how to write a methodology for a journal article

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• How to Write Your Methods

Ensure understanding, reproducibility and replicability

What should you include in your methods section, and how much detail is appropriate?

Why Methods Matter

The methods section was once the most likely part of a paper to be unfairly abbreviated, overly summarized, or even relegated to hard-to-find sections of a publisher’s website. While some journals may responsibly include more detailed elements of methods in supplementary sections, the movement for increased reproducibility and rigor in science has reinstated the importance of the methods section. Methods are now viewed as a key element in establishing the credibility of the research being reported, alongside the open availability of data and results.

A clear methods section impacts editorial evaluation and readers’ understanding, and is also the backbone of transparency and replicability.

For example, the Reproducibility Project: Cancer Biology project set out in 2013 to replicate experiments from 50 high profile cancer papers, but revised their target to 18 papers once they understood how much methodological detail was not contained in the original papers.

What to include in your methods section

What you include in your methods sections depends on what field you are in and what experiments you are performing. However, the general principle in place at the majority of journals is summarized well by the guidelines at PLOS ONE : “The Materials and Methods section should provide enough detail to allow suitably skilled investigators to fully replicate your study. ” The emphases here are deliberate: the methods should enable readers to understand your paper, and replicate your study. However, there is no need to go into the level of detail that a lay-person would require—the focus is on the reader who is also trained in your field, with the suitable skills and knowledge to attempt a replication.

A constant principle of rigorous science

A methods section that enables other researchers to understand and replicate your results is a constant principle of rigorous, transparent, and Open Science. Aim to be thorough, even if a particular journal doesn’t require the same level of detail . Reproducibility is all of our responsibility. You cannot create any problems by exceeding a minimum standard of information. If a journal still has word-limits—either for the overall article or specific sections—and requires some methodological details to be in a supplemental section, that is OK as long as the extra details are searchable and findable .

Imagine replicating your own work, years in the future

As part of PLOS’ presentation on Reproducibility and Open Publishing (part of UCSF’s Reproducibility Series ) we recommend planning the level of detail in your methods section by imagining you are writing for your future self, replicating your own work. When you consider that you might be at a different institution, with different account logins, applications, resources, and access levels—you can help yourself imagine the level of specificity that you yourself would require to redo the exact experiment. Consider:

• Which details would you need to be reminded of? 
• Which cell line, or antibody, or software, or reagent did you use, and does it have a Research Resource ID (RRID) that you can cite?
• Which version of a questionnaire did you use in your survey? 
• Exactly which visual stimulus did you show participants, and is it publicly available? 
• What participants did you decide to exclude? 
• What process did you adjust, during your work? 

Tip: Be sure to capture any changes to your protocols

You yourself would want to know about any adjustments, if you ever replicate the work, so you can surmise that anyone else would want to as well. Even if a necessary adjustment you made was not ideal, transparency is the key to ensuring this is not regarded as an issue in the future. It is far better to transparently convey any non-optimal methods, or methodological constraints, than to conceal them, which could result in reproducibility or ethical issues downstream.

Visual aids for methods help when reading the whole paper

Consider whether a visual representation of your methods could be appropriate or aid understanding your process. A visual reference readers can easily return to, like a flow-diagram, decision-tree, or checklist, can help readers to better understand the complete article, not just the methods section.

Ethical Considerations

In addition to describing what you did, it is just as important to assure readers that you also followed all relevant ethical guidelines when conducting your research. While ethical standards and reporting guidelines are often presented in a separate section of a paper, ensure that your methods and protocols actually follow these guidelines. Read more about ethics .

Existing standards, checklists, guidelines, partners

While the level of detail contained in a methods section should be guided by the universal principles of rigorous science outlined above, various disciplines, fields, and projects have worked hard to design and develop consistent standards, guidelines, and tools to help with reporting all types of experiment. Below, you’ll find some of the key initiatives. Ensure you read the submission guidelines for the specific journal you are submitting to, in order to discover any further journal- or field-specific policies to follow, or initiatives/tools to utilize.

Tip: Keep your paper moving forward by providing the proper paperwork up front

Be sure to check the journal guidelines and provide the necessary documents with your manuscript submission. Collecting the necessary documentation can greatly slow the first round of peer review, or cause delays when you submit your revision.

Randomized Controlled Trials – CONSORT The Consolidated Standards of Reporting Trials (CONSORT) project covers various initiatives intended to prevent the problems of  inadequate reporting of randomized controlled trials. The primary initiative is an evidence-based minimum set of recommendations for reporting randomized trials known as the CONSORT Statement . 

Systematic Reviews and Meta-Analyses – PRISMA The Preferred Reporting Items for Systematic Reviews and Meta-Analyses ( PRISMA ) is an evidence-based minimum set of items focusing  on the reporting of  reviews evaluating randomized trials and other types of research.

Research using Animals – ARRIVE The Animal Research: Reporting of In Vivo Experiments ( ARRIVE ) guidelines encourage maximizing the information reported in research using animals thereby minimizing unnecessary studies. (Original study and proposal , and updated guidelines , in PLOS Biology .) 

Laboratory Protocols Protocols.io has developed a platform specifically for the sharing and updating of laboratory protocols , which are assigned their own DOI and can be linked from methods sections of papers to enhance reproducibility. Contextualize your protocol and improve discovery with an accompanying Lab Protocol article in PLOS ONE .

Consistent reporting of Materials, Design, and Analysis – the MDAR checklist A cross-publisher group of editors and experts have developed, tested, and rolled out a checklist to help establish and harmonize reporting standards in the Life Sciences . The checklist , which is available for use by authors to compile their methods, and editors/reviewers to check methods, establishes a minimum set of requirements in transparent reporting and is adaptable to any discipline within the Life Sciences, by covering a breadth of potentially relevant methodological items and considerations. If you are in the Life Sciences and writing up your methods section, try working through the MDAR checklist and see whether it helps you include all relevant details into your methods, and whether it reminded you of anything you might have missed otherwise.

Summary Writing tips

The main challenge you may find when writing your methods is keeping it readable AND covering all the details needed for reproducibility and replicability. While this is difficult, do not compromise on rigorous standards for credibility!

• Keep in mind future replicability, alongside understanding and readability.
• Follow checklists, and field- and journal-specific guidelines.
• Consider a commitment to rigorous and transparent science a personal responsibility, and not just adhering to journal guidelines.
• Establish whether there are persistent identifiers for any research resources you use that can be specifically cited in your methods section.
• Deposit your laboratory protocols in Protocols.io, establishing a permanent link to them. You can update your protocols later if you improve on them, as can future scientists who follow your protocols.
• Consider visual aids like flow-diagrams, lists, to help with reading other sections of the paper.
• Be specific about all decisions made during the experiments that someone reproducing your work would need to know.

Don’t

• Summarize or abbreviate methods without giving full details in a discoverable supplemental section.
• Presume you will always be able to remember how you performed the experiments, or have access to private or institutional notebooks and resources.
• Attempt to hide constraints or non-optimal decisions you had to make–transparency is the key to ensuring the credibility of your research.
• How to Write a Great Title
• How to Write an Abstract
• How to Report Statistics
• How to Write Discussions and Conclusions
• How to Edit Your Work

The contents of the Peer Review Center are also available as a live, interactive training session, complete with slides, talking points, and activities. …

The contents of the Writing Center are also available as a live, interactive training session, complete with slides, talking points, and activities. …

There’s a lot to consider when deciding where to submit your work. Learn how to choose a journal that will help your study reach its audience, while reflecting your values as a researcher…

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How to Write the Methodology for Your Journal Article Effectively

Table of contents, a sneak peek, differentiating between methodology and methods, the role of methodology in adding research credibility, how a well-written methodology facilitates peer review, examples of research philosophies and approaches, data collection methods, the significance of discussing your data analysis process, examples of commonly used data analysis techniques, acknowledge potential ethical issues, explain your approach to ethics, discuss data protection, consider cultural sensitivity, step 1: revisit your research questions and objectives, step 2: explain your overall approach and rationale, step 3: describe your research design, step 4: provide details on data collection and instruments, step 5: explain your sampling method, step 6: describe your data analysis procedures, step 7: address ethical considerations, step 8: write in a clear, concise manner, step 9: maintain logical flow and organization, step 10: proofread extensively, being too vague, neglecting to justify choices, inappropriate level of detail, inconsistent structure, ignoring limitations, using jargon, introduction.

This article guides you on how to write the methodology for your journal article effectively and efficiently. In academic publishing , the methodology section is one of the most critical parts of drafting an academic journal article.

You will learn about methodology, why it is vital for your research, and how to craft one that adequately conveys the rationale behind your study design, data collection, and analysis techniques. We will also discuss common pitfalls to avoid when drafting your methodology.

By the end, you will have a solid understanding of how to structure your methodology section perfectly. You can justify your chosen research philosophy, outline your data collection procedures, explain your analysis methods, and address relevant ethical concerns. The tips and examples will help you write a methodology that adds credibility to your work and facilitates future replication studies.

In the coming sections, we will start by clearly defining a methodology and explaining why it is crucial for your academic article. We’ll then provide guidance on identifying your research philosophy and approach, detailing your study design and data collection techniques, discussing your analysis methods, and addressing ethical considerations.

The post will also include a step-by-step walkthrough of how to structure and write your methodology section. You’ll get tips to maintain clarity, precision, and flow in your writing. We’ll end by highlighting common mistakes to avoid when drafting this crucial part of your journal article.

Understanding What a Methodology Is

The methodology section is one of the most important parts of a research paper or journal publishing . It details the procedures and techniques the researcher uses to structure the study and collect and analyze data. But what exactly is a methodology?

In simple terms, the methodology explains the methods used in the research. It provides a description of the approaches, tools, materials, and procedures employed by the researcher to carry out the study. The methodology section allows readers to evaluate a study’s validity and reliability critically.

Some key elements covered in a methodology include:

• Research philosophy ( positivism , interpretivism , etc.)
• Research approach (deductive, inductive, etc.)
• Research design (experimental, survey, case study, etc.)
• Sampling techniques
• Data collection methods (interviews, surveys, observations)
• Data analysis methods (statistical analysis, coding, etc.)

The methodology refers to the overall strategy and rationale for the research process. The methods are specific procedures and techniques for collecting and analyzing data. The methodology provides the reasons for using specific methods and not others in a study. It justifies the research methods.

While the methodology outlines the broad principles and reasoning, the methods section provides meticulous details and a step-by-step account of the techniques applied to gather and make sense of the data. The methods explain how the study was conducted, while the methodology explains why particular methods were used.

To summarize, the methodology describes the overall approach and underpinning research framework, while the methods section offers a detailed account of the practical steps and processes followed in the study.

Why is Methodology Crucial for Your Journal Article?

A sound methodology is the foundation of credible and impactful research. The methodology section demonstrates the validity of your study by detailing how you systematically conducted the research. Here are some key reasons why methodology holds great significance for your journal article:

The methodology provides a window into the research process, allowing readers to evaluate your work critically. A robust methodology indicates that you have carefully considered the research design, data collection, and analysis techniques.

This adds to the overall credibility of the study findings and conclusions. Detailing a logical and scientifically sound methodology reassures readers that you have undertaken a rigorous and unbiased investigation.

During peer review , reviewers scrutinize the methodology to determine the research’s validity, reliability, and reproducibility. A clear, comprehensive, and coherent methodology enables reviewers to assess the technical quality of your work effectively.

Sound methodology allows other researchers to replicate your study and verify the results independently. Replication bolsters the authenticity of your findings. A concise methodology section makes your academic work more amenable to critical peer evaluation and replication – two pillars of the scientific process.

In short, an articulate, well-structured methodology enhances your journal article’s overall cogency and scientific merit. Investing efforts into crafting this crucial section can go a long way in getting your research published and positively received by the academic community. The methodology demonstrates methodological rigor and allows readers to judge the soundness of your work.

Identifying your Research Philosophy and Approach

Defining your research philosophy and approach is crucial when drafting a journal article’s methodology section. Your research philosophy refers to your beliefs about the nature of knowledge and reality, guiding your research. On the other hand, your research approach deals with the overall strategy and plan of action underpinning your study.

