Software and data citation are emerging best practices in scholarly communication. This article provides structured guidance to the academic publishing community on how to implement software and data citation in publishing workflows. These best practices support the verifiability and reproducibility of scientific results; sharing and reuse of valuable data and software tools, and attribution to the creators of the software and data. While data citation is increasingly well-established, software citation is rapidly maturing. With the current intensive use of software, including specialized tools and models for scientific research problems, the research community has begun to recognize that software, as a key research result and resource, requires the same level of transparency, accessibility, and disclosure as data. Software and data that support scientific results should be preserved and shared in scientific repositories for discovery, transparency, and use by other researchers. These goals can be supported by citing these products in the Reference Section of papers and effectively associating them to the software and data preserved in scientific repositories. Publishers need to mark up these references in a specific way to enable downstream processes, specifically those that enable automated attribution. Academic publishers wishing to stay current with best practices in the field are encouraged to follow the guidance provided here.