• 1460 Citations
  • 18 h-Index
19982019
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Research Output 1998 2019

  • 1460 Citations
  • 18 h-Index
  • 47 Article
  • 8 Conference contribution
  • 5 Chapter
  • 1 Conference article
2019

Feature learning using stacked autoencoder for shared and multimodal fusion of medical images

Singh, V., Verma, N. K., Ul Islam, Z. & Cui, Y., Jan 1 2019, Advances in Intelligent Systems and Computing. Springer Verlag, p. 53-66 14 p. (Advances in Intelligent Systems and Computing; vol. 798).

Research output: Chapter in Book/Report/Conference proceedingChapter

Fusion reactions
Image analysis
Learning systems
Deep learning

Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources

Ziebarth, J. D., Bhattacharya, A. & Cui, Y., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 101-120 20 p. (Methods in Molecular Biology; vol. 1970).

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational Biology
MicroRNAs
Mutation
Untranslated RNA
Genetic Databases
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
1 Citation (Scopus)

Optimal feature selection using fuzzy combination of feature subset for transcriptome data

Singh, V., Vardhan, H., Verma, N. K. & Cui, Y., Oct 12 2018, 2018 IEEE International Conference on Fuzzy Systems, FUZZ 2018 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 8491683. (IEEE International Conference on Fuzzy Systems; vol. 2018-July).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Set theory
Feature Selection
Feature extraction
Filter Method
Subset
6 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
7 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
6 Citations (Scopus)

Layerwise feature selection in Stacked Sparse Auto-Encoder for tumor type prediction

Singh, V., Baranwal, N., Sevakula, R. K., Verma, N. K. & Cui, Y., Jan 17 2017, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Burrage, K., Zhu, Q., Liu, Y., Tian, T., Wang, Y., Hu, X. T., Jiang, Q., Song, J., Morishita, S., Burrage, K. & Wang, G. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1542-1548 7 p. 7822750. (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Feature extraction
Tumors
Gene expression
Benchmarking
Neoplasms
1 Citation (Scopus)

Precise network modeling of systems genetics data using the Bayesian network webserver

Ziebarth, J. D. & Cui, Y., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 319-335 17 p. (Methods in Molecular Biology; vol. 1488).

Research output: Chapter in Book/Report/Conference proceedingChapter

Information Systems
Genetic Models
Genotype
Learning
Phenotype
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
3 Citations (Scopus)

Hausdorff distance and global silhouette index as novel measures for estimating quality of biclusters

Verma, N. K., Dutta, E. & Cui, Y., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc., p. 267-272 6 p. 7359691

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Benchmarking
Microarrays
Datasets
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

Bioinformatics Tools for Gene Function Prediction

Cui, Y., Feb 10 2012, Gene Discovery for Disease Models. John Wiley and Sons, p. 93-110 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bioinformatics
Computational Biology
Genes
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
8 Citations (Scopus)

A comparison of biclustering algorithms

Verma, N. K., Meena, S., Bajpai, S., Singh, A., Nagrare, A. & Cui, Y., Dec 1 2010, International Conference on Systems in Medicine and Biology, ICSMB 2010 - Proceedings. p. 90-97 8 p. 5735351. (International Conference on Systems in Medicine and Biology, ICSMB 2010 - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Gene Ontology
Cluster Analysis
Databases
Technology
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
1 Citation (Scopus)

Systems genetics analysis of molecular pathways underlying ethanol-induced behavioral phenotypes

Ziebarth, J. D., Cook, M. N., Li, B., Williams, R., Lu, L. & Cui, Y., Aug 20 2010, Proceedings of the 2010 Biomedical Science and Engineering Conference, BSEC 2010: Biomedical Research and Analysis in Neuroscience, BRAiN. 5510821

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Gene expression
Ethanol
Alcohols
Bayesian networks
Brain
2009

Fuzzy rule based unsupervised approach for salient gene extraction

Verma, N. K., Gupta, P., Agrawal, P. & Cui, Y., Dec 1 2009, Applied Imagery Pattern Recognition 2009: Vision: Humans, Animals, and Machines, AIPR 2009. 5466302

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Fuzzy rules
Genes
Microarrays
Classifiers
Tissue
3 Citations (Scopus)

Medical image segmentation using improved mountain clustering approach

Verma, N. K., Gupta, P., Agrawal, P., Hanmandlu, M., Vasikarla, S. & Cui, Y., Dec 1 2009, ITNG 2009 - 6th International Conference on Information Technology: New Generations. p. 1307-1312 6 p. 5070807

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Image segmentation
X rays
Entropy
8 Citations (Scopus)

MRI brain image segmentation for spotting tumors using improved mountain clustering approach

Verma, N. K., Gupta, P., Agrawal, P. & Cui, Y., Dec 1 2009, Applied Imagery Pattern Recognition 2009: Vision: Humans, Animals, and Machines, AIPR 2009. 5466301

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Magnetic resonance
Image segmentation
Tumors
Brain
Entropy
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
15 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

Bridging genotype and phenotype: Causal pathways from DNA to complex traits

Cui, Y., Jan 1 2007, Current Topics in Human Genetics: Studies in Complex Diseases. World Scientific Publishing Co., p. 433-446 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Genetic Loci
Gene expression
Genotype
Phenotype
Gene Expression
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
15 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
2 Citations (Scopus)

Ranking gene regulatory network models with microarray data and Bayesian Network

Li, H., Zhou, M. & Cui, Y., Dec 1 2004, In : Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science). 3327, p. 109-118 10 p.

Research output: Contribution to journalConference article

Gene Regulatory Network
Bayesian networks
Microarrays
Microarray Data
Bayesian Networks