Traversing the Academic Literature

Throughout my academic career, I have been involved in a wide breadth of research topics. Early on, I was interested in the genetic engineering of plant pathogens for disease prevention. I pivoted to studying sex biases, and their influence on the tenure-track progression of research faculty. Now, I am a part of the British Columbia Cancer Research Center investigating low-grade serous ovarian cancer.

I have had to read a bunch of academic literature over those years. A whole bunch! In this blog post, I will share my strategy and thought process on how to dive into academic literature.

The Academic Literature Landscape

There are multiple forms of academic literature.

We may be familiar with the term “research article”. However, a research article is not the only way we can package our findings. Let’s define the different types of academic articles that exist. Take note, this is a non-exhaustive list.

The Research Article

A research article is a technical report that attempts to answer a research question based on data generated by the authors of the article. Every research article is characterized by a central research question, which is systematically divided into smaller inquiries.

The research article format is fairly standardized. The major sections are:

Section	Description
Abstract	A condensed summary of the article providing an overview of the research question, methodology, findings, and conclusions.
Introduction	A summary of what is known and unknown in the field of study, and the significance of the research question being addressed in the remainder of the article.
Results	A technical description of the experimental design, generated data, and statistical analyses performed to answer the research question.
Discussion	A synthesis of how the generated data and statistical analyses connect to the research question, the contribution to the domain of study, and future direction based on the conclusions presented.
Methods	A technical description of the procedures performed to generate the data being analyzed.

The sections will largely be presented in the order outlined above. The methods section will tend to float around depending on the publishing journal. In general, the methods section will always be after the introduction.

It is crucial to keep in mind, peer-review and publication of a research article does not make the research article or their conclusions into facts. Every experimental or model system will have inherent drawbacks. We, as critical readers, must assess the validity of the data generated via the described methods and the credibility of the authors’ asserted conclusions.

The Review Paper

A review article attempts to synthesize our collective knowledge and understanding, or lack thereof, of a specific field of study.

The main purpose of a review article is to provide a critical summary and assessment of the work that has been done in the field of study. It will identify trends, gaps, and pivots in the academic literature. Often, a review article will contain an abstract and introduction. Afterward, the structure of the review article is defined by the authors and editors.

Review articles may also include a methods section, describing how the authors collected the academic literature they referenced.

The scope of review articles can vary broadly. We could find a review article discussing a category of diseases. Similarly, we could find a review article solely on one specific disease. We could go deeper, and find a review discussing what is known about a protein of significance in our disease of interest. We could then go broader, and grab a review summarizing what is known about the protein family our protein of interest is a part of.

For example, we could find a review article on ovarian carcinomas, which will likely mention low-grade serous ovarian cancer. We could follow up by reading a review solely on low-grade serous ovarian cancer. We would find out that KRAS is a gene often mutated in low-grade serous ovarian cancer, so we can find a review on KRAS.

Now, there won’t be a review article for every topic, but it is always worth searching for one.

Note, review articles are fallible. Verify the citations of key statements in the review article by going through the article’s citations. Moreover, be wary of reviews that have a low diversity of authors in their citations. If the author of the review is mostly citing their articles, then the review may be considered biased. At the same time, we must also weigh the diversity of authors being cited by the size of the research community. If the research community of the domain is small and/or new, then only a few research teams will have publications to reference.

The Research Letter

A research letter is a condensed report on a research question. They are distinct from research articles in that they are shorter in length, yet maintain their rigor and significance. Research letters tend to contain an abstract, a main, and a methods section. The main section is a combination of the introduction, results, and discussion sections you would have seen in a research article.

The Perspective and Opinion

An article that falls under the veil of “perspective” communicates a research team’s conceptualization of a given topic. They synthesize a body of literature, much like a review article. However, perspective articles will tend to be more speculative. For example, it could be the research team’s perspective on the direction the field needs to take or ideations of novel approaches to a current research question.

Perspective articles have an ill-defined structure. However, I find them more enjoyable to read.

Exploring Uncharted Territory

Any time we enter a new research project, we must ask ourselves:

What is my research question? Without a question or objective to guide us, our research project will not be successful. For example, we have to know if our purpose is hypothesis-testing or hypothesis-generating.

What is already known? To make a meaningful contribution to any field, we must first become well-versed in the current understanding of the phenomenon of interest. Without that understanding, our domain-specific intuition will be lacking. The consequence of a meager domain-specific intuition is the inability to identify known and unknown gaps of knowledge.

Which are the landmark research articles? To understand the conceptual framework that established researchers are using in a given domain, we must study the historical context of their field. Landmark articles provide foundational knowledge and conceptual frameworks that most researchers are building from. Without identifying these articles, we would be blind to what may be taken for granted by domain experts.

Which are the established academic journals? Academic journals are companies that publish academic literature. Each journal encompasses a specialized topic, at varying scopes. A journal’s prestige is indicated by the quality and perceived impact of the research articles it publishes. Typically, you will find the landmark research articles being published in prestigious journals. You can identify the prestige of a journal by its impact factor.

