J. Cui

发表

Bioinformatics Databases and Tools on Dietary microRNA

J. Cui, 2017 .

A Comparative Analysis of Gene-Expression Data of Multiple Cancer Types

V. Olman, Kun Xu, Ying Xu, 2010, PloS one.

The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development

T. Ochsenreiter, D. Nilsson, Xiaofeng Song, 2010, Nucleic acids research.

Elucidation of How Cancer Cells Avoid Acidosis through Comparative Transcriptomic Data Analysis

M. Mehta, Fenglou Mao, Kun Xu, 2013, PloS one.

Identification of age- and gender-associated long noncoding RNAs in the human brain with Alzheimer's disease

M. Cao, J. Cui, Huaqing Li, 2019, Neurobiology of Aging.

Identification of potential predictors for subtype IgA nephropathy through analyses of blood biochemical indicators.

Yaping Tian, Yong Wang, Z. Dong, 2011, Clinica chimica acta; international journal of clinical chemistry.

A systematic approach to RNA-associated motif discovery

J. Cui, Tian Gao, Jiang Shu, 2018, BMC Genomics.

Astrocyte EV-Induced lincRNA-Cox2 Regulates Microglial Phagocytosis: Implications for Morphine-Mediated Neurodegeneration

Y. Lyubchenko, Lu Yang, S. Buch, 2018, Molecular therapy. Nucleic acids.

Noncoding RNAs as a Cause of Cancer: Evidence From Genome-Wide Association Studies and Reverse Genetics

J. Cui, 2018 .

Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation

J. Zempleni, J. Cui, Jiang Shu, 2015, PloS one.

An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

Wen-Chi Chou, V. Olman, J. Suo, 2010, Nucleic acids research.

Cancer Classification and Molecular Signature Identification

Ying Xu, J. Cui, D. Puett, 2014 .

Searching for Cancer Biomarkers in Human Body Fluids

Ying Xu, J. Cui, D. Puett, 2014 .

Omic Data, Information Derivable and Computational Needs

Ying Xu, J. Cui, D. Puett, 2014 .

The endothelial lipase protein is promising urinary biomarker for diagnosis of gastric cancer

J. Suo, Ying Xu, Guoqing Wang, 2013, Diagnostic Pathology.

Microarray-based transcriptome profiling of ovarian cancer cells.

Ying Xu, J. Cui, D. Puett, 2013, Methods in molecular biology.

A Comparative Study of Gene-Expression Data of Basal Cell Carcinoma and Melanoma Reveals New Insights about the Two Cancers

Juan Cui, Chi Zhang, M. Mehta, 2012, PloS one.

Transcriptomic Analysis of Human Ovarian Cancer Cells: Changes Mediated by Luteinizing Hormone Receptor Activation

Ying Xu, J. Cui, D. Puett, 2012 .

A Computational Method for Prediction of Excretory Proteins and Application to Identification of Gastric Cancer Markers in Urine

Celine S. Hong, Fan Li, Juan Cui, 2011, PloS one.

Gene-Expression Signatures Can Distinguish Gastric Cancer Grades and Stages

Guoqing Wang, Fan Li, Juan Cui, 2011, PloS one.

Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation

Juan Cui, David Puett, Phuongan Dam, 2011, BMC Cancer.

Nutrition, microRNAs, and Human Health.

J. Zempleni, S. Ross, Beiyan Zhou, 2017, Advances in nutrition.

Cancer After Metastasis: The Second Transformation

Ying Xu, J. Cui, D. Puett, 2014 .

A phylogenetic model for understanding the effect of gene duplication on cancer progression

Jing Zhao, J. Reeves, D. Liberles, 2013, Nucleic acids research.

Elucidation of molecular links between obesity and cancer through microRNA regulation

Haluk Dogan, Zeynep Hakguder, J. Cui, 2020, BMC medical genomics.

