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Papers in press

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  1. Chen, C*., Wang, M., Chen, S. (2023). An Efficient Data Integration Scheme for Synthesizing Information from Multiple Secondary Datasets for the Parameter Inference of the Main Analysis. Biometrics. Accepted.

Papers in revision

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  1. Ye Z., Mo C., Liu S., Gao S., Feng L., Zhao B., Canida T., Wu YC., Hatch K., Ma Y., Mitchell BD., Hong L.E., Kochunov P., Chen C., Zhao B.,  Chen, S*. and Ma, T*., 2022. Deciphering the causal relationship between blood pressure and regional white matter integrity: a two-sample Mendelian randomization study. Under revision in Journal of Neuroscience Research.

2023

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  1. Chen, C., Shen, B., Zhang, L., Yu, T., Wang, M., & Wu, R. (2023). A Cartographic Tool to Predict Disease Risk-associated Pseudo-Dynamic Networks from Tissue-specific Gene Expression. Bio-protocol, 13(1), e4583. https://doi.org/10.21769/BioProtoc.4583

  2. Mo C., Wang J., Ye Z., Ke H., Liu S., Hatch K., Gao S., Magidson J., Chen C., Mitchell BD., Kochunov P., Hong L.E., Chen, S*. and Ma, T*., 2022. Evaluating the causal effect of tobacco smoking on white matter brain aging: a two-sample Mendelian randomization analysis in UK Biobank. Addiction (Abingdon, England), 118(4), 739–749. https://doi.org/10.1111/add.16088

2022

  1. Ryan, M.C., Hong, L.E., Hatch, K.S., Gao, S., Chen, S., Haerian, K., Wang, J., Goldwaser, E.L., Du, X., Adhikari, B.M. and Bruce, H., 2022. The additive impact of cardio‐metabolic disorders and psychiatric illnesses on accelerated brain aging. Human Brain Mapping, 43(6), pp.1997-2010.

  2. Chen, S*., 2022. Statistical Commentary: Church et al.(2018, 2020, 2021) and Spielmans et al.(2020, 2021) Published Debate Regarding the Effectiveness of Acupoint Tapping by Meta-analysis. The Journal of Nervous and Mental Disease, 210(2), pp.137-138.

  3. Ke, H., Ren, Z., Qi, J., Chen, S., Tseng, G.C.,  Ye, Z., and Ma, T*., 2022. High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression. Bioinformatics. 2022 Sep 1;38(17):4078-87.

  4. Ge, Y., Chen, G., Waltz, J.A., Hong, L.E., Kochunov, P. and Chen, S*., 2022. An integrated cluster‐wise significance measure for fMRI analysis. Human Brain Mapping.

  5. Adhikari BM, Hong LE, Zhao Z, Wang DJ, Thompson PM, Jahanshad N, Zhu AH, Holiga S, Turner JA, van Erp TG, Calhoun VD., Hatch KS., Bruce H., Hare SM., Chiappelli J., Goldwaser EL, Kvarta MD, Ma Y., Du X., Nichols TE., Shuldiner AR., Mitchell BD., Dukart J, Chen S, Kochunov P., Cerebral blood flow and cardiovascular risk effects on resting brain regional homogeneity. NeuroImage. 2022 Nov 15;262:119555.

  6. Shao M, Xia D, Zhang Y, Wu Q, Chen S*. Higher-order accurate two-sample network inference and network hashing. arXiv preprint arXiv:2208.07573. 2022 Aug 16.

  7. Sathyasaikumar KV, Notarangelo FM, Kelly DL, Rowland LM, Hare SM, Chen S, Mo C, Buchanan RW, Schwarcz R. Tryptophan Challenge in Healthy Controls and People with Schizophrenia: Acute Effects on Plasma Levels of Kynurenine, Kynurenic Acid and 5-Hydroxyindoleacetic Acid. Pharmaceuticals. 2022 Aug 15;15(8):1003.

  8. Lee H, Chen C, Kochunov P, Elliot Hong L, Chen S. Modeling multivariate age‐related imaging variables with dependencies. Statistics in Medicine. 2022 Jul 7.

  9. Bruce HA, Kochunov P, Kvarta MD, Goldwaser EL, Chiappelli J, Schwartz A, Lightner S, Endres J, Yuen A, Ma Y, Van der Vaart A. Hatch KS., Gao Si, Ye Z., Wu Q., Chen S., Mitchell BD., Hong LE., Frontal white matter association with sleep quality and the role of stress. Journal of Sleep Research. 2022 Jun 14:e13669.

  10. Qadir H, Stewart BW, Van Ryzin J, Wu Q, Chen S, Seminowicz DA, Mathur BN. The mouse claustrum synaptically connects cortical network motifs. bioRxiv. 2022 Jan 1.

  11. Chen C, Shen B, Ma T, Wang M, Wu R. A statistical framework for recovering pseudo-dynamic networks from static data. Bioinformatics. 2022 May 1;38(9):2481-7.

  12. Kochunov P, Ma Y, Hatch KS, Jahanshad N, Thompson PM, Adhikari BM, Bruce H, Van der Vaart A, Goldwaser EL, Sotiras A, Kvarta MD. Ma T., Chen S., Nichols TE., Hong LE., Brain‐wide versus genome‐wide vulnerability biomarkers for severe mental illnesses. Human Brain Mapping. 2022 Aug 30.