Clarifying your philosophical assumptions and approach from the outset is vital for several reasons:

• It helps establish your research’s intent, angle, and perspective from the start.
• It allows readers to understand your worldview and theoretical positioning as a researcher.
• A clear philosophy provides justification for your chosen methods and study design.
• It demonstrates methodological rigor and self-awareness as a researcher.

Some common research philosophies include positivism, interpretivism, pragmatism, constructivism, and post-positivism. Your choice depends on factors like your field of study, research aims, data collection methods, and preferred analysis techniques. When describing your philosophy, explain why it aligns with your research problem and goals.

Similarly, you need to identify and justify your overall research approach. There are three main approaches:

• Quantitative research – objective measures and statistical analysis, focusing on hypothesis testing
• Qualitative research – exploratory, focusing on meanings and experiences
• Mixed methods – combines quantitative and qualitative techniques as needed

Your research approach should logically follow your philosophical assumptions. For instance, a positivist philosophy typically lends itself to a quantitative approach. However, qualitative or mixed methods can also be suitable depending on the context.

The key is to state your chosen philosophy and approach upfront transparently. This provides a conceptual framework for readers to understand your methodology. Any deviations or mixed approaches should adequately justify and align with your research aims.

Here are some examples to illustrate how different research philosophies and approaches are typically described:

• A positivist philosophy with quantitative methods: “This study adopts a positivist philosophy and quantitative approach to test the hypothesis that…”
• An interpretivist philosophy with qualitative methods: “Aligned with an interpretivist philosophy, this study uses qualitative interviews to explore the subjective experiences of…”
• A pragmatist philosophy with mixed methods : “Guided by a pragmatist philosophy, this research employs a mixed methods approach, integrating quantitative surveys and qualitative case studies to…”

The author clearly states their philosophical stance and research approach in each example. This level of transparency is key in the methodology section. Readers can immediately grasp how the researcher’s worldview shapes their inquiry strategy.

In short, articulating your research philosophy and approach provides a conceptual anchor for your methodology. It also demonstrates methodological rigor and alignment between your research aims and techniques. Make sure to provide justification for your chosen philosophy and approach as well.

Detailing Your Research Design and Data Collection Methods

A clear and detailed description of your research design is crucial for a robust methodology section. Your research design refers to the overall strategy you chose to integrate the different components of the study in a coherent way to address your research problem effectively. It provides the blueprint for data collection, measurement, and analysis.

A well-articulated research design shows the logical sequence that connects the empirical data to the initial research questions and, ultimately, the conclusions drawn from the study.

When describing your research design, you need to provide sufficient information for readers to evaluate the appropriateness of your methods and the reliability and validity of your results. Key elements to mention are:

• Research design type (e.g., experimental, quasi-experimental, observational).
• Study setting.
• Population and sample.
• Variables, constructs, or phenomena under study.
• Any control or comparison groups, if applicable.

You should also justify why your chosen design aligns with your research aims and questions. For example, highlight why an experimental design may be preferred over an observational study to establish causality for your research problem.

In addition to the research design, you must elaborate on the techniques and procedures for collecting the required data. Data collection methods are broadly divided into:

• Primary methods: These involve first-hand data collection by the researcher using methods like interviews, surveys, observations, case studies, focus groups, etc.
• Secondary methods: These rely on already available data from sources like journals, census, organizational records, etc. Examples are literature/desk review, content/document analysis, etc.

For both primary and secondary data collection methods, discuss details like:

• Specific techniques (e.g., online survey, semi-structured interviews, etc.).
• Development and testing of data collection instruments (e.g., survey questionnaires).
• Study sample and sampling technique.
• Procedure adopted for data collection.
• Timeframe for data collection.

Providing this level of detail enables readers to judge the appropriateness of your data collection methods for the research problem and assess potential biases.

A detailed account of your research design and data collection techniques is vital for evaluating your research methodology’s overall rigor and quality.

Explaining Your Data Analysis Technique

The data analysis section is a crucial component of your methodology, demonstrating how you made sense of the data you collected. This section should provide a detailed account of your techniques to analyze your data and arrive at your findings.

Explaining your data analysis process allows readers to evaluate the appropriateness of your techniques. It also enables them to assess the reliability and validity of your results. Some key reasons for detailing your data analysis approach are:

• It demonstrates the logic behind your choice of analysis methods.
• It allows readers to judge the suitability of your analysis techniques for your specific research questions and data types.
• It gives credibility to your findings by providing a transparent account of how you analyzed the data.
• It enables other researchers to replicate your analysis process potentially.

Some commonly used qualitative and quantitative data analysis methods include:

• Thematic analysis – Identifying patterns and themes in qualitative data like interview transcripts.
• Content analysis – Systematically categorizing and analyzing qualitative data like documents or images.
• Discourse analysis – Studying language use and linguistic patterns in textual data.
• Statistical analysis – Techniques like regression, ANOVA, and t-tests for quantitative data.
• Data mining – Finding patterns and relationships in large quantitative datasets.

You should provide details like the tests performed, statistical software or tools used, variables examined, steps followed, etc., to allow readers to understand your analysis approach clearly.

Addressing Ethical Considerations

Ethically conducting research is a crucial component of developing a sound methodology. Here are some tips for effectively addressing ethical considerations in your methodology section:

Briefly acknowledge any potential ethical issues that may arise from your research, such as:

• Obtaining informed consent from participants.
• Protecting anonymity and confidentiality.
• Avoiding deception or distress to participants.
• Handling sensitive topics or vulnerable groups appropriately.

After identifying potential issues, explain how you addressed them ethically. For example:

• Note that participation was voluntary and that participants could withdraw at any time.
• Explain that anonymity was protected by using pseudonyms or codes instead of real names.
• Mention that approval was obtained from an ethics review board.

Discuss steps taken to protect data, such as:

• Storing data securely with password protection and encryption.
• Limiting access to identifiable data.
• Anonymizing data for analysis.
• Securely destroying data after a specified period.

If applicable, explain how you approached your research in a culturally sensitive manner, such as:

• Collaborating with local communities or leaders.
• Adapting methodology to cultural norms and values.
• Using culturally appropriate language and methods.

Addressing ethics builds trust with readers that you conducted your research responsibly. A brief but thoughtful discussion shows you are committed to integrity in your work.

Writing the Methodology: Step-by-Step Guide

Writing the methodology for your journal article is more manageable by breaking it down into clear steps. Here is a step-by-step guide on how to structure and write an effective methodology section:

The first step is to revisit the research questions and objectives you outlined at the start of your paper. Your methodology should clearly describe your specific methods to address these questions and meet the stated objectives.

Provide an overview of the approach you took in conducting your research. For example, did you use a quantitative, qualitative, or mixed methods approach? Explain why you selected this approach and how it aligns with your research questions.

Outline the specific type of research design you utilized, such as experimental, quasi-experimental, correlational, qualitative case study, ethnography, etc. Discuss critical details like the study population, variables, data collection timeline, etc.

Thoroughly describe how you collected data for your study. Mention specific instruments, like surveys, interview questions, observation checklists, etc. Include details on their validity and reliability if applicable.

Discuss how you selected participants for your study. Describe the sampling method used (e.g., random, stratified, purposive) and your sample size. Provide key details on the study participants, like demographics.

Outline the specific qualitative or statistical methods you used to analyze the data. Mention any software used and provide details on the specific types of analyses performed in line with your research design.

Discuss how you addressed confidentiality, informed consent, and any other ethical issues that arose during data collection and analysis. Provide information on how you obtained IRB approval, if applicable.

Use straightforward, formal language when writing your methodology section. Avoid unnecessary jargon and clarify discipline-specific terminology. Be concise yet provide sufficient detail and explanation.

Structure your writing in a logical order that flows well. Group related ideas and methods together into paragraphs. Use transitions between paragraphs to guide the reader through the discussion.

Carefully proofread your methodology section several times once completed. Check for typos, grammar errors, inconsistencies, omitted details, and lack of clarity. Refine and revise as needed.

These steps can help you draft a clear, comprehensive, and convincing methodology section for your academic paper. Maintaining precision and coherence in your writing is key to effectively conveying the rigor of your research process.

Common Mistakes to Avoid While Writing Your Methodology

When drafting the methodology section for a journal article, it’s easy to make mistakes that can undermine the credibility of your research. Here are some of the most common pitfalls authors should avoid:

One major mistake is insufficient details about the research methods and procedures. Using vague language like “participants completed surveys” or “data was analyzed” leaves the reader guessing. Be specific when describing sampling techniques, data collection tools, analysis methods, etc.

Simply stating the methods you used is not enough – you need to justify why those particular choices were made. For example, explain why a certain sample size was deemed suitable or why a specific analysis technique was selected. Justifying methodological choices demonstrates thoughtful research design.

Some authors provide excessive trivial detail while skimming over more important aspects. Prioritize key information readers need to evaluate your methodology. For specialized details, you can direct readers to citations or supplementary materials.

The methodology section should follow a logical structure, starting with the research design, sampling strategy, data collection procedures, and data analysis techniques. Jumping around between topics makes the methods confusing to follow.

No research is perfect, so failing to acknowledge limitations comes across as biased. Briefly discuss any methodological weaknesses, biases, or assumptions made to show readers you have critically assessed your research.

Technical terms and acronyms should be defined since not all readers know them. Strike a balance between using appropriate methodology terminology and ensuring your writing is accessible.

Following these tips will help you avoid common pitfalls when drafting the methodology for your journal article. Remember to be detailed yet concise, justify all choices, use consistent structure, acknowledge limitations, and avoid excessive jargon.

We have concluded this comprehensive guide on writing the perfect methodology section for your academic journal article. Let’s do a quick recap of the key points we covered:

We started by understanding the methodology section – the part of your paper where you explain the logic and rationale behind your research design and methods. A good methodology provides credibility to your findings and allows others to replicate your study.

We then examined the importance of early identification of your research philosophy and approach. Defining your worldview and perspective lays the foundation for your choice of methods. Some common philosophies are positivism, interpretivism, critical research, etc.

Next, we discussed the significance of clearly detailing your research design and data collection techniques. Remember to mention primary research methods like surveys, interviews, experiments, and secondary desk research methods.

You must also explain your qualitative, quantitative, or mixed data analysis methods to show how you made sense of the collected data. The use of appropriate data analysis software should be highlighted.

We also touched upon the ethical dimensions of research. Do acknowledge any ethical considerations and how you addressed them.

The step-by-step guide focused on the best practices for structuring your methodology section. Maintain logical flow, use transitions, and ensure coherence in your writing.

Finally, we explored some common mistakes to avoid – like not justifying methods, unclear writing, and lack of ethical considerations.

As you draft the methodology for your next journal article submission, implement the steps and tips suggested in this guide. Pay attention to the logical flow and articulate your methods clearly. This will go a long way in getting your paper accepted.

Here are a few ways you can continue the conversation:

• Share your top tips for writing a clear, comprehensive methodology section. What strategies have worked for you? What common pitfalls have you encountered, and how did you avoid them?
• Let us know if you have any lingering questions about writing methodologies that weren’t fully addressed in this post. We’re happy to provide more clarity and recommendations.
• Tell us about when you received particularly helpful feedback on a journal article methodology you wrote, either from editors, reviewers, or colleagues. What did you learn from that experience?
• Have you ever had a paper rejected due to a poorly written methodology section? What could you have done differently?
• For seasoned academic writers: share your advice for novice scholars writing their first journal article methodology. What do you wish you had known when you started?

Thank you for reading this guide on how to write the methodology for your journal article. We hope you feel equipped with the knowledge and tools to write a clear, comprehensive, compelling methodology section that will set your academic work apart.

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Organizing Your Social Sciences Research Paper

• 6. The Methodology
• Purpose of Guide
• Design Flaws to Avoid
• Independent and Dependent Variables
• Glossary of Research Terms
• Reading Research Effectively
• Narrowing a Topic Idea
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• Extending the Timeliness of a Topic Idea
• Academic Writing Style
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• Choosing a Title
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• The Research Problem/Question
• Theoretical Framework
• Citation Tracking
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• Primary Sources
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• Tiertiary Sources
• Scholarly vs. Popular Publications
• Qualitative Methods
• Quantitative Methods
• Insiderness
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• Common Grammar Mistakes
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The methods section describes actions taken to investigate a research problem and the rationale for the application of specific procedures or techniques used to identify, select, process, and analyze information applied to understanding the problem, thereby, allowing the reader to critically evaluate a study’s overall validity and reliability. The methodology section of a research paper answers two main questions: How was the data collected or generated? And, how was it analyzed? The writing should be direct and precise and always written in the past tense.