What are the different niches in this domain? Each domain asks an overarching question. How have researchers systematized the field’s approach to answering that overarching question? For example, one research team could be focused on understanding the effects of oncogenic mutations by using in vitro experimental systems. Other groups may be addressing similar questions using in vivo experimental systems. Yet again, other groups may be focused on the same question but focused on in silico methods. Different research groups will have different access to resources and expertise. Each specialization will have its drawbacks. Identifying these drawbacks will help your critical assessment of other researcher’s work.

Who are the key researchers? Each domain has its celebrities. They will be prolific within their field of study, but, perhaps, unheard of outside of it. Identifying researchers that had substantial influence in the field is crucial, since they may be trendsetters in the field itself. Moreover, collaborating with the key researchers may grant access to resources and expertise that would otherwise have been inaccessible. You can identify an influential researcher by their h-index.

What are the standard methodologies and statistical methods used? Each field will have standard methodologies that they abide by. It is important to appreciate the domain-accepted data generation process and how that influences statistical analysis. It may differ significantly from your previous projects. There may be specific experimental controls, which without, would lead to erroneous conclusions. However, remain critical of the pre-establish dogma. You can adopt the standard methodologies, but do not let that hinder your creativity.

Where do I fit in? Our final question combines different aspects of what we have touched upon above. Are you bringing in expertise or resources that are lacking in the domain? How does your research question contribute to the field? Are you asking a fundamental question or is there a clear pivot to application? Placing yourself in the field will help you identify how you can best contribute and who may offer synergistic collaborations for your research team.

Planning Your Expedition

To find academic articles, use academic search engines and databases.

I tend to use Web of Science, PubMed, bioRxiv, arXiv and Google Scholar. However, there may be domain-specific search engines and databases that may be better suited for your research question. If you work in an academic institution, your library likely has a list of resources you can access with your institution’s credentials.

There are also other services, such as ConnectedPapers that help find articles that are similar to a query article.

Searching for articles can be chaotic. At times, that is perfectly fine. Not every article needs to be carefully indexed. Yet, there are times when we must be diligent in our search. For example, when you are starting to write a manuscript, thesis, or other type of report.

One approach that I have taken is to keep track of my search metadata. I create a table with the following columns:

• Search Engine/Database: Which tool did I use to search for articles?
• Query String: The search prompt.
• Filter: The types of filters I used. For example, filtering for all articles published in a specific journal.
• Ranking: How I displayed the search results, such as by citation number or publication date.
• Number of Results: The number of articles the query string yielded.
• Number of Articles Collected: The number of articles that I have collected from my search results.

Your Travel Log

Do not store your articles as PDFs in a convoluted arrangement of folders. Start using reference managers.

A reference manager is a piece of software that helps with organizing academic literature. The base functionality of a reference manager is:

1. Centralized storage of all your academic literature.
2. Viewing and annotating articles.
3. Notepad associated with each piece of literature.
4. Text editor integration for seamless citation while writing your manuscripts.

There are many reference managers available for researchers, free and paid. The big names in reference management are: EndNote, Papers, Mendeley and Zotero. The first two are paid software, while the latter two are free. I started my career using Mendeley but later shifted to Papers.

Your research group or institution may already have a subscription to a reference manager.

Unraveling a Research Article

Reading a research article is a technical skill set.

In general, a research article will follow the Introduction, Methods, Results, and Discussion (IMRaD) structure. The objective of IMRaD is to start the article with a broad scope, and gently narrowing into addressing a specific research question. Once the research question has been addressed with data, the article broadens once more into the significance of the findings and future directions.

I will be discussing how I, generally, read a research article. My method may or may not align with you, so take what is useful and feel free to leave the rest.

The Abstract

The first step to unravel a research article is to read the abstract. The abstract will provide you with the gist of the article, and help you determine if the contents of the article are immediately relevant to your project.

An abstract is a structured paragraph or set of paragraphs. Understanding how an abstract is written, will help you understand how to scan through it.

1. The first component in an abstract is a hook. Why should you, the reader, be interested in this article? It may start with a statement on the severity of a disease, a need for novel methodologies, or a lack of current standards in a field. The first component will address the scope of the article, and provide a sense of urgency.
2. The second component in an abstract communicates what was done. Usually, this component starts with “We conducted”, “We developed”, “We performed”, or some other variation of an action statement. Within that action statement, the authors will describe their model system.
3. The third component in an abstract relates to the results of the article. This component will give you the punchline. At times, the authors will preface this component with “Our results” or “This comparison reveals”. While the third component communicates the punchline, it will be mentioned quite generally. To appreciate the nuances of the findings, you must delve into the actual article.
4. The fourth component in an abstract reveals the implications of what was discovered. The authors will touch upon the significance of the paper relating to theoretical or practical applications.

After reading the abstract, you should have a sense of how the article relates to your work.

The Introduction

The introduction is the author’s attempt to provide context for the research question being addressed in the article. The authors will answer four main questions in the introduction:

1. What is already known?
2. What are the gaps in knowledge?
3. Why is addressing these gaps in knowledge important?
4. How have we addressed those gaps?

