Works by Jianhua Xuan

Results: 52

Maternal intake of high n-6 polyunsaturated fatty acid diet during pregnancy causes transgenerational increase in mammary cancer risk in mice.

Published in:

2017

By:

Nguyen, Nguyen M.;
de Oliveira Andrade, Fabia;
Lu Jin;
Xiyuan Zhang;
Macon, Madisa;
Cruz, M. Idalia;
Benitez, Carlos;
Wehrenberg, Bryan;
Chao Yin;
Xiao Wang;
Jianhua Xuan;
de Assis, Sonia;
Hilakivi-Clarke, Leena;
Jin, Lu;
Zhang, Xiyuan;
Yin, Chao;
Wang, Xiao;
Xuan, Jianhua

Publication type:

journal article

SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data.

Published in:

Bioinformatics, 2018, v. 34, n. 1, p. 56, doi. 10.1093/bioinformatics/btx557

By:

Shi, Xu;
Wang, Xiao;
Wang, Tian-Li;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification.

Published in:

Bioinformatics, 2017, v. 33, n. 2, p. 177, doi. 10.1093/bioinformatics/btw605

By:

Xi Chen;
Xu Shi;
Hilakivi-Clarke, Leena;
Shajahan-Haq, Ayesha N.;
Clarke, Robert;
Jianhua Xuan

Publication type:

Article

DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency.

Published in:

Bioinformatics, 2017, v. 33, n. 2, p. 161, doi. 10.1093/bioinformatics/btw596

By:

Xiao Wang;
Jinghua Gu;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Jianhua Xuan

Publication type:

Article

BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.

Published in:

2015

By:

Xu Shi;
Barnes, Robert O.;
Li Chen;
Shajahan-Haq, Ayesha N.;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Yue Wang;
Jianhua Xuan

Publication type:

Product Review

KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring.

Published in:

2015

By:

Tian, Ye;
Zhang, Bai;
Hoffman, Eric P.;
Clarke, Robert;
Zhang, Zhen;
Shih, Ie-Ming;
Xuan, Jianhua;
Herrington, David M.;
Wang, Yue

Publication type:

Case Study

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 137, doi. 10.1093/bioinformatics/btu607

By:

Wang, Niya;
Gong, Ting;
Clarke, Robert;
Chen, Lulu;
Shih, Ie-Ming;
Zhang, Zhen;
Levine, Douglas A.;
Xuan, Jianhua;
Wang, Yue

Publication type:

Article

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.

Published in:

2014

By:

Gu, Jinghua;
Xuan, Jianhua;
Riggins, Rebecca B.;
Chen, Li;
Wang, Yue;
Clarke, Robert

Publication type:

Correction Notice

Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.

Published in:

Bioinformatics, 2012, v. 28, n. 15, p. 1990

By:

Gu, Jinghua;
Xuan, Jianhua;
Riggins, Rebecca B.;
Chen, Li;
Wang, Yue;
Clarke, Robert

Publication type:

Article

DDN: a caBIG® analytical tool for differential network analysis.

Published in:

Bioinformatics, 2011, v. 27, n. 7, p. 1036, doi. 10.1093/bioinformatics/btr052

By:

Zhang, Bai;
Tian, Ye;
Jin, Lu;
Li, Huai;
Shih, Ie-Ming;
Madhavan, Subha;
Clarke, Robert;
Hoffman, Eric P.;
Xuan, Jianhua;
Hilakivi-Clarke, Leena;
Wang, Yue

Publication type:

Article

PUGSVM: a caBIGTM analytical tool for multiclass gene selection and predictive classification.

Published in:

Bioinformatics, 2011, v. 27, n. 5, p. 736, doi. 10.1093/bioinformatics/btq721

By:

Yu, Guoqiang;
Li, Huai;
Ha, Sook;
Shih, Ie−Ming;
Clarke, Robert;
Hoffman, Eric P.;
Madhavan, Subha;
Xuan, Jianhua;
Wang, Yue

Publication type:

Article

Multilevel support vector regression analysis to identify condition-specific regulatory networks.

Published in:

Bioinformatics, 2010, v. 26, n. 11, p. 1416, doi. 10.1093/bioinformatics/btq144

By:

Li Chen;
Jianhua Xuan;
Riggins, Rebecca B.;
Yue Wang;
Hoffman, Eric P.;
Clarke, Robert

Publication type:

Article

Differential dependency network analysis to identify condition-specific topological changes in biological networks.