  13. Chen C, Leung YY, Ionita M, Wang LS, Li M. Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge. Bioinformatics. 2022 Oct 1;38(19):4530-6.

  14. Chen C, Yu T, Shen B, Wang M. Synthesizing secondary data into survival analysis to improve estimation efficiency. Biometrical journal. Biometrische Zeitschrift. 

2021

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  1. Li, Y., Rahman, T., Ma, T.*, Tang, L. and Tseng, G.C., 2021. A sparse negative binomial mixture model for clustering RNA-seq count data. Biostatistics.

  2. Mo C^, Ye Z^, Hatch K, Zhang Y, Wu Q, Liu S, Lu Q, Mitcheel B, Hong LE, Kochunov P, Ma T* and Chen S*. Genetic Fine-Mapping With Dense Linkage Disequilibrium Blocks. Research Square; 2021. DOI: 10.21203/rs.3.rs-649530/v1.

  3. Gao, S., Donohue, B., Hatch, K.S., Chen, S.*, Ma, T.*, Ma, Y., Kvarta, M.D., Bruce, H., Adhikari, B.M., Jahanshad, N. and Thompson, P.M., 2021. Comparing empirical kinship derived heritability for imaging genetics traits in the UK biobank and human connectome project. NeuroImage, 245, p.118700.

  4. Ge Y, Hare S, Chen G, Waltz JA, Kochunov P, Elliot Hong L, Chen S*. Bayes estimate of primary threshold in clusterwise functional magnetic resonance imaging inferences. Stat Med. 2021 Nov 10;40(25):5673-5689. doi: 10.1002/sim.9147. Epub 2021 Jul 26. PMID: 34309050.

  5. Ye, Z.^, Mo, C.^, Ke, H.^, Yan, Q., Chen, C., Kochunov, P., Hong, L.E., Mitchell, B.D., Chen, S*. and Ma, T.*, 2021. Meta-analysis of transcriptome-wide association studies across 13 brain tissues identified novel clusters of genes associated with nicotine addiction. Genes, 13(1), p.37.

  6. Ye Z^, Mo C^, Liu S, Hatch KS, Gao S, Ma Y, Hong LE, Thompson PM, Jahanshad N, Acheson A, Garavan H, Shen L, Nichols TE, Kochunov P, Chen S*, Ma T*. White Matter Integrity and Nicotine Dependence: Evaluating Vertical and Horizontal Pleiotropy. Front Neurosci. 2021 Oct 14;15:738037. doi: 10.3389/fnins.2021.738037. PMID: 34720862; PMCID: PMC8551454.

  7. Luo JH, Liu S, Tao J, Ren BG, Luo K, Chen ZH, Nalesnik M, Cieply K, Ma T, Cheng SY, Chen Q. Pten-NOLC1 fusion promotes cancers involving MET and EGFR signalings. Oncogene. 2021 Feb;40(6):1064-76.

  8. Wu Q, Huang X, Culbreth A, Waltz J, Hong LE, Chen S*. Extracting Brain Disease-Related Connectome Subgraphs by Adaptive Dense Subgraph Discovery. bioRxiv. 2020 Jan 1.

  9. Adenaiye O, Bueno de Mesquita PJ, Wu Q, Hong F, Lai J, Chen S, Milton DK, Prometheus@ UMD Consortium. The effect of COVID‐19 stay‐at‐home order and campus closure on the prevalence of acute respiratory infection symptoms in college campus cohorts. Influenza and other respiratory viruses. 2021 May;15(3):331-5.

  10. Wu Q, Zhang Z, Ma T, Waltz J, Milton D, Chen S*. Link predictions for incomplete network data with outcome misclassification. Statistics in Medicine. 2021 Mar 15;40(6):1519-34.

  11. Kelly DL, Spaderna M, Hodzic V, Coppersmith G, Chen S, Resnik P. Can language use in social media help in the treatment of severe mental illness?. Current Research in Psychiatry. 2021;1(1):1-4.

  12. Wang J, Zheng X, Zhang J, Xue H, Wang L, Jing R, Chen S, Che F, Heng X, Li G, Xue F. An MRI-based radiomics signature as a pretreatment noninvasive predictor of overall survival and chemotherapeutic benefits in lower-grade gliomas. European Radiology. 2021 Apr;31(4):1785-94.

  13. Wu Q, Ma T, Liu Q, Milton DK, Zhang Y, Chen S*. ICN: extracting interconnected communities in gene co-expression networks. Bioinformatics. 2021 Jan 28.

  14. Pan S, Feng W, Li Y, Huang J, Chen S, Cui Y, Tian B, Tan S, Wang Z, Yao S, Chiappelli J. The microRNA-195-BDNF pathway and cognitive deficits in schizophrenia patients with minimal antipsychotic medication exposure. Translational Psychiatry. 2021 Feb 8;11(1):1-8.

  15. Won J, Ranadive SM, Callow DD, Chen S, Carson Smith J. Blood pressure‐related differences in brain health between young African Americans and Caucasian Americans. Physiological Reports. 2021 Mar;9(6):e14819.