If you are unfamiliar with the domain of the research article, you should read the introduction in its entirety. It will provide the necessary pieces of information needed to interpret the results. However, introductions are not always thorough, since authors have to abide by a word limit. Leverage the citations in the introduction to help you better understand what work has already been done that led up to this research article.

If you are already familiar with the domain of the research article, you may find it redundant. However, it is still beneficial to skim through the first few paragraphs and identify any references that you haven’t encountered before.

The last few paragraphs of an introduction are critical. This is where the authors will explicitly tell the reader the research question, discuss their approach to answering the question, and frame it with the implications the research question has for others in the field, or the public at large.

After reading the introduction, you should have a sense of where this article fits in the domain.

The Methods

Now, I strongly recommend that reading the methods section be left to the end of the article or as a supplement while reading the results.

The methods section is a technical description of the data generation process. The authors will discuss the model system, reagents, assays, and statistical analysis. The method section is crucial for a reader to have a proper critical assessment of the data and conclusion being presented in the results and discussion section.

If you are to reproduce a research article, the methods section is where you would start planning your experiments. However, the methods section may vary in depth of detail. At times, there will be supplemental documents that include additional details about the methods used. Other times, you will have to contact the corresponding author(s) for additional information.

The Results

The results section is a technical description of the data that has been generated, and the statistical analysis. It will commonly be compartmentalized into subsections, accompanied by figures.

The order in which the data is presented to you in the results section follows a narrative, much like a story. It will start by providing descriptive data on the model system, to provide confidence that the system behaves as expected before any perturbation. If the paper is investigating a cohort of patients afflicted by a disease, the first subsection of the results will describe the demographic feature of the patients. If the paper is studying the function of a protein in a cell, the first figure will describe how the protein functions and the cell behaves before applying any modifications to the protein or cell. In essence, the authors are describing the main characters in the arc that is the results sections.

Personally, I tend to quickly skim through the headers of each subsection in the results since it gives me an idea of what to expect from the authors. Much like I would look at a table of contents to gather an idea of what a blog post will cover. Each header will be a concise and descriptive statement of the main takeaway from that subsection. I will also glance at the figures and figure captions to get a better sense of the type of data that is being described.

The figures are being displayed in a deliberate and logical order. They are a sequence of events, and should be treated as such. The figure exists to provide a concrete representation of of the technical and abstract description present in the text of the article. An exercise that helps me interpret figures is to associate them with an experimental question. Afterall, each figure is a visual representation of data that was generated to make trends and patterns stand out, to help answer a question or gather insight.

A figure will be composed of multiple panels, typically enumerated as “A”, “B”, “C” and so on. Much like figures, panels are ordered deliberately. Looking at panel “Z” before understanding panel “A”, will present a barrier in your critical assessment of the data. It is much like viewing the season finale of a TV show, without having sat down and watched all the episodes leading up to the finale.

There may be panels that appear redundant in the type of conclusions they suggest. These panels may, very well, be redundant by design. To answer a question thoroughly, you should ask the same question using indepedent methodologies. If each independent methodologies converges to the same conclusion, you have greater confidence that your conclusions are approaching a ground truth. If the independent methodologies do not converge, then further conceptualization of the project is meritted.

Now, if you determine that you do not need to be intimately knowledgeable about the article’s contents, then you could skip straight to the discussion section and leave the results for another time. Regardless, you should still read through the headers and inspect the figures. Otherwise, you may be blind to a glaring oversight by the authors.

Similarly, if you are feeling overwhelmed by the contents of the results, you should feel free to move on to the discussion and then circle back to the results. The discussion section will provide more context and interpretation that may help you digest the results section.

In the results section, you should also consult the methods. The methods section will help you understand how the data was generated and may hint at limitations in the conclusions of the article. Moreover, the methods section will highlight the statistical techniques used. You then can assess if those were the appropriate statistical techniques (i.e. normalization or hypothesis testing) for the type of data the authors generated.

The Discussion

A research article’s discussion section is where you will find the authors’ interpretation and conclusions from the data presented in the results section. The data will be put into context by framing it with prior research. The authors will also hint at future research that their data and conclusions may lead towards.

If the results was a challenging section for you to traverse, then the discussion should help you map out the relevant aspects of the data described. The authors will also provide multiple references, such as other articles and reviews that substantiate any claims that they make. A good discussion will also address articles that contradict the claims the authors are making.

I personally will go through the discussion from top to bottom a few times to make sure I understand what the authors are claiming about their findings. Circling back to the results and methods sections is necessary to determine if the authors’ claims are aligned with their experimental approach and data.

A published research article is not immune to overinterpretation or analytical errors.

Ending Your Journey

Reading research articles can be intimidating at first, but with practice and perseverance, it becomes second nature. Don’t be discouraged if you encounter unfamiliar terms or complex concepts along the way. Remember, every expert was once a beginner too.

As you embark on this intellectual adventure, always remember the importance of critical thinking. Question assumptions, evaluate evidence, and seek diverse perspectives. Engage in discussions, share your insights, and contribute to the scholarly community.

Ultimately, reading research articles is not just about understanding the content but also about becoming an active participant in the academic discourse.