Published in:

Bioinformatics, 2009, v. 25, n. 4, p. 526, doi. 10.1093/bioinformatics/btn660

By:

Bai Zhang;
Huai Li;
Rebecca B. Riggins;
Ming Zhan;
Jianhua Xuan;
Zhen Zhang;
Eric P. Hoffman;
Robert Clarke;
Yue Wang

Publication type:

Article

VISDA: an open-source caBIGTM analytical tool for data clustering and beyond.

Published in:

Bioinformatics, 2007, v. 23, n. 15, p. 2024, doi. 10.1093/bioinformatics/btm290

By:

Jiajing Wang;
Huai Li;
Yitan Zhu;
Malik Yousef;
Michael Nebozhyn;
Michael Showe;
Louise Showe;
Jianhua Xuan;
Robert Clarke;
Yue Wang

Publication type:

Article

Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data.

Published in:

Bioinformatics, 2006, v. 22, n. 6, p. 755, doi. 10.1093/bioinformatics/btk036

By:

Zuyi Wang;
Yue Wang;
Jianhua Xuan;
Yibin Dong;
Marina Bakay;
Yuanjian Feng;
Robert Clarke;
Eric P. Hoffman

Publication type:

Article

Reverse engineering module networks by PSO-RNN hybrid modeling.

Published in:

BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-S1-S15

By:

Yuji Zhang;
Jianhua Xuan;
de los Reyes, Benildo G.;
Clarke, Robert;
Ressom, Habtom W.

Publication type:

Article

ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 7, p. 1, doi. 10.1371/journal.pcbi.1009203

By:

Chen, Xi;
Neuwald, Andrew F.;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

Comparative analysis of semantic segmentation and deep regression models with supervised pretraining for accurate prediction of pig body weight from video data: Insights from industry-scale datasets.

Published in:

Journal of Animal Science, 2024, v. 102, p. 414, doi. 10.1093/jas/skae234.472

By:

Ye Bi;
Jianhua Xuan;
Yijian Huang;
Gota Morota

Publication type:

Article

Asynchronous remodeling is a driver of failed regeneration in Duchenne muscular dystrophy.

Published in:

Journal of Cell Biology, 2014, v. 207, n. 1, p. 139, doi. 10.1083/jcb.201402079

By:

Dadgar, Sherry;
Zuyi Wang;
Johnston, Helen;
Akanchha Kesari;
Kanneboyina Nagaraju;
Yi-Wen Chen;
Hill, D. Ashley;
Partridge, Terence A.;
Mamta Giri;
Freishtat, Robert J.;
Nazarian, Javad;
Jianhua Xuan;
Yue Wang;
Hoffman, Eric P.

Publication type:

Article

A Bayesian approach for accurate de novo transcriptome assembly.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-97015-x

By:

Shi, Xu;
Wang, Xiao;
Neuwald, Andrew F.;
Halakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

Endoplasmic reticulum stress, the unfolded protein response, and gene network modeling in antiestrogen resistant breast cancer.

Published in:

Hormone Molecular Biology & Clinical Investigation, 2011, v. 5, n. 1, p. 35, doi. 10.1515/HMBCI.2010.073

By:

Clarke, Robert;
Shajahan, Ayesha N.;
Yue Wang;
Tyson, John J.;
Riggins, Rebecca B.;
Weiner, Louis M.;
Bauman, William T.;
Xuan, Jianhua;
Zhang, Bai;
Facey, Caroline;
Aiyer, Harini;
Cook, Katherine;
Hickman, F. Edward;
Tavassoly, Iman;
Verdugo, Anael;
Chun Chen;
Zwart, Alan;
W&x00E4;rri, Anni;
Hilakivi-Clarke, Leena A.

Publication type:

Article

Reconstruction of Gene Regulatory Modules in Cancer Cell Cycle by Multi-Source Data Integration.

Published in:

PLoS ONE, 2010, v. 5, n. 4, p. 1, doi. 10.1371/journal.pone.0010268

By:

Yuji Zhang;
Jianhua Xuan;
de los Reyes, Benildo G.;
Clarke, Robert;
Ressom, Habtom W.

Publication type:

Article

Applications of DifferentWeighting Schemes to Improve Pathway-Based Analysis.

Published in:

Comparative & Functional Genomics, 2011, p. 1, doi. 10.1155/2011/463645

By:

Ha, Sook S.;
Kim, Inyoung;
Wang, Yue;
Xuan, Jianhua

Publication type:

Article

CyNetSVM: A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines.