  16. Wang, J., Kochunov, P., Sampath, H., Hatch, K.S., Ryan, M.C., Xue, F., Neda, J., Paul, T., Hahn, B., Gold, J., Waltz, J., Hong, L.E and Chen, S.*, 2021. White matter brain aging in relationship to schizophrenia and its cognitive deficit. Schizophrenia Research, 230, pp.9-16.

  17. Asanad S, O'Neill H, Addis H, Chen S, Wang J, Goldwaser E, Kochunov P, Hong LE, Saeedi OJ. Neuroretinal Biomarkers for Schizophrenia Spectrum Disorders. Translational Vision Science & Technology. 2021 Apr 1;10(4):29-.

  18. Hare SM, Du X, Adhikari BM, Chen S, Mo C, Summerfelt A, Kvarta MD, Garcia L, Kochunov P, Hong LE. Mapping Local and Long-Distance Resting Connectivity Markers of TMS-Related Inhibition Reduction in Schizophrenia. NeuroImage: Clinical. 2021 Apr 30:102688.

  19. Buchanan RW, Kelly DL, Strauss GP, Gold JM, Weiner E, Zaranski J, Chen S, Blatt F, Holden J, Granholm E. Combined Oxytocin and Cognitive Behavioral Social Skills Training for Social Function in People With Schizophrenia. Journal of Clinical Psychopharmacology. 2021 May 1;41(3):236-43.

  20. Saegusa T, Zhao Z, Ke H, Ye Z, Xu Z, Chen S and Ma T*. Detecting survival-associated biomarkers from heterogeneous populations. Scientific Reports. 2021 Feb 5;11(1):1-2.

  21. Tong, J., Zhou, Y., Huang, J., Zhang, P., Fan, F., Chen, S.*, Tian, B., Cui, Y., Tian, L., Tan, S. and Wang, Z., 2021. N-methyl-D-aspartate Receptor Antibody and White Matter Deficits in Schizophrenia Treatment-Resistance. Schizophrenia Bulletin, 47(5), pp.1463-1472.

  22. Zhou, Y., Huang, J., Zhang, P., Tong, J., Fan, F., Gou, M., Cui, Y., Luo, X., Tan, S., Wang, Z., Feng, W., Yang, F., Tian, B., Tian, L., Savransky, A., Hare, S., Ryan, M. C., Goldwaser, E., Chiappelli, J., Chen, S., … Hong, L. E. (2021). Allostatic Load Effects on Cortical and Cognitive Deficits in Essentially Normotensive, Normoweight Patients with Schizophrenia. Schizophrenia bulletin, sbaa196. Advance online publication. https://doi.org/10.1093/schbul/sbaa196

  23. Kochunov, P., Ryan, M. C., Yang, Q., Hatch, K. S., Zhu, A., Thomopoulos, S. I., Jahanshad, N., Schmaal, L., Thompson, P. M., Chen, S., Du, X., Adhikari, B. M., Bruce, H., Hare, S., Goldwaser, E. L., Kvarta, M. D., Nichols, T. E., & Hong, L. E. (2021). Comparison of regional brain deficit patterns in common psychiatric and neurological disorders as revealed by big data. NeuroImage. Clinical, 29, 102574. Advance online publication. https://doi.org/10.1016/j.nicl.2021.102574

  24. Culbreth, A. J., Wu, Q., Chen, S., Adhikari, B. M., Hong, L. E., Gold, J. M., & Waltz, J. A. (2020). Temporal-thalamic and cingulo-opercular connectivity in people with schizophrenia. NeuroImage. Clinical, 29, 102531. Advance online publication. https://doi.org/10.1016/j.nicl.2020.102531

  25. Kochunov, P., Zavaliangos-Petropulu, A., Jahanshad, N., Thompson, P. M., Ryan, M. C., Chiappelli, J., Chen, S., Du, X., Hatch, K., Adhikari, B., Sampath, H., Hare, S., Kvarta, M., Goldwaser, E., Yang, F., Olvera, R. L., Fox, P. T., Curran, J. E., Blangero, J., Glahn, D. C., … Hong, L. E. (2021). A White Matter Connection of Schizophrenia and Alzheimer's Disease. Schizophrenia bulletin, 47(1), 197–206. https://doi.org/10.1093/schbul/sbaa078

  26. Ye Z^, Ke H^, Chen S, ..., Milton D and Ma T*. (2021) Biomarker Categorization in Transcriptomic Meta-Analysis by Concordant Patterns With Application to Pan-Cancer Studies. Frontiers in Genetics, 12(1079). doi:10.3389/fgene.2021.651546

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2020

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  1. Lin, C., Chang, L., Ma, T., Oh, H., French, B., Puralewski, R., Matthews, F., Lewis, D., ..., Nikolova, Y., Tseng GC and Sibille, E. (2020). Older Molecular Brain Aging in Severe Mental Illness. Molecular psychiatry, 1-11.

  2. Saegusa, T., Ma, T., Li, Gang., Chen, Y., Lee, ML. (2020). Variable Selection in Threshold Regression Model with Applications to HIV Drug Adherence Data. Statistics in Biosciences, 1-23.

  3. Ma, T., Ren, Z. and Tseng, GC.. (2020). Variable screening with multiple studies. Statistica Sinica. 30 (2), 925--953.

  4. Zeng, X., Zong, W., Lin, C. W., Fang, Z., Ma, T., Lewis, D. A., ... & Tseng, G. C. (2020). Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis. Genes, 11(6), 696.

