the boundaries of their understanding and doesn't try to invent understanding on the spot. That might be a good strategy for a standardized test but isn't going to fly in a manuscript.

Departments continuously look at in what sub-sub-fields they want to grow. This also means a choice of where they do not want to grow. The internal politics of that department could result in the choice that computational biology is not a priority, and the fact that no person in the committee has a computational lab could  be an indication of that. In that case, you may or may not be a wonderful computational biologist, but if they are not looking for computational biologists, then it does not matter how many publications you have. You are in that case not the right person for that job.
In the end this is all speculation. If you want to know, you have to ask them. They may or may not answer.

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Can my past supervisor use our unpublished data for grants without my permission?
Say I work on a project as a Postdoc/PhD student and conduct an experiment or study, and this results in data that leads to another interesting follow-up question, or possibly even indicates a major area for new investigtion. Can my PI then use this unpublished data, without including me (and other coauthors) to try and win grants?
Im sure this must happen alot (also Postdocs doing similar things i.e not including the PI), but is this ethical? Is it policied? Could doing this practise result in the funding being withdrawn?

Why would it not be ethical?

Who has come up with the follow-up question and the new research idea? If you've, it's possibly unethical not to include you depending on previous agreements between the research team members. If your PI has come up with it, he decides to include or not include whom.

What you're asking about is who "owns" the results and data of a study. I don't think this is generally defined between researchers in academia. This is unlike in industry, where all of this is "intellectual property" owned by the company that employed the people who conducted the study. In that sense, the university owns the results and data, but that is not generally an ownership that is asserted (with the exception of patentable or marketable material). As a consequence, it is typically left up to the researchers themselves how they want to handle that ownership, but it is rarely done in any formal way.
At least informally, though, every participant to a study can use these results however they see fit for purposes other than publication (where one would typically expect that everyone who participated also becomes an author). Thus, most researchers would agree that for presentations at conferences, grant applications, etc., use of study results and data is fair game. I cannot see anything unethical in using data that way in grant applications, for example, and I certainly wouldn't know why anyone would "police" this or withdraw funding.

For presenting (unpublished) results from a study at conferences, it is definitely good form to check with your co-authors if this is OK.

Good form for sure. Is it unethical not to -- maybe not.

Your question seems to assume the premise that being the co-participant in the collection of research data (or more generally in the creation of knowledge in the context of academic research) confers you with certain rights. That is correct. However, I think you fail to identify correctly what those rights are: you do not get a right to control what is done with the data by the other people who have it. The right that you have is a right to be identified as a co-creator of the data.
In other words, I think the right way to look at this issue is that academic knowledge such as research data is not “owned”; that is, it is not conceptually correct to think of it as a form of property (even intellectual property). Rather, it is knowledge that is labeled with the identity of its discoverers/creators. To make clear the distinction between those two things, consider that a researcher cannot create knowledge and then sell to someone else (in a confidential transaction, obviously) the rights to be labeled as the creator. The lack of the ability to sell this right is one clear thing that sets it apart from a property right, including intellectual property.
Coming back to your question, following the above logic, I’d argue that what would be unethical is if your PI were to intentionally misrepresent who created the data. But if they state in their grant application that the data was collected by their lab members and students (and/or state the individual names of the discoverers, assuming that’s relevant enough to be included - in a grant application it might not be, but in a formal publication it probably would be), then it seems to me that they are respecting your rights and the rights of the other data collectors, so I don’t see a reason why that should be considered unethical or problematic.
A famous case in which the rights of the creator of a very important piece of experimental data to be identified appear not to have been honored is the story of Photo 51. Whether the photo was actually significant enough to suggest that Rosalind Franklin was robbed of a Nobel prize, is a separate and, from what I’ve read on the topic, much more controversial question that I don’t have a firm opinion on. But, Nobel prizes aside, credit for the photo to Franklin and to her student Raymond Gosling (who took the photo while working under her supervision) should in any case have been given in the initial publications announcing the double helix structure of DNA, and from what I understand, it wasn’t.


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Which is the easiest way for putting citations and references?
Most easy way to put references & citations?

Maybe edit your question to give a broader description of what your problem is to get better answers.

Zotero is a free, open-source management tool for references and bibliographies.

Please clarify your question.

Reference management software.

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Asking if the position is tenure-track.
I recently obtained my Ph.D., and I am looking in various states for an assistant professor or instructor position. Since I will be moving to another state, I would ideally like to find a tenure-track position. However, some of the jobs postings  I found do not mention whether or not the position is tenure-track. They usually list the position as full-time 9/10 month, with no mention of a contract or fixed term.
Is it considered impolite to email the university's HR and ask if the position is tenure-track? If not, what would be the best way to ask?

What country? Do you mean US states?

@dbliss: How can that be? You're supposed to offer jobs, to accept jobs, without the slightest clue what they are?? That's not "integrity"; that's lunacy.

The main reason I would ask is because I am applying for positions across multiple US states. It would be nice knowing that my family and I would be moving to a more permanent location so we could buy a house, settle down, etc...without having to get up and move a few years later.

@BoundaryImposition You have now been introduced to sarcasm.

@SashoNikolov: I invented it ;)

In many cases, they might think it is clear from the job title.  In the US, job titles with the words "Lecturer", "Instructor", "Adjunct", "Visiting", "Clinical" are almost always non-tenure-track.
The job title "Assistant Professor" is usually tenure-track, though with some exceptions: "named" assistant professorships like "John Doe Assistant Professor" may be effectively postdocs.  But it does not hurt to ask for clarification.
As David says, talk to someone in the department instead of HR.  The HR office is usually not closely involved in a faculty search and isn't likely to be the best source of information.

Thanks for the info. I ended up contacting the chair of the department for a position that didn't have anything listed regarding tenure. They replied and said their system does not offer tenure for instructors. Instead, they work under an annual contract system. Instructors are generally renewed unless there is a serious issue that constitutes a breach of the employment contract. They classified the position as a full-time permanent position. They seemed very enthusiastic that I asked, and I'm glad I did. I'm not sure if applying is worth the 95% job security though. Thanks again!

@josh: Out of curiosity, what was the job title for this position?  And what type of institution was it (private / public university, community college, etc)?

It's an instructor title at a community college.

@josh: Okay, so that fits what I said.

That makes sense. I've seen some instructor positions listed as tenure-track, which again lines up with what you said. I'm just glad knowing it's not frowned upon to ask whether not a position like that is tenured.

How would you classify a position that says " full-time career-track?"

@josh: With the word "tenure" conspicuously absent, I'd say that's not tenure-track.

It is not impolite to ask. Usually the tenure-track and non-tenure-track descriptions are a major consideration of academic job postings. I find it a little odd that any job posting would neglect to mention this.
Getting in touch with the department chair or search committee (or other responsible faculty member listed in the solicitation) might be a better option than contacting the HR department.

Thanks for the reply. I do agree, it is odd that these positions don't mention anything about tenure. I replied to Nate's answer with the department's response to this.

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My PhD supervisor want to add his name on a paper from my MSc work
I just started my PhD and I was planning to submit a paper from my MSc work to a conference soon. The paper was finished before I join my PhD program.
Now my new PhD supervisor want to add his name and his post-doc name on the paper. He asked me to send the paper for his post-doc to review and then add both their names. Although my previous supervisor already reviewed the paper.
How should I proceed? My new supervisor definitely has no contribution in the paper and feels like he just wants his name on more papers with no regard to how he contributed.

