So welcome to week six. So in this week, I'm going to talk, a
little bit about some alternatives to the original research manuscript that you
might consider, writing, And then I'm going to talk a lot about the
publication process. In the last three modules, I'm going to
interview three long time journal editors to get their tips and advice about
navigating the publication process, and how to increase your chances of getting
published. But in this first module, I'm just going
to start by talking about some other types of papers that you might see in the
literature and you might consider writing besides the original research manuscript.
But first, I want to start in here with an example of good writing.
I want to make sure that in this course I'm not just giving you all examples of
bad writing, but also giving you some examples of good writing.
So I was reading this piece by, a Stanford professor who, actually invented something
called optogenetics. He had written a review article about
optogenetics, and I, I find he did a really great job on the writing, and I
pulled a passage that I really liked from this. So he says, the lesson of
optogenetics is that the old, the fragile, and the rare, notice the use of dashes,
here even cells from pond scum or from harsh Saharan salt lakes, can be crucial
to comprehension of ourselves in our modern world.
The story behind this technology underscores the value of protecting rare
environmental niches, I like that verb underscores by the way,
And the importance of supporting true basic science.
We should never forget that we do not know where the long march of science is taking
us, or what would be needed to illuminate our path,
And actually, that illuminate right there is a little pun, a little play on words
because optogenetics is about using light to control the brain,
So he, got in a nice verb there with illuminate.
So that's an example of good writing. I'm going start by talking here about
review articles. So, again, other than original research
manuscripts, there's a lot of other opportunities for you to get published in
the literature and one of those is to write a review article.
Now, a lot of review articles actually are solicited by journal editors.
So, a journal editor might go out and ask a known expert in the field if they want
to write a review article on a specific topic.
Even in those cases, however, somebody who's a little bit more junior like a
graduate student might get involved, because a review article is a lot of work.
So, that expert in the field might solicit some help, from somebody like a graduate
student, who will end up being a co-author on the, on the paper,
So, you might have an opportunity to get involved in a review like that.
Also, as a junior person, especially if you're a graduate student or somebody just
getting into the field, you might actually be in a really good position to write your
own review article. And that's because you know, as a graduate
student you're coming in and you're trying to learn this whole body of literature on
a topic. And that puts you in a really good
position to write a review article, Like I can remember when I was starting
graduate school in the mid 90's, I, I worked on a topic called female athlete
triad. So the first thing I did was, you know,
gathered all of the literature on that topic,
There wasn't actually that much at that time,
And I went through it very carefully. I put it into tables.
I was really trying to get a hold of, of, of that field.
And so, I, I did not write a review article on the topic, but at that point, I
could have, I've sort of done all the groundwork.
So it's a, it's a good way to get published if you're more junior, if you
have taken the time to go through the literature.
It's a good idea, though, if you're going to write a review article, to consider
what, journal you might want to publish it in and think about trying to contact the
journal editor ahead of time, maybe sending them a brief outline, and asking
them if they would be interested in that review article, just so you can establish
ahead of time, that this is something that, you know, they're likely to be
interested in, as opposed to just sending them a whole review article cold.
I mean, you can do that as well, but, one tip would be to contact the journal editor
early in the process. So what's the goal of a review article?
Basically, the idea is you're trying to synthesize the recent primary literature
on a topic. So, there's just, you know, a huge
proliferation of papers these days. Nobody really can keep up with the entire
primary literature, and so, your job as a review article author is to kind of put
together, summarize the recent primary literature, so that somebody can go to
your paper and get a good sense of the field.
You're also summarizing the current state of knowledge on a topic, so what's the
status, what do we know, what do we not know, where are we? review articles often
also address controversies. In fact, you could have a whole review
article that was centered around a controversy, where that was the point of
the article, or just possibly in passing your review article might address some
important controversies. Another I think that a review article
provides is it, In doing the review article you're putting
together sort of a comprehensive, list of citations on a particular topic or
research question. And that can be a good resource for other
authors who later, you know, want to get into the field and get to, up to speed on
the literature. It's a nice, resource for other people to
have a set of references like what are the top and important papers on this topic?
So that's a real, service also, Of course, you want to make sure that your
references are correct and, and we'll talk about that some more.
So there's three basic types of review articles, that you could do.
So, there's what we call non-systematic, systematic, and meta-analysis.
So, a non-systematic review is actually probably the most common type thats done,
you know, sometimes called also a narrative review. And, what distinguishes
it from the other two, is really that it's a little of bit of a less rigorous review.
S, ideally if you're going to take the time to do a review article, you might
consider wanting to do one of the more rigorous types.
