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Do prestigious mathematics journals discriminate against young (undergraduate) authors?
I am an undergraduate mathematics major. I have made a draft of a paper on group theory. My paper is not a breakthrough. After scanning through a lot of journals I have come down to Journal of Group Theory and Journal of Algebra. Both are prestigious math journals. And the recent history of both journals doesn’t support undergraduate authors.
I do have the support of my advisor so editing will not be a big problem for me.
Do undergraduates have a decent shot of publishing in these journals?

Welcome! The second part of your question is probably addressed by this question about journal workflow, though if you need an answer beyond that you can [edit] your question. Congrats on the research!

Welcome. Because the second part of your question has been answered in the link cactus_pardner has provided, I've edited it out of your question.

What is the meaning of "the recent history of both journals doesn't support undergraduate authors"? I doubt that there is any sort of direct discrimination against younger people or undergrads or whatever, but, unsurprisingly, expectations for writing style and substance of results tend to create a high bar for beginners, since you're competing against experienced people.

They set the standards high : up to you to meet or exceed them - it’s not about any sort of « ism »...

There is probably very little discrimination against undergraduates (or even against non-acedemics).  But of course those journals reject lots of papers, even those by known professors.  So: if your paper is rejected, as it may well be, I would not explain it as prejudice against undergraduates.  If that happens, go on and submit to another journal.

I'm voting to close because of the unsubstantiated (and unclear) claim "recent history of both journals doesn’t support undergraduate authors", and because the title and the actual question don't match.  It's unclear what the actual question is.

I think "discrimination against" is the wrong phrase to use (my reasoning being essentially the same as that of @SolarMike ) and may be based on unrealistic expectations

In fact, I published a paper in the Journal of Algebra based on work I did as an undergraduate (I was a graduate student by the time it was published).
Certainly, there's no policy discriminating against undergrads (or anyone for that manner).  It's hard to rule out very subtle ways that cues affect people's judgement; it's actually quite rare that I am asked to referee a paper by someone I've never heard of, so I do notice and probably adopt a more skeptical attitude when asked to referee a paper by someone whose work I have no experience with. Still, this is a subtle effect, and there's nothing to be done about but to do good work and get your name out there.
Actually, there's a decent chance that the editors and referee won't notice that you are an undergrad.  (If they do notice, it will likely because you are affiliated with a university where they expect to know any professor in your field, and thus will investigate when they see an unfamiliar name.)

another way they could notice is if you acknowledge your "advisor".

I'm actually quite surprised that they aren't double blind...

@xuq01 With Arxiv in widespread use, double blinding is not terribly effective. Also, the amount of experts in a given subject is often quite small.

@TommiBrander It makes sense. In my field most major venues are double-blind and quite effective. But it's not a terribly small field either.

@xuq01 I think the flip side of this is that most mathematicians would be horrified by the idea of waiting until their results are refereed to circulate them.

@BenWebster True

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Can Budapest Semesters in Mathematics outset the disadvantage of not attending a prestigious undergraduate for top graduate programs in Mathematics?
I am an international applicant from a less prestigious school. Although with help of my coursework and recommendations letter from my advisor and internship advisor I hope I can make to Budapest Semesters in Mathematics. I also hope to get a letter from those professors in Budapest. However I am skeptical of how can it help my application for top Math graduate schools. Will a A from the toughest courses and a letter help overturn the fact that I am attending less prestigious school ?

Perhaps you could track down some former participants of BSM and ask what they think. Even if the person you ask didn't attend a top graduate program, then they may know (because the groups tend to be pretty close knit, I think) about the experiences of others in the program and how helpful it was for them in getting in a top graduate program.

I have pretty significant anecdotal insight here.  I went to a very good but not quite top tier ( in math ) school and jointly majored in a humanities degree and a math degree.  I was active in the math department, but was not the top student.  I took maybe one or two graduate courses as an undergrad.  By my senior year I decided to focus more on math, but didn't think I would get in to a top tier graduate program ( and, for me, it wasn't worth it not to go to a top tier program.  Please keep in mind that this is not true for everyone and was a personal choice ).  I was confident, and received confirming feedback from professors, that I probably would not be able to achieve this goal with my background.
In my senior year I applied to several scholarships for graduating undergraduates, like Fulbright and Marshall scholarships, but did not succeed.  I then applied to and was accepted into BSM.  It's an excellent program, and I would say that it's an even better opportunity to learn a lot.  When I was there, academics was not 100% the goal for around half of the other students; for many of them it's the "study abroad" experience.  I do not mean to disparage them at all; this experience can be very important for personal growth and perhaps even more important than the academic experience.  I simply mean to point out that you're working with absolutely top tier educators and mathematicians who care very much about the program and if you're there for the academics then you have an opportunity work closely with them and have a lot of access.
I focused extremely hard both during the summer before BSM, and during my time in Budapest, working on a ( small ) independent research project and rounding out my background, while making sure that I excelled while in Budapest.  I can echo the other answer that the courses were quite difficult, probably closer to a graduate level than undergraduate ( although I probably took more advanced courses ).
Anyway, punchline of the story is that I got in to the top school of my choosing for graduate school.  I had recommendation letters from BSM professors and from professors from my undergraduate institution.  I don't know how they evaluated, but I believe that my strong grades from undergrad ( at a near top but not top school ), my activity in undergrad activities within the math department, and my performance and dedication ( eg. research ) in BSM were the major contributing factors.  Regarding the school I attended for graduate school, most students were high school olympiad medalists ( I didn't know what the olympiad was until college ) and/or putnam finalists ( I participated 3 years, never getting honorable mention, but scoring okay ).  I definitely felt like I was the "least" among them, but learned later many of them felt the same about themselves ( see "imposter syndrome").  There were a couple of top tier graduate programs that rejected me, so I'd say that the experience put me in the mix.
So, moral of the story for me is that it can absolutely help you.  It requires, however, a lot of effort and at least a pretty good background on top of that. I would also like to emphasize that I know many people that had amazing experiences and learned a ton at next tier and next next tier graduate programs, some of whom have successful academic careers.  The best of the best students in my graduate program got something out of being with those stratosphere level professors that, to be honest, I was not capable of.  My guess, although every story is different, is that you may have an even better experience at a next tier graduate school rather than top tier.

In short, the answer is yes provided that you do well enough so their professors are willing to write a LoR for you. BSM courses are challenging, ELTE is a top tier research university whose professors are mostly world renowned in their fields. Keep in mind that a sizable portion of local or European participants in the program are students who did well on high school math contests.
That said, this is a big if - most of the courses offered are pure math classes and the highest rigor is to be expected. Much higher than that of a mid or low tier U.S university.

I agree with this answer. A graduate admissions committee should be impressed if you get a letter saying you did as well in BSM as the students from prestigious universities. But doing that well won't be easy.

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Internship to Grad School
Last year I did a year long Quantum Chemistry internship at a very prestigious university. Towards the end of my internship I met another principle investigator from the same institution and got interested in their work (Material Sci). I didn't get time to develop a relationship since I had to move for college in less than a weeks time(transferred from a Junior College into my junior year), but I wanted to try to intern in their lab this summer, and if they liked me enough, go there as a grad student upon graduation.
I was wondering if there is anything wrong with this plan. For example, I've heard often that universities want you to go somewhere else for your grad school than undergrad in order to "meet more people in your field". I wanted to know if this custom also tends to apply with internships done in undergraduate years.
Edit: I am a physics major in case you are wondering.

Could you clarify your question, please? It isn't quite clear what you are asking. If you are asking what is wrong with the plan to do an internship and then apply for grad school at the same institution, the answer is: nothing. However, I'm a bit confused by the background story. Is this material scientist you met from the same institution you are currently in, i.e. your undergrad school? Are you in your freshmen year (based on 'I had to move for college in less than a weeks time')? If so, it might be too early to focus on where to apply for grad school, you'll probably change your mind.

i added that i transferred schools and that the PI was at the university I interned at

I don't think it's so much that universities want their grad students to have attended other schools for undergrad, it's more about achieving a broader experience for yourself which will be especially helpful after grad school.
In my experience, professors (and departments and universities) generally want to attract the best students they can for grad school. The top students in an undergraduate program may be heavily recruited for graduate programs at the same university, especially if they have been participating in research with a professor and he/she is impressed with their work. It can be difficult to judge applicants' grad school potential based solely on application materials and a professor having personal (positive) experience with a student can lead to very strong recommendations and near-certain acceptance.
On the other hand, if you should choose to go to graduate school, it is in your best interest to choose the best (for some definition of best) situation for you. I think this is where it's often beneficial to change institutions. Attending multiple universities broadens your contact base, exposes you to new resources and ways of doing things, gives you perspective on multiple departments, and better prepares you for future moves to new locations/institutions/etc. I think that the importance of developing a broad network of contacts for your postgraduate career is incredibly important and changing institutions for different degrees is almost guaranteed to help you there.
In your case, where you've done an internship at the school you're considering, I would not worry much about potential negatives if you decide to apply there for graduate school. I think an internship is a great way to get a feel for the institution and the professor. It's also a potential way to get yourself a very strong recommendation and an "in" to the department.

