Selected Publications

   See a complete list of publications  * corresponding author
 

Silva TC, Young JI, Zhang L, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L* (2022) Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer’s disease.  Nature Communications  In Press

Silva TC, Young JI, Martin ER, Chen XSWang L* (2022) MethReg: estimating the regulatory potential of DNA methylation in gene transcription. Nucleic Acids Research gkac030  (code) (software)

Lehmann BD*, Colaprico ASilva TC,  Chen J, An H, Ban Y, Huang HWang L, James JL, Balko JM, Gonzalez-Ericsson PI, Sanders ME, Zhang B, Pietenpol JA, Chen XS* (2021) Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes. Nature Communications 12, 6276. (code)

This paper was among the top 25 most downloaded Nature Communications articles in health sciences published in 2021

Lu M, Sha Y, Silva TC, Colaprico A, Sun X, Ban Y,  Wang L, Lehmann BD, Chen XS* (2021) LR Hunting: A Random Forest Based Cell–Cell Interaction Discovery Method for Single-Cell Gene Expression Data. Frontiers in Genetics 12:708835 (code)

Odom JO, Colaprico A, Silva TC, Chen XS, Wang L* (2021) PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples. Frontiers in Genetics 12: 783713 (code) (software)

Zhang L, Young JI, Gomez L, Silva TC, Schmidt MA, Cai J, Chen X, Martin ER, Wang L*   (2021) Sex-specific DNA methylation changes in Alzheimer’s disease pathology. Acta Neuropathologica Communications 9:77  (code)

Zhang L, Silva TC, Young JI, Gomez L, Schmidt MA, Hamilton-Nelson KL, Kunkle BW, Chen X, Martin ER, Wang L* (2020). Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease. Nature Communications 11, 6114 (code

Zhang Y, Wang P, Li X, Ning S, Li X*, Cao Y*, Chen XS* (2021) GABC: A Comprehensive Resource and Genome Atlas for Breast Cancer. International Journal of Cancer. 148 (4) 988-994 

Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, Chen XS*, Papaleo E* (2020). Interpreting pathways to discover cancer driver genes with Moonlight. Nature Communications. 11(1):69. (software)

Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L*, Chen X* (2020) pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection. Proteomics. 20(21-22):e1900409 (code) (software)

Gomez L, Odom GJ, Young JI, Martin ER, Liu L, Chen X, Griswold AJ, Gao Z, Zhang L, Wang L* (2019). coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes. Nucleic Acids Research. 47(17):e9 (code) (software)

Mallik S, Odom GJ, Gao Z, Gomez L, Chen X*, Wang L* (2019). An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays. Brief Bioinform. 20(6):2224-35 (code)

 Prediction models for personalized disease risk assessment using genomics data

Chen X, Ishwaran H (2013) Pathway hunting by random survival forests. Bioinformatics 29(1): 99-105.

Chen X, Ishwaran H (2012) Random forests for genomic data analysis. Genomics. 99(6): 323-9.

Chen X, Wang L, Ishwaran H (2010) An Integrative Pathway-based Clinical-genomic Model for Cancer Survival Prediction. Stat Probab Lett.  80:1313-1319.

Chen X, Wang L (2009) Integrating biological knowledge with gene expression profiles for survival prediction of cancer. J Comput Biol. 16(2):265-78.

  Methodology and tools for genomics and epi-genomics research

Gomez L, Odom GJ, Young JI, Martin ER, Liu L, Chen X, Griswold AJ, Gao Z, Zhang L and Wang L (2019) coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies. [software] Nucleic Acids Research,47(17), e98.

Colaprico, A, Olsen C., Bailey MH, Odom GB, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, CAstiglioni, Cava Claudia, Bontempi G, Chen X, Papaleo E. (2020) Interpreting pathways to discover cancer driver genes with Moonlight. [software] Nature Communications, 11:69.

Odom GJ, Ban Y, Liu L, Sun X, Pico AR, Zhang B, Wang L, Chen X (2019) pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection [software] Proteomics, In Press

Yan A, Ban Y, Gao Z, Chen X, Wang L (2018) PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data. Bioinformatics, 34(18): 3220-3222. [software]

Mallik S, Odom G, Gao Z, Gomez L, Chen X, Wang L (2018) An Evaluation of Supervised Methods for Identifying Differentially Methylated Regions in Illumina Methylation Arrays. Briefings in Bioinformatics.  Sep 17. doi: 10.1093/bib/bby085. [software]

Sheng Q, Shyr Y, Chen X (2014) Dupchecker: a Bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. BMC Bioinformatics 2014; 15(1): 323  [software]

Chen X, Li J, Gray WH, Lehmann BD, Bauer JA, Shyr Y, Pietenpol JA (2012) TNBCtype: A subtyping tool for triple-negative breast cancer. Cancer Informatics 2012; 11: 147-15 [software]

  Integrative analysis of genomics data

Wang L, Chen X, Zhang B (2012) Statistical analysis of patient-specific pathway activities via mixed models. J Biom Biostat S8: 001

Wang L, Jia P, Wolfinger RD, Chen X, Grayson BL, Aune TM, Zhao Z (2011) An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. Bioinformatics, 27, 686-692.

Wang L, Jia P, Wolfinger RD, Chen X, Zhao Z (2011) Gene set analysis of genome-wide association studies: methodological issues and perspectives. Genomics, 98(1):1-8

Chen X (2011) Adaptive elastic-net sparse principal component analysis for pathway association testing. Stat Appl Genet Mol Biol. Oct 24;10(1).

