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Rong Chen, PhD

Academic Title:

Assistant Professor

Primary Appointment:

Diagnostic Radiology and Nuclear Medicine

Location:

100 N Greene St, 411

Phone (Primary):

410-706-3284

Fax:

410-706-1878

Education and Training

Southeast University, China, B.S. 1996, Biomedical Engineering
The Graduate School of Chinese Academy of Sciences, China, M.S. 1999, Electrical Engineering
Washington State University, Pullman, WA, Ph.D. 2003, Electrical and Computer Engineering
University of Pennsylvania, Philadelphia, PA, Postdoctoral Researcher, 2005, Radiology
University of Pennsylvania, Philadelphia, PA, M.T.R 2012, Translational Research

Biosketch

Dr. Chen has a strong background in computational neuroscience, machine learning, biomedical data analysis, and translational research. His research focuses on leveraging machine learning, deep learning, and computational modeling to understand the relationship between brain and behavior, leading to novel therapeutic concepts for brain disorders and brain-inspired AI. He has 20 years of experience in advanced modeling, algorithm, and software development. He has released two open-source biomedical data mining software packages on NITRC: the GAMMA suite and Advanced Connectivity Analysis. Dr. Chen is a senior member of IEEE. He is an editorial member of Frontier of computational neuroscience, Frontiers of neurorobotics, and the Open Neuroimaging journal.

Research/Clinical Keywords

Computational neuroscience, machine learning, translational medicine, biomedical data analysis

Highlighted Publications

 

Barbera G, Liang B, Zhang LF, Gerfen CR, Culurciello E, Chen R#, Li Y#, Lin DT#. Spatially Compact Neural Clusters In The Dorsal Striatum Encode Locomotion Relevant Information. 92(1):202-213, Neuron. 2016. # co-corresponding authors.

 

Chen, R., Arkuszewski M, Krejza J., Zimmerman R., Herskovits, E. H., Melhem E. R. A prospective longitudinal brain-morphometry study of children with sickle-cell disease, AJNR, 36(2), 403-410, 2015.

 

Chen R, Resnick S, Davatzikos C, Herskovits EH, Dynamic Bayesian network modeling for longitudinal brain morphometry. NeuroImage. 59(3):2330-2338, 2011.

 

Chen R, Herskovits EH, Graphical-Model-based Morphometric Analysis. IEEE Transaction on Medical Imaging. Vol 24, 1237-1248, October 2005.

 

Chen R, Sivakumar K, Kargupta H, Collective Mining of Bayesian Networks from Distributed Heterogeneous Data, Knowledge and Information Systems. 6(2):164-187, 2004.

 