Many departments actively forbid their own undergraduates from enrolling as graduate students.

@aeismail Interesting. That has not been my experience at multiple U.S. R1 universities (math or applied math departments). I'd be interested hear examples. I wonder if it's also field dependent.

Pretty much every top-25 department in my field (chemical engineering) won't let their own undergraduates continue on.

I think that's generally better for the students. I was lucky enough to have an undergraduate advisor that pointed out the advantages to me, but I've seen others stay in the same research group from undergrad through PhD. I think that is typically a mistake.

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Is it a violation of copyright if I draw and publish a figure very similar to another person's published figure?
I am pursuing a PhD (computer science) from one of the reputed Indian universities. I have prepared some white papers for publication in coming journals. I prepared these papers by myself. I referred various links and study guides, books etc.
After getting these papers published, I received one notice from the editorial staff of publication that I have violated the contents/copyright law. They provided me some contents and images (they said violated areas).
I am surprised because I prepared all the things by myself. I have already mentioned the referred links, books etc. in the publication.
How can I avoid content violation in my own written material?

Did you use images from other sources in your paper?

@ff524 - no I draw these images, person who claimed for content violation said these image and contents belong to her. I asked my guide and he said that these images are very common like I have created a security model for Cloud computing which is very common so, everyone can draw the same image for security model.

It's hard to make a judgment here without seeing what was allegedly infringed upon, and what you did. However, it is important to remember that ideas cannot be copyrighted. Reconstructed images normally violate copyright only when there is data or novel intellectual content that has been reproduced without permission.

The editorial staff of which journal?  And which country's laws did they say you violated?  (I'm not a lawyer, so I won't be able to answer in any case, but I think it might help other people to answer.)

@TrevorWilson - Publication is in India and editorial staff did not mention that this is a content violation they sent an mail mentioning that XYZ person claims as an original author of these contents

What would probably help somewhat in this situation are the images, if possible.

Copyright protects not only the original content itself but also anything which is clearly derived from the original content.  That is why plagiarism doesn’t depend on whether you copied, retyped, or minorly reworded.
If you created a figure using a figure that somebody else drew as a template, then it does not matter if there are minor differences between your figure and their figure. Because your creation is closely deirved from their creation, then it is still their copyright, from both a moral and legal perspective (personally, as a scientist I find the moral perspective more compelling than the legal).
If you had simply created a figure from scratch, then it is highly unlikely that it would appear closely similar to another person’s figure – there are simply too many possible personal choices in how to diagram the same ideas, even for fairly simple ideas.
At this point, there are two ways to proceed (assuming that the rest of your content is intellectually honest):

Create your own diagrams from scratch with significantly different content, reflecting the different ways in which you think about the area.
Obtain rights permissions from the original publisher, and include “(figure adapted from […])” in your paper. Many publishers have an automated online method for obtaining fragment reuse rights, which can then be sent to the publisher handling your paper.  If the original figure was posted in a free-reuse medium (e.g., a US or UK government report), then you may not have to do formal obtaining of rights.

For what I read in one comment you draw also the images, but still if the figures appears somewhere else you should reference them. For example put something like:
Figure 1: Description... (based/largely based in Professor X)
Try to make those changes.
Good luck!

those figures are mine (I draw those) and how can I mention these belong to someone else. I Completely agreed what did you say in my publication I adapted Microsoft asp.net MVC workflow (images) and I referred that the original source is XXXX. But, how can I mention those images for others which have been drawn by myself only?

for that reason I have said that you should put the term "based on". I recommend you check up the source from where they are making claims you took the figures. Even if its your own drawings and you based those on something you have saw before, then you must put the source.

The figures she was telling is not same as mine I draw it in vertically but other was in horizontally I use 3-different color but other is having a single color in the description I have already mentioned that this is adapted on the theory of Cloud Security

In case that you have never seen the other material, I mean that the model has just came out of your mind, then you can try to argue with the editor that there are no copyright issues. If you based those figures on some material you have seen before then it is your duty to reference that. Even if you have changed the format: colors, style, position, and so on.

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Some metric to find research project for PhD program which lead me to kick the start-up after PhD
I have trouble on finding my field.
 I have a master on computer networks in field  of Wireless Sensor Network. What I did on my master degree was just a pure simulation!
I like academia but What I am looking for is finding a research project which involve me on real world problems and not just simulation.
Ideally I want start my own start-up after finishing my PHD. or fining job in industry as a research associate which they research but they solve the real problems.
In order to more understanding you can see here which they finish their thesis and start their own company.
Now my question is how to find a professor as supervisor which working with his project direct me to those what I said? For example If one professor has lots of citation on google-scholar one will make sure that he has strong knowledge on academia.
I need some metrics to know working with which professor will guarantee my working on industry as a research associate?
Are patents are good metric?
More example are:
In my thesis I have tool to develop which name was NS2. that is appropriate for simulation. I am sure working three to five years  with tools like that never directs me to solving real problem.
PS: 1. I did not said That I want to become developer on industry.
Ps: 2. I say I want to become researcher which direct my to start my own start-up

to down voter : any reason

As you said, publication numbers and citation counts are a way to measure academic prowess. While patents are interesting as a metric, I wouldn't suggest they measure industrial relevance - I know several academics holding patents. None have ever actually been implemented into a product. None has any realistic and practical implementation, at least today. Now, don't get me wrong - one might become relevant in some years, but for now the patents were purely academic.
Instead I suggest taking a look at funding awards - at least in the UK there's a push towards industrially relevant research. Certain types of funding are given for partnerships with industry. For example, a TSB project (now Innovate UK) typically is either fully industrial, or industrial with academic partners. Someone with active and ongoing projects like this should be a good potential advisor.
Another potential way to approach the problem is to look for professors with their own spin-off companies. Generally universities like to shout and boast about their research which leads towards spin-offs! This is perhaps the most relevant indicator as to the industrial relevance of their work. To be clear, they typically hold their academic position while the spin-off company begins and trades, with the university encouraging it (and possibly holding a small investment stake).
Ultimately though, there isn't a reliable metric to guarantee that you would work on industrially relevant work as an RA. While you could certainly look at past industrial funding received (perhaps companies directly sponsoring PhD students), ultimately the only way to know is to talk to potential advisors. Perhaps current researchers too - if someone approached me having found my name on a paper, and asked about where the industrially relevant work was being led from, I could point them towards a few people who would be entirely happy to "promise" anything you worked on would be industrially relevant. Indeed I'm currently in the process of sorting out a new RA for a 100% industrial project.
As to metrics, I therefore suggest their own claimed funding, coming from non-academic sources (this will require some background research). The source of the money for their work generally highlights the motivation and (presence or lack of) industrial relevance. Ultimately you then need to talk to your short-list and see if they sound to be working on the things you want to work on.


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Thesis reviewer requests update to literature review to incorporate last four years of research. Do I need to do this?
I'm about to defend my Phd thesis in November 2016 in software engineering. I  started my Phd in February 2010. One of my thesis reviewers stated in his review comments that my bibliography references are too old: the most recent work I have quoted in my bibliography is from 2012; that was when I was elaborating my thesis' state of the art. He stated that I have to check main works done in the field of research since 2012.
I am not excited about completing a new literature review two weeks before my defense. Thus, I was planning to say at the defense that the bibliography is old because my thesis began several years earlier. Is this an acceptable response? What would you do in this situation?

Well, basically you are saying that you didn't keep abreast of the literature over the last 4 years. You should not need to do a new literature review, since you should have been reading relevant papers as you went along. I would have an issue with not having recent references as well.

Y'know what would be scarier than being told to refresh your lit review?  Finding out -- during your defense -- that someone else has done, and published, "your" research.  Refresh the lit review.

@JonCuster, that's one way to read the Q.  A more optimistic way is to consider that the reading since then hasn't made it into the review because the review was written too early.

@ChrisH even if the review simply hasn't been updated, "the most recent work I have quoted in my bibliography is from 2012" implies that also all of the other chapters done after the literature review have not (according to citations) taken into account any recent publications.

@Peteris: Implies, yes. Some attention to the citations in the rest of the thesis may be required as well

Thanks all for your answers. The reality is close to what @ChisH has stated above. In my university and in my department, along the Phd process we have 3 different exam, aside the thesis defense exam: the first one is the qualification exam, a written one, the second one is the research proposal exam, and the third one is the thesis proposal. So if I count the thesis exam that make in total 4 exams. I have written the litterature review since the thesis proposal and have updated it for the thesis proposal exam I took last year in 2015.

