• 1466 Citations
  • 18 h-Index
19982019
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Research Output 1998 2019

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Article
2019

Type-2 Fuzzy PCA Approach in Extracting Salient Features for Molecular Cancer Diagnostics and Prognostics

Singh, V., Verma, N. K. & Cui, Y., Jul 1 2019, In : IEEE Transactions on Nanobioscience. 18, 3, p. 482-489 8 p., 8718370.

Research output: Contribution to journalArticle

Molecular Pathology
Principal Component Analysis
Principal component analysis
Feature extraction
Neoplasms
2018
2 Citations (Scopus)

Deletion of DGCR8 in VSMCs of adult mice results in loss of vascular reactivity, reduced blood pressure and neointima formation

Zou, Y., Chen, Z., Jennings, B. L., Zhao, G., Gu, Q., Bhattacharya, A., Cui, Y., Yu, B., Malik, K. & Yue, J., Dec 1 2018, In : Scientific Reports. 8, 1, 19660.

Research output: Contribution to journalArticle

DiGeorge Syndrome
Neointima
Vascular Smooth Muscle
Smooth Muscle Myocytes
Blood Vessels
7 Citations (Scopus)

Transfer Learning for Molecular Cancer classification using Deep Neural Networks

Sevakula, R. K., Singh, V., Verma, N. K., Kumar, C. & Cui, Y., Apr 3 2018, (Accepted/In press) In : IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Research output: Contribution to journalArticle

Cancer Classification
Transfer Learning
Tumor
Neural Networks
Tumors
2017
9 Citations (Scopus)

A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules

Bhattacharya, A. & Cui, Y., Dec 1 2017, In : Scientific Reports. 7, 1, 4162.

Research output: Contribution to journalArticle

Gene expression
Genes
Graphics processing unit
2016
2 Citations (Scopus)

Assessing the quality of biclusters using fuzzy biclustering index

Verma, N. K., Dutta, E. & Cui, Y., Jan 1 2016, In : International Journal of Data Mining and Bioinformatics. 15, 4, p. 291-311 21 p.

Research output: Contribution to journalArticle

Data Mining
Data mining
Databases
scenario
present
33 Citations (Scopus)

SomamiR 2.0: A database of cancer somatic mutations altering microRNA-ceRNA interactions

Bhattacharya, A. & Cui, Y., Jan 4 2016, In : Nucleic acids research. 44, D1, p. D1005-D1010

Research output: Contribution to journalArticle

MicroRNAs
Databases
RNA
Mutation
Neoplasms
2015
10 Citations (Scopus)

CbGRiTS: Cerebellar gene regulation in time and space

Ha, T., Swanson, D., Larouche, M., Glenn, R., Weeden, D., Zhang, P., Hamre, K., Langston, M., Phillips, C., Song, M., Ouyang, Z., Chesler, E., Duvvurru, S., Yordanova, R., Cui, Y., Campbell, K., Ricker, G., Phillips, C., Homayouni, R. & Goldowitz, D., Jan 1 2015, In : Developmental Biology. 397, 1, p. 18-30 13 p.

Research output: Contribution to journalArticle

Genes
Gene Expression Profiling
Transcriptome
Databases
Developmental Genes
5 Citations (Scopus)

Knowledge-based analysis of functional impacts of mutations in microRNA seed regions

Bhattacharya, A. & Cui, Y., Oct 1 2015, In : Journal of Biosciences. 40, 4, p. 791-798 8 p.

Research output: Contribution to journalArticle

MicroRNAs
microRNA
Seed
Seeds
mutation
16 Citations (Scopus)

MiR2GO: Comparative functional analysis for microRNAs

Bhattacharya, A. & Cui, Y., Jan 1 2015, In : Bioinformatics. 31, 14, p. 2403-2405 3 p.