I think this is time for a JeffE quote: "Don't walk, run". Someone will probably elaborate more, but if this is the attitude of your advisor, there is a good likelihood that this whole PhD will be a miserable experience with little gain.

Start by saying no. It's your work. You do not need your advisor's permission to publish it. If he objects, fire him and find a new advisor.

Discuss this with your previous supervisor

"Thank you. professor but the paper is already reviewed by my former supervisor and I cannot add any co-authors without his/her consent." Or, you could go by "Thank you for your generous offer, but I'd like to submit paper as it is. Maybe we can work together for a journal version."

Are planning on going to the conference on your own (your own money)? Or your current advisor will pay for the fees? If he is going to sponsor you, perhaps he needs a justification to use some money from a grant or dept. I'm not trying to defend your advisor, but perhaps that's another angle to look at things. PS either way, I still agree with Jeff.

They are trying to stealing your work, without fear of losing face to your Master's advisor. Those people have no shame. You should run away ASAP.

You should not use your real name btw.

@TheFireGuy, that's a good point. I am submitting another paper with him to the same conference, hopefully if it is accepted then the dept will sponsor me and I can present both papers. But if only my MSc paper is accepted, then it is not clear whether I would be sponsored or not

If only to be sponsored for the conference, is this enough to add their names to the paper?

@KM158 in theory, your MSc advisor (or old dept) should sponsor you :) In a different dimension, your current advisor may offer to sponsor you regardless if you added his/her name or not. In reality, since you are the main author, it's really up to you to accept his offer or not! Keep in mind that this is only a conference paper (I don't know what's your exact field, in some fields conference papers don't count as important as journal articles, in others its a really big thing). If you are in the 1st field, Is it worth going to the conference to present it? Is it worth saying "no" to your adv?

@padawan That is a decent approach but I would say your first suggested response does not stress the fact it was original work of the OP as well and the OP's consent is also necessary.

I'm in the social sciences, but I can't imagine that this is a discipline-specific issue. Is your new supervisor pre-tenure? If so, he may be pressured to have a stronger CV and publishing with his post-doc would look extra favorable. Regardless, (from your description) this appears to be an inappropriate request and I'm sorry that you were put in this predicament. I find the fact that the supervisor wants the post-doc to also co-author is especially troubling.
First, I echo that you should find a new supervisor. If there is someone else whose work is close or closer to your interest, you can ask to transfer supervisors and claim this as an academic request and not a personal one.
Second, is your MSc a co-author? If so, you can state that the prior supervisor is the co-author and you do not feel comfortable adding additional co-authors when the previous supervisor put in much of the work.
If not, you can still claim that you did the majority of the work and that if neither your supervisor nor his post-doc have any significant additional contributions to your paper, you do not feel comfortable adding them as co-authors. To further decline with professionalism, you could explain to the supervisor that you have other paper drafts or other projects that you would like to publish and/or present at conferences...if the two are interested in co-authoring you could collaborate on revising something else to publish together.
If your new supervisor is somewhat junior, he may not know that this was inappropriate (I'm giving him the benefit of the doubt), so I would try to be as professional about this as possible. It also might not surprise other faculty or administrators that this person asked you to do this (there are always faculty members here and there who are known to minimize student contribution and credit, though unfortunate).  Good luck!!!

@user2768 If the student is interested in finding out if there is benevolent intent on the part of the supervisor, a larger discussion could start with asking how the supervisor and post-doc plan to help revise with the paper and take it from there. I understand your point - fair enough. However, there is the potential for a bigger them to review and having them assume there will be co-authorship on any and all terms, which may have to be argued against later. Here, it can be established up front, which is how all co-authorship agreements should be.

That seems a bit iffy to me; it's clear from the OP that it is his or her original work and from what was written, probably already publication worthy. The behaviour of the supervisor was inappropriate and I think the best approach is to shut them down clearly.

I largely agree with comments by Tobias Kildetoft, JeffE, and Nicole Ruggiano, but there's another angle that has not been considered, namely, the supervisor might be acting in the OP's best interests.
THIS ANSWER IS CONTROVERSIAL. At the time of adding this remark, down-votes outweigh up-votes. The comments suggest that down-votes are due to the supervisor being presumed guilty of malpractice. This is a serious, worrisome accusation. Let's step-back momentarily and presume innocence.
The OP has stated that their supervisor wants his post-doc to review a paper co-authored by the OP and OP's previous supervisor. It has been assumed that the supervisor is acting in his own interests. This might not be the case. Perhaps the supervisor believes the paper can be improved, after review. The OP should assess whether this might be the case. If so, then the OP should consider whether such improvements are worth adding the supervisor and post-doc as co-authors. They might well be worth it. For instance, if the improvements enable publication at a more prestigious journal, then I'd consider such improvements worth adding the supervisor and post-doc as co-authors.
I fully appreciate that reviewing is insufficient for authorship and, as I have hinted, I fully agree with Tobias Kildetoft, JeffE, and Nicole Ruggiano, if the supervisor wants co-authorship without contribution. That's not the issue I want to address; I want to establish whether the OP has fully understood the supervisor's intent. In particular, I want to establish whether the supervisor/post-doc is also offering a scholarly contribution. If so, then    the OP should consider co-authorship.
(In using the phrase "feels like," the OP is hinting that the supervisor's intent is unclear. Hence, the need for clarification and the potential importance of this response.)

Simply reviewing is not enough, otherwise every peer reviewer should be added as authors after acceptance of a paper. That he asks OP to add him and his postdoc as co-authors after only reviewing the work, and not as a conditional statement dependent on any real contribution, cannot imply anything other than ill intent.

Clearly reviewing is insufficient for authorship! That's not the issue, the issue is whether the OP has understood the supervisor's intent. It's very common for questions to miss crucial details and I'm merely exploring the possibility that a detail has been missed here.

well he explicitly told me the order of the authors including him and his post-doc as me, my ex-supervisor, his post-doc and then him. He did not even mention putting my ex-supervisor in the loop or asking for his advice. He said this will look good because it will be like international collaboration.

I would agree IF the supervisor made this clear. The paper is complete and there was no suggestion that additional theoretical or methodological changes would be made. To simply edit for grammar and such would not suffice for co-authorship.

@KaRim, personally, I recommend that you establish whether he wants to contribute to the paper. His intent should be a crucial factor in your decision and you should make sure there hasn't been any misunderstanding. Especially if drastic actions (e.g., finding a new supervisor) are to be considered.

@KaRimMaGdy This is especially funny because in many (most?) fields, last authorship is actually more prestigious than the second one, as it implies you directed and organized the project.

@NicoleRuggiano, I largely agree with everything you've said, but the OP just started their PhD and maybe they've misunderstood the situation. Jumping to the conclusion that the supervisor is acting in his best interests might have significant consequences and I strongly recommend that the OP delays any action before establishing the supervisor's intent. (Perhaps I'm romanticising that supervisors are generally good people;)

@KaRimMaGdy, what field are you in? (To address user8001's comment.)

@user8001 Exactly what I thought, I will go on and discuss it more to understand his motivation.

@user2768 Computer science

In computer science last author is not more prestigious than any other position.

I completely disagree with your answer. I could see your answer applying to a project in progress, but a person which has power (supervisor) asking to join a completed project (as stated by the OP) should be a big NO in academia. On top of that, asking to be added to the authors list before even seeing IF they can contribute negates your reasoning, at least IMO.