  5. Furman, A.J., Prokhorenko, M., Keaser, M.L., Zhang, J., Chen, S., Mazaheri, A. and Seminowicz, D.A., 2020. Sensorimotor peak alpha frequency is a reliable biomarker of prolonged pain sensitivity. Cerebral Cortex, 30(12), pp.6069-6082.

  6. Buckley T, Kitchen C, Vyas G, Siegfried NA, Tefera E, Chen S, DiPaula BA, Kelly DL. Comparison of novel immunoassay with liquid chromatography/tandem mass spectrometry (LC-MS/MS) for therapeutic drug monitoring of clozapine. Therapeutic Drug Monitoring. 2020 Oct 1;42(5):771-7.

  7. Asanad, S., Addis, H., Chen, S., Wu, J., Kochunov, P., O'Neill, H., ... & Saeedi, O. (2020). Retinal Thickness and Vascular Pathology as Ocular Biomarkers for Schizophrenia: Morphometric Analysis of the Peripapillary and Macular Regions using OCT and OCTA In Vivo. Investigative Ophthalmology & Visual Science, 61(7), 5105-5105.

  8. Kochunov, P., Fan, F., Ryan, M. C., Hatch, K. S., Tan, S., Jahanshad, N., Chen, S., ... & Du, X. (2020). Translating ENIGMA schizophrenia findings using the regional vulnerability index: Association with cognition, symptoms, and disease trajectory. Human Brain Mapping.

  9. Ponomareva, O. Y., Redman, B., Sayer, M. A., Wehring, H. J., Vyas, G., Richardson, C. M., Chen, S., Wang, J., ... & Hoag, S. W. (2020). L-Tetrahydropalmatine, a Novel Dopamine Antagonist, Fails to Improve Psychiatric Symptoms as Adjunctive Treatment for Schizophrenia. Schizophrenia Bulletin Open.

  10. Hare, S.M., Chiappelli, J., Savransky, A., Adhikari, B.M., Wisner, K., Kvarta, M., Goldwaser, E., Du, X., Chen, S., Rowland, L.M. and Kochunov, P., 2020. The role of hippocampal functional connectivity on multisystem subclinical abnormalities in schizophrenia. Psychosomatic medicine, 82(6), pp.623-630.

  11. Adhikari, B., Hong, L. E., Wang, D. J., Rowland, L. M., Thompson, P. M., Jahanshad, N., Chen, S., ... & Kochunov, P. (2020). Genetic Control Over Cerebral Blood Flow and Resting State Regional Homogeneity Signal. Biological Psychiatry, 87(9), S397-S398.

  12. Gold, J.M., Bansal, S., Gaspar, J.M., Chen, S., Robinson, B.M., Hahn, B. and Luck, S.J., 2020. People with schizophrenia show enhanced cognitive costs of maintaining a single item in working memory. Psychological medicine, 50(5), p.867.

  13. Chen, S., Xing, Y., Kang, J., Kochunov, P., & Hong, L. E. (2020). Bayesian modeling of dependence in brain connectivity data. Biostatistics, 21(2), 269-286.

  14. Seminowicz, D. A., Bilska, K., Chowdhury, N. S., Skippen, P., Millard, S. K., Chiang, A. K., Chen, S., ... & Schabrun, S. M. (2020). A novel cortical biomarker signature for predicting pain sensitivity: protocol for the PREDICT longitudinal analytical validation study. Pain Reports.

  15. Turpin, R., Slopen, N., Boekeloo, B., Dallal, C., Chen, S., & Dyer, T. (2020). Testing a syndemic index of psychosocial and structural factors associated with HIV testing among black men. Journal of Health Care for the Poor and Underserved, 31(1), 455-470.

  16. Chen, S., Bowman, F. D., & Xing, Y. (2020). Detecting and testing altered brain connectivity networks with k-partite network topology. Computational Statistics & Data Analysis, 141, 109-122.

  17. Kelly, D.L., Spaderna, M., Hodzic, V., Nair, S., Kitchen, C., Werkheiser, A.E., Powell, M.M., Liu, F., Coppersmith, G., Chen, S. and Resnik, P., 2020. Blinded Clinical Ratings of Social Media Data are Correlated with In-Person Clinical Ratings in Participants Diagnosed with Either Depression, Schizophrenia, or Healthy Controls. Psychiatry Research, 294, p.113496.

  18. Chen, S., Zhang, Z., Mo, C., Wu, Q., Kochunov, P. and Hong, L.E., 2020. Characterizing the Complexity of Weighted Networks via Graph Embedding and Point Pattern Analysis. Entropy, 22(9), p.925.

  19. Buchanan, R.W., Weiner, E., Kelly, D.L., Gold, J.M., Chen, S., Zaranski, J., Blatt, F., Wehring, H. and Carpenter, W.T., 2020. Anti-inflammatory Combination Therapy for the Treatment of Schizophrenia. Journal of Clinical Psychopharmacology, 40(5), pp.444-450.

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2019

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  1. Zhu, L., Huo, Z., Ma, T., Tseng, GC. (2019). Bayesian indicator variable selection model with multi-layer overlapping groups. Annals of Applied Statistics. Accepted. (a preliminary version won the ENAR distinguished student paper award). 