Kallet, Richard H. "How to Write the Methods Section of a Research Paper." Respiratory Care 49 (October 2004): 1229-1232.

Importance of a Good Methodology Section

You must explain how you obtained and analyzed your results for the following reasons:

• Readers need to know how the data was obtained because the method you chose affects the results and, by extension, how you interpreted their significance in the discussion section of your paper.
• Methodology is crucial for any branch of scholarship because an unreliable method produces unreliable results and, as a consequence, undermines the value of your analysis of the findings.
• In most cases, there are a variety of different methods you can choose to investigate a research problem. The methodology section of your paper should clearly articulate the reasons why you have chosen a particular procedure or technique.
• The reader wants to know that the data was collected or generated in a way that is consistent with accepted practice in the field of study. For example, if you are using a multiple choice questionnaire, readers need to know that it offered your respondents a reasonable range of answers to choose from.
• The method must be appropriate to fulfilling the overall aims of the study. For example, you need to ensure that you have a large enough sample size to be able to generalize and make recommendations based upon the findings.
• The methodology should discuss the problems that were anticipated and the steps you took to prevent them from occurring. For any problems that do arise, you must describe the ways in which they were minimized or why these problems do not impact in any meaningful way your interpretation of the findings.
• In the social and behavioral sciences, it is important to always provide sufficient information to allow other researchers to adopt or replicate your methodology. This information is particularly important when a new method has been developed or an innovative use of an existing method is utilized.

Bem, Daryl J. Writing the Empirical Journal Article. Psychology Writing Center. University of Washington; Denscombe, Martyn. The Good Research Guide: For Small-Scale Social Research Projects . 5th edition. Buckingham, UK: Open University Press, 2014; Lunenburg, Frederick C. Writing a Successful Thesis or Dissertation: Tips and Strategies for Students in the Social and Behavioral Sciences . Thousand Oaks, CA: Corwin Press, 2008.

Structure and Writing Style

I.  Groups of Research Methods

There are two main groups of research methods in the social sciences:

• The e mpirical-analytical group approaches the study of social sciences in a similar manner that researchers study the natural sciences . This type of research focuses on objective knowledge, research questions that can be answered yes or no, and operational definitions of variables to be measured. The empirical-analytical group employs deductive reasoning that uses existing theory as a foundation for formulating hypotheses that need to be tested. This approach is focused on explanation.
• The i nterpretative group of methods is focused on understanding phenomenon in a comprehensive, holistic way . Interpretive methods focus on analytically disclosing the meaning-making practices of human subjects [the why, how, or by what means people do what they do], while showing how those practices arrange so that it can be used to generate observable outcomes. Interpretive methods allow you to recognize your connection to the phenomena under investigation. However, the interpretative group requires careful examination of variables because it focuses more on subjective knowledge.

II.  Content

The introduction to your methodology section should begin by restating the research problem and underlying assumptions underpinning your study. This is followed by situating the methods you used to gather, analyze, and process information within the overall “tradition” of your field of study and within the particular research design you have chosen to study the problem. If the method you choose lies outside of the tradition of your field [i.e., your review of the literature demonstrates that the method is not commonly used], provide a justification for how your choice of methods specifically addresses the research problem in ways that have not been utilized in prior studies.

The remainder of your methodology section should describe the following:

• Decisions made in selecting the data you have analyzed or, in the case of qualitative research, the subjects and research setting you have examined,
• Tools and methods used to identify and collect information, and how you identified relevant variables,
• The ways in which you processed the data and the procedures you used to analyze that data, and
• The specific research tools or strategies that you utilized to study the underlying hypothesis and research questions.

In addition, an effectively written methodology section should:

• Introduce the overall methodological approach for investigating your research problem . Is your study qualitative or quantitative or a combination of both (mixed method)? Are you going to take a special approach, such as action research, or a more neutral stance?
• Indicate how the approach fits the overall research design . Your methods for gathering data should have a clear connection to your research problem. In other words, make sure that your methods will actually address the problem. One of the most common deficiencies found in research papers is that the proposed methodology is not suitable to achieving the stated objective of your paper.
• Describe the specific methods of data collection you are going to use , such as, surveys, interviews, questionnaires, observation, archival research. If you are analyzing existing data, such as a data set or archival documents, describe how it was originally created or gathered and by whom. Also be sure to explain how older data is still relevant to investigating the current research problem.
• Explain how you intend to analyze your results . Will you use statistical analysis? Will you use specific theoretical perspectives to help you analyze a text or explain observed behaviors? Describe how you plan to obtain an accurate assessment of relationships, patterns, trends, distributions, and possible contradictions found in the data.
• Provide background and a rationale for methodologies that are unfamiliar for your readers . Very often in the social sciences, research problems and the methods for investigating them require more explanation/rationale than widely accepted rules governing the natural and physical sciences. Be clear and concise in your explanation.
• Provide a justification for subject selection and sampling procedure . For instance, if you propose to conduct interviews, how do you intend to select the sample population? If you are analyzing texts, which texts have you chosen, and why? If you are using statistics, why is this set of data being used? If other data sources exist, explain why the data you chose is most appropriate to addressing the research problem.
• Provide a justification for case study selection . A common method of analyzing research problems in the social sciences is to analyze specific cases. These can be a person, place, event, phenomenon, or other type of subject of analysis that are either examined as a singular topic of in-depth investigation or multiple topics of investigation studied for the purpose of comparing or contrasting findings. In either method, you should explain why a case or cases were chosen and how they specifically relate to the research problem.
• Describe potential limitations . Are there any practical limitations that could affect your data collection? How will you attempt to control for potential confounding variables and errors? If your methodology may lead to problems you can anticipate, state this openly and show why pursuing this methodology outweighs the risk of these problems cropping up.

NOTE :   Once you have written all of the elements of the methods section, subsequent revisions should focus on how to present those elements as clearly and as logically as possibly. The description of how you prepared to study the research problem, how you gathered the data, and the protocol for analyzing the data should be organized chronologically. For clarity, when a large amount of detail must be presented, information should be presented in sub-sections according to topic. If necessary, consider using appendices for raw data.

ANOTHER NOTE : If you are conducting a qualitative analysis of a research problem , the methodology section generally requires a more elaborate description of the methods used as well as an explanation of the processes applied to gathering and analyzing of data than is generally required for studies using quantitative methods. Because you are the primary instrument for generating the data [e.g., through interviews or observations], the process for collecting that data has a significantly greater impact on producing the findings. Therefore, qualitative research requires a more detailed description of the methods used.

YET ANOTHER NOTE :   If your study involves interviews, observations, or other qualitative techniques involving human subjects , you may be required to obtain approval from the university's Office for the Protection of Research Subjects before beginning your research. This is not a common procedure for most undergraduate level student research assignments. However, i f your professor states you need approval, you must include a statement in your methods section that you received official endorsement and adequate informed consent from the office and that there was a clear assessment and minimization of risks to participants and to the university. This statement informs the reader that your study was conducted in an ethical and responsible manner. In some cases, the approval notice is included as an appendix to your paper.

III.  Problems to Avoid

Irrelevant Detail The methodology section of your paper should be thorough but concise. Do not provide any background information that does not directly help the reader understand why a particular method was chosen, how the data was gathered or obtained, and how the data was analyzed in relation to the research problem [note: analyzed, not interpreted! Save how you interpreted the findings for the discussion section]. With this in mind, the page length of your methods section will generally be less than any other section of your paper except the conclusion.

Unnecessary Explanation of Basic Procedures Remember that you are not writing a how-to guide about a particular method. You should make the assumption that readers possess a basic understanding of how to investigate the research problem on their own and, therefore, you do not have to go into great detail about specific methodological procedures. The focus should be on how you applied a method , not on the mechanics of doing a method. An exception to this rule is if you select an unconventional methodological approach; if this is the case, be sure to explain why this approach was chosen and how it enhances the overall process of discovery.

Problem Blindness It is almost a given that you will encounter problems when collecting or generating your data, or, gaps will exist in existing data or archival materials. Do not ignore these problems or pretend they did not occur. Often, documenting how you overcame obstacles can form an interesting part of the methodology. It demonstrates to the reader that you can provide a cogent rationale for the decisions you made to minimize the impact of any problems that arose.

Literature Review Just as the literature review section of your paper provides an overview of sources you have examined while researching a particular topic, the methodology section should cite any sources that informed your choice and application of a particular method [i.e., the choice of a survey should include any citations to the works you used to help construct the survey].

It’s More than Sources of Information! A description of a research study's method should not be confused with a description of the sources of information. Such a list of sources is useful in and of itself, especially if it is accompanied by an explanation about the selection and use of the sources. The description of the project's methodology complements a list of sources in that it sets forth the organization and interpretation of information emanating from those sources.

Azevedo, L.F. et al. "How to Write a Scientific Paper: Writing the Methods Section." Revista Portuguesa de Pneumologia 17 (2011): 232-238; Blair Lorrie. “Choosing a Methodology.” In Writing a Graduate Thesis or Dissertation , Teaching Writing Series. (Rotterdam: Sense Publishers 2016), pp. 49-72; Butin, Dan W. The Education Dissertation A Guide for Practitioner Scholars . Thousand Oaks, CA: Corwin, 2010; Carter, Susan. Structuring Your Research Thesis . New York: Palgrave Macmillan, 2012; Kallet, Richard H. “How to Write the Methods Section of a Research Paper.” Respiratory Care 49 (October 2004):1229-1232; Lunenburg, Frederick C. Writing a Successful Thesis or Dissertation: Tips and Strategies for Students in the Social and Behavioral Sciences . Thousand Oaks, CA: Corwin Press, 2008. Methods Section. The Writer’s Handbook. Writing Center. University of Wisconsin, Madison; Rudestam, Kjell Erik and Rae R. Newton. “The Method Chapter: Describing Your Research Plan.” In Surviving Your Dissertation: A Comprehensive Guide to Content and Process . (Thousand Oaks, Sage Publications, 2015), pp. 87-115; What is Interpretive Research. Institute of Public and International Affairs, University of Utah; Writing the Experimental Report: Methods, Results, and Discussion. The Writing Lab and The OWL. Purdue University; Methods and Materials. The Structure, Format, Content, and Style of a Journal-Style Scientific Paper. Department of Biology. Bates College.

Writing Tip

Statistical Designs and Tests? Do Not Fear Them!

Don't avoid using a quantitative approach to analyzing your research problem just because you fear the idea of applying statistical designs and tests. A qualitative approach, such as conducting interviews or content analysis of archival texts, can yield exciting new insights about a research problem, but it should not be undertaken simply because you have a disdain for running a simple regression. A well designed quantitative research study can often be accomplished in very clear and direct ways, whereas, a similar study of a qualitative nature usually requires considerable time to analyze large volumes of data and a tremendous burden to create new paths for analysis where previously no path associated with your research problem had existed.

To locate data and statistics, GO HERE .

Another Writing Tip

Knowing the Relationship Between Theories and Methods

There can be multiple meaning associated with the term "theories" and the term "methods" in social sciences research. A helpful way to delineate between them is to understand "theories" as representing different ways of characterizing the social world when you research it and "methods" as representing different ways of generating and analyzing data about that social world. Framed in this way, all empirical social sciences research involves theories and methods, whether they are stated explicitly or not. However, while theories and methods are often related, it is important that, as a researcher, you deliberately separate them in order to avoid your theories playing a disproportionate role in shaping what outcomes your chosen methods produce.

Introspectively engage in an ongoing dialectic between the application of theories and methods to help enable you to use the outcomes from your methods to interrogate and develop new theories, or ways of framing conceptually the research problem. This is how scholarship grows and branches out into new intellectual territory.

Reynolds, R. Larry. Ways of Knowing. Alternative Microeconomics . Part 1, Chapter 3. Boise State University; The Theory-Method Relationship. S-Cool Revision. United Kingdom.