So to avoid the criticism I got from the reviewer, in 2015 and 2016 I cared about having in the bibliography many references from 2015 and 2016. The criticism is about a big section of the literature review where I present some models. The most recent work presented in that section is from 2012. @ScottSeidman answer below is very interesting.

A bit more related to @BobBrown's comment - Often at first glance it looks like someone else has done the same research, but on closer inspection it's clear that there are significant differences.  You probably haven't had someone else publish this research, but it would not be at all surprising if someone could ask you "how is this different from the following paper published 3 years ago?"  If you get that question and your answer is "I don't know that paper", you're in a LOT of trouble.  If you get it and your answer is "they were focusing on this set of parameters, for which..." you're okay

@Joel Correct.  That actually happened to me.  I encountered a paper with work very similar to mine and went to my committee chair in a panic.  He told me to include that paper in my lit review.  I did so, with enough detail to show the differences.  Problem solved.

The criticism is that you're not up to date on the current state of your own field of specialty, and it is not a light matter.  If the "reviewer" is some sort of committee member that can throw a wrench into your exit process, you should address the criticism.
The real issue is how to address it.  My assumption here is that your defense will be "typical", with a formal presentation followed by some sort of closed session.
You have a very limited amount of time before your defense, and you need to use it wisely.  To start, I'd pick the five most relevant citations to your work that you have, and search them forward to see who cited them, and read those papers-- there will probably be less than 20.  If nothing earth-shattering has happened, you will eventually add those to your reference list, and all should be good.  If there is something earth shattering and pertinent to your work, you probably have more research to do at this point.
How will your reviewer know you did it?  Well, for the closed session, you should have a slide in your rack entitled "review of recent literature".  In closed session, make the opportunity to say "in review, a criticism of how up to date my knowledge of the field was came up.  This was accurate, and this is how I've responded...  I think I've covered this, and will continue to stay up to date with the literature".
To add, they may require a bit of a rewrite-- that's actually fairly common-- but worry about that when the time comes.  The strategy is to to convince them that you've done the work, and you're ready to do that rewrite.  You don't have the time to do it between now and your defense, and my experience is that the document is largely sealed until it's defended anyway.  You're trying to set things up so your revised dissertation will be signed off on without a thorough going-through.

+1 for the pragmatic suggestions instead of "Yew dunne screwed up."

Actually, I like this answer better than mine. I hesitated to give advice on a situation I was unsure about, but this answer seems to address what can be done accurately and realistically.

First, if a reviewer stated that you should better do something, then you better do something (in most cases, do what the reviewer says, unless you have a very good reason to do something else).
Second, the reviewer is right here. You have to keep up to date with the literature, and provide a literature review in your thesis which is up to date at the time of submission. Four years is a pretty long time for fast-moving fields, and even for slower-moving fields it is still not negligible. On the other hand, refreshing a literature review for four years of new research is a doable task.
If it really is the case that you did not keep up with the literature in the past four years, it may be that you missed some important developments. Many things may have happened and I can't answer the question "what now?" without knowing more details.

I don't think it's always true that you must do something because the reviewer says so. It's not unheard of for them to say something should be done when there is a good reason not to.

@JessicaB: That's true in the general case, but it's hard to see how that applies in this specific case

@JessicaB Agreed - since my I formulated my first paragraph in a general way, I took that into account now, thanks!

@ChrisH I'm not disputing that. But it's stated in this answer as a general truth, and I'd expect others to read the question and answer at some point.

@JessicaB As a bit of background: At least in the German system, a reviewer can officially request (as opposed to recommend) changes in the thesis, and if the committee concurs (which usually happens, because this is a step not taken lightly), these become mandatory -- meaning that even if the defense is passed, the degree won't be conferred before a suitably revised thesis is (re)submitted.

While writing a lierature review early is a good idea, it's a mistake to regard this as the literature review.  The early literature review is better though of as something for your own use (plus your supervisor and any internal requirements).
It's quite possible that you've kept up with the literature but not demonstrated that in the thesis -- which is essentially the same as not putting the thesis in context.
From where you are now, it seems like you really should update (not rewrite) it.  If you have kept up this shouldn't be too hard.  Even if you haven't you could be lucky and find a good recent review paper that you can use as an index to developments with some context and weighting.  Even if you're unlucky and there isn't such a paper, looking for it is helpful to writing your review.  Check for recent/relevant publications from anyone involved in your defense.
Actually getting stuck in to recent literature on your subject is a good  way to prepare; although the writing side of it is a chore, you're not in such a bad position as you seem to fear.

Many of the answers above are quite good, and I don't want to re-state them except to highlight things that they have already said:

Surely you have been reading papers over the past 4 years, and have used this scholarship to enhance your own research.  Part of your response to this reviewer can highlight this fact.
You should take this reviewer's request seriously.  This person gets a vote on whether you graduate or not.  The only reason not to do so is that literally every other person on your committee thinks this guy is an idiot and that they will vote to support you regardless.

In addition to this advice, I would also add:

You should also find out what your advisor thinks.  Do what your advisor says.
Do not waste too much time on this.  Do good work, but do the minimum work necessary.  Unless software engineering is wildly different from physics, this is not a "book field," that is, you do not get tons of credit from writing a scholarly book.  Instead, peer-reviewed articles are the preferred form of scholarship.

My own thesis was printed and bound in a gorgeous black volume with gold embossing.  It has sat on my shelf, lo these (not so) many years.  Instead, I cite the 3 peer-reviewed articles that form the basis for this thesis.  In fact, my own dissertation was written using the "staple method" taking these three peer-reviewed articles and weaving them together in about an hour.  This may make @qsp's disgruntled examiner even more disgruntled, but that is the way that my field is moving...

"Surely you have been reading papers over the past 4 years, and have used this scholarship to enhance your own research." ...exactly!

Given that only a couple of weeks are available at most, is there really danger of wasting too much time on this?

It is a serious problem. It means that you don't know what happened in your field during the last four years. You should try to update the literature review by adding newer references, including at least some 2015 and 2016 references.
It does not matter when you started your work. Even if you started your Ph.D. in 2010 and did the literature review in 2012, you should have updated your literature review during the last few years. You need to keep the literature review up to date.

There are two very different things in your question, and I get confused because you mentioned it like the same thing.

Your literature review is only until 2012.
The latest paper you cited is in 2012.

IMHO, 1) is OK, and 2) is not. Actually I did 1). In my thesis, I had a small subsection of only 3 pages, called "state-of-the-art", which briefly summarized all the techniques and more importantly their limitations up to 2011, the time I started my PhD. This helped showing my motivations to choose the topic, and what I had achieved in the thesis (in one paragraph).
After 2011, there were papers that developed alternative approaches to mine. There were papers that were incremental to my work. My reasoning is that if I put them all in the literature review, one may ask why I propose the slow technique in Chapter 1 (published in 2012), while there are already much faster technique in the literature review (published in 2015, and based some parts on my work).
For each chapter, I have a related work section that cited all the papers up to that time. Therefore, my bibliography is complete until 2015, although literature review is only until 2011.
My thesis is not a good one, an examiner in particular commented that "thesis reads in place like a bundle of papers rather than a thesis". However, both examiners are very established in my field (also Software Engineering), and none of them complained about the literature review.

I'm surprised he or she did not encourage you much sooner to include more recent literature. Other than seminal work, often including research older than 3-5 years is discouraged by advisers. I don't think you can get around "modernizing" your literature review and always do what your dissertation chair says if you want to finish on time!


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How do I handle a colleague's gender change when citing their paper?
We are currently working on a conference paper where we plan to cite and discuss a paper as a related work. It was written by a colleague at the same university who has kindly offered to help us understand its specifics.
After publishing said paper, the colleague has changed name and gender. For example, suppose that the paper is authored by George Smith and she now uses the name Mary Smith (not the real names). The problem is that she insists that her new name/gender is used everywhere, including our citation of her publication. She explicitly asked us to change the citation from G. Smith to M. Smith.
I’m not sure how to handle this. The publisher still lists George as name as do most citation data bases. Our scientific handbook demand that external sources should be cited as precisely as possible and should not be modified. (I asked about this specific case and got back a multi-page document that stresses the importance of respecting gender identity [no problem for me] but the document does not address this issue.) On the other hand, the paper has a distinct title, journal name, volume, number, pages and a DOI so everybody should be able to find it, even if one author is listed as M. Smith instead of G. Smith.
Do you have any advice on how to handle this situation? Would a change from G. Smith to M. Smith be acceptable/reasonable?

Comments are not for extended discussion; this conversation has been moved to chat.

Related: If you change your name while doing research, can you list both names on a publication? and Citing an author who changed his name

I wonder if there is an established procedure for women who change their name after getting married. Perhaps that procedure can inform this one, although the sensitivity issues are most certainly different.

Is it an option to ask M Smith if she would be ok if the first citation were to read as the following?