  2. Huo, Z., Zhu, L., Ma, T., Liu, H, Han, S, Liao, D, Zhao J and Tseng, GC. (2019). Two-way Horizontal and Vertical Omics Integration for Disease Subtype Discovery. Statistics in Bioscience. Accepted. 

  3. Wijtenburg, S. A., Kapogiannis, D., Korenic, S. A., Mullins, R. J., Tran, J., Gaston, F. E., Chen S., ... & Rowland, L. M. (2019). Brain insulin resistance and altered brain glucose are related to memory impairments in schizophrenia. Schizophrenia research, 208, 324-330.

  4. Clark, S. M., Notarangelo, F. M., Li, X., Chen, S., Schwarcz, R., & Tonelli, L. H. (2019). Maternal immune activation in rats blunts brain cytokine and kynurenine pathway responses to a second immune challenge in early adulthood. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 89, 286-294.

  5. Baratta, A. M., Buck, S. A., Buchla, A. D., Fabian, C. B., Chen, S., Mong, J. A., & Pocivavsek, A. (2018). Sex differences in hippocampal memory and kynurenic acid formation following acute sleep deprivation in rats. Scientific reports, 8(1), 1-11.

  6. Wijtenburg, S. A., Near, J., Korenic, S. A., Gaston, F. E., Chen, H., Mikkelsen, M., Chen, S.,... & Rowland, L. M. (2019). Comparing the reproducibility of commonly used magnetic resonance spectroscopy techniques to quantify cerebral glutathione. Journal of Magnetic Resonance Imaging, 49(1), 176-183.

  7. Adhikari, B. M., Hong, L. E., Sampath, H., Chiappelli, J., Jahanshad, N., Thompson, P. M., Chen, S.,... & Kochunov, P. (2019). Functional network connectivity impairments and core cognitive deficits in schizophrenia. Human brain mapping, 40(16), 4593-4605.

  8. Kim, E., Keskey, Z., Kang, M., Kitchen, C., Bentley, W. E., Chen, S., ... & Payne, G. F. (2019). Validation of oxidative stress assay for schizophrenia. Schizophrenia research, 212, 126-133.

  9. Kochunov, P., Huang, J., Chen, S., Li, Y., Tan, S., Fan, F., ... & Du, X. (2019). White matter in schizophrenia treatment resistance. American Journal of Psychiatry, 176(10), 829-838.

  10. Kim, E., Li, J., Kang, M., Kelly, D. L., Chen, S., Napolitano, A., ... & Shen, J. (2019). Redox Is a Global Biodevice Information Processing Modality. Proceedings of the IEEE, 107(7), 1402-1424.

  11. Turpin, R. E., Slopen, N., Chen, S., Boekeloo, B., Dallal, C., & Dyer, T. (2019). Latent class analysis of a syndemic of risk factors on HIV testing among black men. AIDS care, 31(2), 216-223.

  12. Wang, J., Zheng, X., Zhang, J., Xue, H., Wang, L., Jing, R., Chen, S.,... & Xue, F. (2019). Pretreatment MRI Radiomics Analysis Allows for Reliable Noninvasive Prediction of Survival and TERT Promoter Mutation in Lower-Grade Gliomas. Available at SSRN 3487723.

  13. Chiappelli, J., Rowland, L. M., Wijtenburg, S. A., Chen, H., Maudsley, A. A., Sheriff, S., Chen, S.,... & Bruce, H. A. (2019). Cardiovascular risks impact human brain N-acetylaspartate in regionally specific patterns. Proceedings of the National Academy of Sciences, 116(50), 25243-25249.

  14. Bruce, H. A., Kochunov, P., Mitchell, B., Strauss, K. A., Ament, S. A., Rowland, L. M., Chen, S.,... & Wisner, K. (2019). Clinical and genetic validity of quantitative bipolarity. Translational psychiatry, 9(1), 1-8.

  15. Shaw, E. P., Rietschel, J. C., Shuggi, I. M., Xu, Y., Chen, S., Miller, M. W., ... & Gentili, R. J. (2019). Cerebral cortical networking for mental workload assessment under various demands during dual-task walking. Experimental brain research, 237(9), 2279-2295.

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2018

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  1. Fang Z, Ma T, Zhu L, Yan Q, Chen W, Tang G and Tseng GC. (2018). A Bayesian Model for Integrating High-Throughput Multi-Omics Data with Missingness Handling. Bioinformatics. Accepted. [Software]

  2. Ma, T.^, Huo Z.^ , Kuo A.^ , Zhu, L, Fang, Z, ..., Song S and Tseng GC. (2018). MetaOmics - Comprehensive Analysis Pipeline and Web-based Software Suite for Transcriptomic Meta-Analysis. Bioinformatics. Accepted. [Link] [Software] 

  3. Scifo, E., Pabba, M., Kapadia, F., Ma, T., Lewis, D. A., Tseng, G. C., & Sibille, E. (2018). Sustained molecular pathology across episodes and remission in major depressive disorder. Biological psychiatry, 83(1), 81-89.

  4. Gold, J. M., Robinson, B., Leonard, C. J., Hahn, B., Chen, S., McMahon, R. P., & Luck, S. J. (2018). Selective attention, working memory, and executive function as potential independent sources of cognitive dysfunction in schizophrenia. Schizophrenia bulletin, 44(6), 1227-1234.