Chen X, Wang L, Hu B, Guo M, Barnard J, Zhu X (2010) Pathway-based analysis for genome-wide association studies using supervised principal components. Genet Epidemiology. 34(7):716-24.

Wang L, Chen X, Wolfinger RD, Franklin JL, Coffey RJ, Zhang B (2009) A unified mixed effects model for gene set analysis of time course microarray experiments. Stat Appl Genet Mol Biol 8: Article 47.

Chen X, Wang L, Smith JD, Zhang B (2008) Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics. 24(21):2474-81.

Wang L, Zhang B, Wolfinger RD, Chen X (2008) An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet 4: e1000115.

    Cancer genomics analysis

Lehmann BD, Bauer JA, Chen X, Sander ME, Chakravarthy B, Shyr Y, Pietenpol JA (2011) Identification of triple negative breast cancer subtypes and preclinical models for selection of targeted therapies. Journal of Clinical Investigation 121(7): 2750-2767.

 

Tanner JF, Smith JJ, Chen X, Washington MK, Roland JT, Means AL, Eschrich SA, Yeatman TJ, Deane NG, Beauchamp RD (2012) Smad4-mediated signaling inhibits intestinal neoplasia by inhibiting beta-catenin gene expression. Gastroenterology 142(3): 562-571.

Yu KD, Zhu R, Zhan M, Rodriguez AA, Yang W, Wong S, Makris A, Lehmann BD, Chen X, Mayer I, Pietenpol JA, Shao ZM, Symmans F, Chang JC (2013) Identification of prognosis-relevant subgroups in patients with chemoresistant triple negative breast cancer. Clinical Cancer Research 19:2723-2733.

Grieb BC, Chen X, Eischen CM.MTBP is over-expressed in triple negative breast cancer and contribute to its growth and survival. Molecular Cancer Research 2014; 12(9):1216-1224.

Lehmann BD, Bauer JA, Schafer JM, Pendleton CS, Tang L, Johmson KC, Chen X, Balko JM, Gomez H, Arteaga CL, Mills GB, Sanders ME, Pietenpol JA. PIK3CA mutations in androgen receptor-positive triple negative breast cancer confer sensitivity to the combination of PI3K and androgen receptor inhibitors. Breast Cancer Research 2014; 16:406.

Lovly CM, McDonald NT, Chen H, Ortiz-Cuaran S, Heukamp LC, Yang Y, Florin A, Ozretic L, Lim D, Wang L, Chen Z, Chen X, Lu P, Pail PK, Shen R, Jin H, Buettner R, Ansen S, Perner S, Brockman M, Bos M, Wolf J, Gardizi M, Wright GM, Soloman B, Russell PA, Rogers TM, Suehara Y, Red-Brewer M, Tieu R, Stanchina ED, Wang Q, Zhan Z, Johnson D, Horn L, Wong KK, Thomas RK, Ladanyi M, Pao W.Rationale for co-targeting IGF-1R and ALK in ALK fusion positive lung cancer. Nature Medicine 2014; 20:1027-1034.

Nagathihalli NS, Castellanos JA, Shi C, Beesetty Y, Reyzer ML, Caprioli R, Chen X, Walsh AJ, Skala MC, Moses HL, Merchant NP. STAT3 mediated remodeling of the rumor microenvironment results in enhanced tumor drug delivery in a mouse model of pancreatic cancer. Gastroenterology 2015; 149(7): 1932-1943.

Lehmann BD, Jovanović B, Chen X, Estrada MV, Johnson KN, Shyr Y, Pietenpol J.Refinement of triple-negative breast cancer molecular subtypes: implications for neoadjuvant chemotherapy selection. PloS One. 2016; 11(6):e0157368.

Chen X*, Deane NG, Lewis KB, Li J, Zhu J, Washington MK, Beauchamp RD. Comparison of nanostring nCounter® data on FFPE colon cancer samples and Affymetrix microarray data on matched frozen tissues. PloS One. 2016; 11(5): e0153784.

Zhu J, Deane NG, Lewis KB, Padmanabhan C, Washington MK, Ciombor KK, Timmers C, Goldberg RM, Beauchamp RD, Chen X*. Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples. Scientific Reports. 2016; 6:33273.

Cheng G, Liu F, Asai T, Lai F, Man N, Xu H, Chen S, Greenblatt S, Hamard P-J, Ando K, Chen X, Wang L, Martinex C, Tadi M, Wang L, Xu M, Yang F-C, Shiekhattar R, Nimer SD. Loss of p300 accelerates MDS-associated leukemogenesis. Leukemia. 2017; 31(6):1382-1390.

Wei Q, Ye Z, Zhong X, Li L, Wang C, Myers R, Palazzo JP, Fortuna D, Waldman SA, Chen X, Posey JA, Basu-Mallick A, Jiang BH, Hou L, Shu J, Sun Y, Xing J, Li B, Yang H.Multiregion whole-exome sequencing of matched primary and metastatic tumors revealed genomic heterogeneity and suggested polyclonal seeding in colorectal cancer metastasis. Annals of Oncology. 2017;28(9):2135-41.

Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM.Colorectal cancer cell line proteomes are representative of primary tumors and predict drug sensitivity. Gastroenterology. 2017;153(4):1082-95.

Li Z, Zhang P, Yan A, Guo Z, Ban Y, Li J, Chen S, Yang H, He Y, Li, J, Guo Y, Zheng W, Hajiramezanali E, An H, Fajardo D, Harbour JW, Ruan Y, Nimer SD, Yu P, Chen X*, Xu M*, Yang FC*. AXL1 interacts with the cohesion complex to maintain chromatid separation and gene expression for normal hematopoiesis. Science Advances. 2017; 3(1): e1601602