I agree with @NickS.  The explanation offered by user2768 might make sense except that the supervisor asked to be added to the paper at the same time that he asked to send it to his postdoc (not even to him!) to read.  So the supervisor has neither done nor proposed any contributions to the paper but asks to be added as a coauthor.  I don't see how this could be okay.

But yes, it is possible that the OP has badly misunderstood the situation.  That is always possible on this site (and in academic life).  So I agree that the OP should not begin by trying to jettison his advisor.  Rather, he should talk to the advisor in person and explain why adding him as a coauthor is not appropriate.  If they still can't see eye to eye at the end of the conversation, then it is time to find another advisor.

@KM158, are you willing to share the outcome?

This answer has 0 up votes and 9 downvotes. The statement that it is controversial and that only currently do downvotes outweigh upvotes, is misleading and should be removed.

@Nij, I don't know how you can see up-votes, but the statistics I'm seeing on my side seemingly contradict your claim, in particular, the site advised me that I had received "-14" on this post a couple of days ago, yet only "-7" was being listed a few hours ago, thus, there were surely 7 up-votes. My apologises in advance if StackExchange's rating system has bamboozled me. I'll certainly edit if that is indeed the case.

I'm intrigued that @PeteL.Clark has received 6 up-votes for essentially summarising my point...

I've discovered that votes don't correspond to reputation, and I'll edit. My apologises.

@user2768, Sorry for the late reply.
As you all suggested, I asked my previous supervisor and he told me this is unacceptable. I then told my current supervisor that my previous one does not think this is justifiable and he told me it is alright, it is fine by him.

@KM158, presumably your new supervisor did not justify why "it is alright"? As others have highlighted, there seems to be a problem with your new supervisor. I stand by my "innocent until proven guilty" position, but I think we've demonstrated "guilt" here.


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How to handle one's own academic misconduct, long after it occurred?
I got my PhD in data engineering in 2014 from a reputed university in a developed country. I am now an associate professor in a well-reputed university. Between my PhD and my current position, I took several postdoc positions in very good universities in several countries.
The papers with which I got my PhD (with distinction) are problematic. These papers were published in very good journals and proceedings. However, I didn't conduct the experiments as I mentioned in the papers. They aren't fully falsified, I had assistance and some are true only for specific parameters.  I knew this when I published.
More than two years, I began to feel terrible about this. I feel that my PhD is fake and everything I am doing now is based on academic misconduct.
I now excessively try to make everything very correct in my papers and to be extremely honest in presenting the results. I often disagree with my coauthors when they want to publish a paper with weak experimental validation. They always argue that at this rate, we can publish only a few papers and we can never compete with our fellows.
I don't think this will ever be discovered.  Even if you execute the experiments, you always find different results, the details of the approach are not given in the papers so any missing details can change the results.
What should I do now?

The title says "many years later" but your fourth paragraph seems to suggest it was only two years ago.  Am I misreading this?

@Michael "Now, I feel terrible about these papers [...] for more than two years already and I am wondering what I should do. " The pain started two years ago.

I find it strange that most of the answers you receive focus on the emotional/evaluative response of guilt (not a word you actually used) rather than focusing on the final sentence ... "what should I do now", which I take to mean, "What should I do now,about the fact of there being in existence papers whose results are incorrect or false?"

How hard is it for a reader (who, say, is doing a thorough literature review on the subject) to arrive at the conclusion that your papers are crap?

Btw. what does your old mentor say about the subject? He's the one who should be ashamed.

Separate two things: The guilt over having obtained your PhD in a dishonest way, and the guilt over having falsified papers in the literature.
First, the PhD. While you may not have deserved your PhD at the time you received it, it seems that you have accomplished good work afterwards. You are qualified for your role now, and there isn't really anything you can do to fix the past. If you need to atone, consider making a sizable (compared to your disposable income) donation to charity - maybe something helping disadvantaged students to access university education (in case you feel guilt over having "taken" a spot from someone else)?
Second, the papers. This is a different situation, because the continued presence of falsified results in the literature is an ongoing harm. You could perform the experiments now, and issue a correction with the actual results. If you have omitted any restrictions from the paper, issue a correction stating those. If it is not possible to fix a paper, you need to withdraw it. These actions obviously come with risks to your reputation, but there is no way around them if you want to do the right thing now.

I think there is another aspect you might want to mention: do others also perceive that these papers contain misconduct. Maybe they follow the standards of the field but Alice's personal standards are higher.

@Christian The OP is clear about having published partially falsified data. Whether or not their immediate subfield considers this aceptable is irrelevant.

The OP also wrote "After that, I got a phobia and I was excessively trying to make everything very correct " - this is what made me take the previous statements with a grain of salt.

Wait, wait, "If you're feeling guilty, just buy off your guilt with the money you made from the very thing you're guilty about" doesn't seem like very ethical advice.

Once you get beyond the standard knee-jerk reactions here, welcome to the beginnings of the actual human experience. You made a mistake, bless you, turns out that’s the stuff that makes you, and the rest of us, less than the angels. Don’t burn in Hell, just learn.

I have some reservations regarding the paragraph concerning the PhD. It pretty much justifies cheating as long as you improve later on and promotes the selling of indulgences. Is that really the best way to handle the PhD situation ? Is there no way to restore scientific integrity, lifting the feeling of guilt, without ruining the career ?

@corsiKa It's strictly better than not buying off your guilt; many people would just come to terms with it, go “the past is the past”, then (eventually) forget about it.

@HansWurst The cheating has already happened, OP can't undo it. There is no specific injured individual OP could do restitution to. Advising OP to seek punishment for punishment's sake feels wrong to me. If you have better ideas, please share them.

@Arno I do not advise to seek punishment nor do I think that you should recommend it. My comment is not "against" you or the op, I just think that your answer could be improved if another way was found and I wish I knew such a solution but I'm afraid my limited abilities only allow me to identify some shortcomings. Perhaps someone else will read that comment and manage to come up with a better way to handle the situation and can help to improve that part. I just hope that the current solution is not the final word on the problem, as it has the downsides that I mentioned.

Donating money to whatever charity seems as unrelated to the situation as building a shed in your backyard, and reads as a very odd suggestion. You rightly observe that OP has made a mistake that cannot be corrected. That's life. Learn from it and move on. If and when the opportunity arises, prevent yourself and others from making the same mistake.

@Thissitehasbecomeadump. No, it's not at all unrelated. The reasoning the answer author gives is that if OP feels like they took a spot from someone more deserving of the PhD, donating to a charity that would benefit people who do deserve a PhD but otherwise might not be able to get one would negate the societal harm they feel they've caused.

@RadvylfPrograms Whether it "would negate the societal harm" is very much up for debate. Perhaps it is a matter of cultural difference, but I'd say this approach is actively harmful if one believes that throwing money at someone (or something) else absolves you from your personal responsibilities towards society. Anyway this is rather off-topic.

@Thissitehasbecomeadump. It's hardly off-topic if we're discussing how correct the answer is, in my opinion. But I don't see this as "throwing money ... to absolve you from your personal responsibilities", it's to make up for an action long in the past. The options aren't "don't do misconduct" or "do misconduct and pay money to a charity", it's "have done misconduct in the past" or "have done misconduct in the past and want to make up for it in some way". And measuring the net benefit or harm to society is hard, sure, but I'm sure a lot of money being donated to a charity is better than none.