Smith, M. (published G.) 2014, recent advances in foo, international journal of foo sciences 12:56, 427-865

This would eliminate the only reason I can think of for misgendering the person, namely that readers might be unsure whether they are looking up the correct source. This would be a weak reason, though, since we have DOIs (Digital Object Identifiers) now.
Edited on second thought: What is the worst thing that could happen if you use the new name? Someone might find it more difficult to look up the paper; that's a minor inconvenience. Compare this to the frustration, if not anger and distress, that it would cause M. Smith to be referred to in cold print by a name that doesn't reflect her identity and that she is struggling to leave behind.

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It's been a few years and I've now voted to delete this answer. (Apparently I can't unilaterally delete my own answers once accepted.). There is at least one much better answer now, written by an actual expert on gender transition in academia.

@henning You could also edit your answer to reference the other one. (I'm not sure which one did you mean actually. Also, props for acknowledging.)

One of the primary goals of citing literature is to help others find that literature. Citing a paper differently than it exists in a journal is antithetical to this goal. Unless Smith changes George to Mary on the article you are citing, you should cite it as it exists.

Yes, but suppose a Russian whose Russian papers had been transliterated under the name Chaikovskii suddenly started publishing in English under the name Tchaikovsky (very similar things have happened). Isn't having half her papers under one name and half under another name in the bibliography even more confusing?

@PeterShor Only if you are using the citations to figure out which papers were written by the same author...

The point of a citation is to serve as pointer to an archived piece of literature, nothing more. It's not there to reinforce or undermine anyone's gender preference, fluff egos, compute h-index, Right Great Wrongs, or anything else.
I will copy the citation as it appears in the cited journal, with the author names exactly as they appear in that journal. If the authors do not like the way they are cited by the journal, that is between them and the journal.
As for the gender, no gendered pronoun needs to appear in your text in the first place.

Honest question: does that matter when the literature (or at least the correct info) is only a Scholar query away? Just look for the title in quotes and be done? I'm sure that fails in other fields, but I have no clue what's the status.

This is not universally true. Remember that author's name is not mandatory for a journal citation. Only mandatory fields for a citation are: (1) journal name or abbreviation, (2) volume (and issue number given each issue starts on page 1) and (3) page number of the first page of the journal.

@PeterShor APA style handles this: you cite what was published, but can sort based on person (although they are a little unclear as to how much sorting leeway you have).

@PeterShor That is the usual case. It is the case for women who change their names on marriage and then publish under their married names. The citation goes under the published name. A reprint may be published under a different name than the original for this reason. [Not everyone changes her name, obviously. Not all who change their names publish under their married names. But it certainly happens.]

This is really making a mountain out of a mole hill. Do the thing that will make the author happy. Even hyper famous papers have all sorts of oddities and mistakes in them; it is likely that nobody is even going to notice this. On the subject of citations:

I thought myself a good typo spotter, and yet it took me a minute and some googling to figure out what was wrong about that journal!

@LeonMeier "Brain" (part of the central nervous system) vs. "Brian" (a first name).

I suggest doing the thing that makes the publisher happy since they are going to change it in the end to match their style guide.

To be fair, it's not making a mountain out of a molehill. It's making a StackExchange question out of a moral dilemma. People have done far worse with their time and got less out of it!

@StrongBad well if the publisher changes it you can apologise to the collaborator and say it was out of your hands. I don't think the publisher will notice this though. Clearly 77 "Brian"s got past a publisher, and I've seen a lot worse. Really the only person who will notice is the academic with a gender change, and if the OP wants to keep working with them it would be best to stay on good terms.

SCNR: as of 2021-09-06, there are now 105 results for "Experimental Brian Research" on Google Scholar. The field is developing nicely.

Do you have any advice on how to handle this situation?

Name them exactly as in the publication, using the old name for publications before the name change and the new one for publications after the name change. Your scientific handbook requires that, the conference organizers or journal publishers (or the citations style1 they mandate) will probably require it and it is the common convention in scientific writing for practical purposes: References are (primarily) for re-finding the source work itself, not (primarily) for re-finding or identifying its authors.
References are, in many citations styles, highly redundant for a reason: Keeping their function to accurately point to the source work even in the case of accidental errors. Relying on the redundancy to suffice when introducing deliberate changes is counter-productive.
Thus, the only case when you could cite an old work under the new name would be if it has been re-published under the new name and is thus findable under the new name, too. (This sometimes happens when originally pseudonymously published works are published again under the author's canonical name after they claim authorship for their "true" identity. Probably more common with fanfiction than with scientific writing, but not unheard of there either, I assume.)
This means that in this case, this isn't really your own choice to make.2 The same rules apply whether someone changed their name due to marriage, due to becoming a monk or nun, due to being elected pope and also when authors didn't change their name per-se but just published different works under different names (like the already mentioned pseudonyms). So ask your colleague to please not take it personally when you disregard her wish in this case and that you are happy to respect her preference when referring to her outside of scientific citations.

Would a change from G. Smith to M. Smith be acceptable/reasonable?

As harsh as that might be on your colleague's feelings: No, this wouldn't be acceptable, especially not if rules (like the handbook you mentioned, and probably more rules by the journal publisher etc.) apply, that clearly state that it isn't and it wouldn't be reasonable to ignore or willingly violate those rules.

1 You didn't say anything about the citations style mandated or used, but for the example of APA Style, this blog post on the official APA Style blog covers name changes, explicitly including changes due to gender changes.
2 Unless of course the different rules that might apply disagree. But even then, as the journal publisher has the final say about whether your paper will be published especially concerning formalities like this, ask your publisher which rules take precedent.

I advise you strongly to use their new name and gender. Especially in the period right after the change, she's very sensitive about this. It's very upsetting when people remind you of your previous gender and cite you with your previous name. After thirty years, it doesn't matter that much. Today, I wouldn't care any more.
I ask of you to not consult the person about it. She needs all support she can get, citing her by her right name without asking her will make her feel good.
I speak from experience: been there, done that. I wrote papers and publications before and after. People have always handled this in a way I appreciate: by using my after-change gender and first name.

There is strong precedent to cite published research as it was published. Is sensitivity a compelling reason to break precedent?

I'm just saying what I prefered when I was in the same situation. I must say, my current name isn't that different from what it was before, for the reason you mentioned.

In my field, initials are often used instead of first names. That was smart to only make a small change :)

That helped me in most cases. And afaik, nobody reading my name didn't immediately know I was the same person with the name that differed only in the last two letters.

I wish I could plus this for being insightful and appreciated without possibly being the best resolution to this question.

The first answer suggests asking the person. Whatever is decided, that's the worst thing to do.

Can you cite or give quotes from specific journal editors who approved of changing the citation name?

@chessofnerd Such precedent is not strong at all, for instance Don Knuth prefers to have names in citations as complete and as precise as possible, no matter how they appeared in the publication. And also, the names are not even mandatory for a reference, so I don't understand the big deal you make out of it.

@curiousdannii don't know anyone who says to change names, but APA specifically says DO NOT change the name.

@StrongBad That's why I'm asking this answerer, who says they've been able to do it before.

Asking the person is irrelevant: the person requested the change on reading (presumably) a draft.

Upvoted for the suggestion to not discuss this with the person.  That's valuable info that wasn't obvious to me, or apparently to most people.

@curiousdannii Although i am not much in favor of this, it looks like some journals are allowing name changes in previously published work. There is a science article on this just published today.

Very similar things have happened previously. The following really happened, but the name has been changed.
A Russian whose papers had been translated under the name Chaikovskii suddenly started publishing papers in English under the name Tchaikovsky. So his papers in old translated Russian journals all have the name Chaikovskii, and his papers after he started publishing in English all have the name Tchaikovsky. Would you really want to list half his papers under one name and half under the other? That really would be confusing, especially since the two names are quite far apart alphabetically.
What people sometimes do in this instance is list all his papers under the new name. Sometimes they put something like (pubished as Chaikovskii) in the reference and sometimes they don't.
I don't really see why we should treat transgender people worse than Russians.
I would recommend people do the same thing in this case. List all the papers in the bibliography with her new name. Add (published as G. Smith) if you feel people will be confused by the change of initials. When your colleague becomes world-famous and has many publications under the name M. Smith, then G. Smith will be the confusing citation.
If you really feel that academic honesty requires you to list the paper as G. Smith in the bibliography, then depending on the reference style the journal requires, you could use

M. Smith [G. Smith 2016] showed that ...

or

M. Smith [6] showed that ...
References
  [6] G. Smith, "paper title" ...

About the name change causing confusion: a very famous computer scientist insists on listing everybody in his bibliographies with their full names (Xavier Yawkey Zacharias Jones), even if they put just Z. Jones on all their publications. This has not caused widespread confusion.

You would want half of them cited under the old name because that's what you need to search to find them.

@immibis: A citation has a journal, a year, a page number, and often a title. You don't actually need the author's name to find the paper.