Additional Publication Citations

Peer-reviewed journal articles

  1. Chen, R., Zhang, X.M., The Development of a New Type of Intelligent Surface Pressure Measuring Instrument, Instrument Technique and Sensor, Dec. 1997
  2. Chen, R., Liu, X.J., Zou, M.Y., Binary Image Restoration Based on MRF, Journal of Image and Graphics, Oct. 1999
  3. Chen, R., Sivakumar, K, Kargupta, H, Collective Mining of Bayesian Networks from Distributed Heterogeneous data, Knowledge and Information Systems, 6(2):164-187, 2004
  4. Chen, R., Herskovits, E. H., Graphical-Model-based Morphometric Analysis, IEEE Transaction on medical imaging, Vol 24, 1237-1248, Oct. 2005
  5. Chen, R., Herskovits, E. H., Network analysis of Mild Cognitive Impairment, NeuroImage, Vol 29, 1252-1259, 2006
  6. Chen, R., Herskovits E. H., Clinical Diagnosis based on Bayesian Classification of Functional Magnetic-resonance Data. Neuroinformatics, 5(3):178-88, Fall, 2007
  7. Chen, R., Herskovits E. H., Graphical-model-based Multivariate Analysis of Functional Magnetic Resonance Data, NeuroImage, Vol 35, 635-647, Apr. 2007
  8. Chen, R., Hillis A. E., Pawlak M., and Herskovits E. H., Voxelwise Bayesian Lesion Deficit Analysis, NeuoImage, Vol 40, 1633-1642, May, 2008
  9. Herskovits E. H., Chen, R., Integrating Data-Mining Support into a Brain-Image Database Using Open-Source Components, Advance in Medical Sciences, 18:1-10, Apr. 2008
  10. Chen, R., Pawlak, M., Flynn, T., Krejza, J., Herskovits, E. H., Melhem, E., Brain morphometry and IQ measurements in children with sickle cell disease, Journal of Developmental & Behavioral Pediatrics, 30(6):509-17, 2009
  11. Jiao, Y., Chen, R., Ke, X, Chu, KK, Lu ZH, Herskovits, E. H, Predictive models of autism spectrum disorder based on brain regional cortical thickness, NeuroImage, 50(2):589-99, 2010 (Experimental design, data analysis)
  12. Chen, R., Herskovits E. H, Voxel-based Bayesian lesion-symptom mapping, NeuroImage, 49:1, 597-602, 2010
  13. Chen, R., Herskovits E. H, Machine-learning techniques for building a diagnostic model for very mild dementia, NeuroImage, 52(1):234-44, 2010
  14. Krejza J, Chen R, Romanowicz G, Kwiatkowski JL, Ichord R, Arkuszewski M, Zimmerman R, Ohene-Frempong K, Desiderio L, Melhem ER., Sickle cell disease and imaging: inter-hemispheric differences in blood flow Doppler parameters, Stroke.42:1, 81-6, 2011 (Data analysis)
  15. Chen, R., Jiao Y., Herskovits E. H, Structural MRI in Autism Spectrum Disorder, invited paper, Pediatric Research, 69:63r-8r, 2011.
  16. Arkuszewski, M., Krejza, J., Chen, R., Kwiatkowski, J., Ichord, R., Zimmerman, R., Ohene-Frempong, K., Desiderio, L., E.R. Melhem, Sickle Cell Disease: Reference Values and Interhemispheric Differences of Nonimaging Transcranial Doppler Blood Flow Parameters, American Journal of Neuroradiology, 32(8):1444-50, 2011
  17. Jiao, Y., Chen, R., Cheng, L., Ke, X., Chu K., Lu ZH., Herskovits. E. H., Predictive models for subtypes of autism spectrum disorder based on single-nucleotide polymorphisms and magnetic resonance imaging, Advance in Medical Sciences, 56(2):334-42, 2011
  18. Jiao, Y., Chen, R., Ke, X., Cheng Li, Chu, K., Lu ZH, Herskovits, E. H., Single Nucleotide Polymorphisms Predict Symptom Severity of Autism Spectrum Disorder, Journal of Autism and Developmental Disorders, 42(6):971-83, 2011
  19. Chen, R., Herskovits E. H, Graphical model based multivariate analysis (GAMMA): an open-source, cross-platform neuroimaging data analysis software package, Neuroinformatics, 10(2):119-27, 2011
  20. Chen, R., Resnick, S., Davatzikos, C., Herskovits E. H., Dynamic Bayesian network modeling for longitudinal brain morphometry, NeuroImage, 59(3):2330-8, 2011
  21. Chen, R., Young, K., Chao L. L., Miller, B., Yaffe K., Weiner, M., Herskovits E. H., Prediction of Conversion from Mild Cognitive Impairment to Alzheimer Disease Based on Bayesian Data Mining with Ensemble Learning, The Neuroradiology Journal, 25:1, 5-16, 2012
  22. Kumar, M., Kim, S., Pickup, S., Chen, R., Fairless A., Ittyerah, R., Abel, T., Brodkin, E., Poptani, H., Longitudinal in-vivo diffusion tensor imaging for assessing brain developmental changes in BALB/cJ mice, a model of reduced sociability relevant to autism, Brain Research, 1455:56-67, 2012
  23. Chen, R., Wang, S., Poptani, H., Melhem, E. R., Herskovits, E. H. A Bayesian diagnostic system to differentiate glioblastomas from solitary brain metastases. Neuroradiol J. 10;26(2):175-83. 2013
  24. Arkuszewski M., Krejza J., Chen R., Melhem E. R., Sickle cell anemia: reference values of cerebral blood flow determined by continuous arterial spin labeling MRI. Neuroradiol J. 10;26(2):191-200. 2013
  25. Arkuszewski, M., Krejza, J., Chen, R., Ichord, R., Kwiatkowski, J., Bilello M., Zimmerman R., Ohene-Frempong K., Melhem, E. R., Prevalence of intracranial stenosis and silent cerebral infarcts in children with sickle cell anemia and low risk of stroke, International Journal of Stroke. 8(7):E50-1. DOI:10.1111/ijs.12115. 2013
  26. Arkuszewski, M., Krejza, J., Chen, R., Ichord, R., Kwiatkowski, JL., Bilello, M., Zimmerman, R., Ohene-Frempong, K., Melhem, E., Sickle cell anemia: intracranial stenosis and silent cerebral infarcts in children with low risk of stroke. Adv Med Sci. Mar;59(1):108-13, 2014
  27. Liu, Y., Wang, T., Chen, X., Zhang, J., Zhou, G., Wang, Z., Chen, R., Tract-based Bayesian multivariate analysis of mild traumatic brain injury. Comput Math Methods Med. 2014:120182. doi: 10.1155/2014/120182, 2014