@RadvylfPrograms Sure, although it seems you are replying to someone else. To emphasize my earlier point, "It's better than doing nothing" is a rather low moral standard, perhaps the lowest after no standard at all, and is actively harmful if one believes that this is good enough. Again, this may be a cultural difference.

Your guilt is rooted in the fact that you completed a PhD without taking the time to properly (according to your standards, standards that are higher than your colleagues and mentors at the time) complete the papers.
So you feel your current professorship is undeserved.
Ask yourself: if at the time you had enough time and resources, would you publish proper (according to your standards) papers?
From what you describe, I would say yes. And this is the most important teaching you have to share and enable with the M.Sc and PhD students you are tutoring, this is what makes you valuable in the academia. You learned it the hard (wrong?) way, by doing it, make this step unnecessary for others.
Give your students resources, give them time, take into account for each PhD a buffer of 6 months to wrap up (additional to whatever length is average in your country) read the papers from candidates to the positions you have open, do not simply read their h-index/citations or other metrics that are there just to be gamed (and the way you published during your PhD is the consequence of these metrics ... it would be extremely irrational not to game them).
Regarding doing science, you are evidently on par with the others, since you obtained various postdocs and you landed a professorship, so you did not take a valuable spot.
Final note:

if you execute the experiments, you always find different results and
the details of the approach are not given in the papers

So your papers are very weak, or even inconclusive: these papers are needed in science, because they can trigger discussion. Is this a waste of money? in the world where results are the goals of science, yes, and if you feel like that you would find yourself better aligned working in the industry, in a world where science is the goal of research results, one cannot expect to have high impact results from all the funded research...

Why would it be "extremely irrational" not to game the h-index/citation metrics? Yes it can be done, and yes it isn't hard and yes those metrics are bad for a multitude of reasons, but that doesn't meant the "rational" course of action is to game them! Is that really what you meant to say?

@terdon what else is rational, if your career depends on some stupid metrics and you are at the bottom of the scale, with no power of changing it?
Remember, we are discussing about PhDs and the like, they are already slaves of lousy working conditions, although they have some marginal control on that, expecting they immolate their career to prove those metrics are useless is not something I force on them.
From higher rank academics, I absolutely expect them to fight against these metrics. And they don't. For accepted rational reasons like:

@tendon

How can I evaluate the 100s candidates? I cannot read all their papers, I need an objective measure!
How can I evaluate the goodness of a project? It must have produced some high impact in the following 2-3 years
and so on ... if these are rational reasons to have those metrics in place, then it is absolutely rational to game them.

@tendon As any software developer working in a company can prove to you, if you set dummy metrics like "I give you a bonus of 0.01% for every line of code we sell to our clients" you end up with crappy code, because the software developer will rationally spend time to increase the line of codes while building the proper codes. Given that time is a scarce resource, the optimization of metrics takes away time from real productive work. Science: the more you publish, the less you spend on each publication (or you get burn out, your call).

I am not defending the metrics. However, gaming them is immoral and I see no reason to call it "rational", sorry. Falsifying information and unethical conduct is very hard to defend as "rational". I'm sure some people do it, but that's their problem and we shouldn't promote the practice. (Also, my name is terdon, not tendon :) ).

@terdon you can game the citation metrics and at the same time having each single publication perfectly moral. You do not need to falsify your publications to get more work published, but you surely cannot spend the same amount of time on each publication.
Do not expect the system to change while holding these metrics in place, do not expect rational entities to fight or ignore these metrics as long as these metrics are considered valid.

@terdon: I think there is a difference between "making sure that a crappy paper is published in a prestigious journal to get the credit * index" and "falsify the results". The first one is a normal consequence of the idiotic way science is measured and everyone will make attempts to get whatever published. It does not mean falsifying the results, it may just mean making extraordinary claims and hope for the best, or publish nice but useless information. This is the sad reality of a failed system.

@terdon Then, when someone is a Nobel Prize winner, they should publicly claim that such a system is crap and use all their powers to change it. Or if they are head of Stanford or Yale - to publicly state that they will not pay for the journals and that they will not look at indexes. Or something else. But before they are such great figures of academia they have to pay for their food.

@WoJ dunno. I have very little respect for colleagues who are favoring quantity over quality. I might accept calling it "pragmatic" but I refuse to consider it "extremely irrational" to try to do the best work you can instead of gaming the system.

@terdon yes, "unfortunately pragmatic" is something that sounds good to me :)

-1 for the cynical answer that says in essence "the careerist ends justify the means" and "bad or even falsified research might be useful, don't bother correcting it".

Dear @SylvainRibault , not everyone can afford to see the world in black&white and it is in the human nature to commit mistakes. But I congratulate you for setting an equivalence between bad and falsified research, I hope you burn your Physics degree because of the way Galileo falsified his experiments.

@terdon accept the fact that the human nature is of animal nature: it's exactly our rational side that makes us behave so pragmatically. If you start having a moral in what you do, then you are bound to suffer. And you will be exploited by the pragmatic ones that are "just" following the metrics.
Exploited because:

at some point you collaborate with them, thus helping them.
if you produce less papers, their efforts in increasing their papers output to stand out has even more reward, because someone is lowering the average output.
Is suffering and being exploited rational?

Support reproducibility
First, I subscribe to @Arno's answer and I have already upvoted it. I am also in data science at a reputable Western university and what he/she advises are the standard practices in this field. I would just add that, if you find that the journals where you have published your papers do not accept corrections, you can post the corrections on your web page, along with links to the original papers.
Moreover, you may want to learn about the reproducibility movement and promote it more systematically with your collaborators or in the classes you teach. For instance, I teach a project class about research practices; in it we also discuss publishing reproducible research. Advocating for reproducible research will not fix your previous papers, but will improve your field of research as a whole, and will  make it less likely that the misconduct you committed is accepted (see e.g. Donoho's paper below).
One classic article I use is
 An invitation to reproducible computational research by
David L. Donoho. In machine learning, from 2019 on, conferences have introduced reproducibility checklists and reproducibility challenges, as shown in this paper. For a behavioral research themed discussion you can look through the posts of datacolada.org. I am citing the last source because psychology was one of the first fields where the reproducibility crisis was openly recognised, and you are more likely to find concrete suggestions.
Hope this helps. Science makes mistakes, but it corrects itself. Humans make mistakes, but they can learn to become better. [Please allow for the following less than objective insertion: I
respect you very much for caring enough to do something about research ethics.]
I also suggest that, if you aren't doing it already, you take on peer reviewing as a service to the community. At the serious journals and peer reviewed conferences, your work ethics will be valued.

A lot of answers here are suggesting a middle of the road fix - donate to charity, see that you've done good work since etc. quite frankly this will (probably) not work.
If you made the mistake of thinking the papers were of sufficient and publish worthy quality, not knowing of any errors then you could quite easily fix the issue by issuing corrections, withdrawals etc. but for this is not the case.
The issue here is guilt. You feel guilt for your intentional wrong doing. Giving any amount of your income to charity won't help with the guilt, because it doesn't rectify it. Here's what could:

Redo the bad work in full, at your own expense
Go back to your issuing body and come clean. Explain if there were any circumstances that lead to your poor judgement, but own up. Tell them you have since fully corrected the work and are ready to issue corrections etc.
Follow the advice/suggestions/enforcement they tell you to

This will mean you've not only paid for tour wrong doing, you've made good on your previous commitments.

obtained with some assistance and some of them are true only for some specific parameters

the details of the approach are not given in the papers so any missing details can change the results

If these are the worst parts of the papers, don't worry too much. It is a widespread problem in science that cherry-picking of "statistically significant" results occurs, and that reproducing results is difficult.
And indeed it is a big and important problem, but you are already on a good path by recognizing the shortcomings of your prior work.
I would suggest that you check if your prior publications get referenced in other work. If not, don't worry - the results apparently weren't very important, and the main result was your personal learning.
If they do get referenced, read the new publications to see if the shortcomings in your work could affect them. If it does, then you should work on making a follow-up that will point out circumstances under which the original research is valid, and also that will make it possible to more easily reproduce the results.