Yet Another Writing Tip

Methods and the Methodology

Do not confuse the terms "methods" and "methodology." As Schneider notes, a method refers to the technical steps taken to do research . Descriptions of methods usually include defining and stating why you have chosen specific techniques to investigate a research problem, followed by an outline of the procedures you used to systematically select, gather, and process the data [remember to always save the interpretation of data for the discussion section of your paper].

The methodology refers to a discussion of the underlying reasoning why particular methods were used . This discussion includes describing the theoretical concepts that inform the choice of methods to be applied, placing the choice of methods within the more general nature of academic work, and reviewing its relevance to examining the research problem. The methodology section also includes a thorough review of the methods other scholars have used to study the topic.

Bryman, Alan. "Of Methods and Methodology." Qualitative Research in Organizations and Management: An International Journal 3 (2008): 159-168; Schneider, Florian. “What's in a Methodology: The Difference between Method, Methodology, and Theory…and How to Get the Balance Right?” PoliticsEastAsia.com. Chinese Department, University of Leiden, Netherlands.

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Here's What You Need to Understand About Research Methodology

Table of Contents

Research methodology involves a systematic and well-structured approach to conducting scholarly or scientific inquiries. Knowing the significance of research methodology and its different components is crucial as it serves as the basis for any study.

Typically, your research topic will start as a broad idea you want to investigate more thoroughly. Once you’ve identified a research problem and created research questions , you must choose the appropriate methodology and frameworks to address those questions effectively.

What is the definition of a research methodology?

Research methodology is the process or the way you intend to execute your study. The methodology section of a research paper outlines how you plan to conduct your study. It covers various steps such as collecting data, statistical analysis, observing participants, and other procedures involved in the research process

The methods section should give a description of the process that will convert your idea into a study. Additionally, the outcomes of your process must provide valid and reliable results resonant with the aims and objectives of your research. This thumb rule holds complete validity, no matter whether your paper has inclinations for qualitative or quantitative usage.

Studying research methods used in related studies can provide helpful insights and direction for your own research. Now easily discover papers related to your topic on SciSpace and utilize our AI research assistant, Copilot , to quickly review the methodologies applied in different papers.

The need for a good research methodology

While deciding on your approach towards your research, the reason or factors you weighed in choosing a particular problem and formulating a research topic need to be validated and explained. A research methodology helps you do exactly that. Moreover, a good research methodology lets you build your argument to validate your research work performed through various data collection methods, analytical methods, and other essential points.

Just imagine it as a strategy documented to provide an overview of what you intend to do.

While undertaking any research writing or performing the research itself, you may get drifted in not something of much importance. In such a case, a research methodology helps you to get back to your outlined work methodology.

A research methodology helps in keeping you accountable for your work. Additionally, it can help you evaluate whether your work is in sync with your original aims and objectives or not. Besides, a good research methodology enables you to navigate your research process smoothly and swiftly while providing effective planning to achieve your desired results.

What is the basic structure of a research methodology?

Usually, you must ensure to include the following stated aspects while deciding over the basic structure of your research methodology:

1. Your research procedure

Explain what research methods you’re going to use. Whether you intend to proceed with quantitative or qualitative, or a composite of both approaches, you need to state that explicitly. The option among the three depends on your research’s aim, objectives, and scope.

2. Provide the rationality behind your chosen approach

Based on logic and reason, let your readers know why you have chosen said research methodologies. Additionally, you have to build strong arguments supporting why your chosen research method is the best way to achieve the desired outcome.

3. Explain your mechanism

The mechanism encompasses the research methods or instruments you will use to develop your research methodology. It usually refers to your data collection methods. You can use interviews, surveys, physical questionnaires, etc., of the many available mechanisms as research methodology instruments. The data collection method is determined by the type of research and whether the data is quantitative data(includes numerical data) or qualitative data (perception, morale, etc.) Moreover, you need to put logical reasoning behind choosing a particular instrument.

4. Significance of outcomes

The results will be available once you have finished experimenting. However, you should also explain how you plan to use the data to interpret the findings. This section also aids in understanding the problem from within, breaking it down into pieces, and viewing the research problem from various perspectives.

5. Reader’s advice

Anything that you feel must be explained to spread more awareness among readers and focus groups must be included and described in detail. You should not just specify your research methodology on the assumption that a reader is aware of the topic.  

All the relevant information that explains and simplifies your research paper must be included in the methodology section. If you are conducting your research in a non-traditional manner, give a logical justification and list its benefits.

6. Explain your sample space

Include information about the sample and sample space in the methodology section. The term "sample" refers to a smaller set of data that a researcher selects or chooses from a larger group of people or focus groups using a predetermined selection method. Let your readers know how you are going to distinguish between relevant and non-relevant samples. How you figured out those exact numbers to back your research methodology, i.e. the sample spacing of instruments, must be discussed thoroughly.

For example, if you are going to conduct a survey or interview, then by what procedure will you select the interviewees (or sample size in case of surveys), and how exactly will the interview or survey be conducted.

7. Challenges and limitations

This part, which is frequently assumed to be unnecessary, is actually very important. The challenges and limitations that your chosen strategy inherently possesses must be specified while you are conducting different types of research.

The importance of a good research methodology

You must have observed that all research papers, dissertations, or theses carry a chapter entirely dedicated to research methodology. This section helps maintain your credibility as a better interpreter of results rather than a manipulator.

A good research methodology always explains the procedure, data collection methods and techniques, aim, and scope of the research. In a research study, it leads to a well-organized, rationality-based approach, while the paper lacking it is often observed as messy or disorganized.

You should pay special attention to validating your chosen way towards the research methodology. This becomes extremely important in case you select an unconventional or a distinct method of execution.

Curating and developing a strong, effective research methodology can assist you in addressing a variety of situations, such as:

• When someone tries to duplicate or expand upon your research after few years.
• If a contradiction or conflict of facts occurs at a later time. This gives you the security you need to deal with these contradictions while still being able to defend your approach.
• Gaining a tactical approach in getting your research completed in time. Just ensure you are using the right approach while drafting your research methodology, and it can help you achieve your desired outcomes. Additionally, it provides a better explanation and understanding of the research question itself.
• Documenting the results so that the final outcome of the research stays as you intended it to be while starting.

Instruments you could use while writing a good research methodology

As a researcher, you must choose which tools or data collection methods that fit best in terms of the relevance of your research. This decision has to be wise.

There exists many research equipments or tools that you can use to carry out your research process. These are classified as:

a. Interviews (One-on-One or a Group)

An interview aimed to get your desired research outcomes can be undertaken in many different ways. For example, you can design your interview as structured, semi-structured, or unstructured. What sets them apart is the degree of formality in the questions. On the other hand, in a group interview, your aim should be to collect more opinions and group perceptions from the focus groups on a certain topic rather than looking out for some formal answers.

In surveys, you are in better control if you specifically draft the questions you seek the response for. For example, you may choose to include free-style questions that can be answered descriptively, or you may provide a multiple-choice type response for questions. Besides, you can also opt to choose both ways, deciding what suits your research process and purpose better.

c. Sample Groups

Similar to the group interviews, here, you can select a group of individuals and assign them a topic to discuss or freely express their opinions over that. You can simultaneously note down the answers and later draft them appropriately, deciding on the relevance of every response.

d. Observations

If your research domain is humanities or sociology, observations are the best-proven method to draw your research methodology. Of course, you can always include studying the spontaneous response of the participants towards a situation or conducting the same but in a more structured manner. A structured observation means putting the participants in a situation at a previously decided time and then studying their responses.

Of all the tools described above, it is you who should wisely choose the instruments and decide what’s the best fit for your research. You must not restrict yourself from multiple methods or a combination of a few instruments if appropriate in drafting a good research methodology.

Types of research methodology

A research methodology exists in various forms. Depending upon their approach, whether centered around words, numbers, or both, methodologies are distinguished as qualitative, quantitative, or an amalgamation of both.

1. Qualitative research methodology

When a research methodology primarily focuses on words and textual data, then it is generally referred to as qualitative research methodology. This type is usually preferred among researchers when the aim and scope of the research are mainly theoretical and explanatory.

The instruments used are observations, interviews, and sample groups. You can use this methodology if you are trying to study human behavior or response in some situations. Generally, qualitative research methodology is widely used in sociology, psychology, and other related domains.

2. Quantitative research methodology

If your research is majorly centered on data, figures, and stats, then analyzing these numerical data is often referred to as quantitative research methodology. You can use quantitative research methodology if your research requires you to validate or justify the obtained results.

In quantitative methods, surveys, tests, experiments, and evaluations of current databases can be advantageously used as instruments If your research involves testing some hypothesis, then use this methodology.

3. Amalgam methodology

As the name suggests, the amalgam methodology uses both quantitative and qualitative approaches. This methodology is used when a part of the research requires you to verify the facts and figures, whereas the other part demands you to discover the theoretical and explanatory nature of the research question.

The instruments for the amalgam methodology require you to conduct interviews and surveys, including tests and experiments. The outcome of this methodology can be insightful and valuable as it provides precise test results in line with theoretical explanations and reasoning.

The amalgam method, makes your work both factual and rational at the same time.

Final words: How to decide which is the best research methodology?

If you have kept your sincerity and awareness intact with the aims and scope of research well enough, you must have got an idea of which research methodology suits your work best.

Before deciding which research methodology answers your research question, you must invest significant time in reading and doing your homework for that. Taking references that yield relevant results should be your first approach to establishing a research methodology.

Moreover, you should never refrain from exploring other options. Before setting your work in stone, you must try all the available options as it explains why the choice of research methodology that you finally make is more appropriate than the other available options.

You should always go for a quantitative research methodology if your research requires gathering large amounts of data, figures, and statistics. This research methodology will provide you with results if your research paper involves the validation of some hypothesis.

Whereas, if  you are looking for more explanations, reasons, opinions, and public perceptions around a theory, you must use qualitative research methodology.The choice of an appropriate research methodology ultimately depends on what you want to achieve through your research.

Frequently Asked Questions (FAQs) about Research Methodology

1. how to write a research methodology.

You can always provide a separate section for research methodology where you should specify details about the methods and instruments used during the research, discussions on result analysis, including insights into the background information, and conveying the research limitations.

2. What are the types of research methodology?

There generally exists four types of research methodology i.e.

• Observation
• Experimental
• Derivational

3. What is the true meaning of research methodology?

The set of techniques or procedures followed to discover and analyze the information gathered to validate or justify a research outcome is generally called Research Methodology.

4. Where lies the importance of research methodology?

Your research methodology directly reflects the validity of your research outcomes and how well-informed your research work is. Moreover, it can help future researchers cite or refer to your research if they plan to use a similar research methodology.

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Journal Article: Methods

Criteria for success.

A successful Methods section:

• provides the reasons for choosing your methodology
• allows readers to confirm your findings through replication

Compare Authentic Annotated Examples for Methods and Results . Note the correspondence of subheadings between the two sections.

Identify Your Purpose

The purpose of a Methods section is to describe how the questions/knowledge gap posed in the Introduction were answered in the Results section. Not all readers will be interested in this information. For those who are, the Methods section has two purposes:

1. Allow readers to judge whether the results and conclusions of the study are valid.

The interpretation of your results depends on the methods you used to obtain them. A reader who is skeptical of your results will read your Methods section to see if they can be trusted. They’ll want to know that you chose the most appropriate methods and performed the necessary controls. Without this content, skeptical readers might think your data and any conclusions drawn from them are unreliable.

2. Allow readers to repeat the study.

For readers interested in replicating your study, the Methods section should provide enough information for them to obtain the same or similar results.

Analyze your audience

Typically, only readers in your field will want to replicate your study or have the knowledge to assess your methodology. More general audiences will read the Introduction and then proceed straight to the Results. You can therefore assume that people reading your Methods understand methodologies that are frequently used in your field. To gauge the level of detail necessary for a given method, you can look at articles previously published in your target journal.

If your paper is designed to appeal to experts in more than one field, you still need to write your Methods for a single set of experts. For example, say you applied a novel computational approach to gain new insight into a well-characterized biological system. Is your goal to get to show biologists the value of your computational tool or to show computational scientists how they can help study biology? In the former case, assume less computational expertise: provide more extensive explanations for how methods work and why they were chosen.