  28. Chen, R., Herskovits, E. H., Examining the multifactorial nature of a cognitive process using Bayesian brain-behavior modeling. Comput Med Imaging Graph, 41:117-25, 2014
  29. Hickok, G., Rogalsky, C., Chen, R., Herskovits, E. H., Townsley, S., Hillis, A., Partially Overlapping Sensorimotor Networks Underlie Speech Praxis and Verbal Short-Term Memory: Evidence from Apraxia of Speech Following Acute Stroke, 8:649, Hum. Neurosci. 2014
  30. Chen, R., Herskovits, E. H., Bayesian predictive modeling based on multidimensional connectivity profiling, Neuroradiol J. 28(1), 5-11, 2015
  31. Chen, HJ., Chen, R., Yang, M., Teng, GJ., Herskovits, E. H., Identification of minimal hepatic encephalopathy in patients with cirrhosis based on white matter imaging and Bayesian data mining, AJNR, 36(3):481-7, 2015 (Experimental design, data analysis, data interpretation)
  32. Chen, R., Arkuszewski M, Krejza J., Zimmerman R., Herskovits, E. H., Melhem E. R. A prospective longitudinal brain-morphometry study of children with sickle-cell disease, AJNR, 36(2), 403-410, 2015
  33. Yang M, Yang YR, Li HJ, Lu XS, Shi YM, Liu B, Chen HJ, Teng GJ, Chen R, Herskovits EH. Combining diffusion tensor imaging and gray matter volumetry to investigate motor functioning in chronic stroke. PLoS One. May 12;10(5), 2015
  34. Herskovits EH, Hong LE, Kochunov P, Sampath H, Chen R. Edge-Centered DTI Connectivity Analysis: Application to Schizophrenia. Neuroinformatics. 13(4):501-509, 2015
  35. Chen, R.*, Herskovits, E. H. and ADNI, Predictive structural dynamic network analysis, Journal of neuroscience methods, 245:58-63, 2015
  36. Wang Q, Chen R, JaJa J, Jin Y, Hong LE. Herskovits EH, Connectivity-Based Brain Parcellation - A Connectivity-Based Atlas for Schizophrenia Research, Neuroinformatics, 14(1):83-97, 2016
  37. Wang Z, Wu W, Liu Y, Wang T, Chen X, Zhang J, Zhou G, Chen R. Altered cerebellar white matter integrity in patients with mild traumatic brain injury in the acute stage. PLoS One, 11(3): e0151489, 2016
  38. Chen, R., Nixon, E., Herskovits, E. H., Advanced Connectivity Analysis (ACA): a large scale functional connectivity data mining environment, Neuroinformatics, 14(2): 191-9, 2016
  39. Chen, R., Krejza, J., Arkuszewski, M., Zimmerman, R., Herskovits, E., Melhem, E., Brain morphometric analysis predicts decline of intelligence quotient in children with sickle cell disease: a preliminary study, Advances in Medical Sciences, 62(1): 151-157, 2017
  40. Barbera G, Liang B, Zhang LF, Gerfen CR, Culurciello E, Chen R#, Li Y#, Lin DT#. Spatially compact neural clusters in the dorsal striatum encode locomotion relevant information. 92(1):202-213, Neuron. 2016. # Co-corresponding authors.
  41. Jiao Y, Wang XH, Chen R, Tang TY, Zhu XQ, Teng GJ., Predictive models of minimal hepatic encephalopathy for cirrhotic patients based on large-scale brain intrinsic connectivity networks, Sep 14;7(1):11512, Sci Rep. 2017
  42. Chen HJ, Shi HB, Jiang LF, Chen L, Chen R., Disrupted topological organization of brain structural network associated with prior overt hepatic encephalopathy in cirrhotic patients, European Radiology, 28(1): 85-95, 2017
  43. Chen R., Zheng YJ, Nixon E, Herskovits E, Dynamic network model with continuous valued nodes for longitudinal brain morphometry, NeuroImage, 155:605-611, 2017
  44. Dreizin D., Bodanapally U., Boscak A., Tirada N., Issa G., Nascone J., Bivona L., Mascarenhas D., O’Toole R., Nixon E., Chen R., Siegel E., CT Prediction Model for Major Arterial Injury after Blunt Pelvic Ring Disruption, Radiology, 287(3): 1061-1069, 2017
  45. Naragum V., Jindal G., Miller T., Kole M., Shivashankar R., Merino J., Cole J., Chen R., Kohler N., Gandhi D., Functional Independence After Stroke Thrombectomy Using Thrombolysis in Cerebral Infarction Grade 2c, A New Aim of Successful Revascularization, World Neurosurgery, 119:e928-e933. doi: 10.1016/j.wneu.2018.08.006, 2018
  46. Miller TR, Giacon L, Kole MJ, Chen R., Jindal G., Gandhi D., Onyx embolization with the Apollo detachable tip microcatheter: A single-center experience. Interv Neuroradiol, 24(3):339-344. doi: 10.1177/1591019918758494, 2018
  47. Liang HJ., Chang L., Chen R., Oishi K., Ernst T., Independent and Combined Effects of Chronic HIV-Infection and Tobacco Smoking on Brain Microstructure, Journal of Neuroimmune Pharmacology, 13(4):509-522. doi: 10.1007/s11481-018-9810-9, 2018
  48. Yan T., Wang W., Yang L., Chen K., Chen R., Han Y., Rich club disturbances of the human connectome from subjective cognitive decline to Alzheimer’s disease, Theranostics, 8(12):3237-3255, 2018
  49. Qiu WL, Chen R., Chen X, Zhang HF, Song L, Cui WJ, Zhang JJ, Ye DD, Zhang YF, Wang ZQ, Oridonin-loaded and GPC1 Targeted Gold Nanoparticle for Multimodal Imaging and Therapy in Pancreatic Cancer, International Journal of Nanomedicine, 13:6809-6827, doi: 10.2147/IJN.S177993, 2018 (Data analysis)
  50. Liang B., Zhang LF., Barbera G., Fang WT., Zhang J., Chen XC, Chen R., Li Y., LinDT., Distinct and Dynamic ON and OFF Neural Ensembles in the Prefrontal Cortex Code Social Exploration, Neuron, 100(3):700-714, doi: 10.1016/j.neuron.2018.08.043, 2018 (Data analysis)
  51. White C., Dharaiya E., Dalal S., Chen R., Haramati L., Vancouver Risk Calculator compared to ACR LungRads in Predicting Malignancy: Analysis of the National Lung Screening Trial, Radiology, in press, 2019