Cutting to the chase here, you cheated and you obtained very large benefits from your cheating. The first question, surprisingly unexplained by you, is exactly why you did this. Please say something about this.
Cheating carries unsuspected penalties. Building a career in academia is grueling and exhausting. People who jump through all the hoops successfully end up with increased strength of character, determination, and persistence. In fact they change remarkably during those long years of training.
When you cut corners or cheat to get ahead, you eliminate yourself from the group of people who came about their credentials the hard way and built the skills and character needed for a successful career. The demands don't stop with the PhD; for many people things get harder after that when they're faced with the larger demands of tenure, promotions, and more sophisticated research and publications. The competition continues too, such that those who aren't willing to put in the work or who don't have superior skills (because they didn't do their own academic work earlier) are culled from the pack. When things get really tough, those who learned honest toughness at the lower levels of their training pull ahead of the rest.
As you've found out, the psychological burden of cheating is large. There's small guilt and Big Guilt. How big is the fault in your case? Well, it's enough to get you ejected from your career and to have your PhD revoked. I'm really wondering why these thoughts didn't cross your mind when you were contemplating cheating. Please say more about this.
What to do now is a moral and philosophical question about your basic beliefs about life. For that reason, I suggest that you post your question in a moral and ethics forum or, better, get guidance from a skilled person like a therapist, life coach, minister, etc. I think you should start by asking yourself, "Why did I do this?" What does your conduct say about you? Are you happy with that? Next I would assess whether actual harm was done to others and the extent of the harm. Then, is it possible to make reparations to those who were harmed? Finally, ask how you can make this right within yourself. Many people have committed serious errors. They must find a way to make peace with their actions and move on. You will never forget this error you've made, but perhaps you can come to terms with it by correcting whatever flaw within you allowed it to happen and by accumulating enough positive actions to offset it.
At the extreme end, the hardest question for you is whether you would be willing to set everything back to moral zero by admitting your mistake to your PhD institution and accepting the consequences, which I think would be grave. This is a complex moral question that can only be answered with considerable introspection.

"When you cut corners or cheat to get ahead, you eliminate yourself from the group of people who came about their credentials the hard way and built the skills and character needed for a successful career."
https://xkcd.com/1827/

The way you have framed this question, you make the "black and white" answer seem to be: come clean and announce to the world publicly that you committed some kind of misconduct with the papers you wrote and issue a correction.
However there are several factors here that I am reading between the lines that make me doubt that the "black and white" answer really applies here.

Guilt -- especially guilt over something that has been festering -- can skew your perspective on how important something is. It's not clear to me, in objective terms, how serious the ommission is, but my suspicion is that it is fairly minor. To me, "major" would mean that the main result of your paper is not reproducible even in principle; "minor" would mean that you did not provide enough information to fully reproduce the results but that the main conclusions are correct and reproducible (perhaps with some additional input that can't be reconstructed from the text of the paper).

Our own faults are very clear to us, while the faults of others are often less obvious. Are you sure that your assessment of your work is fair, in the sense that other papers in the literature do not contain similar omissions/simplifications? This is particularly the case since according to your description, your standards are higher than many of your peers.

Science can be brutal, and we are hard on ourselves. People make mistakes, and deserve the room to learn from those mistakes. Be kind to yourself.

Furthermore, it's important to be accurate in your assessment of this, because "going too far" in the direction of "apparent good" can lead to damage to your reputation -- if you tell people you are guilty of something, people will tend to take you at your word. Admitting to falsifying results in a paper, even approximately falsifying them, is a pretty major offense in the scientific world.
I think you need to evaluate as honestly as possible, without guilt, whether the papers currently in the literature actively causing harm. Are people citing these papers? Are they building experiments based on the parts you know are wrong? And... realistically, do you believe your omissions are significantly larger than others in the literature in your field? If not, then let it go. I promise you, you are not the only one who has done something like this, and from your description I seriously doubt that what you did is the worst thing that exists in the scientific literature.
If there are really wrong results in those papers and those wrong results are being used as a basis for follow-up studies today, then that does make the situation more complicated. But I would still proceed cautiously. I would publish an erratum or some updated paper addressing the issue, but I would strongly recommend to keep the focus on the science, and not admit fault or falsification of the results. Just state that you became aware of errors or omissions and you are submitting a clarification.
The problem you have is that by raising the issue now, particularly if you frame the issue as something serious like "falsification", years and years after the paper was published, is that (a) people will wonder why you are brining it up (they may question your motives), and (b) you bring attention to the issue. If harm is not actively being caused, and your guilt is causing you to overestimate how significant the actual offense was, then there is a serious risk that the net result will be self-sabatoge without helping yourself, anyone in community, or, I would argue, even "the cause of justice" in an abstract sense.
You seem to be a very serious and dedicated scientist. Focus on doing good science and bringing positive and exciting new results into the world. Don't let this consume you.

Exploit your unique* experience to better the world
* Ok academic misconduct is definitely not unique but go with me here
I've seen people who change careers, or people who have done regrettable things, do things using their past experience that nobody else would have thought of. Whether it's a dentist that becomes a software developer and solves some major problems in his industry, or a murderer that becomes a lawyer or journalist and fights for a better system, these people bring a unique insight that allows them to do things most people can't.
You would be better placed than most people to answer questions like:

how widespread is the problem in your field
what impact does it have
what factors contribute to the psychology of academic misconduct
what can be done to change the culture
what can be done to minimise the harm/detect occurrences
what is an acceptable level of rigour (i.e. what is the sweet spot between invalid results and slowing down valid scientific progress in the field)

Trying to impose standards on your collaborators seems a bit of a waste of potential. If the system is generating strong pressure to fabricate results, people within the system should be having open discussions about how to improve the system. You could be one of the people driving these conversations across your field as a whole.
To go public or not?
Of course, going public with what you have done puts your career at risk. It is not something to do lightly. But remember, how you frame things can make a big difference to how they are received. If you tell people you fraudulently obtained your PhD, you will likely be in a lot more trouble than if you tell people you cut some corners you shouldn't have, you know you're not the only one and you want to do something about it.
A useful question to ask yourself is, what would you want someone else in your field to do if they were in a similar situation? Then, perhaps you should lead by example and do it.
Another useful question is, how would you want the academic community to respond to someone else in your field voluntarily admitting to a similar level of misconduct? A slap on the wrist? An investigation? Revoking the PhD? A dialogue? Although there are no guarantees that something worse won't happen, at least you'll be able to make an argument for why you think a certain thing is appropriate.
The final question is: what are the consequences of staying silent? Are people who read your PhD papers in turn going to produce invalid results or significantly wrong opinions? Or is it niche/obsolete work that won't affect anyone much?
(Actually there is one more question: would you jeopardise anyone else's career if you admit to the misconduct?)
Instead of going public you may want to write up your story and publish it anonymously, in a place where people from your field gather, and perhaps participate in an ongoing conversation about how to improve the problem.

they were obtained with some assistance

That is not bad. Scientific research is usually conducted in groups. If you are feeling guilty about not crediting someone you got help from, consider that if they were relevant enough as contributors, they would have been included as authors (PhD students, in my experience, are not the ones who choose that).
If they were not, it is true that you could have included them in the "acknowledgements" section (if that is used in your field), but that is mostly ornamental when you are thanking people, so you shouldn't worry. You could always thank them, probably even now.

and some of them are true only for some specific parameters

That is not fabrication. If you didn't provide enough information to reproduce your results, it just means that people may refute you some day. If you did provide the necessary conditions, it makes those papers more specific (and less interesting), but they are still valid.
What you seem to be worried is that you knew about these limitations, and decided to "hide" them, and feel that you were dishonest. There's always the option to publish a new paper continuing your research on that topic, explaining how those elements affect your research -be as exhaustive as you need this time!-. That would certainly remove the risk of someone extrapolating your results (although again, if they did, they would just find out that what you published is not as general as stated).