State the reasons for choosing your methodology

A reader looking to assess your methodology will read your Methods section to judge your experimental design. When describing your approach, place more emphasis on how you applied a method rather than on how you performed the method. For example, you don’t need to explain how to perform a western blot, but you might want to describe why a western blot is an appropriate approach for the task at hand (and, potentially, why you didn’t use another method).

Use subheadings to organize content

As recommended for your Results section , use subheadings within your Methods to group related experiments and establish a logical flow. Write your Results section first, and then follow the order of Results subheadings when writing your Methods. The parallel structure will make it easy for readers to locate corresponding information in the two sections.

Subheadings for Methods and Results may not exactly correspond. Sometimes you may need multiple Methods subheadings to explain one Results subheading. Other times, one Method subheading is enough to explain multiple Result subheadings.

Provide minimal essential detail

Provide only those details necessary for a reader to replicate the experiments presented in your study; anything more is extraneous. Remember that readers use Methods to help them assess the validity of your conclusions, so specify any methodological details that might cause someone to reach a different conclusion.

You can cite papers for standard methods, but any modifications or alterations should be clearly stated. When citing methods, cite the original paper in which a method was described instead of a paper that used the method. This helps avoid chains of citations that your reader must follow to find information about the method.

Avoid “we did…” or “the authors did…”

The Methods section should focus on the experiments, not the authors. Avoid phrasing your experiments as “We/The authors did ___”, even if it requires you to write in the passive voice.

“Samples were processed with standard DNA extraction protocols.”

“We processed the samples with standard DNA extraction protocols.”

This content was adapted from from an article originally created by the  MIT Biological Engineering Communication Lab .

Resources and Annotated Examples

Annotated example 1.

Zetsche et al. , "Cpf1 is a single RNA-guided endonuclease...", Cell 2015. Compare to the annotated examples in the Results section. 2 MB

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Scholarly Articles: How can I tell?

• Journal Information
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Methodology

• Research sponsors
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The methodology section or methods section tells you how the author(s) went about doing their research. It should let you know a) what method they used to gather data (survey, interviews, experiments, etc.), why they chose this method, and what the limitations are to this method.

The methodology section should be detailed enough that another researcher could replicate the study described. When you read the methodology or methods section:

• What kind of research method did the authors use? Is it an appropriate method for the type of study they are conducting?
• How did the authors get their tests subjects? What criteria did they use?
• What are the contexts of the study that may have affected the results (e.g. environmental conditions, lab conditions, timing questions, etc.)
• Is the sample size representative of the larger population (i.e., was it big enough?)
• Are the data collection instruments and procedures likely to have measured all the important characteristics with reasonable accuracy?
• Does the data analysis appear to have been done with care, and were appropriate analytical techniques used? 

A good researcher will always let you know about the limitations of his or her research.

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Research Guide: Scholarly Journals

Methodology.

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Reviewing the methodology section

The image below show the Methods section of the article, where the authors are outlining how they carried out their study.

(click on image to enlarge)

• The Methodology section of the article describes the procedures, or methods, that were used to carry out the research study.
• The methodology the authors follow will vary according to the discipline, or field of study, the research relates to. 
• Types of methodology include case studies, scientific experiments, field studies, focus groups, and surveys.
• You may not need to spend much time focusing on the details of this section unless you want to replicate the experiment yourself.
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How To Write The Methodology Chapter

The what, why & how explained simply (with examples).

By: Jenna Crossley (PhD) | Reviewed By: Dr. Eunice Rautenbach | September 2021 (Updated April 2023)

So, you’ve pinned down your research topic and undertaken a review of the literature – now it’s time to write up the methodology section of your dissertation, thesis or research paper . But what exactly is the methodology chapter all about – and how do you go about writing one? In this post, we’ll unpack the topic, step by step .

Overview: The Methodology Chapter

• The purpose  of the methodology chapter
• Why you need to craft this chapter (really) well
• How to write and structure the chapter
• Methodology chapter example
• Essential takeaways

What (exactly) is the methodology chapter?

The methodology chapter is where you outline the philosophical underpinnings of your research and outline the specific methodological choices you’ve made. The point of the methodology chapter is to tell the reader exactly how you designed your study and, just as importantly, why you did it this way.

Importantly, this chapter should comprehensively describe and justify all the methodological choices you made in your study. For example, the approach you took to your research (i.e., qualitative, quantitative or mixed), who  you collected data from (i.e., your sampling strategy), how you collected your data and, of course, how you analysed it. If that sounds a little intimidating, don’t worry – we’ll explain all these methodological choices in this post .

Why is the methodology chapter important?

The methodology chapter plays two important roles in your dissertation or thesis:

Firstly, it demonstrates your understanding of research theory, which is what earns you marks. A flawed research design or methodology would mean flawed results. So, this chapter is vital as it allows you to show the marker that you know what you’re doing and that your results are credible .

Secondly, the methodology chapter is what helps to make your study replicable. In other words, it allows other researchers to undertake your study using the same methodological approach, and compare their findings to yours. This is very important within academic research, as each study builds on previous studies.

The methodology chapter is also important in that it allows you to identify and discuss any methodological issues or problems you encountered (i.e., research limitations ), and to explain how you mitigated the impacts of these. Every research project has its limitations , so it’s important to acknowledge these openly and highlight your study’s value despite its limitations . Doing so demonstrates your understanding of research design, which will earn you marks. We’ll discuss limitations in a bit more detail later in this post, so stay tuned!

Need a helping hand?

How to write up the methodology chapter

First off, it’s worth noting that the exact structure and contents of the methodology chapter will vary depending on the field of research (e.g., humanities, chemistry or engineering) as well as the university . So, be sure to always check the guidelines provided by your institution for clarity and, if possible, review past dissertations from your university. Here we’re going to discuss a generic structure for a methodology chapter typically found in the sciences.

Before you start writing, it’s always a good idea to draw up a rough outline to guide your writing. Don’t just start writing without knowing what you’ll discuss where. If you do, you’ll likely end up with a disjointed, ill-flowing narrative . You’ll then waste a lot of time rewriting in an attempt to try to stitch all the pieces together. Do yourself a favour and start with the end in mind .

Section 1 – Introduction

As with all chapters in your dissertation or thesis, the methodology chapter should have a brief introduction. In this section, you should remind your readers what the focus of your study is, especially the research aims . As we’ve discussed many times on the blog, your methodology needs to align with your research aims, objectives and research questions. Therefore, it’s useful to frontload this component to remind the reader (and yourself!) what you’re trying to achieve.

In this section, you can also briefly mention how you’ll structure the chapter. This will help orient the reader and provide a bit of a roadmap so that they know what to expect. You don’t need a lot of detail here – just a brief outline will do.

Section 2 – The Methodology

The next section of your chapter is where you’ll present the actual methodology. In this section, you need to detail and justify the key methodological choices you’ve made in a logical, intuitive fashion. Importantly, this is the heart of your methodology chapter, so you need to get specific – don’t hold back on the details here. This is not one of those “less is more” situations.

Let’s take a look at the most common components you’ll likely need to cover. 

Methodological Choice #1 – Research Philosophy

Research philosophy refers to the underlying beliefs (i.e., the worldview) regarding how data about a phenomenon should be gathered , analysed and used . The research philosophy will serve as the core of your study and underpin all of the other research design choices, so it’s critically important that you understand which philosophy you’ll adopt and why you made that choice. If you’re not clear on this, take the time to get clarity before you make any further methodological choices.

While several research philosophies exist, two commonly adopted ones are positivism and interpretivism . These two sit roughly on opposite sides of the research philosophy spectrum.

Positivism states that the researcher can observe reality objectively and that there is only one reality, which exists independently of the observer. As a consequence, it is quite commonly the underlying research philosophy in quantitative studies and is oftentimes the assumed philosophy in the physical sciences.

Contrasted with this, interpretivism , which is often the underlying research philosophy in qualitative studies, assumes that the researcher performs a role in observing the world around them and that reality is unique to each observer . In other words, reality is observed subjectively .

These are just two philosophies (there are many more), but they demonstrate significantly different approaches to research and have a significant impact on all the methodological choices. Therefore, it’s vital that you clearly outline and justify your research philosophy at the beginning of your methodology chapter, as it sets the scene for everything that follows.

Methodological Choice #2 – Research Type

The next thing you would typically discuss in your methodology section is the research type. The starting point for this is to indicate whether the research you conducted is inductive or deductive .

Inductive research takes a bottom-up approach , where the researcher begins with specific observations or data and then draws general conclusions or theories from those observations. Therefore these studies tend to be exploratory in terms of approach.

Conversely , d eductive research takes a top-down approach , where the researcher starts with a theory or hypothesis and then tests it using specific observations or data. Therefore these studies tend to be confirmatory in approach.

Related to this, you’ll need to indicate whether your study adopts a qualitative, quantitative or mixed  approach. As we’ve mentioned, there’s a strong link between this choice and your research philosophy, so make sure that your choices are tightly aligned . When you write this section up, remember to clearly justify your choices, as they form the foundation of your study.

Methodological Choice #3 – Research Strategy

Next, you’ll need to discuss your research strategy (also referred to as a research design ). This methodological choice refers to the broader strategy in terms of how you’ll conduct your research, based on the aims of your study.

Several research strategies exist, including experimental , case studies , ethnography , grounded theory, action research , and phenomenology . Let’s take a look at two of these, experimental and ethnographic, to see how they contrast.

Experimental research makes use of the scientific method , where one group is the control group (in which no variables are manipulated ) and another is the experimental group (in which a specific variable is manipulated). This type of research is undertaken under strict conditions in a controlled, artificial environment (e.g., a laboratory). By having firm control over the environment, experimental research typically allows the researcher to establish causation between variables. Therefore, it can be a good choice if you have research aims that involve identifying causal relationships.

Ethnographic research , on the other hand, involves observing and capturing the experiences and perceptions of participants in their natural environment (for example, at home or in the office). In other words, in an uncontrolled environment.  Naturally, this means that this research strategy would be far less suitable if your research aims involve identifying causation, but it would be very valuable if you’re looking to explore and examine a group culture, for example.

As you can see, the right research strategy will depend largely on your research aims and research questions – in other words, what you’re trying to figure out. Therefore, as with every other methodological choice, it’s essential to justify why you chose the research strategy you did.

Methodological Choice #4 – Time Horizon

The next thing you’ll need to detail in your methodology chapter is the time horizon. There are two options here: cross-sectional and longitudinal . In other words, whether the data for your study were all collected at one point in time (cross-sectional) or at multiple points in time (longitudinal).

The choice you make here depends again on your research aims, objectives and research questions. If, for example, you aim to assess how a specific group of people’s perspectives regarding a topic change over time , you’d likely adopt a longitudinal time horizon.

Another important factor to consider is simply whether you have the time necessary to adopt a longitudinal approach (which could involve collecting data over multiple months or even years). Oftentimes, the time pressures of your degree program will force your hand into adopting a cross-sectional time horizon, so keep this in mind.

Methodological Choice #5 – Sampling Strategy

Next, you’ll need to discuss your sampling strategy . There are two main categories of sampling, probability and non-probability sampling.

Probability sampling involves a random (and therefore representative) selection of participants from a population, whereas non-probability sampling entails selecting participants in a non-random  (and therefore non-representative) manner. For example, selecting participants based on ease of access (this is called a convenience sample).

The right sampling approach depends largely on what you’re trying to achieve in your study. Specifically, whether you trying to develop findings that are generalisable to a population or not. Practicalities and resource constraints also play a large role here, as it can oftentimes be challenging to gain access to a truly random sample. In the video below, we explore some of the most common sampling strategies.

Methodological Choice #6 – Data Collection Method

Next up, you’ll need to explain how you’ll go about collecting the necessary data for your study. Your data collection method (or methods) will depend on the type of data that you plan to collect – in other words, qualitative or quantitative data.

Typically, quantitative research relies on surveys , data generated by lab equipment, analytics software or existing datasets. Qualitative research, on the other hand, often makes use of collection methods such as interviews , focus groups , participant observations, and ethnography.

So, as you can see, there is a tight link between this section and the design choices you outlined in earlier sections. Strong alignment between these sections, as well as your research aims and questions is therefore very important.

