• 1372 Citations
  • 16 h-Index
19952019
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Research Output 1995 2019

2019
Penalized Regression
Sequencing
DNA
Tuning
DNA Copy Number Variations
2018
DNA Sequencing
DNA Sequence Analysis
DNA
Genes
Genome
2016

A statistical change-point analysis approach for modeling the ratio of next generation sequencing reads

Chen, J. & Li, H., Jan 1 2016, Association for Women in Mathematics Series. Springer, p. 283-300 18 p. (Association for Women in Mathematics Series; vol. 6).

Research output: Chapter in Book/Report/Conference proceedingChapter

Change-point Analysis
Sequencing
Statistical Analysis
Change Point
Point Location
2 Citations (Scopus)
Data Depth
Sequencing
Statistical Model
Experiment
Genomics
2015

An online copy number variant detection method for short sequencing reads

Yiğiter, A., Chen, J., An, L. & Danacioğlu, N., Jul 3 2015, In : Journal of Applied Statistics. 42, 7, p. 1556-1571 16 p.

Research output: Contribution to journalArticle

Count Data
Sequencing
Change Point
Change-point Detection
Lung Cancer
4 Citations (Scopus)

Modeling the next generation sequencing read count data for DNA copy number variant study

Ji, T. & Chen, J., Aug 1 2015, In : Statistical Applications in Genetics and Molecular Biology. 14, 4, p. 361-374 14 p.

Research output: Contribution to journalArticle

DNA Copy Number Variations
Count Data
Sequencing
DNA
Genes
6 Citations (Scopus)

Use a survival model to correlate single-nucleotide polymorphisms of DNA repair genes with radiation dose-response in patients with non-small cell lung cancer

Jin, J. Y., Wang, W., Ten Haken, R. K., Chen, J., Bi, N., Sadek, R., Zhang, H., Lawrence, T. S. & Kong, F. M., Oct 2015, In : Radiotherapy and Oncology. 117, 1, p. 77-82 6 p.

Research output: Contribution to journalArticle

Non-Small Cell Lung Carcinoma
DNA Repair
Single Nucleotide Polymorphism
Radiation
Survival
2014
1 Citation (Scopus)
Compound Poisson Process
Change Point
Bayesian Approach
Sliding Window
Poisson distribution
12 Citations (Scopus)

Natural Antioxidants Exhibit Chemopreventive Characteristics through the Regulation of CNC b-Zip Transcription Factors in Estrogen-Induced Breast Carcinogenesis

Chatterjee, A., Ronghe, A., Singh, B., Bhat, N. K., Chen, J. & Bhat, H. K., Dec 1 2014, In : Journal of Biochemical and Molecular Toxicology. 28, 12, p. 529-538 10 p.

Research output: Contribution to journalArticle

Ascorbic Acid
Estrogens
Carcinogenesis
Breast
Transcription Factors
22 Citations (Scopus)
Change-point Analysis
Change-point Model
Finance
Medicine
Change-point Problem
2013
2 Citations (Scopus)

SeqBBS: A change-point model based algorithm and R package for searching CNV regions via the ratio of sequencing reads

Li, H., Vallandingham, J. & Chen, J., Dec 1 2013, 2013 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2013 - Proceedings. p. 40-43 4 p. 6735925

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

Tumors
Technology
DNA Copy Number Variations
Cells
Bayes Theorem
2012
5 Citations (Scopus)

A Mouse Model for Adolescent Alcohol Abuse: Stunted Growth and Effects in Brain

Huang, C., Titus, J. A., Bell, R. L., Kapros, T., Chen, J. & Huang, R., Oct 1 2012, In : Alcoholism: Clinical and Experimental Research. 36, 10, p. 1728-1737 10 p.

Research output: Contribution to journalArticle

Growth Disorders
Alcoholism
Brain
Ethanol
Alcohols
73 Citations (Scopus)

Change-point analysis as a tool to detect abrupt climate variations

Beaulieu, C., Chen, J. & Sarmiento, J. L., Mar 13 2012, In : Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 370, 1962, p. 1228-1249 22 p.