@immibis:
The papers in Russian journals appeared under the name Чайко́вский, and that never changed. It's only the English translations (which were regularly published by Western publishers in translated versions of the journals a year or two after the Russian versions) that used the name Chaikovskii. And many citations of them indeed use the name Chaikovskii (although remarkably, Google scholar actually has some of the translated versions that were published with the name Chaikovskii filed under the name Tschaikowsky).

@immibis:  Should you cite the author of Laughter in the Dark as "Vladimir Nabokoff" and of Lolita
as "Vladimir Nabokov"? Does anybody? And if you're writing his biography, do you use the first spelling for the years before 1940 and the second for the years afterward?

I think your last comment mixes two things. One is citing a work as it appears. The other is referring specifically to a person. While I see the arguments for keeping the old name in the citation (not that I can make up my mind on what I would do myself in the situation), certainly one should use the current name when referring to the person.

This does not really matter in this discussion, but AFAIK Tchaikovsky in Russian is a name used for a male person, whereas the female form would be Tchaikovskaya. So your use of the pronoun "her" in your example confuses the matter.

@Tobias: a problem may be that when you write the text, for some journal styles the citations are of the form "Chaikovskii [1973] proved Tchaikovsky's theorem." I would say that in this style, you are referring to a person as well as a reference.  But I suppose you could write "Tchaikovsky [Chaikovskii 1973] proved Tchaikovsky's theorem."

@cfh: fixed. I changed the gender back to male.

@PeterShor In your second paragraph, you wrote "Tchaikovsky" and then "Tschaikovsky". You have also used both spellings in comments (as well as "Tschaikowsky"). Are there several spellings for the "new name"? (also : you have forgotten an "l" in "published as Chaikovskii")

I'd go for this. Use M.Smith in the article, use G.Smith in the reference list. Or even "G.Smith (now M.Smith)" in the reference list.

Use the name the author prefers. There is little chance of confusion. In a given citation style, there are at least three and possibly more separate factors pointing toward the correct citation: 1) author's last name, 2) actual page/volume citation, 3) doi, 4) article title, 5) author ORCID id in case of name confusion.
Beyond simple courtesy (search "deadnaming" for how seriously many trans folks take this), the arguments for using the author's preferred name are internal consistency and Google-ability.
1) You are going to be using the author's name in many different contexts. For instance, in the acknowledgments, you will say, "We thank Mary Smith for helpful discussion of her paper, Ref. 24" (as Mary has requested you use her current name, and you're presumably not a jerk.) If Ref. 24 is attributed to George Smith, you have confused readers just as much as if you cited "M. Smith," and they later found G. Smith. You may also want to use her name within the paper body - "Work by Mary Smith's group..." (though here it might be more common to say "Smith et al.").
2) Sometimes, readers (and especially people who hear talks) don't check citations. They just hear you say, "Mary Smith at University of X" and google that. The same applies when you repeatedly refer to someone's work by their name within the paper. You want that name to lead to the current online presence - presumably in the author's preferred name.
As a side note, telling trans authors that preferring their current name means they "don't like facts" or that changing a citation to match the current name is ignoring "professionalism, scientific fact and established standards" seems a wildly disproportionate response to a fairly straightforward request. If someone said, "By the way, I know that the original paper spells my name Gorge, but it's really spelled George, we never got around to issuing a correction," what would you do?
Edited to add: I looked up a trans friend's research in the standard archive/search engine for her field. Because she has gone through a formal name change process, most of her pre-transition papers are listed under her current name. If you searched her deadname, you do not find those papers. Using the author's current name is not just polite, but the only way to not be misleading here.

"You want that name to lead to the current online presence" - that depends. Especially when looking at a citation, a reader may be more interested in works by the same author from around the same time, when they still used to call themselves "G." "the original paper spells my name Gorge, but it's really spelled George" - that seems like a different case, given that "Gorge" was already considered incorrect at the time of writing. Even so, the spelling mistake would have to be highlighted, thereby calling additional attention to the gender change (which, according to others here, might be bad).

No matter what time period you are interested in, you probably still want to know the author's current affiliation. It's not like their papers will drop off of their webpage or CV! In the cases of the trans researcher I know best, searching for their original name would get you nothing useful unless you were literally searching the internet archive.

+1 for mentioning ORCID id. I'm not sure whether ORCID have a policy for name changes, but I suspect that this should be treated in the same way as a more familiar name change would be.

Some people still need to find papers in printed, bound journals in libraries ....

TL;DR: I have this problem when citing my own papers.  I concluded that I'm citing a paper, not a person, and generally cite my old papers as they stand (example below).  However, if someone asked me to cite their papers in a certain way, I would do so: it's a minuscule cost, and makes them feel like you value their identity.
I feel the worst option is to cite both names: this "outs" them, and permanently reveals personal and identifying information.

Basically, there's four five options, and we'll weight up the pros and cons:

Don't cite the paper.
This is just a workaround, and is probably not appropriate unless the paper is only tangentially relevant.  It might also only be a temporary solution (i.e., the problem might arise in your next paper).
Cite the paper as it's published.
This is what I do in my papers.  For example, in Partial Latin rectangle graphs ... (DOI), this is how I cite my papers:

After a not-small amount of reflection, I eventually came to the conclusion that I'm citing a paper, not a person.
The consequences?

People who don't already know about the transition, do not realize papers under the old name are my papers.  At conferences, people ask if they were published by my brother or husband.  They don't equate "that name" with me.
Realistically, most people are going to cite the paper this way without asking me.  They simply don't know about what's happened since then.
These citations do not stand out as abnormal.  It's more private.

Cite the paper under the author's real name.
If someone asked me to cite their name in a particular way, that's what I would do.  If you don't do it, you're acting against their will---it's a violation; you're joining the chorus of people who declare that person has little worth.

I know personally how painful this can be first hand.  E.g. I went a bit crazy at my former supervisor when he had "that initial" on a talk slide.  (Sorry Ian.)  Things like this have made me seriously reconsider staying in academia.
Early on in a transition, virtually everyone constantly contests your gender, and your identity.  Every day, you're required to demonstrate that you are who you say you are.  You cannot give people the slightest hint that it's acceptable to deadname you---people will use it as evidence that you're identity is not genuine, and use that as a reason to not treat you with basic human dignity (and encourage others to do likewise).
As transition progresses, and you become more established in your gender, the people who contest your gender become the "fringe".  If someone contests my gender nowadays, people will just think they're being an arsehole.  The need to defend one's gender decreases over time.
Also, have you seen how many errors there are in published references?  One character is going to go unnoticed.  (In only the most contrived circumstances will someone be hindered in finding a paper because of this one character.)

Cite the paper under the author's real name, and mention it was published under a different name.
I recognize that this is currently the top answer.  I respectfully, but strongly contest this: I consider this the worst thing to do.  This outs them, permanently.
The norm in academia is not to reveal personal and identifying information; it's considered unethical to do so.  That's what this amounts to.
Show them this post.
At the risk of sounding arrogant, perhaps you can consider showing the person this post.  It might change their mind.
If not, I'd go with what they wish.

Thanks for taking the time to write this answer, and the other answers you've given on similar topics. They've been very informative for me, and I'm sure, many other people.

You're weighing up factors against vs. in favour of a particular action, namely using your colleague's new initial.
Points in favour:

Your colleague feels strongly about it
Your colleague has explicitly asked you to do it
It meets social norms regarding trans peoples' names
When you asked for clarification of the regulations, you received a document stressing the importance of doing it
It would show respect for your colleague and help your working relationship with her

Points against:

It's just about conceivable that the discrepancy in the initial could cause someone to fail to find the paper, for example if they try to look it up using a system that doesn't return partial matches, and if they then don't follow it up by Googling the paper's title, looking up the journal issue it appears in, etc.

If that last possibility happens, it does hurt your colleague's career a little bit (it's a potential loss of a reference to her work) and you're right to worry about it. However, you should know that it also hurts your colleague's career if you cite her under a name that she no longer uses. For example, what if a top professor loves the paper by G. Smith but passes over a job application from M. Smith? That would hurt her career a lot more.
As a general rule of thumb in such situations, you should trust your colleague to have weighed these up and made the right decision for herself. After all, she's the one who's made the huge decision to go through a gender change and all that that entails; she has her reasons for this and she knows a lot more about the consequences than you do. She's made a specific request of you, and if your concern is for her career then there's nothing to do other than listen to her and act on it.

Well, this whole depends on how you do feel. Any discussion about whether the reference is "correct" or "possible to follow" are rubbish, for two reasons:

You can list both names, at least in the references. You can actually do this for any person with two names, even in cases of Kucherov/Kutcherov, even in cases of maiden names, whereever you wish. The way how you do it is discussed in the other answers. And once the references contain the correct information, you can divert in the text itself, because either people know what work you cite or they will have to check the references anyway. I also translate titles of cited works into English and provide both, if the reference is not in English.
Names are not even a mandatory part of a reference. So while it's confusing to put the wrong name in the references, the reference should be trackable without the name, based solely on journal title, volume and page. Based on this, even the citation services such as ZB, AMS-MR, ISI or Scopus should be able to pick up; if not, a manual correction is always possible.

