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How to cite and reference properly

I still remember the disappointment I felt when I first learnt about citations.

I think it was in high school, during a religious studies class. We had to write an essay and it had to include citations.

The whole notion of writing something and backing it up with evidence to support it, by essentially quoting someone else…

It just ruined my free form writing style.

I don’t plan my texts?!

I just write everything down as I think it. The idea of properly forming ideas, jotting them down, coming up with texts to support them, then finally compiling it all together in one large paragraph, page/s, essay…

I hated it.

Obviously my mind has changed since then, because you can’t really make it through undergrad, or postgrad, without learning how to cite properly.

But how do you cite and reference properly?

I’ll write this post in the context of a scientific report, journal article, or thesis, because that’s my area of expertise.

If you wish to learn more about the different sections of a scientific report, journal, or thesis, you should check out my previous posts on this topic.

Firstly, what the hell do I mean by ‘citations’?

If you’ve never seen a piece of text that looks something like this:

‘A typical infection with C. burnetii occurs via inhalation of contaminated aerosols into the lungs, where bacteria are phagocytosed by alveolar macrophages (2, 3).’

Then welcome to the world of citations.

It’s those weird numbers at the end of a sentence- the ‘(2, 3)’ in the above example.

Sometimes it might be, ‘(Person et. al. 2021, People et. al. 2020)’- it just depends on the chosen style. Generally, all citations are usually denoted by bracketed numbers or people’s names, sometimes with the year that the article was published in.

At the end of the text, you’ll see their reference list or bibliography, where all the in-text citations (i.e. the bracketed, inserted references amongst the main text), are listed in order of appearance (or alphabetical order), with more details of where it is from. Usually it’s the author/s’ names, year of publication, the title of the publication, the journal or book it was published in, the volume, issue, page numbers, and maybe the digital object identifier (doi) number.


  1. Person AB, People CD, Peeps E. 2014. Insert a cool and catchy title here. Fancy journal 44:339 โ€“353.

All citations are used as a way to back up the claim you make in your sentence.

In the above example, references ‘2’ and ‘3’ are scientific articles that support my claim that typical C. burnetii infection occurs by inhaling bacteria into your lungs, where the Pac Man of the immune system gobbles them up like those white dots in the game.

Because without references, then there’s essentially no ‘proof’ or ‘evidence’ to substantiate the claim I make. If I don’t reference, then for all the reader cares, I’m talking out of my arse.

It’s vital that you reference appropriately when you’re writing scientific (or academic) text, because linking your statements to real data is what makes science evidence-based.

When should you reference?

Again, in the context of scientific text.

Any time you make a claim that you don’t show directly in the results section of your report or article- you should reference an article that did.

This again ties into the need to provide evidence to back your claims.

Any time you borrow data, including explanatory figures, from someone else- you should reference the original article where it came from.

Otherwise you are plagiarising their work. If you don’t reference, then you are making a bold claim that you performed the experiments yourself, or that you made the figure yourself. That’s just stomping on someone else’s hard work, or spitting in their face. Please. Don’t. Plagiarise.

Just don’t

What should I use for my references?

In the context of scientific writing- primary research articles, where the results section of the article definitively and directly shows the findings, are your best bet.

More examples on the uses of primary research articles as a reference include:

  1. Using the data from another article to back up the claims in your text (like the example I gave with C. burnetii)
  2. Using the article to reference a methodology or protocol that you also used (cite in your methods section), or want to use (perhaps it’s for your discussion, where you talk about future directions)
  3. Using the discussion point raised in another article to introduce your own article, or back up your own discussion point (‘someone else thought it was a good idea, too’)
  4. Using someone else’s result/s or discussion point to justify your experimental direction (person A did this in their article, and so I will also do this/not do the same thing)

Hopefully you can get the gist that you can use primary research articles to support the direction you take in your experiments and/or text.

But what if the claim you make it more generic, that might not have a primary research article associated with it?

If it’s something like, ‘Humans are a type of animal’, then it might actually be okay not to cite… because it’s a very well-known fact. If it’s something so fundamentally well-accepted and known, then you can get away with not citing. That’s why you might notice that a lot of scientific articles skip references for the first couple sentences, which might be like a common or generic fact in their field.

But if you really want to reference, for something that’s a bit more generic or broad, then a review paper might be okay.

Review articles are just that- they review a particular topic or field.

So you can imagine that it’s awfully convenient to use as a citation, if the point you’re making is somewhat broad. I’ve used review papers to cite generic statements about symptoms, because the review I used was a clinical one that listed all the possible symptoms a person might get for said illness.

But here’s the stern warning:

Don’t just use review articles for your citations

This is a huge no no.

You can use a few review articles, but only if there are literally no other options to do so. For every reference you make, you should always, always use primary research articles. Basically, you should exhaust all efforts to find a primary research article, before using a review as last resort.

That being said, a review paper is a very handy way to find said primary research articles, because if it’s a good review, they’ll cite them. A review is a good place to start to familiarise yourself with that topic, and use it as like a way point to finding the real sources. So they do have their place in the writing process- just don’t use them to directly cite.

Beyond that… that’s kind of… it. There are some book chapters that contain experimental data, but usually these get published as primary research articles as well. Any other literature being used as a reference is strongly discouraged.

Now, does anyone know why? What makes a primary research article more special than… say… a blog?

What happens to a primary research article before it gets published (that definitely doesn’t happen in a blog)?


It gets peer-reviewed.

An ‘expert panel’ (hopefully expert) will (hopefully) rigorously analyse your article, and make suggestions to fix any issues or gaps that the article might have. Whatever gets published has gone through assessment from the journal quality control team, the assigned editor, and 2 or more reviewers, before it’s finally out in the world.