Research output: Contribution to journalArticle

Functional analysis
MicroRNA
Functional Analysis
MicroRNAs
Comparative Analysis
2014
3 Citations (Scopus)

Genetic control of weight loss during pneumonic Burkholderia pseudomallei infection

Emery, F. D., Parvathareddy, J., Pandey, A. K., Cui, Y., Williams, R. & Miller, M., Jan 1 2014, In : Pathogens and Disease. 71, 2, p. 247-262 16 p.

Research output: Contribution to journalArticle

Burkholderia Infections
Burkholderia pseudomallei
Weight Loss
Lung
Melioidosis
5 Citations (Scopus)

In silico mapping of polymorphic miRNA-mRNA interactions in autoimmune thyroid diseases

Cui, Y., Jan 1 2014, In : Autoimmunity. 47, 5, p. 327-333 7 p.

Research output: Contribution to journalArticle

Thyroid Diseases
MicroRNAs
Computer Simulation
Autoimmune Diseases
Messenger RNA
133 Citations (Scopus)

PolymiRTS Database 3.0: Linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways

Bhattacharya, A., Ziebarth, J. D. & Cui, Y., Jan 1 2014, In : Nucleic Acids Research. 42, D1

Research output: Contribution to journalArticle

MicroRNAs
Databases
Messenger RNA
Ligation
Seeds
15 Citations (Scopus)

Pre-transplant predictors of one yr weight gain after kidney transplantation

Cashion, A. K., Hathaway, D., Stanfill, A., Thomas, F., Ziebarth, J. D., Cui, Y., Cowan, P. A. & Eason, J., Nov 1 2014, In : Clinical Transplantation. 28, 11, p. 1271-1278 8 p.

Research output: Contribution to journalArticle

Kidney Transplantation
Weight Gain
Transplants
Kidney
Bayes Theorem
2013
15 Citations (Scopus)

Bayesian network webserver: A comprehensive tool for biological network modeling

Ziebarth, J. D., Bhattacharya, A. & Cui, Y., Nov 1 2013, In : Bioinformatics. 29, 21, p. 2801-2803 3 p.

Research output: Contribution to journalArticle

Network Modeling
Biological Networks
Web Server
Bayesian networks
Bayesian Networks
60 Citations (Scopus)

CTCFBSDB 2.0: A database for CTCF-binding sites and genome organization

Ziebarth, J. D., Bhattacharya, A. & Cui, Y., Jan 1 2013, In : Nucleic Acids Research. 41, D1

Research output: Contribution to journalArticle

Binding Sites
Genome
Databases
Publications
Gene Expression
24 Citations (Scopus)

miRNA Biogenesis Enzyme Drosha Is Required for Vascular Smooth Muscle Cell Survival

Fan, P., Chen, Z., Tian, P., Liu, W., Jiao, Y., Xue, Y., Bhattacharya, A., Wu, J., Lu, M., Guo, Y., Cui, Y., Gu, W., Gu, W. & Yue, J., Apr 18 2013, In : PLoS ONE. 8, 4, e60888.

Research output: Contribution to journalArticle

MicroRNAs
microRNA
Vascular Smooth Muscle
blood vessels
smooth muscle
49 Citations (Scopus)

SomamiR: A database for somatic mutations impacting microRNA function in cancer

Bhattacharya, A., Ziebarth, J. D. & Cui, Y., Jan 1 2013, In : Nucleic Acids Research. 41, D1

Research output: Contribution to journalArticle

MicroRNAs
Databases
Mutation
Germ-Line Mutation
Neoplasms
2012
15 Citations (Scopus)

Host genetics and Chlamydia disease: Prediction and validation of disease severity mechanisms

Miyairi, I., Ziebarth, J., Laxton, J. D., Wang, X., van Rooijen, N., Williams, R., Lu, L., Byrne, G. I. & Cui, Y., Mar 16 2012, In : PloS one. 7, 3, e33781.