Methodological Choice #7 – Data Analysis Methods/Techniques

The final major methodological choice that you need to address is that of analysis techniques . In other words, how you’ll go about analysing your date once you’ve collected it. Here it’s important to be very specific about your analysis methods and/or techniques – don’t leave any room for interpretation. Also, as with all choices in this chapter, you need to justify each choice you make.

What exactly you discuss here will depend largely on the type of study you’re conducting (i.e., qualitative, quantitative, or mixed methods). For qualitative studies, common analysis methods include content analysis , thematic analysis and discourse analysis . In the video below, we explain each of these in plain language.

For quantitative studies, you’ll almost always make use of descriptive statistics , and in many cases, you’ll also use inferential statistical techniques (e.g., correlation and regression analysis). In the video below, we unpack some of the core concepts involved in descriptive and inferential statistics.

In this section of your methodology chapter, it’s also important to discuss how you prepared your data for analysis, and what software you used (if any). For example, quantitative data will often require some initial preparation such as removing duplicates or incomplete responses . Similarly, qualitative data will often require transcription and perhaps even translation. As always, remember to state both what you did and why you did it.

Section 3 – The Methodological Limitations

With the key methodological choices outlined and justified, the next step is to discuss the limitations of your design. No research methodology is perfect – there will always be trade-offs between the “ideal” methodology and what’s practical and viable, given your constraints. Therefore, this section of your methodology chapter is where you’ll discuss the trade-offs you had to make, and why these were justified given the context.

Methodological limitations can vary greatly from study to study, ranging from common issues such as time and budget constraints to issues of sample or selection bias . For example, you may find that you didn’t manage to draw in enough respondents to achieve the desired sample size (and therefore, statistically significant results), or your sample may be skewed heavily towards a certain demographic, thereby negatively impacting representativeness .

In this section, it’s important to be critical of the shortcomings of your study. There’s no use trying to hide them (your marker will be aware of them regardless). By being critical, you’ll demonstrate to your marker that you have a strong understanding of research theory, so don’t be shy here. At the same time, don’t beat your study to death . State the limitations, why these were justified, how you mitigated their impacts to the best degree possible, and how your study still provides value despite these limitations .

Section 4 – Concluding Summary

Finally, it’s time to wrap up the methodology chapter with a brief concluding summary. In this section, you’ll want to concisely summarise what you’ve presented in the chapter. Here, it can be a good idea to use a figure to summarise the key decisions, especially if your university recommends using a specific model (for example, Saunders’ Research Onion ).

Importantly, this section needs to be brief – a paragraph or two maximum (it’s a summary, after all). Also, make sure that when you write up your concluding summary, you include only what you’ve already discussed in your chapter; don’t add any new information.

Methodology Chapter Example

In the video below, we walk you through an example of a high-quality research methodology chapter from a dissertation. We also unpack our free methodology chapter template so that you can see how best to structure your chapter.

Wrapping Up

And there you have it – the methodology chapter in a nutshell. As we’ve mentioned, the exact contents and structure of this chapter can vary between universities , so be sure to check in with your institution before you start writing. If possible, try to find dissertations or theses from former students of your specific degree program – this will give you a strong indication of the expectations and norms when it comes to the methodology chapter (and all the other chapters!).

Also, remember the golden rule of the methodology chapter – justify every choice ! Make sure that you clearly explain the “why” for every “what”, and reference credible methodology textbooks or academic sources to back up your justifications.

If you need a helping hand with your research methodology (or any other component of your research), be sure to check out our private coaching service , where we hold your hand through every step of the research journey. Until next time, good luck!

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How to Write a Research Methodology for Your Academic Article

This article is part of an ongoing series on academic writing help of scholarly articles. Previous parts explored how to write an introduction for a research paper and a literature review outline and format .

The Methodology section portrays the reasoning for the application of certain techniques and methods in the context of the study.

For your academic article, when you describe and explain your chosen methods it is very important to correlate them to your research questions and/or hypotheses. The description of the methods used should include enough details so that the study can be replicated by other Researchers, or at least repeated in a similar situation or framework.

Every stage of your research needs to be explained and justified with clear information on why you chose those particular methods, and how they help you answer your research question or purpose.

As the Authors, in this section you get to explain the rationale of your article for other Researchers. You should focus on answering the following questions:

• How did you collect the data or how did you generate the data?
• Which research methods did you use?
• Why did you choose these methods and techniques?
• How did you use these methods for analyzing the research question or problem?

The responses to these questions should be clear and precise, and the answers should be written in past tense.

First off, let’s establish the differences between research methods and research methodology.

Research Methods and Research Methodology

As an Academic and Author of valuable research papers, it’s important not to confuse these two terms.

Research Methodology Definition

Research Methodology refers the discussion regarding the specific methods chosen and used in a research paper. This discussion also encompasses the theoretical concepts that further provide information about the methods selection and application.

In other words, you should highlight how these theoretical concepts are connected with these methods in a larger knowledge framework and explain their relevance in examining the purpose, problem and questions of your study. Thus, the discussion that forms your academic article’s research methodology also incorporates an extensive literature review about similar methods, used by other Authors to examine a certain research subject.

Research Method Definition

A Research Method represents the technical steps involved in conducting the research. Details about the methods focus on characterizing and defining them, but also explaining your chosen techniques, and providing a full account on the procedures used for selecting, collecting and analyzing the data.

Important Tips for a Good Methodology Section

The methodology section is very important for the credibility of your article and for a professional academic writing style.

Data Collection or Generation for Your Academic Article

Readers, academics and other researchers need to know how the information used in your academic article was collected. The research methods used for collecting or generating data will influence the discoveries and, by extension, how you will interpret them and explain their contribution to general knowledge.

The most basic methods for data collection are:

Secondary data

Secondary data are data that have been previously collected or gathered for other purposes than the aim of the academic article’s study. This type of data is already available, in different forms, from a variety of sources.

Secondary data collection could lead to Internal or External secondary data research.

Primary data

Primary data represent data originated for the specific purpose of the study, with its research questions. The methods vary on how Authors and Researchers conduct an experiment, survey or study, but, in general, it uses a particular scientific method.

Primary data collection could lead to Quantitative and Qualitative research.

Readers need to understand how the information was gathered or generated in a way that is consistent with research practices in a field of study . For instance, if you are using a multiple choice survey, the readers need to know which questionnaire items you have examined in your primary quantitative research. Similarly, if your academic article involves secondary data from FED or Eurostat it is important to mention the variables used in your study, their values, and their time-frame.

For primary research, that involve surveys, experiments or observations, for a valuable academic article, Authors should provide information about:

• Study participants or group participants,
• Inclusion or exclusion criteria

Selecting and Applying Research Methods

Establishing the main premises of methodology is pivotal for any research because a method or technique that is not reliable for a certain study context will lead to unreliable results, and the outcomes’ interpretation (and overall academic article) will not be valuable.

In most cases, there is a wide variety of methods and procedures that you can use to explore a research topic in your academic article. The methods section should fully explain the reasons for choosing a specific methodology or technique .

Also, it’s essential that you describe the specific research methods of data collection you are going to use , whether they are primary or secondary data collection.

For primary research methods, describe the surveys, interviews, observation methods, etc.

For secondary research methods, describe how the data was originally created, gathered and which institution created and published it.

Reasons for Choosing Specific Research Methods

For this aspect that characterizes a good research methodology, indicate how the research approach fits with the general study , considering the literature review outline and format , and the following sections.

The methods you choose should have a clear connection with the overall research approach and you need to explain the reasons for choosing the research techniques in your study, and how they help you towards understanding your study’s purpose.

Data Analysis Methods

This section should also focus on information on how you intend to analyze your results .

Describe how you plan and intend to achieve an accurate assessment of the hypotheses, relationships, patterns, trends, distributions associated with your data and research purpose.

The data type, how it was measured, and which statistical tests were conducted and performed, should be detailed and reported in an accurate manner.

For explaining the data analysis methods, you should aim to answer questions, such as:

• Will your research be based on statistical analysis?
• Will you use theoretical frameworks to help you (and your Readers) analyze a set of hypotheses or relationships?
• Which data analysis methods will you choose?
• Which other Authors or studies have used the same methods and should be cited in your academic article?

Issues to Avoid

There are certain aspects that you need to pay extra attention in relation to your research methodology section. The most common issues to avoid are:

• Irrelevant details and complicated background information that provides too information and does not provide accurate understanding for Readers
• Unnecessary description and explanations of basic or well-known procedures, for an academic audience who is already has a basin understanding of the study
• For unconventional research approaches, it is important to provide accurate details and explain why your innovative method contributes to general knowledge (save more details for your Discussion/ Conclusion section in which you can highlight your contributions)
• Research limitations and obstacles should be described in a separate section (Research Limitations)
• The methodology should include sources and references that support your choice of methods and procedures, compared to the literature review that provides a general outlook and framework for your study.

Which aspects are you generally focusing on when writing your academic article’s research methodology section?

You may also like, related policies and links, responsibilities of the publisher in the relationship with journal editors, general duties of publisher.

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• Published: 22 April 2024

Memorability shapes perceived time (and vice versa)

• Alex C. Ma   ORCID: orcid.org/0000-0001-5824-0806 1 ,
• Ayana D. Cameron 1 &
• Martin Wiener   ORCID: orcid.org/0000-0001-5963-5439 1  

Nature Human Behaviour ( 2024 ) Cite this article

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• Human behaviour
• Pattern vision
• Sensory processing

Visual stimuli are known to vary in their perceived duration. Some visual stimuli are also known to linger for longer in memory. Yet, whether these two features of visual processing are linked is unknown. Despite early assumptions that time is an extracted or higher-order feature of perception, more recent work over the past two decades has demonstrated that timing may be instantiated within sensory modality circuits. A primary location for many of these studies is the visual system, where duration-sensitive responses have been demonstrated. Furthermore, visual stimulus features have been observed to shift perceived duration. These findings suggest that visual circuits mediate or construct perceived time. Here we present evidence across a series of experiments that perceived time is affected by the image properties of scene size, clutter and memorability. More specifically, we observe that scene size and memorability dilate time, whereas clutter contracts it. Furthermore, the durations of more memorable images are also perceived more precisely. Conversely, the longer the perceived duration of an image, the more memorable it is. To explain these findings, we applied a recurrent convolutional neural network model of the ventral visual system, in which images are progressively processed over time. We find that more memorable images are processed faster, and that this increase in processing speed predicts both the lengthening and the increased precision of perceived durations. These findings provide evidence for a link between image features, time perception and memory that can be further explored with models of visual processing.

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Data availability.

All behavioural data for these experiments, as well as the rCNN results and memorability images used, are available at https://doi.org/10.17605/OSF.IO/FX3N2 (ref. 96 ).

Code availability

All relevant toolboxes and code repositories are cited in the text. The code is available at https://doi.org/10.17605/OSF.IO/FX3N2 (ref. 96 ).

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Acknowledgements

We thank A. Oliva, J. Ongchoco, T. Konkle and T. Kietzmann for their helpful comments relating to the stimuli, results and findings in this manuscript. The authors received no specific funding for this work.

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M.W., A.D.C. and A.C.M. conceived of and designed the experiments. A.D.C. and A.C.M. collected and analysed the data, with consultation and additional analyses by M.W. A.C.M. and M.W. wrote the manuscript.

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Ma, A.C., Cameron, A.D. & Wiener, M. Memorability shapes perceived time (and vice versa). Nat Hum Behav (2024). https://doi.org/10.1038/s41562-024-01863-2

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Volume 30, Number 7—July 2024

Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024

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We report highly pathogenic avian influenza A(H5N1) virus in dairy cattle and cats in Kansas and Texas, United States, which reflects the continued spread of clade 2.3.4.4b viruses that entered the country in late 2021. Infected cattle experienced nonspecific illness, reduced feed intake and rumination, and an abrupt drop in milk production, but fatal systemic influenza infection developed in domestic cats fed raw (unpasteurized) colostrum and milk from affected cows. Cow-to-cow transmission appears to have occurred because infections were observed in cattle on Michigan, Idaho, and Ohio farms where avian influenza virus–infected cows were transported. Although the US Food and Drug Administration has indicated the commercial milk supply remains safe, the detection of influenza virus in unpasteurized bovine milk is a concern because of potential cross-species transmission. Continued surveillance of highly pathogenic avian influenza viruses in domestic production animals is needed to prevent cross-species and mammal-to-mammal transmission.