But sometimes, you know, a graduate student might put together some kind of
non-systematic review. It's, it may not be completely
comprehensive, that is it may not look at all of the papers on a particular topic,
and it tends to be a little bit more qualitative, than say a systematic review
or a meta-analysis, rather than a quantitative, so you just, sort of say,
well this was a good study because of these reasons and you're not neccesarily
scoring the studies. In contrast, a systematic review, as the
term systematic implies, it attempts to find and summarize sort of all the
relevant studies on a particular research question or particular topic.
Others have even gone so far as to solicit, you know, to try to find
unpublished work, so if they know of researchers who are working on a study but
haven't publish the final results, They may contact them to try to get
information about that even though it hasn't been published yet.
When you're going to do a systematic review it, it posts a pretty specific
process. So, the first step, is that you have to,
To, to come up with a rigorous search strategy, so you define,
Well, what is, is the specific topic that I am interested in looking at and you want
to be kind of narrow in this. You don't want to make it too broad or
you're just going to, you're going to run into a literature that's, that's too big.
So you're going to have some kind of narrow, pre-defined topic, research
question you're trying to answer. And then you're going to def, you're going
to define some exclusion and inclusion criteria for the studies you want to
include in your review. And you're going to write these out before
you even go and do the search. You're also going to target what are the
databases that I'm going to be searching. So for example, maybe what,
Look at all the randomized trials on a particular drug.
So maybe that would be your inclusion criteria.
You're looking for studies where you're searching, you get the words randomize
trial and the drug name. Then you would go through those studies in
more detail and use some exclusion criteria to exclude some of them.
So maybe you only want placebo controlled studies, so you would exclude the ones
that didn't have a placebo control. So you're going to come up with a search
strategy. It's a good idea to involve an information
specialist, especially if you're at a university that has a library.
There are people over there that their expertise is on doing searches,
So go and talk to them to make sure that you're doing the proper search so that you
can capture all the relevant studies. You're also going to ahead of time, set up
a set of, criteria for evaluating the quality of these studies.
And these, these are often a quantitative measurement.
So you might have a scoring system where you're going to rate the studies from a
low of one to a high of four or something like that based on the quality of the
evidence in those studies, So it's often a quantitative evaluation
and you've got some predefined criteria that you've set ahead of time for
evaluating the papers, in your review. And then finally, the meta-analysis.
What distinguishes it from a systematic review is that there's and additional
step. You're going to use some kind of
statistical techniques to actually pool the data from those different studies,
Even, sometimes, some data that's unpublished.
So pool that data and come up with a final summary measure that answers a particular
question. So, for example, if you were looking at
all the studies that looked at whether or not zinc can help prevent colds.
You would maybe pool all of the studies, all the randomized trials, or all the
studies that looked at that, And you'd take the outcomes of those
studies, or sometimes even people will do meta-analysis on raw data, but that,
requires you go out and get the raw data from all the investigators.
So more typically, you'll take the summary measures from those individual studies,
like maybe, you know, the colds, zinc doubled the risk of colds or zinc cuts the
risk of colds in half. You'll take those numbers from the
individual studies, and you'll somehow pool them into a single, summary measure
that tries to answer the question, does zinc prevent colds?
So, so that is, higher level of rigor and also more work, because you're actually
doing some very defined statistics, trying to pool that data into some kind of final
summary, measure. So, what's a structure of a review
article? In general sometimes they'll have an
abstract, sometimes they won't. It varies by journal.
Then there'll be an introduction section, and that's going to give, it's going to be
very similar to the introduction section, that we use for an original, research
manuscript. So it gives some general background, sort
of the what's known, what's unknown, what are the gaps in the literature, and then
it gives a clear statement of the aim of the review.
What is the purpose of this review, are you trying to evaluate a new experimental
technique, are you trying to evaluate, or answer a particular research question, are
you trying, to, answer a particular controversy and give one point of view?
Of, or not controversy, so a review must. Have a clear purpose and that's probably
the biggest problem that I see with reviews, when I'm editing students
reviews. Is that they kind of are just this sort
of, this litany of all these different papers, and they're not synthesized in any
coherent way, Sort of around a central focus.
So, I'll go back to that student and ask them, well, what's the point, what are
you, what question are you trying to answer in doing this review?
And so, you need to define that question early on and you need to state it very
clearly in the introduction section. Then you're going to have what's the body
of the paper, sort of the main analysis. That's going to be the bulk of the paper.
You're going to explain what you did, so explain your search strategy, what data
bases did you search, what were your exclusions and inclusion criteria for the
studies, Then you're going to summarize the
literature that you founded, that you included in your review.
