Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

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

Signaling Recognition Events with Fluorescent Sensors and Switches.

A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed the Perseus software platform (http://www.perseus-framework.org) to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing. A machine learning module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signatures. Central to Perseus is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. All activities in Perseus are realized as plugins, and users can extend the software by programming their own, which can be shared through a plugin store. We anticipate that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.

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The Perseus computational platform for comprehensive analysis of (prote)omics data.

This review compiles positively and negatively solvatochromic compounds which have been used to establish empirical scales of solvent polarity by means of UV/vis/near-IR spectroscopic measurements in solution-with particular emphasis on the E ~ ( 3 0 ) scale derived from negatively solvatochromic pyridinium N-phenolate betaine dyes. This requires a short discussion of the concept of solvent polarity and how empirical parameters of solvent polarity can be derived and understood in the framework of linear free-energy relationships. The preconditions for the occurrence of solvatochromism, and further requirements of solvatochromic compounds for them to be useful as solvent polarity indicators will be discussed. In addition to spectroscopically based single parameters of solvent polarity, multiparameter treatments of solvent effects by means of solvatochromic parameters will also be mentioned. The mutual interrelation between some of the more important W/vis/near-IR spectroscopically derived solvent scales, and their correlations with solvatochromic multiparameter equations will be exemplarily given.

Solvatochromic Dyes as Solvent Polarity Indicators

Vol. 197 No. 5, May 28, 2012. [Pages 643–658][1].

Several months ago it came to our attention that one of the expression constructs used in this publication, which we had obtained as a gift from another laboratory, was incorrect. What we had described as a fusion of GFP with full-length N-WASp

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Correction: Stoichiometry of Nck-dependent actin polymerization in living cells.

Disclosed are tethered chromophore compositions comprising a membrane-spanning tether. The compounds can include covalently tethered fluorophore-quencher combinations useful for measuring action potentials and other fast electrical events in cells and tissues.

Leslie M. Loew

Papers

Correction: Stoichiometry of Nck-dependent actin polymerization in living cells.

Compounds and methods for optical sensing of electrical activity in biological systems

Noise regulation by heterotypic biomolecular condensates

Near infrared voltage sensitive dyes based on chromene electron donors.

The maximum solubility product marks the threshold for condensation of multivalent biomolecules