• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• SUVANNABHUMI
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• v.14 no.2
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• pp.117-148
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• 2022

The full impact of COVID-19 has yet to be felt: while it may not define the new decade, it is clear that its immediate significance was to test many of the basic operating assumptions and procedures of global civilization. Even as vaccines are developed and utilized and even as it is possible to see the beginning of the end of COVID-19 as a discrete historical event, it remains unclear as to its ultimate importance. That said, it is evident that the academic exploration of Southeast Asia will also be affected by both the global and regional experiences of the pandemic. "Breakthroughs of Area Studies and ASEAN in the Era of Homo Untact" promises to help reconceptualize the study of the region by highlighting the importance of redefined spatial relationships and new potentially depersonalized modes of communication. This paper acknowledges these issues by suggesting that the transformations caused by the pandemic should motivate scholars to raise new questions about how to understand humanity-particularly as it is defined by societies, nations and regions. Given that COVID-19 (and the response to it) has altered many of the fundamental rhythms of globalized regions, there is sufficient warrant for re-examining both the ways in which disease, health and their related spaces affect the perceptions of Southeast Asia. To achieve "breakthroughs" into the investigation of the region, it makes sense to have another glance at the ways in which the discourses about diseases and health may have helped to inscribe definitions of Southeast Asia-or, at the very least, the nations, societies and peoples who live within it. In order to at least consider these larger issues, the discussion will concentrate on a formative moment in the conceptualization of Southeast Asia-British engagement with the region in the late 18^th and early 19^th centuries. To that end three themes will be highlighted: (1) the role that British diplomatic and military narratives played in establishing the information priorities required for the construction of colonial knowledge; (2) the importance not only of "colonial knowledge" but information making in its own right; (3) in anticipation of the use of big data, the manner in which manufactured information (related to space and disease) could function in shaping early British perceptions of Southeast Asia-particularly in Batavia and Java. This discussion will suggest that rather than see social distancing or increased communication as the greatest outcome of COVID-19, instead it will be the use of data-that is, big, aggregated biometric data which have not only shaped responses to the pandemic, but remain likely to produce the reconceptualization of both information and knowledge about the region in a way that will be at least as great as that which took place to meet the needs of the "New Imperialism." Furthermore, the definition and articulation of Southeast Asia has often reflected political and security considerations. Yet, the experience of COVID-19 could prove that data and security are now fused into a set of interests critical to policy-makers. Given that the pandemic should accelerate many existing trends, it might be foreseen these developments will herald the triumph of homo indicina: an epistemic condition whereby the human subject has become a kind of index for its harvestable data. If so, the "breakthroughs" for those who study Southeast Asia will follow in due course.