  5. Chiappelli, J., Chen, S., Hackman, A., & Hong, L. E. (2018). Evidence for differential opioid use disorder in schizophrenia in an addiction treatment population. Schizophrenia research, 194, 26-31.

  6. Kang, M., Kim, E., Chen, S., Bentley, W. E., Kelly, D. L., & Payne, G. F. (2018). Signal processing approach to probe chemical space for discriminating redox signatures. Biosensors and Bioelectronics, 112, 127-135.

  7. Warren, K. R., Wehring, H. J., Liu, F., McMahon, R. P., Chen, S., Chester, C., & Kelly, D. L. (2018). Effects of intranasal oxytocin on satiety signaling in people with schizophrenia. Physiology & Behavior, 189, 86-91.

  8. Chen, S., Kang, J., Xing, Y., Zhao, Y., & Milton, D. K. (2018). Estimating large covariance matrix with network topology for high-dimensional biomedical data. Computational Statistics & Data Analysis, 127, 82-95.

  9. Grabosch S, Bulatovic M, Zeng F, Ma T, Zhang L, Ross M, Brozick J, Fang Y, Tseng G, Kim E, Gambotto A, Elishaev E, Edwards R and Vlad, A. Cisplatin-induced immune modulation in ovarian cancer mouse models with distinct inflammation profiles. Oncogene: 38(13):2380-2393. [Link]

  10. Andersen CL, Boisen MM, Sikora MJ, Ma T, Tseng G, Suryawanshi S, Vlad AM, Elishaev E, Edwards RP and Oesterreich S. (2018). The evolution of estrogen receptor signaling in the progression of endometriosis to endometriosis-associated ovarian cancer. Hormones and Cancer 9.6: 399-407. [Link]

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2017

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  1. Andersen, C.L., Sikora, M.J., Boisen, M.M., Ma, T., Christie, A., Tseng, G., Park, Y., Luthra, S., Chandran, U., Haluska, P. & Mantia-Smaldone, G.M., (2017). Active estrogen receptor-alpha signaling in ovarian cancer models and clinical specimens. Clinical Cancer Research, 23(14), pp.3802-3812.

  2. French, L., Ma, T., Oh, H., Tseng, G.C. & Sibille, E., (2017). Age-related gene expression in the frontal cortex suggests synaptic function changes in specific inhibitory neuron subtypes. Frontiers in aging neuroscience, 9, p.162.

  3. Linkov, F., Goughnour, S. L., Ma, T., Xu, Z., Edwards, R. P., Lokshin, A. E., ... & Bovbjerg, D. H. (2017). Changes in inflammatory endometrial cancer risk biomarkers in individuals undergoing surgical weight loss. Gynecologic oncology, 147(1), 133-138.

  4. Ma, T., Liang, F., Oesterreich, S., & Tseng, G. C. (2017). A joint Bayesian model for integrating microarray and RNA sequencing transcriptomic data. Journal of Computational Biology, 24(7), 647-662.

  5. Pabba, M., Scifo, E., Kapadia, F., Nikolova, Y. S., Ma, T., Mechawar, N., ... & Sibille, E. (2017). Resilient protein co-expression network in male orbitofrontal cortex layer 2/3 during human aging. Neurobiology of aging, 58, 180-190.

  6. Ma, T., Liang, F., & Tseng, G. (2017). Biomarker detection and categorization in ribonucleic acid sequencing meta-analysis using bayesian hierarchical models. Journal of the Royal Statistical Society. Series C, Applied statistics, 66(4), 847.

  7. Grabosch, S., Tseng, G., Edwards, R.P., Lankes, H.A., Moore, K., Odunsi, K., Vlad, A., Ma, T., Strange, M., Brozick, J. & Lugade, A., (2017). Multiplex profiling identifies distinct local and systemic alterations during intraperitoneal chemotherapy for ovarian cancer: An NRG Oncology/Gynecologic Oncology Group Study. Gynecologic oncology, 146(1), pp.137-145.

  8. Grabosch, S., Boisen, M. M., Ma, T., Philips, B., Strange, M., Elishaev, E., ... & Huang, M. (2017). Uterine leiomyosarcoma: Are novel therapeutics on the horizon?. Gynecologic Oncology, 145, 89-90.

  9. Grabosch, S., Zeng, F., Ma, T., Zhang, L., Guido, E., Tseng, G., ... & Brozick, J. (2017). Novel combination immunotherapy with MUC1 vaccination and immune checkpoint blockade in ovarian cancer. Gynecologic Oncology, 145, 86.

  10. Kochunov, P., Coyle, T. R., Rowland, L. M., Jahanshad, N., Thompson, P. M., Kelly, S., Chen S., ... & Ryan, M. (2017). Association of white matter with core cognitive deficits in patients with schizophrenia. JAMA psychiatry, 74(9), 958-966.

  11. Chen, S., Xing, Y., & Kang, J. (2017). Latent and abnormal functional connectivity circuits in autism spectrum disorder. Frontiers in neuroscience, 11, 125.

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2016

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  1. Chen, C. Y., Logan, R. W., Ma, T., Lewis, D. A., Tseng, G. C., Sibille, E., & McClung, C. A. (2016). Effects of aging on circadian patterns of gene expression in the human prefrontal cortex. Proceedings of the National Academy of Sciences, 113(1), 206-211.

