抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

http://www.maths.qmul.ac.uk/%7Elatora/report_06.pdf

Complex networks: Structure and dynamics

A key aim of postgenomic biomedical research is to systematically catalogue all molecules and their interactions within a living cell. There is a clear need to understand how these molecules and the interactions between them determine the function of this enormously complex machinery, both in isolation and when surrounded by other cells. Rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize our view of biology and disease pathologies in the twenty-first century.

/pdf/network-biology-understanding-the-cell-s-functional-589nl2mnk6.pdf

Network biology: understanding the cell's functional organization

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

We have used 199 million papers over 5 decades and 21 million patents to demonstrate that teams increasingly dominate solo authors in the production of knowledge Research is increasingly done in teams across nearly all fields Teams typically produce more frequently cited research than individuals do, and this advantage has been increasing over time Teams now also produce the exceptionally high-impact research, even where that distinction was once the domain of solo authors These results are detailed for sciences and engineering, social sciences, arts and humanities, and patents, suggesting that the process of knowledge creation has fundamentally changed

/pdf/the-increasing-dominance-of-teams-in-production-of-knowledge-h591ohwfzk.pdf

The Increasing Dominance of Teams in Production of Knowledge

This paper demonstrates that teamwork in science increasingly spans university boundaries, a dramatic shift in knowledge production that generalizes across virtually all fields of science, engineering, and social science. Moreover, elite universities play a dominant role in this shift. By examining 4.2 million papers published over three decades, we found that multi-university collaborations (i) are the fastest growing type of authorship structure, (ii) produce the highest-impact papers when they include a top-tier university, and (iii) are increasingly stratified by in-group university rank. Despite the rising frequency of research that crosses university boundaries, the intensification of social stratification in multi-university collaborations suggests a concentration of the production of scientific knowledge in fewer rather than more centers of high-impact science.

/pdf/multi-university-research-teams-shifting-impact-geography-189qbt4fgc.pdf

Multi-University Research Teams: Shifting Impact, Geography, and Stratification in Science

An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities, such as the partition function or measures for structural diversity. The density of states at low energies and its associated structures are crucial in assessing from a thermodynamic point of view how well-defined the ground state is. We demonstrate this by exploring the role of base modification in tRNA secondary structures, both at the level of individual sequences from Escherichia coli and by comparing artificially generated ensembles of modified and unmodified sequences with the same tRNA structure. The two major conclusions are that (1) base modification considerably sharpens the definition of the ground state structure by constraining energetically adjacent structures to be similar to the ground state, and (2) sequences whose ground state structure is thermodynamically well defined show a significant tendency to buffer single point mutations. This can have evolutionary implications, since selection pressure to improve the definition of ground states with biological function may result in increased neutrality.

Complete suboptimal folding of RNA and the stability of secondary structures.

Distrust in scientific expertise1–14 is dangerous. Opposition to vaccination with a future vaccine against SARS-CoV-2, the causal agent of COVID-19, for example, could amplify outbreaks2–4, as happened for measles in 20195,6. Homemade remedies7,8 and falsehoods are being shared widely on the Internet, as well as dismissals of expert advice9–11. There is a lack of understanding about how this distrust evolves at the system level13,14. Here we provide a map of the contention surrounding vaccines that has emerged from the global pool of around three billion Facebook users. Its core reveals a multi-sided landscape of unprecedented intricacy that involves nearly 100 million individuals partitioned into highly dynamic, interconnected clusters across cities, countries, continents and languages. Although smaller in overall size, anti-vaccination clusters manage to become highly entangled with undecided clusters in the main online network, whereas pro-vaccination clusters are more peripheral. Our theoretical framework reproduces the recent explosive growth in anti-vaccination views, and predicts that these views will dominate in a decade. Insights provided by this framework can inform new policies and approaches to interrupt this shift to negative views. Our results challenge the conventional thinking about undecided individuals in issues of contention surrounding health, shed light on other issues of contention such as climate change11, and highlight the key role of network cluster dynamics in multi-species ecologies15. Insights into the interactions between pro- and anti-vaccination clusters on Facebook can enable policies and approaches that attempt to interrupt the shift to anti-vaccination views and persuade undecided individuals to adopt a pro-vaccination stance.

/pdf/the-online-competition-between-pro-and-anti-vaccination-50fvl99vj2.pdf

The online competition between pro- and anti-vaccination views.

Understanding why some cellular components are conserved across species but others evolve rapidly is a key question of modern biology 1–3 . Here we show that in Saccharomyces cerevisiae, proteins organized in cohesive patterns of interactions are conserved to a substantially higher degree than those that do not participate in such motifs. We find that the conservation of proteins in distinct topological motifs correlates with the interconnectedness and function of that motif and also depends on the structure of the overall interactome topology. These findings indicate that motifs may represent evolutionary conserved topological units of cellular networks molded in accordance with the specific biological function in which they participate.

/pdf/evolutionary-conservation-of-motif-constituents-in-the-yeast-2fh9t8hmlq.pdf

Stefan Wuchty

Papers

The Increasing Dominance of Teams in Production of Knowledge

Multi-University Research Teams: Shifting Impact, Geography, and Stratification in Science

Complete suboptimal folding of RNA and the stability of secondary structures.

The online competition between pro- and anti-vaccination views.

Evolutionary conservation of motif constituents in the yeast protein interaction network