Exploring the post-genomic world: differing explanatory and manipulatory functions of post-genomic sciences

CPGminer: An Interactive Dashboard to Explore the Genomic Features and Taxonomy of Complete Prokaryotic Genomes

Prokaryotes, the earliest forms of life on Earth, play crucial roles in global biogeochemical processes in virtually all ecosystems. The ever-increasing amount of prokaryotic genome sequencing data provides a wealth of information to examine fundamental and applied questions through systematic genome comparison. Genomic features, such as genome size and GC content, and taxonomy-centric genomic features of complete prokaryotic genomes (CPGs) are crucial for various fields of microbial research and education, yet they are often overlooked. Additionally, creating systematically curated datasets that align with research concerns is an essential yet challenging task for wet-lab researchers. In this study, we introduce CPGminer, a user-friendly tool that allows researchers to quickly and easily examine the genomic features and taxonomy of CPGs and curate genome datasets. We also provide several examples to demonstrate its practical utility in addressing descriptive questions.

Precision medicine journey through omics approach

It has been well established that understanding the underlying heterogeneity of numerous complex disease process needs new strategies that present in precision medicine for prediction, prevention and personalized treatment strategies. This approach must be tailored for each individual's unique omics that lead to personalized management of disease. The correlation between different omics data should be considered in precision medicine approach. The interaction provides a hypothesis which is called domino effect in the present minireview. Here we review the various potentials of omics data including genomics, transcriptomics, proteomics, metabolomics, pharmacogenomics. We comprehensively summarize the impact of omics data and its major role in precision medicine and provide a description about the domino effect on the pathophysiology of diseases. Each constituent of the omics data typically provides different information in associated with disease. Current research, although inadequate, clearly indicate that the information of omics data can be applicable in the concept of precision medicine. Integration of different omics data type in domino effect hypothesis can explain the causative changes of disease as it is discussed in the system biology too. While most existing studies investigate the omics data separately, data integration is needed on the horizon of precision medicine by using machine learning.

Ethical Principles, Constraints and Opportunities in Clinical Proteomics

Recent advances in mass spectrometry (MS)-based proteomics have vastly increased the quality and scope of biological information that can be derived from human samples. These advances have rendered current workflows increasingly applicable in biomedical and clinical contexts. As proteomics is poised to take an important role in the clinic, associated ethical responsibilities increase in tandem with impacts on the health, privacy, and wellbeing of individuals. We conducted and here report a systematic literature review of ethical issues in clinical proteomics. We add our perspectives from a background of bioethics, the results of our accompanying paper extracting individual-sensitive results from patient samples, and the literature addressing similar issues in genomics. The spectrum of potential issues ranges from patient re-identification to incidental findings of clinical significance. The latter can be divided into actionable and unactionable findings. Some of these have the potential to be employed in discriminatory or privacy-infringing ways. However, incidental findings may also have great positive potential. A plasma proteome profile, for instance, could inform on the general health or disease status of an individual regardless of the narrow diagnostic question that prompted it. We suggest that early discussion of ethical issues in clinical proteomics can ensure that eventual healthcare practices and regulations reflect the considered judgment of the community and anticipate opportunities and problems that may arise as the technology matures.

How Do Postgenomic Innovations Emerge? Building Legitimacy by Proteomics Standards and Informing the Next-Generation Technology Policy

How do postgenomic innovations emerge and become legitimate? Proteomics, a frequently utilized postgenomic technology, provides a valuable case study of the sociotechnical strategies used by an emergent scientific field to establish its legitimacy and assert political power. Chief among these strategies is standard making, an inherently political process that requires examination through a critical social science lens. We report in this study an original case study from interviews with proteomics scientists and observations at conferences of the Human Proteome Organization and Australasian Proteomics Society over a 5-year period (2011-2015). The study contributes new knowledge on how an emerging postgenomic science uses standard-setting practices to politically legitimize a hitherto contested technology. Drawing on legitimacy theory, we show how proteomics scientists and organizations used standards as strategic tools to establish the legitimacy of this postgenomic field and affirm that proteomics can generate verifiable and reproducible results, thereby establishing it as a legitimate scientific field. Notably, legitimacy can be leveraged, at the same time, to maximize political power vis-à-vis other fields of science and as such embodies power relationships. These data collectively inform the broader context, in which postgenomic innovations emerge and legitimize, both technically and politically, through standards making. These findings have relevance for the design of next generation technology policies by demonstrating that standards are not "just" standards or neutral constructs but also tools to leverage political power of and by science and innovation actors, as shown in this case study of the emerging early phase of proteomics from 2011 to 2015.