Let's break down the aspects:

You (co-)authored a paper which contains scientific misconduct, which you conducted
You co-authored other papers which did not meet your standards
You authored other publications which you PHD is based on correctly
I assume that, even after removing the tainted contribution, your PHD holds enough merit to justify it

Let's see what you could do:

Ask the ombudsperson of the institution in question
Inform the editor of the tainted paper on the nature of the misconduct and ask for retraction if you believe that the core content doesn't hold
Inform the editor about the fact "that the results are not reproducible" and suggest a correction
Write a comment (if such a mechanism exists in the publications in question)

However,

you should try to do this via the corresponding author
I read between the lines that the ethical standards of you co-authors may be not that high, so be prepared that they will block it or, if you circumvent this by going to the editor directly, try to throw you under the bus, which is more problematic if your PHD supervisor is directly involved (they may try to attack your PHD).

When it comes to your PHD, it depends a little but how much of it was tainted and if it was hard misconduct (falsification, fraud, plagiarism) or soft misconduct (cherry picking as far as usual or expected in the discipline). Imagine throwing away all parts of your PHD thesis affected by potential retractions and see if it still has enough value.
If you are independent enough (e.g. postdoc in different field), most of your PHD is not affected by the really problematic parts you can ignore the personal feeling of your former workgroup, but that also depends much on the location of the university.

The OP's wording leads me to think this is a case of hard misconduct. First, it's not one paper, but "papers." Second, he didn't "fully falsify" them; therefore he "partially falsified them."

Reading your post again, I see that your position is that you've reformed yourself and you're now doing honest work. What concerns me about your reform is that it was done out of fear---"I got a phobia." Though you say that your misconduct (your word) can't be discovered, it appears that your fear is based on the risk that it will be discovered and that you will suffer the consequences. You ask to not be judged. It's hard to withhold judgment when you haven't expressed any specific moral regret about your actions.
Data engineers deal with things that directly impact public safety, like self-driven cars. Now imagine that your surgeon, who's about to repair your heart valve, got his medical degree the same way you got your PhD, by not doing proper research or falsifying his studies. Hence he didn't really get the training he needs to operate on you. This is a problem, no? If he teaches in a medical school that's a bigger problem.
Since you're convinced that your misconduct can't be detected, what exactly is the problem in your eyes? You seem to be looking for exoneration. What exactly would justify exoneration in your case? Is there some special circumstance that would exempt you from the usual penalties in cases of academic misconduct?

Your answer works within a framework of retributive justice, rather than restorative justice.  I think that the OP should work to repair the harm they have done (as mentioned by many other answers), rather than "pay the price" for what they have done.

I actually agree that restorative justice is a better Plan A, and my post below (which was actually my first post) reflects this in part. I'm not sure it's possible here because the damage done can't really be calculated. I also feel that restorative justice needs to be undertaken soberly, beginning with a self-examination of the causes and impacts of the deed. I don't see that in the original post. Compare, for example, to racial restorative justice: reparations payments will help, but they're not enough without heartfelt acknowledgement of the harm done by oppression.

From the point of view of outside of academy: stop worrying, fix the problem, and learn techniques to work with pangs of guilt.

Stop worrying: these things happen. I guarantee you that 99% of all adults have some kind of skeleton in their closet that gives them a nice little adrenaline kick every few years when they remember it. Even if it's just some careless comment they said at an inappropriate moment. Shame and guilt are really common feelings that are built into all of us (or at least hopefully so). Life goes on.
Fix the problem: don't overthink it. Gather a few ways to tackle it, make it objective and not subjective, pick one way to go, and do it. In your particular case, although I am not familiar with the ways to get add-on articles into those publications, I could imagine you writing further papers which expound the issues from the previous one. Do not bother worrying about somehow "setting it right". Science is based on the principle of creating falsifiable theorems, and then by all means falsifying them when possible. If you really feel that you must comment on it, you can write a half sentence in your preface (e.g., "this paper fixes some systematic errors  in the previous one"...). Nobody cares or should care how these errors came up or your personal story. Obviously, don't lie or make up an elaborate story about things nobody except yourself knows anyways.
Techniques: one technique to work on things like guilt and shame is mindfulness meditation. There are plenty of possible ways to tackle that; the usual approaches are dead simple to perform ("watching the breath"). There is nothing religious or mystical about this; the beauty is that it is fundamentally an experimental approach. You immediately see what happens, you do not have to believe anything at all. You do not need to "make belief" (this is not about imagining energy balls or stuff like that). Granted, I know people who hate stuff like this with a passion, but you might as well see if that resonates with you.


text:
Proper way of responding to reviewers' comments
I need to resubmit a revised version of my paper to a journal. While submitting, I was asked to provide a list of responses to the reviewers' comments. I've started wondering about an accepted way of organizing these responses.
Should it be a text in free form? Or a bullet-point list?
Given the reviewers' comments in a free form, how would they know to which comments I provide a response? Should I copy the text of the reviewers?
Also, as for responding to changes in the manuscript, what tense is usually used? For example, how should I say that "The introduction has been/is/was modified ..."?

Although there are no rules (unless there are rules... read the decision email properly!), I'd always copy the review text, normally without leaving anything out (the reviewer may not like the impression that you try to sweep something under the carpet), and respond to any specific thing directly after. For example:

Symbol x has not been defined.

Done now on p. 4, l.11.

I suggest shortening and re-organising Chapter 4.

We have removed the last paragraph, however we think that the current
organisation is fine because (...), and the reviewer hasn't explained
what kind of re-organisation they want.

(End example.)
As reviewer and editor I find this way of doing it most easy to handle. I have seen authors adding something like "Thank you for this important remark" to every single response, which is bad as it makes reading more difficult. But starting with a general "We'd like to thank the reviewers for their valuable suggestions that led to an improvement of the paper" note can't hurt.  Regarding the use of tenses I'm in favour of "The introduction has been modified", but then I'm not a native speaker. Also language errors in the response to reviewers are hardly important.

I agree entirely. Although one might have carte-blanche, an ad-hoc approach is only likely to annoy the reviewers when they come to look once again at the paper. Reminding them of what they said, and then saying what one has done about it seems by far the best way to go.

I think it is also very useful to accompany such a revision with a diff file, visually showing the changes made in the paper. It helps the reviewer/editor to see what changes were actually made and they do not have to try to track them by themselves. If you use latex, latexdiff is great for this.