You can organize it in a number of different ways, but it's got to be well
organized. You might organize it based on
methodology, like, so I'm going to put it, I'm going to talk about all the randomized
trials and then I'm going to talk about all the observational studies
Or you might organize it based on the theme or on, you know, the experimental
technique if you're doing something in the lab.
So you find some way to organize it that makes sense and you're going to be
analyzing, interpreting, critiquing, evaluating those studies, and also trying
to synthesize what is it as body of research that what.
You know, takeaway messages can we conclude,
What can we conclude from these different studies?
Based on these studies what are the recommendations you would give or you
might also be saying here are the questions that we haven't answer, so
here's the gaps in the literature that remain that need to be answered.
So then you'll give some kind of conclusion and future directions and this
section will probably be a little bit shorter.
You're going to make recommendations based on what you found and identify those gaps
in the literature. What future studies do we need to answer
this question? And then you're going to give your
literature cited and again, this provides a resource for other authors to go to, to
kind of know lay of the land in terms of the literature in a particular discipline.
So you really want to make sure that you, you've got that, those references are
accurate, and that you've been comprehensive.
So, just a couple of examples, There was a nice little overview article I
was reading recently for a paper feature story I was writing.
And so I pulled the abstract and introduction from this article, cuz I
thought they were good examples of some good writing.
And, so, this was a, review where he was looking at different, competitions that
are used in biomedical computing, to evaluate how are people are doing in the
field. They get together and solve some problems,
it, as a group and, you know, it's a competition but they're also just trying
to that, different methods. So, in the abstract, it says, in
principle, given the amino acid sequence of a protein, it is possible to compute
the corresponding three dimensional structure.
Notice he's giving a really, He's telling a very wide audience what
this is about. He's not assuming anything,
Methods for modeling structure, based on this premise, have been under development
for more than 40 years. Giving a little history there.
For the past decade, a series of community wide experiments,
These are the competitions, They're called CASP.
Have assessed the state of the art, providing a detailed picture of what has
been achieved in the field, where we are making progress, and what major problems
remain. That's a really good summary of the
purpose of CASP. The rigorous evaluation procedure of CASP,
have been accompanied by substantial progress in the field.
Lessons from this area of computation, computational biology suggest a set of
principles for increasing rigor in the field as a whole.
So you know what he's going to be doing in this review.
He's going to be reviewing CASP. The, this set of competitions that's been
going on for a number of years now, and suggesting from that experience some
principles that could be applied to the wider field of computational biology.
And I think this a bit, again, I think both of this abstract in this sort of,
introduction has some nice writing in them.
You can see it's very clear, it's very easy for somebody who's not in the field
to immediately understand what he's saying.
Again, I was writing a feature story and that was the reason I was reading his
article and I just, I was so happy when I came upon his article because it was it
was so well written. So and then this is the introduction
section, notice it's pretty short. And again a little bit of history.
In the 1950's, work by Anfinsen and colleagues conclusively showed that the
information determining the 3D structure of a protein molecule is contained in the
amino acid sequence. Recognition of this relationship rapidly
led to the development of methods for computing structure from sequence.
There were many early encouraging reports of partial successes starting in the 1960s
and continuing through the 1970s and 1980s, and yet,
During this long period, there were very few reports of computed structures in any
way competing with those obtained experimentally.
That's a really nice statement of the problem there.
The mismatch, that's a good word, between apparent success and a lack of useful
application suggested that the traditional peer reviewed publication system is not
sufficient to ensure rigor in this area of computational biology.
So the CASP experiments, these are the competitions, were devised as a means of
addressing the specific needs of methods, evaluation and structure modeling.
Notice that sentences, I just want to point out here, is actually in the passive
voice. As I mention, there are some instances
sometimes when the passive voice works and I think it works here, because it wasn't
important for him to say who came up with these competitions.
So he left out the subject from this. And so I think it works, it's still a very
clear sentence. Casp is one of a number of ways in which
this problem may be addressed as discussed later.
The fundamental differences between computational and experimentally biology
dictate that new procedures be adopted in the field as a whole.
So again I just think there's some really easy to understand, well written good
writing going on here. Probably all of you even if you are not
coming from any kind of field related to computational biology can understand that
introduction section. So that's really well done.
So a couple of tips for writing reviews. So again, you might consider if you're a
junior person contacting a journal editor early in the process, maybe sending them
some kind of outline, to find out if the journal is interested in your review.
That's a helpful because if you just send the review cold, maybe it's not something
that they were not really interested in publishing.
Make sure you're again defining a clear narrow purpose for the review.
It's not just hey, I'm going to talk about all the literature on a topic.
It has to have some kind of focus that you can organize your whole review around.