The Roles of Glycodelin in Cancer Development and Progression

J. Cui, Yanguo Liu, Xiuwen Wang, 2017, Front. Immunol..

In Silico Investigation of Cancer Using Publicly Available Data

Ying Xu, J. Cui, D. Puett, 2014 .

Dynamic and Modularized MicroRNA Regulation and Its Implication in Human Cancers

J. Cui, Tian Gao, Jiang Shu, 2017, Scientific Reports.

Elucidation of Cancer Drivers Through Comparative Omic Data Analyses

Ying Xu, J. Cui, D. Puett, 2014 .

Analysis of genetic and nongenetic factors influencing triglycerides-lowering drug effects based on paired observations

Q. Duan, Q. Jia, Yumou Qiu, 2018, BMC Proceedings.

Genome-scale search of tumor-specific antigens by collective analysis of mutations, expressions and T-cell recognition.

J. Jia, Yuzong Chen, Yuquan Wei, 2009, Molecular immunology.

MicroRNA Expression and Regulation in Human Ovarian Carcinoma Cells by Luteinizing Hormone

Ying Xu, J. Cui, D. Puett, 2011, PloS one.

Abnormal beta-catenin gene expression with invasiveness of primary hepatocellular carcinoma in China.

J. Cui, Z. Tang, M. Zile, 2001, World journal of gastroenterology.

A markov clustering based link clustering method to identify overlapping modules in protein-protein interaction networks

Yan Wang, Enrico Blanzieri, Lan Huang, 2016 .

Progesterone receptor-mediated up-regulation of transthyretin in preimplantation mouse uterus.

J. Chun, Ying Xu, J. Cui, 2010, Fertility and sterility.

A study of health effects of long-distance ocean voyages on seamen using a data classification approach

Juan Cui, Ying Xu, Yunmei Lu, 2010, BMC Medical Informatics Decis. Mak..

MicroRNA-15b-5p inhibits tumor necrosis factor alpha-induced proliferation, migration, and extracellular matrix production of airway smooth muscle cells via targeting yes-associated protein 1

J. Cui, Z. Zheng, Jun Meng, 2022, Bioengineered.

Computational learning of small RNA regulation in pancreatic cancer progression

Haluk Dogan, J. Cui, Roland Madadjim, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Genomic Data Analysis for Personalized Medicine

Juan Cui, J. Cui, 2015, Healthcare Data Analytics.

Concentrations of Purine Metabolites Are Elevated in Fluids from Adults and Infants and in Livers from Mice Fed Diets Depleted of Bovine Milk Exosomes and their RNA Cargos.

J. Adamec, J. Zempleni, A. Andres, 2018, The Journal of nutrition.

A diet defined by its content of bovine milk exosomes and their RNA cargos has moderate effects on gene expression, amino acid profiles and grip strength in skeletal muscle in C57BL/6 mice.

J. Adamec, J. Zempleni, J. Cui, 2018, The Journal of nutritional biochemistry.

Dietary Bovine Milk Exosomes Elicit Changes in Microbial Communities in C57BL/6 Mice

S. Fernando, J. Zempleni, S. Kachman, 2018, bioRxiv.

Human absorbable microRNA prediction based on an ensemble manifold ranking model

Juan Cui, Kevin Chiang, Jiang Shu, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

HBFP: a new repository for human body fluid proteome

Yan Wang, Xueteng Cui, Wei Du, 2021, Database J. Biol. Databases Curation.

Functional Discovery of Small Non-coding RNA Through Computational Inference

Juan Cui, Adam Voshall, Adam Voshall, 2021 .

Gene regulation by dietary microRNAs.

J. Zempleni, J. Cui, K. Howard, 2015, Canadian journal of physiology and pharmacology.

Hypoxia and miscoupling between reduced energy efficiency and signaling to cell proliferation drive cancer to grow increasingly faster.

V. Olman, X. Mao, Ying Xu, 2012, Journal of molecular cell biology.

Understanding Cancer at the Genomic Level

Ying Xu, J. Cui, D. Puett, 2014 .

Basic Cancer Biology

Ying Xu, J. Cui, D. Puett, 2014 .

