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This article discusses the responsible conduct of research, questionable research practices, and research misconduct. Responsible conduct of research is often defined in terms of a set of abstract, normative principles, professional standards, and ethics in doing research. In order to accommodate the normative principles of scientific research, the professional standards, and a researcher’s moral principles, transparent research practices can serve as a framework for responsible conduct of research. We suggest a 'prune-and-add' project structure to enhance transparency and by extension, responsible conduct of research. Questionable research practices are defined as practices that are detrimental to the research process. The prevalence of questionable research practices remains largely unknown and reproducibility of findings has been shown to be problematic. Questionable practices are discouraged by transparent practices because practices that arise from them will become more apparent to scientific peers. Most effective might be preregistrations of research design, hypotheses, and analyses, which reduce particularism of results by providing an a priori research scheme. Research misconduct has been defined as fabrication, falsification, and plagiarism (FFP), which is clearly the worst type of research practice. Despite it being clearly wrong, it can be approached from a scientific and legal perspective. The legal perspective sees research misconduct as a form of white-collar crime. The scientific perspective seeks to answer the question "were results invalidated because of the misconduct?" We review how misconduct is typically detected, how its detection can be improved, and how prevalent it might be. Institutions could facilitate detection of data fabrication and falsification by implementing data auditing. Nonetheless, the effect of misconduct is pervasive: many retracted articles are still cited after the retraction has been issued.