Highly pathogenic avian influenza (HPAI) viruses pose a threat to wild birds and poultry globally, and HPAI H5N1 viruses are of even greater concern because of their frequent spillover into mammals. In late 2021, the Eurasian strain of H5N1 (clade 2.3.4.4b) was detected in North America ( 1 , 2 ) and initiated an outbreak that continued into 2024. Spillover detections and deaths from this clade have been reported in both terrestrial and marine mammals in the United States ( 3 , 4 ). The detection of HPAI H5N1 clade 2.3.4.4b virus in severe cases of human disease in Ecuador ( 5 ) and Chile ( 6 ) raises further concerns regarding the pandemic potential of specific HPAI viruses.

In February 2024, veterinarians were alerted to a syndrome occurring in lactating dairy cattle in the panhandle region of northern Texas. Nonspecific illness accompanied by reduced feed intake and rumination and an abrupt drop in milk production developed in affected animals. The milk from most affected cows had a thickened, creamy yellow appearance similar to colostrum. On affected farms, incidence appeared to peak 4–6 days after the first animals were affected and then tapered off within 10–14 days; afterward, most animals were slowly returned to regular milking. Clinical signs were commonly reported in multiparous cows during middle to late lactation; ≈10%–15% illness and minimal death of cattle were observed on affected farms. Initial submissions of blood, urine, feces, milk, and nasal swab samples and postmortem tissues to regional diagnostic laboratories did not reveal a consistent, specific cause for reduced milk production. Milk cultures were often negative, and serum chemistry testing showed mildly increased aspartate aminotransferase, gamma-glutamyl transferase, creatinine kinase, and bilirubin values, whereas complete blood counts showed variable anemia and leukocytopenia.

In early March 2024, similar clinical cases were reported in dairy cattle in southwestern Kansas and northeastern New Mexico; deaths of wild birds and domestic cats were also observed within affected sites in the Texas panhandle. In > 1 dairy farms in Texas, deaths occurred in domestic cats fed raw colostrum and milk from sick cows that were in the hospital parlor. Antemortem clinical signs in affected cats were depressed mental state, stiff body movements, ataxia, blindness, circling, and copious oculonasal discharge. Neurologic exams of affected cats revealed the absence of menace reflexes and pupillary light responses with a weak blink response.

On March 21, 2024, milk, serum, and fresh and fixed tissue samples from cattle located in affected dairies in Texas and 2 deceased cats from an affected Texas dairy farm were received at the Iowa State University Veterinary Diagnostic Laboratory (ISUVDL; Ames, IA, USA). The next day, similar sets of samples were received from cattle located in affected dairies in Kansas. Milk and tissue samples from cattle and tissue samples from the cats tested positive for influenza A virus (IAV) by screening PCR, which was confirmed and characterized as HPAI H5N1 virus by the US Department of Agriculture National Veterinary Services Laboratory. Detection led to an initial press release by the US Department of Agriculture Animal and Plant Health Inspection Service on March 25, 2024, confirming HPAI virus in dairy cattle ( 7 ). We report the characterizations performed at the ISUVDL for HPAI H5N1 viruses infecting cattle and cats in Kansas and Texas.

Materials and Methods

Milk samples (cases 2–5) and fresh and formalin-fixed tissues (cases 1, 3–5) from dairy cattle were received at the ISUVDL from Texas on March 21 and from Kansas on March 22, 2024. The cattle exhibited nonspecific illness and reduced lactation, as described previously. The tissue samples for diagnostic testing came from 3 cows that were euthanized and 3 that died naturally; all postmortem examinations were performed on the premises of affected farms.

The bodies of 2 adult domestic shorthaired cats from a north Texas dairy farm were received at the ISUVDL for a complete postmortem examination on March 21, 2024. The cats were found dead with no apparent signs of injury and were from a resident population of ≈24 domestic cats that had been fed milk from sick cows. Clinical disease in cows on that farm was first noted on March 16; the cats became sick on March 17, and several cats died in a cluster during March 19–20. In total, >50% of the cats at that dairy became ill and died. We collected cerebrum, cerebellum, eye, lung, heart, spleen, liver, lymph node, and kidney tissue samples from the cats and placed them in 10% neutral-buffered formalin for histopathology.

At ISUVDL, we trimmed, embedded in paraffin, and processed formalin-fixed tissues from affected cattle and cats for hematoxylin/eosin staining and histologic evaluation. For immunohistochemistry (IHC), we prepared 4-µm–thick sections from paraffin-embedded tissues, placed them on Superfrost Plus slides (VWR, https://www.vwr.com ), and dried them for 20 minutes at 60°C. We used a Ventana Discovery Ultra IHC/ISH research platform (Roche, https://www.roche.com ) for deparaffinization until and including counterstaining. We obtained all products except the primary antibody from Roche. Automated deparaffination was followed by enzymatic digestion with protease 1 for 8 minutes at 37°C and endogenous peroxidase blocking. We obtained the primary influenza A virus antibody from the hybridoma cell line H16-L10–4R5 (ATCC, https://www.atcc.org ) and diluted at 1:100 in Discovery PSS diluent; we incubated sections with antibody for 32 minutes at room temperature. Next, we incubated the sections with a hapten-labeled conjugate, Discovery anti-mouse HQ, for 16 minutes at 37°C followed by a 16-minute incubation with the horse radish peroxidase conjugate, Discovery anti-HQ HRP. We used a ChromoMap DAB kit for antigen visualization, followed by counterstaining with hematoxylin and then bluing. Positive controls were sections of IAV-positive swine lung. Negative controls were sections of brain, lung, and eyes from cats not infected with IAV.

We diluted milk samples 1:3 vol/vol in phosphate buffered saline, pH 7.4 (Gibco/Thermo Fisher Scientific, https://www.thermofisher.com ) by mixing 1 unit volume of milk and 3 unit volumes of phosphate buffered saline. We prepared 10% homogenates of mammary glands, brains, lungs, spleens, and lymph nodes in Earle’s balanced salt solution (Sigma-Aldrich, https://www.sigmaaldrich.com ). Processing was not necessary for ocular fluid, rumen content, or serum samples. After processing, we extracted samples according to a National Animal Health Laboratory Network (NAHLN) protocol that had 2 NAHLN-approved deviations for ISUVDL consisting of the MagMax Viral RNA Isolation Kit for 100 µL sample volumes and a Kingfisher Flex instrument (both Thermo Fisher Scientific).

We performed real-time reverse transcription PCR (rRT-PCR) by using an NAHLN-approved assay with 1 deviation, which was the VetMAX-Gold SIV Detection kit (Thermo Fisher Scientific), to screen for the presence of IAV RNA. We tested samples along with the VetMAX XENO Internal Positive Control to monitor the possible presence of PCR inhibitors. Each rRT-PCR 96-well plate had 2 positive amplification controls, 2 negative amplification controls, 1 positive extraction control, and 1 negative extraction control. We ran the rRT-PCR on an ABI 7500 Fast thermocycler and analyzed data with Design and Analysis Software 2.7.0 (both Thermo Fisher Scientific). We considered samples with cycle threshold (Ct) values <40.0 to be positive for virus.

After the screening rRT-PCR, we analyzed IAV RNA–positive samples for the H5 subtype and H5 clade 2.3.4.4b by using the same RNA extraction and NAHLN-approved rRT-PCR protocols as described previously, according to standard operating procedures. We performed PCR on the ABI 7500 Fast thermocycler by using appropriate controls to detect H5-specific IAV. We considered samples with Ct values <40.0 to be positive for the IAV H5 subtype.

We conducted genomic sequencing of 2 milk samples from infected dairy cattle from Texas and 2 tissue samples (lung and brain) from cats that died at a different Texas dairy. We subjected the whole-genome sequencing data to bioinformatics analysis to assemble the 8 different IAV segment sequences according to previously described methods ( 8 ). We used the hemagglutinin (HA) and neuraminidase (NA) sequences for phylogenetic analysis. We obtained reference sequences for the HA and NA segments of IAV H5 clade 2.3.4.4 from publicly available databases, including GISAID ( https://www.gisaid.org ) and GenBank. We aligned the sequences by using MAFFT version 7.520 software ( https://mafft.cbrc.jp/alignment/server/index.html ) to create multiple sequence alignments for subsequent phylogenetic analysis. We used IQTree2 ( https://github.com/iqtree/iqtree2 ) to construct the phylogenetic tree from the aligned sequences. The software was configured to automatically identify the optimal substitution model by using the ModelFinder Plus option, ensuring the selection of the most suitable model for the dataset and, thereby, improving the accuracy of the reconstructed tree. We visualized the resulting phylogenetic tree by using iTOL ( https://itol.embl.de ), a web-based platform for interactive tree exploration and annotation.

Gross Lesions in Cows and Cats

All cows were in good body condition with adequate rumen fill and no external indications of disease. Postmortem examinations of the affected dairy cows revealed firm mammary glands typical of mastitis; however, mammary gland lesions were not consistent. Two cows that were acutely ill before postmortem examination had grossly normal milk and no abnormal mammary gland lesions. The gastrointestinal tract of some cows had small abomasal ulcers and shallow linear erosions of the intestines, but those observations were also not consistent in all animals. The colon contents were brown and sticky, suggesting moderate dehydration. The feces contained feed particles that appeared to have undergone minimal ruminal fermentation. The rumen contents had normal color and appearance but appeared to have undergone minimal fermentation.

The 2 adult cats (1 intact male, 1 intact female) received at the ISUVDL were in adequate body and postmortem condition. External examination was unremarkable. Mild hemorrhages were observed in the subcutaneous tissues over the dorsal skull, and multifocal meningeal hemorrhages were observed in the cerebrums of both cats. The gastrointestinal tracts were empty, and no other gross lesions were observed.

Microscopic Lesions in Cows and Cats

Figure 1 . Mammary gland lesions in cattle in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. A, B) Mammary gland...

The chief microscopic lesion observed in affected cows was moderate acute multifocal neutrophilic mastitis ( Figure 1 ); however, mammary glands were not received from every cow. Three cows had mild neutrophilic or lymphocytic hepatitis. Because they were adult cattle, other observed microscopic lesions (e.g., mild lymphoplasmacytic interstitial nephritis and mild to moderate lymphocytic abomasitis) were presumed to be nonspecific, age-related changes. We did not observe major lesions in the other evaluated tissues. We performed IHC for IAV antigen on all evaluated tissues; the only tissues with positive immunoreactivity were mastitic mammary glands from 2 cows that showed nuclear and cytoplasmic labeling of alveolar epithelial cells and cells within lumina ( Figure 1 ) and multifocal germinal centers within a lymph node from 1 cow ( Table 1 ).

Figure 2 . Lesions in cat tissues in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Tissue sections were stained with...

Both cats had microscopic lesions consistent with severe systemic virus infection, including severe subacute multifocal necrotizing and lymphocytic meningoencephalitis with vasculitis and neuronal necrosis, moderate subacute multifocal necrotizing and lymphocytic interstitial pneumonia, moderate to severe subacute multifocal necrotizing and lymphohistiocytic myocarditis, and moderate subacute multifocal lymphoplasmacytic chorioretinitis with ganglion cell necrosis and attenuation of the internal plexiform and nuclear layers ( Table 2 ; Figure 2 ). We performed IHC for IAV antigen on multiple tissues (brain, eye, lung, heart, spleen, liver, and kidney). We detected positive IAV immunoreactivity in brain (intracytoplasmic, intranuclear, and axonal immunolabeling of neurons), lung, and heart, and multifocal and segmental immunoreactivity within all layers of the retina ( Figure 2 ).

PCR Data from Cows and Cats

We tested various samples from 8 clinically affected mature dairy cows by IAV screening and H5 subtype-specific PCR ( Table 3 ). Milk and mammary gland homogenates consistently showed low Ct values: 12.3–16.9 by IAV screening PCR, 17.6–23.1 by H5 subtype PCR, and 14.7–20.0 by H5 2.3.4.4 clade PCR (case 1, cow 1; case 2, cows 1 and 2; case 3, cow 1; and case 4, cow 1). We forwarded the samples to the National Veterinary Services Laboratory, which confirmed the virus was an HPAI H5N1 virus strain.