Research output: Contribution to journalArticle

Change-point Analysis
Climate
climate
Change Point
Autocorrelation
20 Citations (Scopus)

Identification and characterization of abrupt changes in the land uptake of carbon

Beaulieu, C., Sarmiento, J. L., Mikaloff Fletcher, S. E., Chen, J. & Medvigy, D., Jan 30 2012, In : Global Biogeochemical Cycles. 26, 1, GB1007.

Research output: Contribution to journalArticle

Carbon
Carbon Monoxide
carbon
Volcanic Eruptions
carbon sink
9 Citations (Scopus)

Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis

Zhao, J., Chen, J., Yang, T. H. & Holme, P., Jul 16 2012, In : BMC Systems Biology. 6, SUPPL.1, S4.

Research output: Contribution to journalArticle

Spondylarthropathies
Pathway
Genes
Gene
Proteins
49 Citations (Scopus)

Noncoding RNA expression in myocardium from infants with tetralogy of fallot

O'Brien, J. E., Kibiryeva, N., Zhou, X. G., Marshall, J. A., Lofland, G. K., Artman, M., Chen, J. & Bittel, D. C., Jun 1 2012, In : Circulation: Cardiovascular Genetics. 5, 3, p. 279-286 8 p.

Research output: Contribution to journalArticle

Small Nucleolar RNA
Untranslated RNA
Tetralogy of Fallot
Myocardium
MicroRNAs
2011
8 Citations (Scopus)

A Bayesian approach to inference about a change point model with application to DNA copy number experimental data

Chen, J., Yiǧiter, A. & Chang, K. C., Sep 1 2011, In : Journal of Applied Statistics. 38, 9, p. 1899-1913 15 p.

Research output: Contribution to journalArticle

Change-point Model
Bayesian Approach
Experimental Data
Genomics
Cancer
35 Citations (Scopus)

Gene expression in cardiac tissues from infants with idiopathic conotruncal defects

Bittel, D. C., Butler, M. G., Kibiryeva, N., Marshall, J. A., Chen, J., Lofland, G. K. & O'Brien, J. E., Jan 7 2011, In : BMC Medical Genomics. 4, 1.

Research output: Contribution to journalArticle

Tetralogy of Fallot
Heart Ventricles
Reconstructive Surgical Procedures
Gene Expression
Pulmonary Valve

Pathogenesis of axial spondyloarthropathy in a network perspective

Zhao, J., Chen, J., Yang, T. H. & Holme, P., Oct 28 2011, 2011 IEEE International Conference on Systems Biology, ISB 2011. p. 41-46 6 p. (2011 IEEE International Conference on Systems Biology, ISB 2011).

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

Spondylarthropathies
Genes
Bone
Microarrays
Genetic Databases
2010
2 Citations (Scopus)

A Bayesian analysis for identifying DNA copy number variations using a compound poisson process

Chen, J., Yiǧiter, A., Wang, Y. P. & Deng, H. W., Nov 22 2010, In : Eurasip Journal on Bioinformatics and Systems Biology. 2010, 268513.

Research output: Contribution to journalArticle

DNA Copy Number Variations
Compound Poisson Process
Comparative Genomic Hybridization
Bayes Theorem
Comparative Genomics
13 Citations (Scopus)

Variations in Carotid Artery Intima-Media Thickness during the Cardiac Cycle in Children

Menees, S., Zhang, D., Le, J., Chen, J. & Raghuveer, G., Jan 1 2010, In : Journal of the American Society of Echocardiography. 23, 1, p. 58-63 6 p.

Research output: Contribution to journalArticle

Carotid Intima-Media Thickness
Carotid Arteries
Electrocardiography
Blood Pressure
Linear Models
44 Citations (Scopus)

Vascular age is advanced in children with atherosclerosis-promoting risk factors

Le, J., Zhang, D., Menees, S., Chen, J. & Raghuveer, G., Jan 1 2010, In : Circulation: Cardiovascular Imaging. 3, 1, p. 8-14 7 p.