Published in:

PLoS ONE, 2017, v. 12, n. 1, p. 1, doi. 10.1371/journal.pone.0170482

By:

Shi, Xu;
Banerjee, Sharmi;
Chen, Li;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks.

Published in:

BMC Systems Biology, 2014, v. 8, n. 1, p. 1, doi. 10.1186/s12918-014-0087-1

By:

Ye Tian;
Bai Zhang;
Hoffman, Eric P.;
Clarke, Robert;
Zhen Zhang;
Ie-Ming Shih;
Jianhua Xuan;
Herrington, David M.;
Yue Wang

Publication type:

Article

mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks.

Published in:

BMC Systems Biology, 2013, v. 7, p. 1, doi. 10.1186/1752-0509-7-S5-S4

By:

Xu Shi;
Jinghua Gu;
Xi Chen;
Shajahan, Ayesha;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Jianhua Xuan

Publication type:

Article

The CAM Software for Nonnegative Blind Source Separation in R-Java.

Published in:

Journal of Machine Learning Research, 2013, v. 14, p. 2899

By:

Niya Wang;
Fan Meng;
Li Chen;
Madhavan, Subha;
Clarke, Robert;
Hoffman, Eric P.;
Jianhua Xuan;
Yue Wang

Publication type:

Article

Matched Gene Selection and Committee Classifier for Molecular Classification of Heterogeneous Diseases.

Published in:

Journal of Machine Learning Research, 2010, v. 11, n. 8, p. 2141

By:

Guoqiang Yu;
Yuanjian Feng;
Miller, David J.;
Jianhua Xuan;
Hoffman, Eric P.;
Clarke, Robert;
Davidson, Ben;
Ie-Ming Shih;
Yue Wang

Publication type:

Article

Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-020-79603-5

By:

Chen, Xi;
Gu, Jinghua;
Neuwald, Andrew F.;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

Author Correction: BICORN: An R package for integrative inference of de novo cis-regulatory modules.

Published in:

2020

By:

Chen, Xi;
Gu, Jinghua;
Neuwald, Andrew F.;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Correction Notice

BICORN: An R package for integrative inference of de novo cis-regulatory modules.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-63043-2

By:

Chen, Xi;
Gu, Jinghua;
Neuwald, Andrew F.;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

Inactivation of Arid1a in the endometrium is associated with endometrioid tumorigenesis through transcriptional reprogramming.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16416-0

By:

Suryo Rahmanto, Yohan;
Shen, Wenjing;
Shi, Xu;
Chen, Xi;
Yu, Yu;
Yu, Zheng-Cheng;
Miyamoto, Tsutomu;
Lee, Meng-Horng;
Singh, Vivek;
Asaka, Ryoichi;
Shimberg, Geoffrey;
Vitolo, Michele I.;
Martin, Stuart S.;
Wirtz, Denis;
Drapkin, Ronny;
Xuan, Jianhua;
Wang, Tian-Li;
Shih, Ie-Ming

Publication type:

Article

BMRF-MI: integrative identification of protein interaction network by modeling the gene dependency.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/1471-2164-16-S7-S10

By:

Xu Shi;
Xiao Wang;
Shajahan, Ayesha;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Jianhua Xuan

Publication type:

Article

Automatic detection of foreign objects in computed radiography.

Published in:

Journal of Biomedical Optics, 2000, v. 5, n. 4, p. 425, doi. 10.1117/1.1289771

By:

Jianhua Xuan;
Adali, Tulay;
Yue Wang;
Siegel, Eliot

Publication type:

Article

The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.

Published in:

Nature Reviews Cancer, 2008, v. 8, n. 1, p. 37, doi. 10.1038/nrc2294

By:

Clarke, Robert;
Ressom, Habtom W.;
Antai Wang;
Jianhua Xuan;
Liu, Minetta C.;
Gehan, Edmund A.;
Yue Wang

Publication type:

Article

Isoflavones in soy flour diet have different effects on whole-genome expression patterns than purified isoflavone mix in human MCF-7 breast tumors in ovariectomized athymic nude mice.

Published in:

Molecular Nutrition & Food Research, 2015, v. 59, n. 8, p. 1419, doi. 10.1002/mnfr.201500028

By:

Liu, Yunxian;
Hilakivi‐Clarke, Leena;
Zhang, Yukun;
Wang, Xiao;
Pan, Yuan‐Xiang;
Xuan, Jianhua;
Fleck, Stefanie C.;
Doerge, Daniel R.;
Helferich, William G.