 

Selected Conference Publications

  1. Chen, R., Liu, X.J., Zou, M.Y., New Gibbs Sampling Algorithm with Application to Texture Synthesis, Proceedings of SPIE, Vol 3545, Aug.1998
  2. Chen, R.*, Hyperparameter Estimation for Markov Random Fields Using Genetic Algorithm, Proceedings of ICNN&B'98, Oct.1998
  3. Chen, R., Sivakumar, K., Kargupta, H., An Approach to Online Bayesian Learning from Multiple Data Streams, Proceedings of Workshop on Mobile and Distributed Data Mining, PKDD '01, July, 2001
  4. Chen, R., Sivakumar, K., Kargupta, H., Distributed Web Mining Using Bayesian Networks from Multiple Data Streams, Proceedings of the IEEE Conference on Data Mining, Nov. 2001
  5. Chen, R., Sivakumar, K., A New Algorithm for Learning Parameters of a Bayesian Network from Distributed Data, Proceedings of the IEEE International Conference on Data Mining, 2002
  6. Chen, R., Sivakumar. K, and Kargupta, H., Learning Bayesian Network Structure from Distributed Data, Proceedings of SIAM Data Mining, 2003
  7. Chen, R., Giannella. C, Sivakumar. K, and Kargupta. H, Distributed Data Mining for Earth and Space Science Applications, Proceeding of the fourth annual Earth Science Technology conference (ESTC), June, 2004
  8. Chen, R.*, Herskovits, E. H., A Bayesian Network Classifier with Inverse Tree Structure for Voxel-wise MR Image Analysis, Proceedings of the eleventh conference of SIGKDD, 4-12, 2005
  9. Ide J., Chen, R., Shen DG, and Herskovits EH, Robust Brain Registration using Adaptive Probabilistic Atlas, Med Image Comput Comput Assist Interv (MICCAI), 2009
  10. Chen, R.*, Herskovits E. H, Bayesian Classifier Combination for Microarray Classification, Proceedings of Biocomp, July, 2009
  11. Lee Y., Madayambath S., Liu YZ., Lin DT., Chen, R., Bhattacharyya SS., Online Learning in Neural Decoding Using Incremental Linear Discriminant Analysis, IEEE International Conference on Cyborg and Bionic Systems, 2017
  12. Chen, R.*, Wang H., He J., Lin DT., Dynamic micro-circuit analysis for calcium imaging data, IEEE International Conference on Cyborg and Bionic Systems, 2017.
  13. Chen, R.*, Lin DT., Decoding brain states based on microcircuits, IEEE CBS, 2018

 

Book Chapters

  1. Kargupta, H., Sivakumar, K., Huang, WY, Ayyagari, R., Chen, R., Park, B. H., and Johnson, E., Chapter 16. Toward Ubiquitous Mining of Distributed Data, Data Mining for Scientific and Engineering Applications, page 281-307, Kluwer Academic Publishers, 2001
  2. Bhaduri, K., Das, K., Sivakumar, K., Kargupta, H., Wolff, R., Chen, R., Algorithms for Distributed Data Stream Mining, Data Streams: Models and Algorithms, 2007
  3. Chen, R., Structural magnetic resonance imaging of autism spectrum disorder, Autism Imaging and Devices, CRC Press, February 3, 2017