So in my opinion, it's up to you. I personally prefer to provide as complete and as current authors' names as possible, but this is really just a preference. The only problem could be if the journal insisted on providing the reference "as listed", which sometimes could even be an automated thing. I'm afraid that in that case you'll have to comply with the rules or draw the submission, but even there you can of course try to push, depending on how you feel it.

Whether names are a mandatory part of the reference depends on the style, which will be determined by the publisher/journal. In my field, author/year is common. I've never seen a journal not require name. And I have had journals/publishers query citations when they checked them.

Great point of listing both names. I have never seen a citation style in which you are not allowed to add your own notes to the citation. You could say "Smith, G. Advanced Deconstruction of Spline Reticulation with Respect to Post-Castro Cuban Foreign Policy. Journal of Splines. 1:34. Note that this excellent article by M. Smith was published under the name of G. Smith."

Disclaimer: I'm not active in the field of academia itself.
As others have mentioned there is clear precedent and standardization across this field, and for good reason. It's a field based on fact and evidence and incorrect citations could damage the standing of the citing paper, as it could thus be perceived as incorrect or of lesser quality.
As a reader, It's exceedingly frustrating to not know exactly if I've looked up the correct source, if its because there's a typo in the name, or a namechange, or because the citing paper is simply incorrect.
Diverging from this, purely for social and highly personal views of the individual, even if said view might be shared by a larger percentage of demographics should imho be avoided.
The whole idea that she considers herself to be a different person now, only makes this case stronger and when one considers identity in "Gender Identity" then it is in fact he who wrote the paper, not her.
Yes, the views of said colleague should be respected, as in, one should treat her views with respect, but not as in, her desires (or perhaps demands) should thus be met. That is certainly not what respect means.
Especially in fields such as these, professionalism, scientific fact and established standards, do not and should not be set aside or diminished for volatile social norms, as by definition, they can not be considered set in stone. Bending semantics (or reality) so as to fit the current social norm (if it's a widely accepted norm or not is of little consequence), especially when the field is supposed to be unbiased, neutral and factual, has no basis in a field such as this, if anywhere else.
As a pragmatic solution to your (or her) problem: In other fields, e.g. arts/entertainment, a place where names often change (be it in the form of stage names or changing family names), citations and credits are written in the form Jane Doe (as John Doe). I don't know if a similar construct would be applicable or desirable in the field of academics, but it seems like a sane approach that reflects both past and current situation, without doing the author of the cited paper any injustice.

I doubt that "she considers herself to be a different person now." A transgender person doesn't "change genders"—they change their name, pronouns, and outward expression (or some subset of those) to match their actual gender rather than the gender they were assigned at birth. That's what gender identity means—not how you present externally, but what you are internally. The person who wrote the paper is the same person with the same gender as the person who now publicly identifies as female.

I can also see merit in that point of view. However, in that case I would argue that it is indeed just a change of name and gender pronoun, and less heavily loaded. And as such, the name and gender pronoun under which the article was published, should be the correct one, as that reflects the state of the article when it was published. Same as any other name change, where gender pronoun or identification would not have been a factor. Without going into the semantics of what actual and assigned gender would even mean, as I'm sure it means different things to different people.

I agree, more or less.

The facts, such as they are, don't require the use of a particular gender pronoun. The paper does not state the author's gender, I assume. Just a name. So there's no reason not to respect the author's preference regarding pronouns, even if there's reason to resist her preference regarding name. That particular names are gendered is itself just a social convention, so unless the original paper specified its author's gender, the published paper by itself cannot possibly determine which pronoun should be used.

Our scientific handbook demand that external sources should be cited as precise as possible and should not be modified.

So you cite the policy, and then explore violating this?
For me, DSVA's comment:

This problem also occurs if you change your last name (usually because of marriage). The correct way to cite the old papers is using the old name.

clearly provides the longstanding approach.  People being unable to find information in a database is a real, impacting reason to not pretend like history was something else.
Just because Smith made a decision to change his name is not compellingly professional reason to disregard established data entry standards that provide useful benefit.
I present to you an analogy: If United States President Ronald Reagan, in the final years of that person's life (which happened in 2004), quickly completed the official legal process to have that person's name changed to Rhonda Reagan, would you expect historical documents to change?  For that matter, would you even expect modern texts to say "Rhonda Reagan won the election and she became the next President"?
Doesn't this student's non-fictional request boil down to exactly the same thing as that fictional scenario, which is asking for reference to what historically happened to be referred to different, based on the person's more recent decisions?  Re-writing history is not desirable.

Would a change from G. Smith to M. Smith be acceptable/reasonable?

This change would not be acceptable.  Academia has a goal to prepare students to enter a workforce that often has long-standing established expectations that workers are demanded to abide by.  This goal permeates academia's culture, official policies, and often even coursework grading criteria.  Many students struggle with some of the expected formality, and the demands can feel more traditional than what the students prefer to experience.  Yet, students are expected to adapt if they want to achieve high marks (or even passing marks).  Changing established procedure about name handling, just to accommodate the author's wishes, goes directly against academia pursuing this goal.  That is why this change is not acceptable.
Like other professional environments, academia isn't necessarily the most appropriate platform for people to try to push their own desires, even when those desires may reflect goals that are in line with a currently-popular social stance.

Do you have any advice on how to handle this situation?

Yes.  Resist the author's attempts to get you to overlook the person's name at the time of publication.  The proper response for improper requests is resist.  Decline the request.
Although such a change would be considered desirable by some people, in some environments, academia includes an amount of formality and demands that students accommodate society's expectations, not the other way around.
As policies should be able to be flexible when needed, the motivation of this request may have a significant impact on deciding whether the request should be agreed to.  The motivation for this request appears to be driven from personal interests that are off-topic of most academic subject material.  Therefore, granting an exception to general policy does not really seem to be in academia's best interest.
If a person wishes to have this procedure changed throughout academic culture, the desirable way to do this is not to make a request that an academic institution change long-standing institution behavior just to make a single individual student happier.  So as to not provide an open door welcoming the next person to come up with a reason why policy should be set aside to fulfill personal desires, this request should be declined.

Comments are not for extended discussion; this conversation has been moved to chat.

Depending on how your citations are formatted, you will probably find the initial doesn't matter. For example, a reference listed as:
"Smith, M; Bloggs, J; Jones, A; Brown, B. J. Foo Bar, vol 6, p. 200, 2014."
is unlikely to be difficult to find even if a single initial is different and there's no DOI included. A reader will probably assume the different initial is just a typo, if they even notice it at all. The discrepancy is very minor.
If I saw that reference listed on a paper and tried to look it up I'd mostly use the journal details and publication date to find it, then author surnames as a cross-reference to make sure I'd got the right one.
If you really feel the different initial could be confusing, drop it entirely. Her surname hasn't changed, so by using that on its own you won't confuse any readers who find the names don't precisely match, nor will you be misgendering or deadnaming your colleague. Whatever you do, don't use her old name/initial. This would be exceptionally rude considering that not only do you know what her new name is, but she has also explicitly instructed you to not use her old one in this context.

Downvoted: The old initial was considered appropriate at the time the cited paper was published, so that's what the citation must mirror. The only possibly rude aspect I can see here is for the cited author to expect others to produce a mismatch between cited name and name actually found in the cited work and its metadata.

@O.R.Mapper, although you are the obvious way literally correct, it is my impression that "the change" that trans people go through is so severely upsetting (even if a change for the better) that I'd prefer to "rewrite history" to match...

@paulgarrett: I suppose that's the issue then. I do not believe one can "rewrite history" by modifying a bibliography item - all one can achieve by that is pretend history had been rewritten and thereby create a lot of confusion and mismatching references. I consider causing these effects unethical (and, come to think of it, I consider the entire idea to "rewrite history" in the first place at least as ethically very questionable).


text:
What would be the best way to find foreign professors for a PhD defense panel?
I need some researchers to review my PhD thesis. I am from India and my university is also in India; the research data was collected in India. My university rules say my thesis should be reviewed by experts from the same field and another country before submitting it.
Question: What would be the best way to find specialists in a specific field to participate in a PhD evaluation panel or as reviewers? Should I just leave it to my supervisor?

Unfortunately this isn't a suitable question for this site. You should really discuss this with your supervisor.

Welcome to Academia.SE. I have edited your question in order to comply with the rules of our community. I hope that the answer for this question may also help you.

I voted to reopen your question as I think it is answerable now. Still, it may help if you [edit] your question to include further details regarding your university’s regulations: 1) Why would you need experts to review your thesis before you submit it? Shouldn’t your thesis be submitted/transmitted to the reviewers so they can review it? 2) Why is the origin of your data relevant? 3) How can a thesis be an “international paper”?