Cancer Bioinformatics

Juan Cui, Ying Xu, David Puett, 2014, Springer New York.

Therapy-resistant and -sensitive lncRNAs, SNHG1 and UBL7-AS1 promote glioblastoma cell proliferation

M. Cao, J. Cui, Jian Zhao, 2022, Oxidative medicine and cellular longevity.

Milk exosomes and microRNAs cross the placenta and promote embryo survival in mice.

J. Zempleni, S. Kachman, J. Cui, 2020, Reproduction.

Cancer Development in Competitive and Hostile Environments

Ying Xu, J. Cui, D. Puett, 2014 .

Cell Proliferation from Regulated to Deregulated States Via Epigenomic Responses

Ying Xu, J. Cui, D. Puett, 2014 .

iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis

Qi Liu, Juan Cui, Ruixin Zhu, 2014, Bioinform..

Reconsideration of In-Silico siRNA Design Based on Feature Selection: A Cross-Platform Data Integration Perspective

Ying Xu, Zhiwei Cao, Juan Cui, 2012, PloS one.

Identification of anti‐inflammatory vesicle‐like nanoparticles in honey

Jiujiu Yu, M. Naldrett, S. Kachman, 2021, Journal of extracellular vesicles.

Multiple Routes for Survival: Understanding How Cancer Evades Apoptosis

Ying Xu, J. Cui, D. Puett, 2014 .

Understanding Cancer Invasion and Metastasis

Ying Xu, J. Cui, D. Puett, 2014 .

miR-137 regulates epithelial-mesenchymal transition in gastrointestinal stromal tumor

Guohui Wan, J. Cui, Tailiang Lu, 2014, Tumor Biology.

Comprehensive characterization of the genomic alterations in human gastric cancer

Guoqing Wang, Wen-Chi Chou, Victor Olman, 2015, International journal of cancer.

Human body-fluid proteome: quantitative profiling and computational prediction

Yan Wang, Lan Huang, Qian Chen, 2020, Briefings Bioinform..

Expression of the microRNA-143/145 cluster is decreased in hepatitis B virus-associated hepatocellular carcinoma and may serve as a biomarker for tumorigenesis in patients with chronic hepatitis B

J. Cui, C. Qin, Xiangfei Sun, 2018, Oncology letters.

Circulating microRNA trafficking and regulation: computational principles and practice

Juan Cui, Jiang Shu, J. Cui, 2019, Briefings Bioinform..

Storage of Extracellular Vesicles in Human Milk, and MicroRNA Profiles in Human Milk Exosomes and Infant Formulas.

J. Zempleni, J. Cui, Jiang Shu, 2019, Journal of pediatric gastroenterology and nutrition.

Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs

Jiang Shu, Juan Cui, Janos Zempleni, 2015, PloS one.

Aberrant expression of microRNA induced by high-fructose diet: implications in the pathogenesis of hyperlipidemia and hepatic insulin resistance.

Juan Cui, Hanyuan Zhang, Hanyuan Zhang, 2017, The Journal of nutritional biochemistry.

miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis

Juan Cui, Hanyuan Zhang, Bruno Vieira Resende e Silva, 2017, Briefings Bioinform..

A New Approach to Batch Effect Removal Based on Distribution Matching in Latent Space

Huaqing Li, Juan Cui, Haluk Dogan, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Hyaluronic Acid: A Key Facilitator of Cancer Evolution

Ying Xu, J. Cui, D. Puett, 2014 .

Computational prediction of human proteins that can be secreted into the bloodstream

Ying Xu, Qi Liu, Juan Cui, 2008, Bioinform..

Is serotonin transporter genotype associated with epigenetic susceptibility or vulnerability? Examination of the impact of socioeconomic status risk on African American youth

S. Beach, G. Brody, M. Lei, 2014, Development and Psychopathology.

Heterogeneous graph inference based on similarity network fusion for predicting lncRNA–miRNA interaction

Cui Juan, Yongxian Fan, QingQi Zhu, 2020, RSC advances.