  2. Liu, S., Tsai, W. H., Ding, Y., Chen, R., Fang, Z., Huo, Z., Huo Z., Kim S., Ma T., Chang T., Priedigkeit, N. M, Lee, A. V., Luo, J. Wang H., Chung I., & Tseng, G. (2016). Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic acids research, 44(5), e47-e47.

  3. Sanei-Moghaddam, A., Ma, T., Goughnour, S. L., Edwards, R. P., Lounder, P. J., Ismail, N., ... & Linkov, F. (2016). Changes in hysterectomy trends after the implementation of a clinical pathway. Obstetrics & Gynecology, 127(1), 139-147.

  4. Zhang, L., Ma, T., Brozick, J., Babalola, K., Budiu, R., Tseng, G., & Vlad, A. M. (2016). Effects of Kras activation and Pten deletion alone or in combination on MUC1 biology and epithelial-to-mesenchymal transition in ovarian cancer. Oncogene, 35(38), 5010-5020.

  5. Mansuria, S. M., Comerci, J., Edwards, R., Moghaddam, A. S., Ma, T., & Linkov, F. (2016). Changes in hysterectomy trends and patient outcomes following the implementation of a clinical pathway [7]. Obstetrics & Gynecology, 127, 3S.

  6. Grabosch, S., Zeng, F., Zhang, L., Ma, T., Tseng, G., Edwards, R. P., & Vlad, A. M. (2016). Chemo-induced biology of PD-L1 and in vivo combination immune therapy for ovarian cancer.

  7. Chen, S., Bowman, F. D., & Mayberg, H. S. (2016). A Bayesian hierarchical framework for modeling brain connectivity for neuroimaging data. Biometrics, 72(2), 596-605.

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2015 and before

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  1. Liao, S., Hartmaier, R.J., McGuire, K.P., Puhalla, S.L., Luthra, S., Chandran, U.R., Ma, T., Bhargava, R., Modugno, F., Davidson, N.E. & Benz, S., (2015). The molecular landscape of premenopausal breast cancer. Breast Cancer Research, 17(1), pp.1-13.

  2. Mony, J. T., Zhang, L., Ma, T., Grabosch, S., Tirodkar, T. S., Brozick, J., ... & Vlad, A. M. (2015). Anti-PD-L1 prolongs survival and triggers T cell but not humoral anti-tumor immune responses in a human MUC1-expressing preclinical ovarian cancer model. Cancer Immunology, Immunotherapy, 64(9), 1095-1108.

  3. Zhang, L., Ma, T., Brozick, J., Babalola, K., Budiu, R., Tseng, G., & Vlad, A. (2015). Lung metastasis of ovarian cancer in a transplantable MUC1. Tg mouse model is accompanied by upregulation of MUC1 expression and epithelial to mesenchymal transition.

  4. Chen, S., Kang, J., Xing, Y., & Wang, G. (2015). A parsimonious statistical method to detect groupwise differentially expressed functional connectivity networks. Human brain mapping, 36(12), 5196-5206.

  5. Chen, S., Kang, J., & Wang, G. (2015). An empirical Bayes normalization method for connectivity metrics in resting state fMRI. Frontiers in neuroscience, 9, 316.

  6. Oh, H., Hatfield, B. D., Jaquess, K. J., Lo, L. C., Tan, Y. Y., Prevost, M. C., Chen, S.,... & Blanco, J. A. (2015). A composite cognitive workload assessment system in pilots under various task demands using ensemble learning. In International Conference on Augmented Cognition (pp. 91-100). Springer, Cham.

  7. Suryawanshi, S., Huang, X., Elishaev, E., Budiu, R.A., Zhang, L., Kim, S., Donnellan, N., Mantia-Smaldone, G., Ma, T., Tseng, G. & Lee, T., (2014). Complement pathway is frequently altered in endometriosis and endometriosis-associated ovarian cancer. Clinical Cancer Research, 20(23), pp.6163-6174.

  8. Hou, L., Ma, T., & Zhao, H. (2014). Incorporating functional annotation information in prioritizing disease associated SNPs from genome wide association studies. Science China Life Sciences, 57(11), 1072-1079.

  9. Burke, D. T., Al-Adawi, S., Bell, R. B., Easley, K., Chen, S., & Burke, D. P. (2014). Effect of body mass index on stroke rehabilitation. Archives of physical medicine and rehabilitation, 95(6), 1055-1059.

  10. Huang, C., Guo, C., Nichols, C., Chen, S., & Martorell, R. (2014). Elevated levels of protein in urine in adulthood after exposure to the Chinese famine of 1959–61 during gestation and the early postnatal period. International journal of epidemiology, 43(6), 1806-1814.

  11. Chen, S., Grant, E., Wu, T. T., & Bowman, F. D. (2014). Some recent statistical learning methods for longitudinal high‐dimensional data. Wiley Interdisciplinary Reviews: Computational Statistics, 6(1), 10-18.

  12. He, X., Lu, X., Chen, S., Hochberg, M. C., & Lee, M. L. T. (2014). Association between Obesity, Race and Knee Osteoarthritis: The Multicenter Osteoarthritis Study. International Journal of Statistics in Medical Research, 3(3), 224-230.