@Sim Similar in intent is a check of submitted pdf files is for example diffpdf (the free, frozen version, basis for Debian's package) and diff-pdf.

Spot on. It makes the reviewer's life much easier to explain how exactly you reacted to their review, and you want to make your reviewer's life easier. I currently have a revision to review where the authors simply submitted a Word file with review mode turned on, so I need to read my original review in parallel and figure out whether all my points have been satisfactorily addressed. I already saw that some points were not addressed - but without a response letter, I will need to deduce the reason for this from the revision itself. Don't make the reviewer's life harder than necessary.

Would someone like to post these suggestions (provide some kind of graphical diff of the original vs. revised versions) as an additional answer? (Please?)

Is there any latex format regarding to this?

While I agree with Christian Hennig's answer, I would like to focus on one specific aspect of your question which I believe is the crux---you mention that the reviewer's comments are in the form of free text (not structured as a list).
My technique for this situation is to convert the free text into a list and then address the list items.
Say reviewer 1 submits:

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do
eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad
minim veniam, quis nostrud exercitation ullamco laboris nisi ut
aliquip ex ea commodo consequat. Duis aute irure dolor in
reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla
pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
culpa qui officia deserunt mollit anim id est laborum.

and reviewer 2 submits:

Sed ut perspiciatis unde omnis iste natus error sit voluptatem
accusantium doloremque laudantium, totam rem aperiam, eaque ipsa quae
ab illo inventore veritatis et quasi architecto beatae vitae dicta
sunt explicabo. Nemo enim ipsam voluptatem quia voluptas sit
aspernatur aut odit aut fugit, sed quia consequuntur magni dolores eos
qui ratione voluptatem sequi nesciunt. Neque porro quisquam est, qui
dolorem ipsum quia dolor sit amet, consectetur, adipisci velit, sed
quia non numquam eius modi tempora incidunt ut labore et dolore magnam
aliquam quaerat voluptatem. Ut enim ad minima veniam, quis nostrum
exercitationem ullam corporis suscipit laboriosam, nisi ut aliquid ex
ea commodi consequatur? Quis autem vel eum iure reprehenderit qui in
ea voluptate velit esse quam nihil molestiae consequatur, vel illum
qui dolorem eum fugiat quo voluptas nulla pariatur?

You can break the sentences into a list like so:

R1.1 Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do
eiusmod tempor incididunt ut labore et dolore magna aliqua.
A: Your response
R1.2 Ut enim ad minim veniam, quis nostrud exercitation ullamco
laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor
in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla
pariatur.
A: Your response
R1.3 Excepteur sint occaecat cupidatat non proident, sunt in culpa
qui officia deserunt mollit anim id est [here I used square brackets
to clarify some term that the reviewer used that doesn't make sense
out of context].
A: Your response
R2.1 etc

The power of this method is that it allows you to swap around the order of the reviewer's comments, or to group comments together, or even to group together a comment from reviewer 1 with a comment from review 2. It is highly flexible. The only rule is that you must include all text of the reviews. This technique has been highly valuable whenever I received a long rambling review.

This is the best answer so far +1

I agree with the answer by Chrisitian Hennig --- it is best to copy the entire referee report and respond directly to all comments that require a response.  I highlight all the referee comments in a different colour (and use black for my own responses and contextual information) so that it is clear which parts are from the referee and which parts are my responses.  To add further to that answer, I will note that I use a practice of giving a simple bold statement of the general tenor of my response (agree, disagree, partially agree, revised, no revision, etc.) and then I elaborate more on what I think of the referee suggestion, what I have done, and why.  This helps the reviewer see up-front where I have revised things and where I disagree with them or chose not to revise.  Typically I have four types of main responses:

Agree - revised: Used when I agree with the referee and have revised accordingly.
Partially agree - revised: Used when I partially agree with the referee and have revised accordingly.
Disagree - no revision: Used when I disagree and see no way to improve the paper from the comment.
Disagree - revised anyway: Used when I disagree but the point raised in the disagreement allows me to improve the paper (e.g., tighted up my own argument to head off a misunderstanding).

Here is an example of what a response to referees might look like (using italicisation of referee comments, since I can't change their colour):

The paper is well-written and I like the writing style of the author.  However, I am concerned that the introductory parts lack sufficient literature review and they author does not do a good job of making it clear what parts of their work are novel and what parts are existing knowledge.  I recommend that the author provide a more comprehensive literature review and be more specific about the novel aspects of the contribution of the paper.
Agree - revised: I am glad the referee liked the writing style of the paper.  I have now revised the introductory section (Sec. 1, pp. 1-3) to provide a more comprehensive literature review.  Specifically, I have added reference to James et al (1981), Harrington (1983), Xi and Wang (1990), Wang and Evans (1991), Craig and Watts (1992) and Bonjorno (2013).  I have also revised aspects of the paper to be more explicit about the main contribution of the paper.  I have added a paragraph discussing the contribution of the paper on p. 3 and I have also revised Section 3 of the paper to say which of the theorems I give are new and which are repititions or variations from existing literature.  This new material should allow the reader to see which parts of the paper are novel contributions and which parts are contextual information using results from previous literature.
...
I also found the presentation of the simulation analysis on p. 16 to be unusual.
Usually a simple barplot would be used.  The violin plot used in Figure 4 is unusual in this area and it has not been used in other literature in the field.  I recommend using a simple barplot instead.
Disagree - no revision: I have constructed a barplot of the data to see if it is an improvement over the violin plot used in Figure 4.  While I appreciate the suggestion of the referee, my view is that a mere barplot of the data obscures important information about the shape of the distribution that is discussed in pp. 16-17.  The existing violin plot already has an embedded barplot that shows the median, quantiles, etc., and this is noted in the caption for the figure.  The use of the violin plot shows the estimated shape of the distribution in greater detail than a barplot would, and this is necessary for my later discussion (e.g., my discussion of bimodality, etc.).  I am aware that other literature in this field has typically used a barplot for this kind of simulation analysis, but I consider the use of a violin plot (with an embedded barplot) to be an improvement.  For this reason I have not revised this figure.

The general rule, similar to any document, is to make it easier for the reader to find the necessary information.
To this end, I use a different color for reviewer comments and my responses.  I use a bullet list to highlight key facts.   Further, I include relevant background from the paper in my responses; this ensures my responses are self-contained.

Unless the journal specifies a particular format, it's almost entirely up to you.
Here's a formula that has worked well for me. The goal is to convey that a) you've taken the feedback seriously and b) show how the manuscript has changed in response, so that the decision-makers can quickly and easily accept it--hopefully!
Start with a short summary of the reviewers' comments and the changes made in response to them. This should highlight any major themes: "All three reviewers asked about X, so we performed experiment Y and analysis Z; two reviewers asked us to comment on A in light of B, so we've added a new section to the Discussion on page 9". This does not need to be comprehensive, but should serve as an overview for the editor.
Next, go point-by-point through each reviewer's comments. I reproduce whatever they've written (in a distinctive font/color), and then write my response to that point below it in another style. These responses vary in length: a simple "fixed" is fine for comments about typos or minor errors. A major point might require an entire page, possibly with a bespoke figure. If you have changed the manuscript in response to address this comment, include the location of the changes (e.g., "Discussion, p. 9--10"). If the change is 1--2 paragraph or less, quote the revised text in the response too.
If the review is "free-form" text, break it into discrete "issues" however you see fit, but do not remove or paraphrase text and try to keep the points in the same order. Some people number them, using RX.Y to refer to the yth comment raised by Reviewer #x.
Write something for every comment. If you feel certain that the reviewer is incorrect, it may be tempting to rant about their apparent ignorance. I would avoid doing this unless it's an objective, factual error. Instead, consider the possibility that there's a germ of a good idea, badly expressed, or that the writing failed to properly convey your own brilliance. At the very least, your text can often be revised to make points more clearly.
Try to make each Reviewer's section self-contained. If a reviewer repeatedly returns to the same point, it's fine to occasionally say "As mentioned above in R1.4", especially within a single reviewer's section. If several reviewers ask for a small change, I would just list them in each section. Prefer repeating "We now include the participant's ages, heights, and weights on page. 9 [quote]" to "See R1.3." For longer responses, references are fine but if multiple reviewers have the same major comment, address it in your overview. Some of your responses may rely on specific data from references. It's sometimes helpful to include relevant quotes or figures from those. Give the citation as well, obviously.
Here's a complete example of this format from one of our papers. A growing number of journals now publish peer review files, so it might be worth checking whether examples are available from your field or target journal.