Research output: Contribution to journalArticle

Inborn Genetic Diseases
Chlamydia
Pathogens
disease severity
GTP Phosphohydrolases
23 Citations (Scopus)

Integrative Analysis of Somatic Mutations Altering MicroRNA Targeting in Cancer Genomes

Ziebarth, J. D., Bhattacharya, A. & Cui, Y., Oct 16 2012, In : PloS one. 7, 10, e47137.

Research output: Contribution to journalArticle

somatic mutation
MicroRNAs
microRNA
Genes
Genome
90 Citations (Scopus)

PolymiRTS database 2.0: Linking polymorphisms in microRNA target sites with human diseases and complex traits

Ziebarth, J. D., Bhattacharya, A., Chen, A. & Cui, Y., Jan 1 2012, In : Nucleic Acids Research. 40, D1

Research output: Contribution to journalArticle

MicroRNAs
Databases
Single Nucleotide Polymorphism
Quantitative Trait Loci
Genome-Wide Association Study
15 Citations (Scopus)

Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome

Bhattacharya, A., Ziebarth, J. D. & Cui, Y., Sep 25 2012, In : PloS one. 7, 9, e46176.

Research output: Contribution to journalArticle

Human Genome
MicroRNAs
microRNA
Genes
genome
14 Citations (Scopus)

Treatment- and population-dependent activity patterns of behavioral and expression QTLs

Ziebarth, J. D., Cook, M. N., Wang, X., Williams, R., Lu, L. & Cui, Y., Feb 16 2012, In : PloS one. 7, 2, e31805.

Research output: Contribution to journalArticle

quantitative trait loci
Genes
Gene Expression
Population
Phenotype
2010
3 Citations (Scopus)

Expression QTL modules as functional components underlying higher-order phenotypes

Bao, L., Xia, X. & Cui, Y., Dec 1 2010, In : PLoS ONE. 5, 12, e14313.

Research output: Contribution to journalArticle

quantitative trait loci
Phenotype
phenotype
Genetic Loci
Gene expression
2008
80 Citations (Scopus)

CTCFBSDB: A CTCF-binding site database for characterization of vertebrate genomic insulators

Bao, L., Zhou, M. & Cui, Y., Jan 1 2008, In : Nucleic Acids Research. 36, SUPPL. 1

Research output: Contribution to journalArticle

Vertebrates
Binding Sites
Databases
Chromatin
Hordeolum
2007
16 Citations (Scopus)

An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes

Bao, L., Peirce, J. L., Zhou, M., Li, H., Goldowitz, D., Williams, R., Lu, L. & Cui, Y., Jun 1 2007, In : Human Molecular Genetics. 16, 11, p. 1381-1390 10 p.

Research output: Contribution to journalArticle

Genetic Loci
Genomics
Phenotype
Quantitative Trait Loci
Genes
122 Citations (Scopus)

PolymiRTS Database: Linking polymorphisms in microRNA target sites with complex traits

Bao, L., Zhou, M., Wu, L., Lu, L., Goldowitz, D., Williams, R. & Cui, Y., Jan 1 2007, In : Nucleic acids research. 35, SUPPL. 1

Research output: Contribution to journalArticle

MicroRNAs
Databases
Phenotype
Quantitative Trait Loci
Gene Expression
2006
16 Citations (Scopus)

Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships

Bao, L., Wei, L., Peirce, J. L., Homayouni, R., Li, H., Zhou, M., Chen, H., Lu, L., Williams, R., Pfeffer, L., Goldowitz, D. & Cui, Y., Jun 1 2006, In : Mammalian Genome. 17, 6, p. 575-583 9 p.

Research output: Contribution to journalArticle

Regulator Genes
Spectrum Analysis
Phenotype
Gene Expression
Protein Kinase C-epsilon
12 Citations (Scopus)

Functional impacts of non-synonymous single nucleotide polymorphisms: Selective constraint and structural environments

Bao, L. & Cui, Y., Feb 20 2006, In : FEBS Letters. 580, 5, p. 1231-1234 4 p.