  13. Raison, C. L., Rutherford, R. E., Woolwine, B. J., Chen, S., Schettler, P., Drake, D. F., ... & Miller, A. H. (2013). A randomized controlled trial of the tumor necrosis factor antagonist infliximab for treatment-resistant depression: the role of baseline inflammatory biomarkers. JAMA psychiatry, 70(1), 31-41.

  14. Bowman, F. D., Zhang, L., Derado, G., & Chen, S. (2012). Determining functional connectivity using fMRI data with diffusion-based anatomical weighting. NeuroImage, 62(3), 1769-1779.

  15. Anderson, A. M., Chane, T., Patel, M., Chen, S., Xue, W., & Easley, K. A. (2012). Warfarin therapy in the HIV medical home model: low rates of therapeutic anticoagulation despite adherence and differences in dosing based on specific antiretrovirals. AIDS patient care and STDs, 26(8), 454-462.

  16. Bouloux, G. F., Chen, S., & Threadgill, J. M. (2012). Small and large titanium plates are equally effective for treating mandible fractures. Journal of oral and maxillofacial surgery, 70(7), 1613-1621.

  17. Zhang, L., Agravat, S., Derado, G., Chen, S., McIntosh, B. J., & Bowman, F. D. (2012). BSMac: A MATLAB toolbox implementing a Bayesian spatial model for brain activation and connectivity. Journal of neuroscience methods, 204(1), 133-143.

  18. Raison, C., Rutherford, R. E., Woolwine, B., Chen, S., Schettler, P., Drake, D., ... & Miller, A. H. (2012). 176. The tumor necrosis factor-alpha antagonist infliximab reduces depressive symptoms in patients with treatment resistant depression and high inflammation. Brain, Behavior, and Immunity, 26, S49.

  19. Chen, S., & DuBois Bowman, F. (2011). A novel support vector classifier for longitudinal high‐dimensional data and its application to neuroimaging data. Statistical Analysis and Data Mining: The ASA Data Science Journal, 4(6), 604-611.

  20. Li, M., Chen, S., Zhang, J., Chen, H., & Shyr, Y. (2011). Wave-spec: a preprocessing package for mass spectrometry data. Bioinformatics, 27(5), 739-740.

  21. Woodhams, D. C., Kenyon, N., Bell, S. C., Alford, R. A., Chen, S., Billheimer, D., ... & Rollins‐Smith, L. A. (2010). Adaptations of skin peptide defences and possible response to the amphibian chytrid fungus in populations of Australian green‐eyed treefrogs, Litoria genimaculata. Diversity and Distributions, 16(4), 703-712.

  22. Liu, C., Agrawal, P., Sarkar, N., & Chen, S. (2009). Dynamic difficulty adjustment in computer games through real-time anxiety-based affective feedback. International Journal of Human-Computer Interaction, 25(6), 506-529.

  23. Salmon, S., Chen, H., Chen, S., Herbst, R., Tsao, A., Tran, H., ... & Massion, P. (2009). Classification by mass spectrometry can accurately and reliably predict outcome in patients with non-small cell lung cancer treated with erlotinib-containing regimen. Journal of Thoracic Oncology, 4(6), 689-696.

  24. Chen, S., Li, M., Hong, D., Billheimer, D., Li, H., Xu, B. J., & Shyr, Y. (2009). A novel comprehensive wave-form MS data processing method. Bioinformatics, 25(6), 808-814.

  25. Bowman, F. D., Derado, G., & Chen, S. (2009). Evaluating functional connectivity using fMRI data with diffusion-based anatomical weighting. NeuroImage, 47(1), S147.

  26. Derado, G., Chen, S., Guo, Y., Mayberg, H., & Bowman, D. (2009). Classification Methods for Identifying the Neural Characteristics of Antidepressant Treatment. In Poster presentation at the 15th annual meeting of the Organization for Human Brain Mapping.

  27. Chen, S., Derado, G., Guo, Y., & Bowman, F. D. (2009). Classification Methods for Identifying the Neural Characterics of Antidepressant Treatment. NeuroImage, (47), S71.

  28. Yildiz, P.B., Shyr, Y., Rahman, J.S., Wardwell, N.R., Zimmerman, L.J., Shakhtour, B., Gray, W.H., Chen, S., Li, M., Roder, H., & Liebler, D.C., (2007). Diagnostic accuracy of MALDI mass spectrometric analysis of unfractionated serum in lung cancer. Journal of Thoracic Oncology, 2(10), pp.893-901.

  29. Agulnik, M., da Cunha Santos, G., Hedley, D., Nicklee, T., Dos Reis, P.P., Ho, J., Pond, G.R., Chen, H., Chen, S., Shyr, Y. & Winquist, E., (2007). Predictive and pharmacodynamic biomarker studies in tumor and skin tissue samples of patients with recurrent or metastatic squamous cell carcinoma of the head and neck treated with erlotinib. Journal of Clinical Oncology, 25(16), pp.2184-2190.

  30. Chen, S., Hong, D., & Shyr, Y. (2007). Wavelet-based procedures for proteomic mass spectrometry data processing. Computational Statistics & Data Analysis, 52(1), 211-220.

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Publication list:  (PI bolded, student underlined; ^co-first author, *corresponding/senior author)

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Dr. Shuo Chen: Google Scholar

Dr. Tianzhou (Charles) Ma: Google Scholar

Dr. Chixiang Chen: Google Scholar

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