Shanghai Jiao Tong University

About: Shanghai Jiao Tong University is a education organization based out in Shanghai, Shanghai, China. It is known for research contribution in the topics: Population & Cancer. The organization has 157524 authors who have published 184620 publications receiving 3451038 citations. The organization is also known as: Shanghai Communications University & Shanghai Jiaotong University.

Ensemble classifier for protein fold pattern recognition

Abstract: Motivation: Prediction of protein folding patterns is one level deeper than that of protein structural classes, and hence is much more complicated and difficult. To deal with such a challenging problem, the ensemble classifier was introduced. It was formed by a set of basic classifiers, with each trained in different parameter systems, such as predicted secondary structure, hydrophobicity, van der Waals volume, polarity, polarizability, as well as different dimensions of pseudo-amino acid composition, which were extracted from a training dataset. The operation engine for the constituent individual classifiers was OET-KNN (optimized evidence-theoretic k-nearest neighbors) rule. Their outcomes were combined through a weighted voting to give a final determination for classifying a query protein. The recognition was to find the true fold among the 27 possible patterns. Results: The overall success rate thus obtained was 62% for a testing dataset where most of the proteins have <25% sequence identity with the proteins used in training the classifier. Such a rate is 6–21% higher than the corresponding rates obtained by various existing NN (neural networks) and SVM (support vector machines) approaches, implying that the ensemble classifier is very promising and might become a useful vehicle in protein science, as well as proteomics and bioinformatics. Availability: The ensemble classifier, called PFP-Pred, is available as a web-server at for public usage. Contact: lifesci-sjtu@san.rr.com Supplementary information: Supplementary data are available on Bioinformatics online.

Infrastructure Planning for Electric Vehicles with Battery Swapping

Abstract: Electric vehicles (EVs) have been proposed as a key technology to help cut down the massive greenhouse gas emissions from the transportation sector. Unfortunately, because of the limited capacity of batteries, typical EVs can only travel for about 100 miles on a single charge and require hours to be recharged. The industry has proposed a novel solution centered around the use of “swapping stations,” at which depleted batteries can be exchanged for recharged ones in the middle of long trips. The possible success of this solution hinges on the ability of the charging service provider to deploy a cost-effective infrastructure network, given only limited information regarding adoption rates. We develop robust optimization models that aid the planning process for deploying battery-swapping infrastructure. Using these models, we study the potential impacts of battery standardization and technology advancements on the optimal infrastructure deployment strategy. This paper was accepted by Dimitris Bertsimas, opti...

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

Abstract: A large number of genetic variants have been associated with human diseases. However, the lack of a genetic diversification approach has impeded our ability to interrogate functions of genetic variants in mammalian cells. Current screening methods can only be used to disrupt a gene or alter its expression. Here we report the fusion of activation-induced cytidine deaminase (AID) with nuclease-inactive clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (dCas9) for efficient genetic diversification, which enabled high-throughput screening of functional variants. Guided by single guide (sg)RNAs, dCas9-AID-P182X (AIDx) directly changed cytidines or guanines to the other three bases independent of AID hotspot motifs, generating a large repertoire of variants at desired loci. Coupled with a uracil-DNA glycosylase inhibitor, dCas9-AIDx converted targeted cytidines specifically to thymines, creating specific point mutations. By targeting BCR-ABL with dCas9-AIDx, we efficiently identified known and new mutations conferring imatinib resistance in chronic myeloid leukemia cells. Thus, targeted AID-mediated mutagenesis (TAM) provides a forward genetic tool to screen for gain-of-function variants at base resolution.