When available, we also tested tissue homogenates (e.g., lung, spleen, and lymph nodes), ocular fluid, and rumen contents from 6 cows by IAV and H5 subtype-specific PCR ( Table 3 ). However, the PCR findings were not consistent. For example, the tissue homogenates and ocular fluid tested positive in some but not all cows. In case 5, cow 1, the milk sample tested negative by IAV screening PCR, but the spleen homogenate tested positive by IAV screening, H5 subtype, and H5 2.3.4.4 PCR. For 2 cows (case 3, cow 1; and case 4, cow 1) that had both milk and rumen contents available, both samples tested positive for IAV. Nevertheless, all IAV-positive nonmammary gland tissue homogenates, ocular fluid, and rumen contents had markedly elevated Ct values in contrast to the low Ct values for milk and mammary gland homogenate samples.

We tested brain and lung samples from the 2 cats (case 6, cats 1 and 2) by IAV screening and H5 subtype-specific PCR ( Table 3 ). Both sample types were positive by IAV screening PCR; Ct values were 9.9–13.5 for brain and 17.4–24.4 for lung samples, indicating high amounts of virus nucleic acid in those samples. The H5 subtype and H5 2.3.4.4 PCR results were also positive for the brain and lung samples; Ct values were consistent with the IAV screening PCR ( Table 3 ).

Phylogenetic Analyses

We assembled the sequences of all 8 segments of the HPAI viruses from both cow milk and cat tissue samples. We used the hemagglutinin (HA) and neuraminidase (NA) sequences specifically for phylogenetic analysis to delineate the clade of the HA gene and subtype of the NA gene.

Figure 3 . Phylogenetic analysis of hemagglutinin gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate different...

For HA gene analysis, both HA sequences derived from cow milk samples exhibited a high degree of similarity, sharing 99.88% nucleotide identity, whereas the 2 HA sequences from cat tissue samples showed complete identity at 100%. The HA sequences from the milk samples had 99.94% nucleotide identities with HA sequences from the cat tissues, resulting in a distinct subcluster comprising all 4 HA sequences, which clustered together with other H5N1 viruses belonging to clade 2.3.4.4b ( Figure 3 ). The HA sequences were deposited in GenBank (accession nos. PP599465 [case 2, cow 1], PP599473 [case 2, cow 2], PP692142 [case 6, cat 1], and PP692195 [case 6, cat 2]).

Figure 4 . Phylogenetic analysis of neuraminidase gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate different...

For NA gene analysis, the 2 NA sequences obtained from cow milk samples showed 99.93% nucleotide identity. Moreover, the NA sequences derived from the milk samples exhibited complete nucleotide identities (100%) with those from the cat tissues. The 4 NA sequences were grouped within the N1 subtype of HPAI viruses ( Figure 4 ). The NA sequences were deposited in GenBank (accession nos. PP599467 [case 2, cow 1], PP599475 [case 2, cow 2], PP692144 [case 6, cat 1], and PP692197 [case 6, cat 2]).

This case series differs from most previous reports of IAV infection in bovids, which indicated cattle were inapparently infected or resistant to infection ( 9 ). We describe an H5N1 strain of IAV in dairy cattle that resulted in apparent systemic illness, reduced milk production, and abundant virus shedding in milk. The magnitude of this finding is further emphasized by the high death rate (≈50%) of cats on farm premises that were fed raw colostrum and milk from affected cows; clinical disease and lesions developed that were consistent with previous reports of H5N1 infection in cats presumably derived from consuming infected wild birds ( 10 – 12 ). Although exposure to and consumption of dead wild birds cannot be completely ruled out for the cats described in this report, the known consumption of unpasteurized milk and colostrum from infected cows and the high amount of virus nucleic acid within the milk make milk and colostrum consumption a likely route of exposure. Therefore, our findings suggest cross-species mammal-to-mammal transmission of HPAI H5N1 virus and raise new concerns regarding the potential for virus spread within mammal populations. Horizontal transmission of HPAI H5N1 virus has been previously demonstrated in experimentally infected cats ( 13 ) and ferrets ( 14 ) and is suspected to account for large dieoffs observed during natural outbreaks in mink ( 15 ) and sea lions ( 16 ). Future experimental studies of HPAI H5N1 virus in dairy cattle should seek to confirm cross-species transmission to cats and potentially other mammals.

Clinical IAV infection in cattle has been infrequently reported in the published literature. The first report occurred in Japan in 1949, where a short course of disease with pyrexia, anorexia, nasal discharge, pneumonia, and decreased lactation developed in cattle ( 17 ). In 1997, a similar condition occurred in dairy cows in southwest England leading to a sporadic drop in milk production ( 18 ), and IAV seroconversion was later associated with reduced milk yield and respiratory disease ( 19 – 21 ). Rising antibody titers against human-origin influenza A viruses (H1N1 and H3N2) were later again reported in dairy cattle in England, which led to an acute fall in milk production during October 2005–March 2006 ( 22 ). Limited reports of IAV isolation from cattle exist; most reports occurred during the 1960s and 1970s in Hungary and in the former Soviet Union, where H3N2 was recovered from cattle experiencing respiratory disease ( 9 , 23 ). Direct detection of IAV in milk and the potential transmission from cattle to cats through feeding of unpasteurized milk has not been previously reported.

An IAV-associated drop in milk production in dairy cattle appears to have occurred during > 4 distinct periods and within 3 widely separated geographic areas: 1949 in Japan ( 17 ), 1997–1998 and 2005–2006 in Europe ( 19 , 21 ), and 2024 in the United States (this report). The sporadic occurrence of clinical disease in dairy cattle worldwide might be the result of changes in subclinical infection rates and the presence or absence of sufficient baseline IAV antibodies in cattle to prevent infection. Milk IgG, lactoferrin, and conglutinin have also been suggested as host factors that might reduce susceptibility of bovids to IAV infection ( 9 ). Contemporary estimates of the seroprevalence of IAV antibodies in US cattle are not well described in the published literature. One retrospective serologic survey in the United States in the late 1990s showed 27% of serum samples had positive antibody titers and 31% had low-positive titers for IAV H1 subtype-specific antigen in cattle with no evidence of clinical infections ( 24 ). Antibody titers for H5 subtype-specific antigen have not been reported in US cattle.

The susceptibility of domestic cats to HPAI H5N1 is well-documented globally ( 10 – 12 , 25 – 28 ), and infection often results in neurologic signs in affected felids and other terrestrial mammals ( 4 ). Most cases in cats result from consuming infected wild birds or contaminated poultry products ( 12 , 27 ). The incubation period in cats is short; clinical disease is often observed 2–3 days after infection ( 28 ). Brain tissue has been suggested as the best diagnostic sample to confirm HPAI virus infection in cats ( 10 ), and our results support that finding. One unique finding in the cats from this report is the presence of blindness and microscopic lesions of chorioretinitis. Those results suggest that further investigation into potential ocular manifestations of HPAI H5N1 virus infection in cats might be warranted.

The genomic sequencing and subsequent analysis of clinical samples from both bovine and feline sources provided considerable insights. The HA and NA sequences derived from both bovine milk and cat tissue samples from different Texas farms had a notable degree of similarity. Those findings strongly suggest a shared origin for the viruses detected in the dairy cattle and cat tissues. Further research, case series investigations, and surveillance data are needed to better understand and inform measures to curtail the clinical effects, shedding, and spread of HPAI viruses among mammals. Although pasteurization of commercial milk mitigates risks for transmission to humans, a 2019 US consumer study showed that 4.4% of adults consumed raw milk > 1 time during the previous year ( 29 ), indicating a need for public awareness of the potential presence of HPAI H5N1 viruses in raw milk.

Ingestion of feed contaminated with feces from wild birds infected with HPAI virus is presumed to be the most likely initial source of infection in the dairy farms. Although the exact source of the virus is unknown, migratory birds (Anseriformes and Charadriiformes) are likely sources because the Texas panhandle region lies in the Central Flyway, and those birds are the main natural reservoir for avian influenza viruses ( 30 ). HPAI H5N1 viruses are well adapted to domestic ducks and geese, and ducks appear to be a major reservoir ( 31 ); however, terns have also emerged as an important source of virus spread ( 32 ). The mode of transmission among infected cattle is also unknown; however, horizontal transmission has been suggested because disease developed in resident cattle herds in Michigan, Idaho, and Ohio farms that received infected cattle from the affected regions, and those cattle tested positive for HPAI H5N1 ( 33 ). Experimental studies are needed to decipher the transmission routes and pathogenesis (e.g., replication sites and movement) of the virus within infected cattle.

In conclusion, we showed that dairy cattle are susceptible to infection with HPAI H5N1 virus and can shed virus in milk and, therefore, might potentially transmit infection to other mammals via unpasteurized milk. A reduction in milk production and vague systemic illness were the most commonly reported clinical signs in affected cows, but neurologic signs and death rapidly developed in affected domestic cats. HPAI virus infection should be considered in dairy cattle when an unexpected and unexplained abrupt drop in feed intake and milk production occurs and for cats when rapid onset of neurologic signs and blindness develop. The recurring nature of global HPAI H5N1 virus outbreaks and detection of spillover events in a broad host range is concerning and suggests increasing virus adaptation in mammals. Surveillance of HPAI viruses in domestic production animals, including cattle, is needed to elucidate influenza virus evolution and ecology and prevent cross-species transmission.

Dr. Burrough is a professor and diagnostic pathologist at the Iowa State University College of Veterinary Medicine and Veterinary Diagnostic Laboratory. His research focuses on infectious diseases of livestock with an emphasis on swine.

Acknowledgment

We thank the faculty and staff at the ISUVDL who contributed to the processing and analysis of clinical samples in this investigation, the veterinarians involved with clinical assessments at affected dairies and various conference calls in the days before diagnostic submissions that ultimately led to the detection of HPAI virus in the cattle, and the US Department of Agriculture National Veterinary Services Laboratory and NAHLN for their roles and assistance in providing their expertise, confirmatory diagnostic support, and communications surrounding the HPAI virus cases impacting lactating dairy cattle.

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• Figure 1 . Mammary gland lesions in cattle in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. A, B) Mammary...
• Figure 2 . Lesions in cat tissues in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Tissue sections were stained...
• Figure 3 . Phylogenetic analysis of hemagglutinin gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate...
• Figure 4 . Phylogenetic analysis of neuraminidase gene sequences in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Colors indicate...
• Table 1 . Microscopic lesions observed in cattle in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024
• Table 2 . Microscopic lesions observed in cats in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024
• Table 3 . PCR results from various specimens in study of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024

Suggested citation for this article : Burrough ER, Magstadt DR, Petersen B, Timmermans SJ, Gauger PC, Zhang J, et al. Highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus infection in domestic dairy cattle and cats, United States, 2024. Emerg Infect Dis. 2024 Jul [ date cited ]. https://doi.org/10.3201/eid3007.240508

DOI: 10.3201/eid3007.240508

Original Publication Date: April 29, 2024

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Analysing the email data using stylometric method and deep learning to mitigate phishing attack

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• Published: 05 May 2024

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• Peace Nmachi Wosah   ORCID: orcid.org/0000-0002-7776-6982 1 ,
• Qublai Ali Mirza 1 &
• Will Sayers 1  

The high-volume usage of email has attracted cybercriminals to the platform and criminals are aware of difficulties users often have in separating legitimate from illegitimate emails and seek to take advantage of those difficulties by impersonating staff of a trusted organisation to persuade users into divulging their private information. To help users overcome the difficulty in detecting phishing attacks, a system is proposed. Recent advancement uses: stylometric features, gender features and personality features to carry out a sender verification process. The existing approaches are more complex and if the system fails to detect bad email, and it gets to users, the possibility of becoming a victim becomes high if not detected by the user. The proposed framework adds Colour Code to Email Verification (CCEV). It conducts sender’s verification at the recipients’ end based on 3-features related with senders, writing pattern, gender, and header.

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The dataset utilised was obtained from the web page of William Cohen, which can be accessed at http://www-2.cs.cmu.edu/~enron/

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Wosah, P.N., Ali Mirza, Q. & Sayers, W. Analysing the email data using stylometric method and deep learning to mitigate phishing attack. Int. j. inf. tecnol. (2024). https://doi.org/10.1007/s41870-024-01839-5

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