My university rules say my thesis should be reviewed by experts What are the criteria your university use to determine the people you find are experts?

In this case, you can find the researchers/professors from the references that you used most in your thesis. This is the best way to find the experts in your area to evaluate your thesis. Then, you may give the list of experts to your supervisor for further processing.

Given that you've written a thesis on the topic, you should know who the experts are.  They are the authors of the papers you read and cited.  Hopefully you have also met them at conferences.  Of course, your advisor should also know these people.


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(How) can you teach a subject effectively for which you are a skeptic without biasing students?
I recently accepted a tenure-track position at a university and will be on a 1-1 load my first year. My first course I will teach, I will get to modify and alter based on my expertise.
In my second semester, I am taking over a graduate course that was taught by a previous faculty member. This course is over a concept that I am extremely skeptical about. The prior professor, who taught the course, is a prominent supporter of the theory and has written articles and books on the subject.
So my concern is that my own biases could bleed out into the class.
My current plan is the following:

First half of the semester: teach the course close the the prior syllabus with some differences.
Midterm: present the evidence as to why I am a skeptic.
Second half of the semester: students either provide evidence in the form of a literature review supporting or objecting to my skepticism.

A little background, I was brought into the department for my computational strength, productive research stream, and subject expertise. The thing is, the subject expertise has nothing to do with this course where I am a skeptic. So I feel a little bit like I would be being unnecessarily disruptive to an already established department curriculum. That said, the faculty member who pushed this subject recently left and I do not know if anyone else in the department is as passionate about it as they were.
I hesitate to outright say the topic due to not wanting to be unmasked. But it can be thought of like this: The idea has a solid foundation built on strong empirical evidence and results. This foundation is largely agreed upon by the field. Where this foundation is not nearly agreed upon is a certain abstraction/extension of this foundation. I believe that this abstraction/extension is trivial and also ill-defined. Others in the field believe that this extension is an important area of study.

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I almost downvoted for intentional vagueness about the field, but then read the last paragraph and held back for now. I think the question would be greatly improved by being up-front about that matter, because "skepticism about a subject" is so frequently a matter of willful error on the "skeptic's" part, and failure to address that right away leads readers of the question to believe you're asking for help doing something many of us would classify as pedagogical misconduct.

What "skepticism" means to an academic is strongly field-dependent.  I am a mathematician, and I would have thought that true skepticism is almost impossible: after all, mathematical results are proved and any standard course would be on things that have been proved, reproved and combed over by the community several times over.  I could however be skeptical of the future trajectory of a mathematical subfield: i.e., maybe I think it is not worth the students' time to learn it.  But this is just a way of saying that I have very little interest in that subject, so...why then would I teach it?  I suppose that's one of the luxuries I have as a tenured faculty member in a reasonably large department.
So I looked at your profile, and I am interested to see that your field is...statistics.  So, hmm: again I wonder what you mean by "skepticism."  Do you mean that the course concerns a statistical technique that is mathematically valid
but whose usefulness is vastly overstated or is typically applied outside its range of validity, or a statistical practice that is actually not grounded well in theory, or...what?  I would think that "belief" has little to do with statistics, but perhaps that is a naive pure mathematician's belief.
On the face of it, if the course is in subject X, then spending some of the course covering X, then in the middle revealing that you don't believe in X, then spending the remaining portion of the course having the students decide which is right sounds, well, weird.  It is liable to leave them wondering why they took the course at all.  Indeed: why is this course being given? You said that there was one "believer" faculty member who is no longer in the department, so...who wants the course now?  Inertia is not a great defense for an academic position.  As a new tenure track professor in your department, in theory you should have some say in the programmatic offerings and also some responsibility.  In practice, the responsibility lies much more with senior people than very junior people.  I recommend that you contact faculty mentors and discuss your concerns with them in a mild way, making clear that you will do what they think is best.  One idea is to propose replacing the course with a totally different course in a subject close to your own expertise and enthusiasm: other things being equal, that sounds like a much better course.  If however the department is really committed to the course: well, you said you would do it, so I would suggest that you really do it, and not include skepticism of X as a main part of the course.  You can rest easier at night knowing that you offered the department some alternatives.  Speaking as someone who currently has an administrative role in my department: believe me, I am painfully aware that on a wide range of topics, "the buck stops with me."  That is my problem; as someone who has not even started the tenure track job, it is not yet yours.

Thank you for your insight into this. I appreciate especially the final paragraph. Also, if you would like to see a lively amount of skepticism among statisticians, witness an argument between a bayesian vs frequentist. Lively debates also involve such topics as: weights, separating variance associated with a group from the individual, and overfitting.

@JWH2006 Bayesians vs frequentists was also my first thought. But amongst people who actually understand both, there doesn’t actually seem to be much conflict; except maybe about the degree to which either mindset is useful in specific applications.

Surely pure mathematicians can be skeptical of the status of outstanding conjectures. (Or possibly what foundational axioms are best/required.) Example 1. Example 2. Example 3.

@KonradRudolph Note that the major conflicts seem to be simmering down, but my understanding is that this use to be a far larger point of contention - see Andrew Gelman's Dr. Seuss-style parable: https://statmodeling.stat.columbia.edu/2018/12/06/parable-regarding-changing-standards-presentation-statistical-evidence/

@DanielR.Collins I don't think outstanding conjectures are typically taught at undergraduate level. Only waved over for interest. I've never heard of any strong debate over the Collatz conjecture for instance.

@DanielR.Collins Sure, but the actual content of a course on conjecture X is probably wholly unrelated to one's opinion on the truthfulness of the conjecture. After all math is math, and if it's proven, it's true. If it's not proven, why are you teaching it in a course?

I guess the only "true" skepticism possible in mathematics is skepticism based on philosophical views about mathematics, e.g. a constructivist having objections over a theorem proved using non-constructive means... Bayesian vs frequentist also falls into this category I guess.

Some commenters are claiming that open conjectures aren't addressed at the undergraduate level. But I have "open problems" (conjectures) sections all through my mass-market freshman Discrete Mathematics textbooks, et. al. Moreover, the question at hand is about a graduate class.

@Daniel: Mathematical conjectures don't seem to be a good analogy.  Sure, I can have different beliefs regarding conjectures than my colleagues -- a few years ago, a collaborator of mine wrote a paper giving a heuristic arguing against an important conjecture in our field.  I tend to still believe the conjecture, but....so what?  The paper is interesting and valuable either way.  If you are skeptical of, say, the Riemann Hypothesis, then you will not be interested in theorems that assume it, but this is a difference in taste.

When you discuss open problems in your math class, you don't attempt to convince the students that the problems have a certain solution without giving a proof, do you?!?  It seems to me that that would be an analogue of what the OP is talking about.

Per Example 2 above, on the day after Atiyah's attempt at presenting a proof of Reimann last fall, I specifically said in class that many mathematicians seemed skeptical of it. Per Example 3 above I might cite Minhyong Kim and quote, "Mathematicians who are already skeptical of Mochizuki’s abc proof may well consider Scholze and Stix’s report the end of the story...". Etc.

So, I think a better analogue would be this: Hypothetically, say that the faculty member who recently left is Michael Atiyah, and that he was teaching a graduate seminar on the history of the Reimann Hypothesis, culminating with the proof he publicly presented in September 2018, asserting (as he did) that this was now a solved problem. One could not say that this result has been "proved, reproved and combed over by the community several times over". If for some reason the department considered this to be one of its crown jewels, then I could see someone like the OP being in this bind.

Regardless of the subject matter, you (and every teacher) should be teaching from a skeptical point of view.  One of the most important things students should learn is that no claim should be accepted without justification.  Otherwise, it's not education but rather catechism.
This doesn't mean you should disparage the previous professor's point of view. It just means you should feel free to present alternative positions and defend them -- or better yet, assign the students to defend one side or other of the situation.
OTOH, if the course title is something like 'Effective Use of Astrology in Selecting Short Positions in the Stock Market,"  then by all means disparage the entire course.

You're right. Astrology is far too serious a field to be applied to economic forecasting!

Depending on the belief system of your senior administrators, your disparagement of Astrology may result in their Boötes coming into opposition with Uranus! :)

I had a seminar where I asked a (speculative) topic to be presented. A student picked the topic, but said, he does not believe in the hypothesis of the paper. I said, fine - present it as accurately as possible, and then the counterargument.
Good science is not just about canned facts, but about the process to get to these facts and if the topic is still being researched and knowledge still "in the making", exposing the uncertainty in current knowledge is beneficial to the education of the students. There is otherwise a tendency to accept lecture material as raining down from heaven rather than the compressed understanding of past knowledge by the scientific community (which can, of course, shift).
You have the opportunity to make it about the scientific process rather than the particular topic. This is an honest take on scientific education. I assume mostly natural science, but I personally believe the principle should at least to some extent also apply to a well-run humanities stream.