text:
How do I cite a translation of a classical author (greek philosopher) in my thesis
I want to cite a quote by Seneca at the start of my economics thesis:

It is not because things are difficult that we do not dare,
it is because we do not dare that things are difficult.

Here is an example blog entry with it: "This quote comes from his Letter to Lucilius, letter 104, section 26, line 5".
However, on the Wikisource page it is translated like this:

Our lack of confidence is not the result of difficulty;
the difficulty comes from our lack of confidence.

I obviously can't cite the blog. The Wikisource has a different translation. I can't cite the original (how would I even do this correctly), because it is probably in ancient Greek, and I can't translate it myself.

This sounds like a great suggestion, thanks! I will see if I can find the translator. If not, I maybe just will print it without a reference. you are probably right about that part too...

Nitpick: Seneca wasn't Greek.

Seneca mainly wrote in Latin. Since you are not working in a field that is even remotely interested in Latin literature, but since this is probably an inspirational quote, you should not include it in the references, but just give the quote and then in parentheses put in the reference.
It is not because things are difficult that we do not dare, it is because we do not dare that things are difficult. (Seneca, Letter to Lucilius, 104)
If the quote were of importance to the academic merits of your thesis, you would need to give more information in a citation, including the translator, and you would probably have to give the Latin original.
Most of the classic literature is freely available online, using often translations from the earlier half of the last century. If you want to be very classy, you can also find the Latin original.

When you make a citation, my expectation is that I can check the citation. So you give me a translation and the citation should tell me where you found it. Since you don’t quote the original, you don’t need a citation.


text:
Can I skip the master's of an American PhD.?
I am interested in studying abroad in America. I am currently doing a M.Sc. in Quantum Science and Technology in Germany and would like to start a Ph.D. in the same subject at one of the big American universities (MIT, Harvard, Caltech ...) after I've finished my degree. I noticed that every one of these programs has another master's integrated, for which I should already have completed the coursework. Can I skip that part's courses? If only a portion, how large of a portion could I skip?
Is there anyone who knows about this stuff (especially for the universities mentioned above) or who might've already gone through what I described above?

Are you asking whether you can skip the courses?

Yes sorry if that wasnt clear

Entirely up to the specific institution/department whether they'd let you skip any courses.

I’m surprised we have not had this question before but I am not turning it up …

@AnonymousM I know, but to stay in academia you have to have visited one of the very prominent research groups - and these, as one could imagine, are usually found at these schools. So this parameter would be my parameter I will base my final decision on rather than list of "top US schools".

"I know, but to stay in academia you have to have visited one of the very prominent research groups" You say that as if it were an established fact.

Ok let me rephrase it: I have observed that in order to substantially increase your chances to stay in academia, you have to have done your Ph.D. at one of the widely known research groups of a specific sub field. Some professors, like Immanuel Bloch from my university, also like to boast about this fact (see his cv link. Other examples include this research group from Yale, where actually 3 of my professors I came in contact with went link. But I would also like to be proven wrong.

I'm not really sure how either of those links provides evidence for your assertion. Yes, doing your Ph.D. at a place which is prestigious in your subfield certainly helps. No, you have not shown that you need to do your Ph.D. at MIT, Harvard, Caltech, ... or else your chances of working in that field are shot to hell.

@AdamPřenosil "No, you have not shown that you need to do your Ph.D. at MIT, Harvard, Caltech, ... or else your chances of working in that field are shot to hell." This is not what I've claimed. However, this discussion is pretty subjective, so maybe we agree on a tie? :P

Most US doctoral students start with only a bachelors. Few require a masters at any point, though many make one available along the way, sometimes just by filing paperwork and sometimes by writing a masters thesis (my case).
Actual requirements vary. In my doctoral program (math, but long ago), there were only two requirements: pass comprehensives and write a dissertation acceptable to the faculty.
But all students took courses as they were more advanced than undergraduate courses and were designed to enable passing comps, as well as giving a broad math background. Quite a number of the courses I took in the doctoral program had the same names as undergraduate courses but the level of instruction and difficulty was quite a bit higher. One way to think of it is that undergrad courses give the basics, but if you want real math insight you may need to go beyond what you can get in undergrad education.
Contrary to a comment, there was no "cohort" of students that needed to progress together. That may be different in other fields than math, I suppose. But you needed to pass those courses that you did take.
A doctoral student will probably have an advisor, not necessarily their research advisor, to help them choose whatever necessary courses are needed. So you get some guidance and aren't entirely on your own. The research advisor can be chosen later and isn't normally needed for admissions. If a student is already skilled enough in the required (comp exam) topics they might need to choose a research advisor relatively soon.
And, as mentioned in a comment, I always recommend students to "cast a wide net" of doctoral institutions. You don't just "enroll" at a place like MIT (or anywhere). You "apply" and are accepted or (most often) not. Top level institutions are very (very) competitive in admissions, accepting some fraction which tends to be smaller at the top since there are a lot of applicants and a limited number of slots. You need good letters of recommendation for admissions.
You won't need to repeat a masters, certainly. You might need some courses. But you probably won't need to take any courses in things you've already mastered, though mastering has a high bar. The masters program you are in might prepare you to take comps in some US institution or not. Probably there will be overlap. Possibly (probably?) there will be some gaps.
There are really two gates. The first is admissions. Your background and potential will be weighed and measured. The second gate is comprehensives, sometimes including orals, and folks may (will?) be looking for insight, not just competence. Now you can do the dissertation, which I'm not terming a gate, though there is a high bar there, also.

You would transfer classes you already took in Germany into the program at the US. Rules for transferring are specific to the university and will depend on the class you took and the class you want to transfer. There are also rules about the amount of classes (credit units) you are allowed to transfer into a program.
For a Ph.D., you usually do not lack credit hours to graduate, so the latter might or might not be a problem.
However, there is (in general) no way to just skip ahead to the thesis part that you know from Germany. You might have to pass a comprehensive examination and defend your thesis approval.

Rules on undergraduate course transfer and PhD course transfer are going to be different. In general, most US PhD programs at that level will require the student to retake the courses with their cohort, in my experience.

@Dawn, in math, I would think that a "cohort" would be very unusual. There are too many different math areas. It may well be the case in some other fields, I guess.

@Buffy Let me rephrase - it is not about the "cohort" as such, but rather that they don't trust the graduate classes at any institute not ranked LOTS higher than theirs.