And again, you need to develop a real clear strategy for searching the
literature. So meet with somebody, an information
specialist who knows about searching. If you're at a university that person is
probably at your library. You're going to be, reviews are a ton of
work by the way, so you're going to be reading lots and lots of papers.
It's very important to have a good organizational strategy.
So you're going to be taking a lot of time, spending a lot of time in this
pre-writing step I've been talking about, making sure that you're organizing all
other relevant papers in a way that it's going to be easy for you to write the
review later. So take a lot of time getting organized up
front. And then, remember that a review article's
really written for a very wide audience. So it's not, you know, even though that
your topic might be kind of narrow, it's written for anybody who wants to learn
about that topic. They're going to your review, because the
material in the primary literature isn't yet, hasn't yet appeared in a text book,
and so you're kind of filling in before there's a text book written on this
subject. Here's a good summary of what's out there
in the primary literature. That means people coming from all sorts of fields,
might pick up your review I'm often reading review articles because, I'm
writing about science, you know, a lot of different science topic for magazines. And
things and I'll pick up a review article to get a sense of the feel because it's
often topics that I'm not inherently familiar with.
I really appreciate when those reviews are well written, because again, I'm not
coming right from that scientific field. And if it's not written for a wide
audience and if it's not well written, it's not very useful to me,
But when I pick up a well written review, I can really get a handle on a feel very
quickly. So the good writing is even more important
for a review article. So that's review articles.
Another really good type of publication to consider to keep in the back of your mind
are letters to the editor. people often forget that those are out there, they're
something that you can write. But they're pretty short, they're pretty
quick to do. I've done a number of letters to the
editor and you know, they're something you can sit down and write in a couple of
hours. And they can lead to some interesting and
good publications. So, so what's the point of a letter to the
editor? In general, you're critiquing or
responding to a specific article that the journal has recently published.
So you're going to be sending your letter to the editor to the journal where that,
that first article was published. Usually you have a very specific critique.
Occasionally letters to the editor can be actually short,
Original research manuscripts which you might send in, in response to another
article, because maybe somebody's published a set of data in that journal
and you have sort of a similar set of data that can add a little bit of information
to, to their research question and you might rather than publishing it as a whole
original article, just send it in as a letter of editor, to the editor in
response. So, so it has a couple of purposes, but
generally usually they're critiquing something and they have to be timely.
Journals have, windows where they will accept letters to the editor and usually
it's a couple of weeks, maybe a month or two at most, after the original paper is
published. They, it has to be timely.
That letter to the editor has to refer to something that's recently been in the
journal. So, look at that guideline because if you
are trying to write about something that was published six months ago, it's
probably too late. Letters to the editor also, also have to
be really concise. Go to the instructions for authors and
figure out, exactly how many words they allow.
Generally it's something in the order of 200 to 400 words,
Maybe a maximum of one table or figure, A maximum of a couple of references.
So make sure you look at that ahead of time.
So you know how to write the article. And the structure is pretty simple.
The first paragraph will give an overview, where you're going to site, the recent
article that you're replying to. You want to give some kind of praise to
the authors in that first paragraph. The fact that you're writing a letter to
the editor about their paper tells you that they must have done something really
interesting. That paper caught your attention enough
for you to bother to read it in great detail and to come up with critique about
it and to bother to write a letter to an editor.
So, so there's obviously something important and interesting in that article,
Make sure you praise the authors for that. You know this study's relevant.
It's well designed. It has an intriguing hypothesis.
We found the article to be excellent and highly well relevant.
Give the authors their due that they've, you know, generated a dialog about their
paper, that's, you know, praise worthy. And then succinctly state the main problem
or issue that you are that you are going to be laying out in your letter.
So something like the paper is misleading due to several problems with the
statistical analysis and interpretation that's the overview and then you go and
state specific problems. So there's some kind of overview in the
first paragraph and then in, in a couple of paragraphs, maybe one to three more
paragraphs and extremely focused manner you're going to succinctly explain the
issues that you've observed maybe its one issue, maybe its multiple issues.
If its one issue, you might only. Take one paragraph.
If it's three issues, it might take three paragraphs probably not much longer than
that so. Very focused, explain what were the
problems. Try to eliminate all unnecessary clutter
from your writing cuz it's going to be very short.
And then if you've got enough space, you often don't, but if you have enough space
you might have a brief conclusion or parting thought.
Maybe one to two sentences within the last paragraph could be some kind of thought to
part on. So tips on letters to the editor, go to
the instructions for letters to the editor for the particular journal you're
targeting and make sure you follow them. They have very specific criteria about
huh, the timeliness and how long it can be, so there's no point in writing a
letter unless you know those. Keep the tone as positive in play as
possible. Yes, you're critiquing the authors, but
you can do that, you can critique somebody in a more positive tone and be polite,
obviously. Again, be specific and focused.