Research output: Contribution to journalArticle

Blood Vessels
Atherosclerosis
Carotid Intima-Media Thickness
Carotid Arteries
Dyslipidemias
2009
35 Citations (Scopus)
DNA Copy Number Variations
Change-point Model
Comparative Genomic Hybridization
Comparative Genomics
Statistical Model
5 Citations (Scopus)

Family-based bivariate association tests for quantitative traits

Zhang, L., Bonham, A. J., Li, J., Pei, Y. F., Chen, J., Papasian, C. J. & Deng, H. W., Dec 1 2009, In : PloS one. 4, 12, e8133.

Research output: Contribution to journalArticle

quantitative traits
Principal component analysis
Genes
Throughput
Statistics
2008
4 Citations (Scopus)

A comparison of fuzzy clustering approaches for quantification of microarray gene expression

Wang, Y. P., Gunampally, M., Chen, J., Bittel, D., Butler, M. G. & Cai, W. W., Mar 1 2008, In : Journal of Signal Processing Systems. 50, 3, p. 305-320 16 p.

Research output: Contribution to journalArticle

Fuzzy clustering
Fuzzy Clustering
Microarrays
Gene expression
Microarray
4 Citations (Scopus)

Discovering statistically significant periodic gene expression

Chen, J. & Chang, K. C., Aug 1 2008, In : International Statistical Review. 76, 2, p. 228-246 19 p.

Research output: Contribution to journalReview article

Gene Expression
Gene
Cell Cycle
Microarray
Familywise Error Rate
7 Citations (Scopus)

HAPSIMU: A genetic simulation platform for population-based association studies

Zhang, F., Liu, J., Chen, J. & Deng, H. W., Aug 5 2008, In : BMC Bioinformatics. 9, 331.

Research output: Contribution to journalArticle

Simulation Platform
Population Structure
Population
Statistical methods
Structure Identification
2007
1 Citation (Scopus)

Accurate quantification of gene expression using fuzzy clustering approaches

Wang, Y. P., Gunampally, M., Chen, J., Bittet, D., Butler, M. G. & Cai, W. W., Dec 1 2007, 5th IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'07. 4365833. (GENSIPS'07 - 5th IEEE International Workshop on Genomic Signal Processing and Statistics).

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

Fuzzy clustering
Microarrays
Gene expression
Cluster Analysis
Gene Expression
2006
300 Citations (Scopus)

A complex oscillating network of signaling genes underlies the mouse segmentation clock

Dequéant, M. L., Glynn, E., Gaudenz, K., Wahl, M., Chen, J., Mushegian, A. & Pourquié, O., Dec 8 2006, In : Science. 314, 5805, p. 1595-1598 4 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Mesoderm
Somites
Wnt Signaling Pathway
Fibroblast Growth Factors
131 Citations (Scopus)

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms

Glynn, E. F., Chen, J. & Mushegian, A. R., Feb 1 2006, In : Bioinformatics. 22, 3, p. 310-316 7 p.

Research output: Contribution to journalArticle

Periodogram
Gene expression
Gene Expression
Time series
Fourier Analysis
2 Citations (Scopus)

Detection of DNA copy number changes using statistical change point analysis

Chen, J. & Wang, Y. P., Dec 1 2006, 2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006. p. 11-12 2 p. 4161752. (2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006).

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

DNA Copy Number Variations
Change-point Analysis
Statistical Analysis
DNA
Cells
2005
4 Citations (Scopus)

Fast frequency estimation by zero crossings of differential spline wavelet transform

Wang, Y. P., Chen, J., Wu, Q. & Castleman, K. R., May 21 2005, In : Eurasip Journal on Applied Signal Processing. 2005, 8, p. 1251-1260 10 p.

Research output: Contribution to journalArticle

Frequency estimation
Splines
Wavelet transforms
Signal analysis
Computer vision
25 Citations (Scopus)

Identification of significant periodic genes in microarray gene expression data

Chen, J., Nov 30 2005, In : BMC Bioinformatics. 6, 286.

Research output: Contribution to journalArticle

Microarrays
Gene Expression Data
Microarray Data
Gene expression
Genes
237 Citations (Scopus)

Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling

Li, B., Pattenden, S. G., Lee, D., Gutiérrez, J., Chen, J., Seidel, C., Gerton, J. & Workman, J. L., Dec 20 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 51, p. 18385-18390 6 p.