Aberrant expression of microRNAs in gastric cancer and biological significance of miR-574-3p.

Jihan Wang, Ying Xu, Guoqing Wang, 2012, International immunopharmacology.

Identification of Glycoproteins on the Surface of Cow's Milk Exosomes that Mediate the Uptake of Exosomes into Human Colon Carcinoma Caco‐2 Cells

J. Adamec, J. Zempleni, Hanyuan Zhang, 2016 .

Understanding Cancer as an Evolving Complex System: Our Perspective

Ying Xu, J. Cui, D. Puett, 2014 .

Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification

Yanchun Liang, Wei Du, Yan Wang, 2013, PloS one.

A Mobile-Based Diet Monitoring System for Obesity Management.

Bruno Vieira Resende E Silva, Milad Ghiasi Rad, Juan Cui, 2018, Journal of health & medical informatics.

Isolation of extracellular vesicles from byproducts of cheesemaking by tangential flow filtration yields heterogeneous fractions of nanoparticles.

J. Adamec, J. Zempleni, J. Cui, 2021, Journal of dairy science.

A Survey on Automated Food Monitoring and Dietary Management Systems.

Juan Cui, Bruno Vieira Resende e Silva, J. Cui, 2017 .

MiRDR-OSG: MicroRNA dynamic regulation analysis utilizing open science grid

Juan Cui, Jiang Shu, J. Cui, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

DeepSec: a deep learning framework for secreted protein discovery in human body fluids

Yan Wang, Yao Wang, J. Cui, 2021, Bioinform..

In-silico prediction of blood-secretory human proteins using a ranking algorithm

Ying Xu, Qiang Yang, Qi Liu, 2010, BMC Bioinformatics.

A simulation model of glucose-insulin metabolism and implementation on OSG

Massimiliano Pierobon, Juan Cui, Milad Ghiasi Rad, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

The RNA cargo in small extracellular vesicles from chicken eggs is bioactive in C57BL/6 J mice and human peripheral blood mononuclear cells ex vivo

J. Zempleni, J. Cui, Jiang Shu, 2023, Frontiers in Nutrition.

Sonication and Short-term Incubation Alter the Content of Bovine Milk Exosome Cargos and Exosome Bioavailability (OR26-08-19).

J. Adamec, J. Zempleni, J. Cui, 2019, Current Developments in Nutrition.

Dietary Depletion of Milk Exosomes and Their MicroRNA Cargos Elicits a Depletion of miR-200a-3p and Elevated Intestinal Inflammation and Chemokine (C-X-C Motif) Ligand 9 Expression in Mdr1a−/− Mice

J. Zempleni, S. Kachman, Hatem Kittana, 2019, Current developments in nutrition.

Reply to B Fromm et al.

J. Zempleni, J. Cui, 2018, Journal of NutriLife.

Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

Jiang Shu, Zeynep Hakguder, Juan Cui, 2018, BMC Genomics.

A new statistical model for genome-scale MicroRNA target prediction

Juan Cui, Jiang Shu, Zeynep Hakguder, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Progesterone receptor-mediated up-regulation of transthyretin in preimplantation mouse uterus.

J. Chun, Ying Xu, J. Cui, 2010, Fertility and sterility.

A new system for human microRNA functional evaluation and network

Juan Cui, Jiang Shu, Jiachun Han, 2016, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning

Haluk Dogan, Zeynep Hakguder, Stephen Scott, 2021, Briefings Bioinform..

Elucidation of MicroRNA-Gene Regulation in Human Cancer with Integrative Network Models

Zeynep Hakguder, Juan Cui, Haluk Dogan, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Dietary Bovine Milk Exosomes Elicit Changes in Bacterial Communities in C57BL/6 Mice.

S. Fernando, J. Zempleni, S. Kachman, 2019, American journal of physiology. Gastrointestinal and liver physiology.

An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

Wen-Chi Chou, V. Olman, J. Suo, 2010, Nucleic acids research.