Research output: Contribution to journalArticle

Polymorphism
Single Nucleotide Polymorphism
Nucleotides
33 Citations (Scopus)

Integrative genetic analysis of transcription modules: Towards filling the gap between genetic loci and inherited traits

Li, H., Chen, H., Bao, L., Manly, K. F., Chesler, E. J., Lu, L., Wang, J., Zhou, M., Williams, R. & Cui, Y., Feb 1 2006, In : Human Molecular Genetics. 15, 3, p. 481-492 12 p.

Research output: Contribution to journalArticle

Genetic Transcription
Genetic Loci
Gene Regulatory Networks
Viverridae
Quantitative Trait Loci
91 Citations (Scopus)

Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression

Deng, W., Zhu, X., Skogerbø, G., Zhao, Y., Fu, Z., Wang, Y., He, H., Cai, L., Sun, H., Liu, C., Li, B., Bai, B., Wang, J., Jia, D., Sun, S., He, H., Cui, Y., Wang, Y., Bu, D. & Chen, R., Jan 1 2006, In : Genome Research. 16, 1, p. 20-29 10 p.

Research output: Contribution to journalArticle

Caenorhabditis elegans
Transcriptome
Caenorhabditis
Small Nucleolar RNA
RNA
26 Citations (Scopus)

Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray

He, H., Cai, L., Skogerbø, G., Deng, W., Liu, T., Zhu, X., Wang, Y., Jia, D., Zhang, Z., Tao, Y., Zeng, H., Aftab, M. N., Cui, Y., Liu, G. & Chen, R., Oct 17 2006, In : Nucleic acids research. 34, 10, p. 2976-2983 8 p.

Research output: Contribution to journalArticle

Untranslated RNA
Caenorhabditis elegans
Transcriptome
Genes
Small Nucleolar RNA
2005
70 Citations (Scopus)

Inferring gene transcriptional modulatory relations: A genetical genomics approach

Li, H., Lu, L., Manly, K. F., Chesler, E. J., Bao, L., Wang, J., Zhou, M., Williams, R. & Cui, Y., May 1 2005, In : Human molecular genetics. 14, 9, p. 1119-1125 7 p.

Research output: Contribution to journalArticle

Genomics
Gene Regulatory Networks
Quantitative Trait Loci
Population Genetics
Single Nucleotide Polymorphism
122 Citations (Scopus)

nsSNPAnalyzer: Identifying disease-associated nonsynonymous single nucleotide polymorphisms

Bao, L., Zhou, M. & Cui, Y., Jul 1 2005, In : Nucleic acids research. 33, SUPPL. 2

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Software
Genome
Machine Learning
Forests
104 Citations (Scopus)

Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information

Bao, L. & Cui, Y., May 15 2005, In : Bioinformatics. 21, 10, p. 2185-2190 6 p.

Research output: Contribution to journalArticle

Single nucleotide Polymorphism
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Prediction
2004

Autosomal similarity revealed by eukaryotic genomic comparison

Qi, Z., Cui, Y., Fang, W., Ling, L. & Chen, R., Dec 1 2004, In : Journal of Biological Physics. 30, 4, p. 305-312 8 p.

Research output: Contribution to journalArticle

organisms
genes
proteome
eukaryotes
Eukaryota
19 Citations (Scopus)

GeneInfoViz: Constructing and visualizing gene relation networks

Zhou, M. & Cui, Y., Dec 17 2004, In : In Silico Biology. 4, 3, p. 323-333 11 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Genes
Gene
Gene Ontology
Databases
12 Citations (Scopus)

Integrated analysis of microarray data and gene function information

Cui, Y., Zhou, M. & Wong, W. H., Aug 9 2004, In : OMICS A Journal of Integrative Biology. 8, 2, p. 106-117 12 p.

Research output: Contribution to journalArticle

Microarray Analysis
Microarrays
Genes
Statistical methods
Display devices
2002
6 Citations (Scopus)

Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms

Ling, L., Wang, J., Cui, Y., Li, W. & Chen, R., Oct 29 2002, In : Molecular Phylogenetics and Evolution. 25, 1, p. 101-111 11 p.

