How to Begin Writing a Great Academic Manuscript?

A properly organized research paper begins with an outline

Why do I need an outline?

Whether you are a novice writer or an expert, a well-developed outline is the most important step in writing a manuscript because it serves as a framework to organize your major hypotheses, questions, arguments, and conclusions prior to writing your manuscript. 

Despite these benefits, many authors skip this step because they have not been taught how to construct an outline, or they simply ignore this step because of the time commitment. Even many seasoned writers feel they can rely on their experience instead of an outline. As a result, many authors begin writing their manuscripts without a clear strategy and organization. 

This can be seen in the common mistake of writing the full Results section first. This section appears to be a logical starting point because the data and figures are at hand, and it takes less thought to start at this point. However, authors who begin writing without clearly defined ideas and organization will ultimately waste their time and the time of their colleagues and editors as they try to develop key messages and conclusions while writing, rather than organizing before writing. 

Such basics should already be incorporated into the first draft of the manuscript so that you and your colleagues can focus on the essential logical arguments, hypotheses, and conclusions necessary for an impactful manuscript. A thoughtful outline will keep the manuscript well focused, and the framework can be reused for future manuscripts. Follow the guidelines below to ensure a carefully crafted outline. 

Steps for preparing an effective outline

Think before writing

A manuscript is the culmination of the questions and evidence that led to your major conclusions and their implications. To compose a manuscript that readers will feel compelled to read, it is critical to first think carefully about what you want to communicate. 

  • Is the manuscript describing a method? If so, focus the manuscript upon the technical details, how the method improves upon existing ones, and its utility for research or practical uses.
  • Is it communicating basic research leading to physical, sociological, or biological conclusions? If so, your manuscript should focus upon conclusions of scientific interest that are meaningful to your field and society, if possible. For example, discovering a new biochemical pathway leading to cancer can lead to scientific conclusions (a new biochemical pathway), practical benefits (potential new drug targets), and broader impacts on society (potential cancer cure).
  • Is it challenging existing hypotheses? If so, the existing hypothesis should be introduced and evidence presented that supports the new or modified hypothesis.  

Because the organization of our writing mirrors our thinking, it is highly beneficial to organize ideas formally before writing. This will result in a manuscript that focuses on your major results and conclusions. An outline will provide a means for you to construct this crucial mental framework so that readers will follow a logical progression through the story your research is presenting. 

Construct your outline in the following order

The order in which we construct the outline is different from that in a publication. An outline begins with the Results section because the outline is built around the results of your research. The Discussion section then provides the major conclusions and implications based upon the Results section. Once these sections are clearly outlined, the Introduction and Methods are added to provide the necessary context to understand your research questions and the relevant protocols to provide details for independent replication. Below is a breakdown of each section, in order of preparation:

  1. Results: From each result or set of results state the specific questions or hypotheses that are addressed. Then state your conclusions from the data sets addressing each question. You should have specific conclusions for each data set you present. You should also note which data you will be included in specific figures. For example, Figure 1 may include data from experiments A, B and C. If a conclusion raises a question to be addressed by the next data set, state it explicitly. 
  2. Discussion: State your key conclusions based on a synthesis of each set of results and their conclusions. Aim for two or more major conclusions in the outline that impact your scientific field (i.e., new cancer pathway) or society (i.e., new cancer treatment). The manuscript overall will be written towards these major conclusions and are the key messages you want readers and reviewers to retain. An overall conclusion using the cancer pathway example would be the discovery of a new cancer pathway that could lead to improved treatment, with each of the individual results supporting the overall conclusions. Also, briefly add explanations or other points that will clarify your data or conclusions for readers. For example, are there alternative explanations or limitations to the data that reviewers or readers might question? 
  3. Adjust your results and discussion points. Consider whether the order of the presentation in the Results section best supports the conclusions outlined in the Discussion and adjust the order of presentation in the Results section as needed. Focusing your results towards the major conclusions has the added benefit of helping determine the order of the figures and tables. Results that are relevant, but do not support the key conclusions directly, should be incorporated as supplemental data. Data not relevant to any of your results or conclusions, directly or indirectly, should be considered for exclusion from the manuscript to maintain its focus.
  4. Introduction: Now that you have a grasp of what you want to communicate in writing, consider the Introduction section of your outline. Here, use the outline to keep the Introduction section succinct and focused upon the research results you are presenting. List the essential literature readers can review to understand the current knowledge underlying your research questions. 

Using the cancer pathway example again, what is understood generally about cancer pathways? What is known or hypothesized about new cancer pathways? What are the pathways that current cancer drugs target? Many fields such as cancer are extensive and should not be reviewed extensively. The outline will help to focus upon the essential knowledge needed to understand your research questions and conclusions.   

Methods: Now that you have outlined the questions, organization, and conclusions, list your methods. Authors often write their methods almost as an afterthought, and peer reviewers may not examine them deeply enough as they focus on the major results and their relevance to the conclusions. However, the methods are critical for independent replication which underlies the scientific method. Start this section of your outline with the methods required for the main figures. Methods that require lengthy explanation or support your supplementary figures exclusively should be listed as Supplementary Methods. Methods that are altered significantly or are novel should be described in full detail in the manuscript.  

Organization of your outline

Your outline should have a final form such as that below with all your details.

  1. Introduction
  • Key background and citations for readers to understand the questions and conclusions


  1. Methods
  • Primary methods that support the figures, tables, or other data presented in the Results section
  • Methods that require lengthy explanation or support Supplementary Results exclusively


  1. Results 
  • Research questions
  • Data sets presented to answer the question
  • Experiments incorporated into each figure
  • Conclusions from each experiment
  • Questions posed by each conclusion to be addressed by the next research question


  1. Discussion section
  • Two or more major conclusions supported by the Results section
  • Details of the research that will clarify the data or conclusions presented in the Results section


Give it more thought

Give yourself time to revisit and reconsider the outline. As you spend time thinking through the outline, new points will be added resulting in a detailed outline that logically incorporates your ideas and major points. 

Now you can start writing

Now that you are satisfied with your outline, proceed to manuscript writing. If well-constructed, an outline will permit you to write your sections in the same order that will appear in the manuscript or eventual publication. In other words, you can start by writing the Introduction followed by the Methods, Results, and Discussion. The benefit of writing in this order is a manuscript that will read more smoothly for readers with the correct level of detail throughout. 

Whether you are a novice scientific writer or an expert, you will be rewarded with a manuscript that is organized, refined logically, and a pleasure for colleagues and editors to review. Through the creation of outlines, you also will improve your focus on key questions and results needed for publication while conducting your research. Thus, the outline can ultimately make your research and your writing more impactful.

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