A blog, or book chapter, doesn’t get this sort of treatment. Reviews do, to an extent, but it’s not quite as rigorous as what a research article gets put through.

And that’s basically why there’s that hierarchy. The primary research article has been peer-reviewed, so, in theory, it should be treated as more reliable than, say, a blog that has only one person looking over it.

Moral of the story is, always use peer-reviewed text for citations.

How often should I reference?

Again, any time you make a claim that isn’t shown by you in your report/article/thesis.

Fact 1 (cite 1). Fact 2 (cite 2). Data in report. Fact 3 (cite 3, cite 4).

It’s not enough to go,

Fact 1, Fact 2, Fact, 3. Data in report. Fact 4, Fact 5. Data in report. (cite 1, 2, 3, 4).

Because each ‘Fact’ is a sentence, as is the data. While that’s one line in my example, in reality the whole thing might end up being one lengthy paragraph. You can’t just dump all citations at the end of a paragraph. It has to be associated with the fact that you state.

To flip it around a little, imagine someone else was looking through your text, and they see something that they also want to use as a claim.

How the hell are they supposed to figure out which reference is for which fact, if you’ve put them in one lump sum at the end?

Be nice to your reader.

Sure, it might look a little messy, but in all honesty, the more papers you read, the easier it becomes to just omit the citations and skim over them. In fact, if you get really good, you’ll notice it more when they don’t cite, and you don’t have something to skip over. Then you can judge them harshly and be all, ‘where’s that reference, huh?!’. Or at least, that’s what I do, because I’m very bitter. ๐Ÿ˜‚

Is it possible to cite too much?

Definitely. If you have one statement, have five different references to back that up, and do that throughout your text… that’s overkill. But I find that most people throw citations in just so it looks like they did a lot of reading, when in fact, only one (or two) are actually valid citations. If you genuinely think that all the citations belong there, because they perfectly match what you’re saying- then yes, you can leave it in…

But be honest- do they really fit the bill? All of them?

How do you manage to keep track of all the references?

When I started, I may have only had 5 or so references to worry about, so it was quite easy to just write them in by hand.

But quickly, the list became 10, 20, 60… 120…

So how does one manage all of the different texts? Sure, you can try and do it by hand, but what if the references are listed in order of appearance (like the C. burnetii example), and you edit the text and move bits and pieces around, so you need to go back and reorder everything?

At that point, the only reason to push on manually is just… self torture.

The rest of us tend to use citation managers, or special programs that keep a track of all your references for you.

My university used Endnote as the default, supported software, so I’ve only ever used it. I know Microsoft Word has an in-built citation manager, but I preferred Endnote to it, so I don’t have any extensive knowledge in its use.

Direct from the Endnote website

Both Word and Endnote are citation managers that help you keep track of all the references you’ve used for your text. The screenshot above from the Endnote website shows you that the reference library contained a whopping 4617 references in total. Using the Endnote plugin for Word, you can directly insert citations into your text, and it automatically adds a reference list at the end of your document. You can go to PubMed and other databases that have scientific journals, and download electronic citation files for Endnote, that contain all the relevant info for said citation. All you have to do is click download. Endnote will also automatically re-arrange numbers for your in-text citations if you move bits of text around, and let you choose your citation format out of hundreds in their collection.

I won’t delve any further (if you really want to learn how to use citation managers, you should watch any of the hundreds of online tutorial videos), but this is the thing- it has gotten much, much easier to cite properly. Learning how to use these tools can only help you make your life easier.

The only downside to these, just as an FYI, is that they don’t italicise binomial/scientific names for different organisms. I had to italicise them in the Endnote app/program when I would download and import references, so that they appeared italicised in my text. You’ve been warned.

APA, Harvard, Chicago… What are all these different names for citations?

APA, Harvard, and Chicago are all names for the styles of referencing. You’ll need to double check what the required style is when you’re writing scientific text, because each one can be very different. They’re all very finicky, too, with different requirements for when you italicise, or capitalise, or include first initials… Again, you should check which one you’re supposed to be using, before you start citing.

If you’re writing for a scientific journal, there should be an ‘instructions for authors’ document that you can use as reference (hahah, reference… get it?? … Sorry). That instruction document will tell you what style the journal would like their writing in.

Yes- it’s a giant pain in the arse. I know.

I remember the frustration when I discovered that one journal wanted me to write 13C-glucose, while another wanted [13C]glucose. Both explicitly requested that authors adhere to their rules. I had to painstakingly go through and change all these differences in nomenclature. At least for citations, if you have a citation manager, all you need to do is change the journal and it’ll automatically do it for you. Unfortunately that only extends to citations, not finicky differences in preferred nomenclature. ๐Ÿ˜”

So that’s a crash course on how to reference properly! Definitely aim to over-cite than to under-cite.

Use primary research articles as your main references, with reviews being the only other real alternative.

Get to grips with a good citation manager, so that you’re not left doing all the hard work. Bow down to your electronic overlords.

Don’t plagiarise. If you don’t cite appropriately, you run the risk of stealing other people’s hard work.

And most important of all, the best way to learn is to read examples of what youโ€™re writing. Reading journal articles is the only way you can get better at writing them.

Good luck!

Categories: Ph D posts

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A Ph. D graduate in Microbiology, residing in Victoria, Australia. Currently working in multiple locations but still in the STEM field. ๐Ÿ‘€ ๐Ÿฆ  ๐Ÿงซ ๐Ÿงฌ

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