Publication type:

Article

Improved Diagnostics Using Polarization Imaging and Artificial Neural Networks.

Published in:

International Journal of Biomedical Imaging, 2007, p. 1, doi. 10.1155/2007/74143

By:

Jianhua Xuan;
Uwe Klimach;
Hongzhi Zhao;
Qiushui Chen;
Yingyin Zou;
Yue Wang

Publication type:

Article

Nonrigid Medical Image Registration by Finite-Element Deformable Sheet-Curve Models.

Published in:

International Journal of Biomedical Imaging, 2006, p. 1, doi. 10.1155/IJBI/2006/73430

By:

Jianhua Xuan;
Yue Wang;
Freedman, Matthew T.;
Tulay Adali;
Shields, Peter

Publication type:

Article

Modeling and Reconstruction of Mixed Functional and Molecular Patterns.

Published in:

International Journal of Biomedical Imaging, 2006, p. 1, doi. 10.1155/IJBI/2006/29707

By:

Yue Wang;
Jianhua Xuan;
Srikanchana, Rujirutana;
Choyke, Peter L.

Publication type:

Article

BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data.

Published in:

BMC Bioinformatics, 2014, v. 15, p. 1, doi. 10.1186/1471-2105-15-S9-S6

By:

Jinghua Gu;
Xiao Wang;
Halakivi-Clarke, Leena;
Clarke, Robert;
Jianhua Xuan

Publication type:

Article

Motif-guided sparse decomposition of gene expression data for regulatory module identification.

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 82, doi. 10.1186/1471-2105-12-82

By:

Ting Gong;
Jianhua Xuan;
Li Chen;
Riggins, Rebecca B.;
Huai Li;
Hoffman, Eric P.;
Clarke, Robert;
Yue Wang

Publication type:

Article

Knowledge-guided gene ranking by coordinative component analysis.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 162, doi. 10.1186/1471-2105-11-162

By:

Chen Wang;
Jianhua Xuan;
Huai Li;
Yue Wang;
Ming Zhan;
Hoffman, Eric P.;
Clarke, Robert

Publication type:

Article

Motif-directed network component analysis for regulatory network inference.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S1-S21

By:

Chen Wang;
Jianhua Xuan;
Li Chen;
Po Zhao;
Yue Wang;
Clarke, Robert;
Hoffman, Eric

Publication type:

Article

caBIG VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-383

By:

Yitan Zhu;
Huai Li;
Miller, David J.;
Zuyi Wang;
Jianhua Xuan;
Clarke, Robert;
Hoffman, Eric P.;
Yue Wang

Publication type:

Article

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-203

By:

Yuji Zhang;
Jianhua Xuan;
de los Reyes, Benildo G.;
Clarke, Robert;
Ressom, Habtom W.

Publication type:

Article

Multilevel learning-based segmentation of ill-defined and spiculated masses in mammograms.

Published in:

Medical Physics, 2010, v. 37, n. 11, p. 5993, doi. 10.1118/1.3490477

By:

Tao, Yimo;
Lo, Shih-Chung B.;
Freedman, Matthew T.;
Makariou, Erini;
Xuan, Jianhua

Publication type:

Article

IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles.

Published in:

Bioinformatics, 2021, v. 37, n. 5, p. 650, doi. 10.1093/bioinformatics/btaa852

By:

Shi, Xu;
Neuwald, Andrew F;
Wang, Xiao;
Wang, Tian-Li;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data.

Published in:

Bioinformatics, 2018, v. 34, n. 10, p. 1733, doi. 10.1093/bioinformatics/btx827

By:

Chen, Xi;
Gu, Jinghua;
Wang, Xiao;
Jung, Jin-Gyoung;
Wang, Tian-Li;
Hilakivi-Clarke, Leena;
Clarke, Robert;
Xuan, Jianhua

Publication type:

Article

ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 7, p. e65, doi. 10.1093/nar/gkv1491

By:

Xi Chen;
Jung, Jin-Gyoung;
Shajahan-Haq, Ayesha N.;
Clarke, Robert;
Shih, Ie-Ming;
Yue Wang;
Magnani, Luca;
Wang, Tian-Li;
Jianhua Xuan

Publication type:

Article

Identifying protein interaction subnetworks by a bagging Markov random field-based method.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 2, p. e42, doi. 10.1093/nar/gks951

By:

Chen, Li;
Xuan, Jianhua;
Riggins, Rebecca B.;
Wang, Yue;
Clarke, Robert

Publication type:

Article