Research output: Contribution to journalArticle

Proteome
proteome
Cluster Analysis
phylogenetics
protein
76 Citations (Scopus)

Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes

Cui, Y., Wong, W. H., Bornberg-Bauer, E. & Chan, H. S., Jan 22 2002, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 2, p. 809-814 6 p.

Research output: Contribution to journalArticle

Point Mutation
Proteins
Physics
Mutation Rate
Hydrophobic and Hydrophilic Interactions
2000
5 Citations (Scopus)

Multiple-sequence information provides protection against mis-specified potential energy functions in the lattice model of proteins

Cui, Y. & Wong, W. H., Jan 1 2000, In : Physical Review Letters. 85, 24, p. 5242-5245 4 p.

Research output: Contribution to journalArticle

potential energy
proteins
enumeration
9 Citations (Scopus)

The coevolution of cell senescence and diploid sexual reproduction in unicellular organisms

Cui, Y., Chen, R. S. & Wong, W. H., Mar 28 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 7, p. 3330-3335 6 p.

Research output: Contribution to journalArticle

Cell Aging
Diploidy
Reproduction
Asexual Reproduction
Computer Simulation
1999
1 Citation (Scopus)

Molecular dynamics simulation of site-directed mutagenesis of HIV-1 Tat trans-activator

Cui, Y., Ling, L., Chen, R., Bai, L., Yuan, J. & Qiang, B., Jan 1 1999, In : Chinese Science Bulletin. 44, 8, p. 708-711 4 p.

Research output: Contribution to journalArticle

Trans-Activators
Molecular Dynamics Simulation
Site-Directed Mutagenesis
HIV-1
Human Immunodeficiency Virus tat Gene Products
1998

Molecular dynamic simulation of chaperonin-mediated protein folding

Cui, Y., Chen, R. S. & Wong, W. H., Dec 1 1998, In : Protein Journal. 17, 4, p. 377-380 4 p.

Research output: Contribution to journalArticle

Chaperonins
Protein folding
Protein Folding
Molecular Dynamics Simulation
Molecular dynamics
2 Citations (Scopus)

Molecular dynamic simulation of chaperonin-mediated protein folding

Cui, Y., Chen, R. S. & Wong, W. H., Jun 8 1998, In : Journal of Protein Chemistry. 17, 4, p. 377-380 4 p.

Research output: Contribution to journalArticle

Chaperonins
Protein folding
Protein Folding
Molecular Dynamics Simulation
Molecular dynamics

Molecular dynamics simulation of protein folding with supersecondary structure constraints

Sun, Z. R., Cui, Y., Ling, L. J., Guo, Q. & Chen, R. S., Dec 1 1998, In : Journal of Protein Chemistry. 17, 8, p. 765-769 5 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Molecular Dynamics Simulation
Molecular dynamics
Crystal structure
3 Citations (Scopus)

Molecular dynamics simulation of protein folding with supersecondary structure constraints

Sun, Z. R., Cui, Y., Ling, L. J., Guo, Q. & Chen, R. S., Dec 1 1998, In : Journal of Protein Chemistry. 17, 8, p. 765-769 5 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Molecular Dynamics Simulation
Molecular dynamics
Crystal structure
57 Citations (Scopus)

Protein folding simulation with genetic algorithm and supersecondary structure constraints

Cui, Y., Chen, R. S. & Wong, W. H., May 15 1998, In : Proteins: Structure, Function and Genetics. 31, 3, p. 247-257 11 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Genetic algorithms
Amino Acid Motifs
Proteins
2 Citations (Scopus)

Torsional relaxation for biopolymers

Wong, W. H., Cui, Y. & Chen, R. S., Jan 1 1998, In : Journal of Computational Biology. 5, 4, p. 655-665 11 p.

Research output: Contribution to journalArticle

Biopolymers
Energy Function
Hydrogen Bonds
Van Der Waals
Hydrogen bonds