Well, you are admittedly heavily guarding your subject details.  So, I'll just make up something that's very controversial, but something we can all relate to.
Suppose the course is called "Why God exists", and you are an atheist.  Ok, obvious conflict.  So suppose you determine that the syllabus of the course includes several topics which define the main course.
Perhaps, then, your method of teaching must change.  Tell the students outright "You're here to learn why God exists, but I don't believe he does".
For some students (and I bet a few commenters here) that can raise the hackles, "How dare you", "Are you here to teach against what I believe", or they conjure up some other ulterior motivation for you.
So you cater to that, just as if you are engaging in a debate contest: a subject you must argue for or against, despite your personal beliefs.  To do that in a competition is admittedly different than in a classroom setting, but that's the point: you need a method to teach a subject for which you have a bias against.  One way is to force the students into a debate by way of essays, demonstrable proofs, physical exertion, or maybe even an actual debate - and all topic by topic according to the subject's syllabus.
If you are up front about your bias, your students should not feel that they've been cheated at the end of the course.  Or maybe they've changed their minds.  Either way can't be bad.  But if at the end of the course, they then find out about your bias, then they wonder if they've been taught all that could have been taught.
I would offer that you adopt a methodology that the mob uses: keep your friends close, but keep your enemies closer.  Allowing the students to know of your bias can be better than them knowing you are fervently in support of them, because they may want to go the extra step of proving you wrong.
I am a martial arts instructor, and this subject comes up all the time.  Personal biases - instructor and student - can often collide and become an issue in class.  So, make the students prove their point.  They'll be forced to research and argue.
So it goes something like this: "2 + 2 does not equal 4. Prove me wrong. I can prove I'm right."  In order for them to prove you wrong, they'll have to first find out what your proof is: that can only be done one of two ways.  First is to research historical ways you might be supporting.  The second is for you to tell them.  Either way, that research can be very educational.

I don't see much wrong with your plan.
It does of course depend on the subject matter... Trying to be skeptical about gravity (engineer's joke: gravity is a myth, the earth sucks... :) ) is one thing - but skeptical about other "theories" which are held to be "true" until something better comes along, and it normally does, is not a crime.
If you explain your position and why, then the students can evaluate their position as per the second part of the semester.
It will be more interesting for you developing the assessments to avoid bias... But that will be part of your learning curve.
I don't think you have much to worry about - you are already considering both "sides" - if you held the position that the other side did not exist then the students would have an issue.
Best of luck.

First time I heard someone gripping about the earth. Wait, I mean griping.

Your plan is good. However, I might do it slightly differently. I would start by identifying what issues/problems this theory can address/solve. I would also clearly outline the set of possible theories etc. that can also address this same set of questions/issues/problems. Then:

I would begin my course by defining the questions/issues/problems and situate them within the broader context of the field.
Introduce and teach this theory as a potential solution. I would be clear about perceived strengths and weaknesses.
Introduce alternative solutions in the same manner.
Have my students take a well-reasoned stand on a particular alternative. Or take a well-reasoned stand on how/why/when to select among alternative solutions.

I had to be general because you were general. But i think that this is a viable format for discussing unsettled and possibly contentious areas of resesarch.

I believe the answer is very simple and deductive.  Have your students provide counter-arguments themselves to the exact prior syllabus. That establishes a zero prejudice solution while providing continuity within the course.  Any other option obscures or over emphasizes available information.  Collaboration can define potential.  In truth your very question and your plan of action betray your wish to not inject bias.  It just sounds like your using the fact that all theory is inductive in nature to provide a cover for your bias..


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Correct grammatical errors after getting PhD
I have a question I cannot find the answer in any place. After receiving my PhD degree I found in my thesis some stupid grammatical errors which dont change anything in my work but still embarrassing. Can I correct these errors? Is anybody has the same experience. Sometimes I found mistakes in books which are 5th edition so it can happen.. but still..

Welcome to Academia SE. Please [edit] your question to clarify: How is your thesis published (if at all) and how would you correct those errors?

It is still not published. Now I know where is these grammatical errors and I can fix them. I ask is there any rules in universities for cases like this?

Well, if the publication is independent of your degree, then you can do whatever you want with it. Otherwise, you have to check your institution’s rules and we cannot possibly answer this question.

you mean publications from my thesis. no.. I dont have yet. but interesting how the rules work if I want to fix grammatical corrections. how it works? if there any rules I can find? can you give me some link?

Okay, let me rephrase this: There are two possibilities: 1) You have to publish your thesis in some way as a requirement for obtaining your degree. In this case the institution granting the degree makes the rules and you have to ask them. 2) You want to publish your thesis for other reasons. In this case, there are no rules (at least regarding fixing minor errors). Why do you think there would be?

Strongly related questions: Correcting a thesis after publication and Found an error in my thesis

I should speak with my supervisor to find out what to do.

If you wish to amend it, then use some of the results from your thesis and get some papers published which the whole world sees. Ph.D. viva is an examination which has been graded. Forget about the thesis and move on with life not to make unnecessary mistakes anymore


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How to build research collaboration?
I am an assistant professor of chemistry. My department strongly values international collaborations. I contacted some research groups working on the same topics as mine, but half of them wanted my fund, and the other half thought I want theirs.
My imagination of research collaboration was that two groups do parts of a research idea by their available funds, and then preparing a joint paper by combining the results.
For example, a common suggestion I received is that they can host a PhD student or a postdoc fellow (for a minimum period of one year for the sake of official paperwork and adaptability) if I have a fund. How can I fund someone to work somewhere else on a project different from my funded project? And how is it a collaboration after all?
In my experience, it is very difficult to spend research funds in another country. It is even impractical to send joint proposals (unless there are governmental agreements between two countries). I wonder how do researchers from various countries plan international collaborations (which is apparently very common based on the joint papers)?

Go to international conferences and present papers. Meet people with similar work.

@Dawn while I agree with you that personal conversions are much more effective (though the OP has not mentioned the means of his/her contacts), I believe that the question is about working models of collaboration rather than where to find it.

Generally, and as many questions here on Academia.SE reflect, collaboration typically does not grow from blind-mailing people that you have never spoken to and which, presumably, have little to no idea who you actually are. The fact that many of them thought you are interested in leeching of their funds is not surprising, because that's what a lot of these blind mails boil down to.
Dawn is on the right track in a comment - before you can have collaborations, you need connections. A common way to establish connections is by going to conferences and chatting with people - initially not even necessarily about common work, although the discussion often tends to go there fairly naturally.
Optimally, you would have started this process long before you were an Assistant Professor - in fact, arguably one of the key tasks of an academic supervisor lies in introducing their students into their academic network, exactly so that they have an easier time bootstrapping future collaborations of their own.
Even if you have no real network right now, you can probably still fix this, but you should see this as a marathon, not a sprint. You will need to go to a number of conferences, talk to a lot of people, and and generally be present in the community for some time before your name starts to come up naturally when people think about who to collaborate with on a given topic.
However, once you have started to be somewhat known in the community, even as fast as after your first conference, you can still approach the people that you talked to there with concrete ideas for collaboration. Be prepared that especially initially you may need to put in a bit more effort than they do, particularly if you collaborate with somebody more senior than you. This does not mean that you should do all the work and just put them on the paper, but if a collaboration is your idea it is often assumed that you are also driving the project and ask your collaborator(s) for concrete, actionable input.

Look at all of this from the view of the other researchers. They're happily working away in their lab or office and they get contacted out of the blue from some assistant Professor in America who is basically saying "Hi! I want to collaborate!". What do you think is going through their minds? If I, a researcher here in America, were suddenly contacted by some assistant Professor in, say, Switzerland or Singapore who I had never heard of before about collaborating, a number of questions would be going through my mind: Who is this guy? What is his sub-field? Does he have any character or personality issues? What of benefit is he offering to bring into a collaboration? Is he a good, productive researcher who is worth my time?
Now since you're in a relatively junior position and early in your career, you're pretty much of an unknown entity and you probably can't claim to have a wealth of valuable experience and knowledge that a more senior researcher would have, so that puts you at a disadvantage. You probably do have lots of energy and may be more up-to-date and willing to jump fully into the latest emerging technologies and developments (whereas senior researchers tend to be more conservative and tend to stay with what they're familiar with), so those may be some of your strengths.
I would say that before trying to contact scores of foreign researchers about possible collaborations which you don't know will really benefit you and your research, you first need to do some homework and groundwork. First, think really hard about how the other guy sees you and ask yourself what of value you really have to offer in an international collaboration. The honest answer may be "nothing", in which case you're jumping the gun and need to first work on developing a good research program rather than reaching out for international collaboration. Secondly, if you do have something of value to offer in an collaboration, you need to get out and get more recognition by publishing and attending international conferences where you can meet potential collaborators face-to-face, better exchange ideas, including collaboration ideas, and establish a rapport and make them comfortable with the idea of collaborating with you. Collaborations can come together naturally in those circumstances.