Research output: Contribution to journalArticle

Histone Code
Chromatin Assembly and Disassembly
Histones
Nucleosomes
Genome
2004
8 Citations (Scopus)

Distribution and percentage points of the likelihood ratio statistic for testing circular symmetry

Nagar, D. K., Chen, J. & Gupta, A. K., Aug 1 2004, In : Computational Statistics and Data Analysis. 47, 1, p. 79-89 11 p.

Research output: Contribution to journalArticle

Percentage Points
Inverse transforms
Likelihood Ratio Statistic
Normal distribution
Covariance matrix
11 Citations (Scopus)

Statistical inference of covariance change points in gaussian model

Chen, J. & Gupta, A. K., Feb 1 2004, In : Statistics. 38, 1, p. 17-28 12 p.

Research output: Contribution to journalArticle

Information Criterion
Change Point
Gaussian Model
Statistical Inference
Bivariate Normal
2001
53 Citations (Scopus)

On change point detection and estimation

Chen, J. & Gupta, A. K., Jan 1 2001, In : Communications in Statistics Part B: Simulation and Computation. 30, 3, p. 665-697 33 p.

Research output: Contribution to journalArticle

Change-point Estimation
Change-point Detection
Wavelet Transformation
Cumulative Sum
Information Criterion
2000
1 Citation (Scopus)

Detecting change point for a sequence of random vectors under nonnormality

Chen, J. & Gupta, A. K., Jan 1 2000, In : Random Operators and Stochastic Equations. 8, 2, p. 127-142 16 p.

Research output: Contribution to journalArticle

Non-normality
Null Distribution
Change Point
Random Vector
Asymptotic distribution

On classification of multiple observations with application to marketing analysis

Logan, T. P., Gupta, A. K. & Chen, J., Jan 1 2000, In : American Journal of Mathematical and Management Sciences. 20, 3-4, p. 387-402 16 p.

Research output: Contribution to journalArticle

Marketing
Likelihood
Data analysis
Alternatives
Model
1999
4 Citations (Scopus)

A variable selection technique in discriminant analysis with application in marketing data

Gupta, A. K., Logan, T. P. & Chen, J., Jan 1 1999, In : Journal of Statistical Computation and Simulation. 63, 2, p. 187-199 13 p.

Research output: Contribution to journalArticle

Discriminant analysis
Variable Selection
Discriminant Analysis
Factorization
Marketing
13 Citations (Scopus)

Change point analysis of a Gaussian model

Chen, J. & Gupta, A. K., Jan 1 1999, In : Statistical Papers. 40, 3, p. 323-333 11 p.

Research output: Contribution to journalArticle

Change-point Analysis
Change Point
Gaussian Model
Change-point Problem
Information Criterion
1998
27 Citations (Scopus)

Testing for a change point in linear regression models

Chen, J., Jan 1 1998, In : Communications in Statistics - Theory and Methods. 27, 10, p. 2481-2493 13 p.

Research output: Contribution to journalArticle

Change Point
Linear Regression Model
Simple Linear Regression
Testing
Information Criterion
1997
157 Citations (Scopus)

Testing and Locating Variance Changepoints with Application to Stock Prices

Chen, J. & Gupta, A. K., Jun 1 1997, In : Journal of the American Statistical Association. 92, 438, p. 739-747 9 p.

Research output: Contribution to journalArticle

Information Criterion
Stock Prices
Change Point
Testing
Common Mean
1996
20 Citations (Scopus)

Detecting changes of mean in multidimensional normal sequences with applications to literature and geology

Gupta, A. K. & Chen, J., Dec 1 1996, In : Computational Statistics. 11, 3, p. 211-221 11 p.

Research output: Contribution to journalArticle

Exploratory Data Analysis
Geology
Information Criterion
Change Point
Segmentation
1995
16 Citations (Scopus)

Likelihood procedure for testing change point hypothesis for multivariate Gaussian model

Chen, J. & Gupta, A. K., Jan 1 1995, In : Random Operators and Stochastic Equations. 3, 3, p. 235-244 10 p.

Research output: Contribution to journalArticle

Information Criterion
Multivariate Models
Change Point
Gaussian Model
Asymptotic distribution