You're really going to have to use all your skills for removing unnecessary
clutter from manuscripts. These skills will come in really handy in
writing a good letter to the editor, 'cuz you have to be really succinct.
And, One other thing is. Don't just write a letter to point out
some. Small you know problem...
May be they analyse their data wrong but it doesn't actually affect the conclusions
at all. Don't write a letter to the editor if its
not something that really changes or potentially could affect the main
conclusion because if it doesn't matter, it doesn't matter.
So take something that's actually, you know could have potentially impact the
main conclusion of the original paper and make sure you articulate in your letter
how the problem you have identified might impact that main conclusion.
Otherwise, your letter has no real significance.
There has to be something that matters. Finally the last kind of alternate type of
publication that I'm going to talk about in detail are case reports.
Now obviously, you have to be coming from the medical field in order to write a case
report. So this is mostly for you medical
professionals out there. I have an example of a case report right
here which I'm just going to show you One of the authors on this case report which
was published in 1970 in the New England Journal of Medicine is George Lundberg,
and he's one of the editors that I'm going to be interviewing in my upcoming module.
So he mentioned in my interview with him, that the very first his very first
publication, which is this one. It was in the New England Journal of
Medicine, which is a extremely high impact medical journal.
So that paper got accepted right away in the New England Journal of Medicine which
is a great success story on your first paper.
But, it is a case report, so he said, you know, because it's a case report, he was
immediately obvious why It was significant.
So case reports can be really great publications because they often are
identifying new diseases, new side effects.
They, they can be very high impact. You know, for example the first AIDS cases
were identified as case reports in the literature.
So these can be some of the most highly cited papers.
Usually it's easy to con, if it's a, you know, if it's.
If it's clearly you know, an interesting case, it's often easy to persuade an
editor that it's worth publishing. So, so these are great if you are, are in
the medical field to consider doing some case reports.
Case reports the structure is very similar to an original research manuscript with
some differences. So you'll usually have an abstract.
The introduction section. The point is to say what's the
significance of the cases that you've identified or the case.
Then you'll be getting a description of the cases.
Things like, what were the presenting signs and symptoms?
The medical history of your social cases or case.
What medications were they taking? What were the results of their exams and
lab tests? What's the differential diagnosis, the
final diagnosis? What treatments were given?
What were the outcomes? So it's very much a medical.
Again, this is only for medical audiences and then you'll give a discussion where
you interpret the cases. What do those cases potentially suggest?
What are the questions for further research?
Usually case reports are bringing up a whole host of questions for future
research and then you'll have references and usually case reports will have some
kind of tables and figures. So it's like, it's just a, a good type of
thing to consider. Doing a case report if your in the medical
field and an interesting case comes along. I just want to mention briefly these other
types of papers that do appear in the medical literature.
For the most part these tend to be written by more senior people experts in the
field. But just so you're aware there are
commentaries, which are usually Often solicited by a journal editor.
Even if you're kind of junior, you might have the opportunity to do a commentary.
Because, when you're doing peer review, sometimes the journals will ask you, is
this a piece that's significant enough that it warrants a commentary, and would
you be willing to write a commentary? So you might have an opportunity to write
a commentary that way. Usually commentaries are talking about the
significance of another paper. Maybe raising some questions methodologic
question, but usually are pretty positive. There's also opinion pieces in editorials.
Those tend to be written by the editors of the journals.
Sometimes you'll see book reviews there's explanatory pieces in columns.
Like, I write a statistics column for one of the.
The journals and of course, I was asked to write that so.
But as you get more senior, you may have some opportunities to write things like
this. I just point out final, the last slide
here that, In terms of editorials, one of the, editors I'm going to be interviewing
in one of the upcoming modules is Dr. Gary Freedman, and he's a long-time editor
of the American Journal of Epidemiology. And he did a number of editorials about
good writing in the medical literature. So, I'll just point out those editorials.
I really like his editorial, be kind to your reader.
He talks a lot about the same kinds of writing tips that I'm talking about in
this course. A couple of citations and some further
reading if you want to, to get some more reading on different types of
publications. And particularly that second book there
also has a lot information about doing poster presentations, job applications,
and grants. Things which we're not really going to
focus on in this course and that's written for any scientific discipline.
It's a very thick book, but might be worth reading if you're interested in one of
those topics. The proceeding program is copyrighted by
the Board of Trustees of the Leland Stanford Junior University.
Please visit us at www.med.stanford.edu.