Jianwen Fang

Differential long-term bivalent HPV vaccine cross-protection by variants in the Costa Rica HPV vaccine trial

Jaimie Zhi Shing, Carolina Porras, Maísa Pinheiro, Rolando Herrero et autres

The AS04-adjuvanted human papillomavirus (HPV)16/18 vaccine, an L1-based vaccine, provides strong vaccine efficacy (VE) against vaccine-targeted type infections, and partial cross-protection to phylogenetically-related types, which may be affected by variant-level heterogeneity. We compared VE against incident HPV31, 33, 35, and 45 detections …

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Abstract 6915: Integrated proteogenomic analysis for the NCI patient-derived cancer model repository

Peter Wu, Li Chen, Yuri Kotliarov, Jianwen Fang et autres

Abstract Background: Studying protein expression involved in cancer from patient-derived xenografts (PDX) enhances understanding of tumorigenesis and may shed light on patient therapeutic decisions. Recently, mass spectrometry-based proteomics sequencing techniques have enabled the acquisition of high-throughput PDX protein/phosphoprotein expression profiles and paved …

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Circular RNAs in vascular diseases

Qiaoyuan Liu, Yaofeng Wang, Tinghong Zhang, Jianwen Fang et autres

Vascular diseases are the leading cause of morbidity and mortality worldwide and are urgently in need of diagnostic biomarkers and therapeutic strategies. Circular RNAs (circRNAs) represent a unique class of RNAs characterized by a circular loop configuration and have recently been identified …

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Predicting thermostability difference between cellular protein orthologs

Jianwen Fang

MOTIVATION: Protein thermostability is of great interest, both in theory and in practice. RESULTS: This study compared orthologous proteins with different cellular thermostability. A large number of physicochemical properties of protein were calculated and used to develop a series of machine learning …

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The role of data imbalance bias in the prediction of protein stability change upon mutation

Jianwen Fang

There is a controversy over what causes the low robustness of some programs for predicting protein stability change upon mutation. Some researchers suggested that low-quality data and insufficiently informative features are the primary reasons, while others attributed the problem largely to a …

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Identifying Epstein–Barr virus peptide sequences associated with differential IgG antibody response

Anna E. Coghill, Jianwen Fang, Zhiwei Liu, Chien‐Jen Chen et autres

BACKGROUND: Epstein-Barr virus (EBV) infection contributes to cancers in a fraction of seropositive individuals, but much remains to be learned about variation in EBV-directed humoral immunity in cancer-free adults. METHODS: A protein microarray was used to probe serum from 175 Taiwanese and …

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Molecular genomic features associated with in vitro response of the NCI‐60 cancer cell line panel to natural products

Julia Krushkal, Simarjeet Negi, Laura M. Yee, Jason R. Evans et autres

Natural products remain a significant source of anticancer chemotherapeutics. The search for targeted drugs for cancer treatment includes consideration of natural products, which may provide new opportunities for antitumor cytotoxicity as single agents or in combination therapy. We examined the association of …

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Bioinformatics Tools and Resources for Cancer Immunotherapy Study

Alida Palmisano, Julia Krushkal, Ming‐Chung Li, Jianwen Fang et autres

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A Novel Modified Electromagnetism-like Algorithm for Solving Constrained Optimization Problem

Wenming Cao, Jianwen Fang, Huang Gan

Abstract The original Electromagnetism-like mechanism (EM) is a meta-heuristic algorithm utilizing an attraction-repulsion mechanism (called as force F) to move sample points towards optimality in global optimization problems. To solve the potential problem of stagnation happening in the original algorithm, new searching …

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Exposure time versus cytotoxicity for anticancer agents

David M. Evans, Jianwen Fang, Thomas R. Silvers, René Delosh et autres

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A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation

Jianwen Fang

A number of machine learning (ML)-based algorithms have been proposed for predicting mutation-induced stability changes in proteins. In this critical review, we used hypothetical reverse mutations to evaluate the performance of five representative algorithms and found all of them suffer from the …

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Vaccine-induced or Pre-existing Hemagglutination Inhibiting Antibodies on the Protection Against Influenza Virus Infection: A Systematic Review and Meta-analysis

Qingfang Xiong, Nancy Leung, KL Tsang, Jianwen Fang et autres