Dr. Jin Chen is an associate professor in the Institute for Biomedical Informatics (IBI), Department of Internal Medicine and Department of Computer Science, the University of Kentucky since 2016. Previously he was an assistant professor in Department of Energy Plant Research Laboratory (PRL) and Department of Computer Science and Engineering, Michigan State University from 2009 to 2016. Dr. Chen received his B.E. in Computer Science from Southeast University in Nanjing, China in 1997. After working in the Jiangsu Electric Power Company Information Center for several years, he decided to transition from industry to academia. He received his Ph.D. in Computer Science from the National University of Singapore (NUS) under the supervision of Dr. Wynne Hsu, Dr. Mong Li Lee and Dr. See-Kiong Ng in 2007. He was a research associate in the bioinformatics laboratory of Dr. Seung Y. Rhee at the Carnegie Institution for Science, Stanford University from 2007 to 2009.

Dr. Chen's research focuses on the development of data mining and computer vision algorithms to solve problems in medical and biological informatics. He has developed a series of algorithms for phenomics and genomics data analysis, including inter-functional clustering, heterogeneity pattern recognition, phenotype ontology development, phenotype data quality control, gene ranking, data visualization, etc. He is also interested in biological network reconstruction using high-dimensional omics data. His work covers regulatory module identification, organelle communication pattern mining, and data-driven ontology construction. He has published more than 50 papers in biomedical informatics, computer science, and biology. Dr. Chen's research has been supported by NSF, NIH, DOE, MSU and UKY.

Current Funding

NSF ABI Innovation: A New Framework to Analyze Plant Energy-related Phenomics Data PI (09/01/15 - 08/31/18)

DOE BES: Photosynthetic Energy Capture, Conversion and Storage: From Fundamental Mechanisms to Modular Engineering co-PI (04/01/14 - 04/01/17)

NIH U01 SUDEP Translational Research Alliance Without Walls co-Investigator (09/30/14 - 07/31/19)

NIH U54 Kentucky Center for Clinical and Translational Science co-Investigator (09/30/16 - 07/31/21)

Previous Funding

DOE BES: Interdisciplinary Research and Training in the Plant Sciences co-PI (04/01/11 - 04/01/14)

Publications

2016

1. Yang Y, Xu L, Feng Z, Cruz JA, Savage LJ, Kramer DM*, Chen J*. PhenoCurve: Capturing Dynamic Phenotype-Environment Relationships using Phenomics Data, Bioinformatics, in press, 2016

2. Peng J, Wang T, Wang J, Wang Y*, Chen J*, Extending Gene Ontology with Gene Association Networks. Bioinformatics, 32(8):1185-94, 2016 PDF Highly Accessed

3. Cruz JA, Savage L, Zegarac R, Kovac W, Hall C, Chen J, Kramer DM, Dynamic Environmental Photosynthetic Imaging (DEPI) Reveals Emergent Phenotypes Related to the Environmental Responses of Photosynthesis. Cell Systems, 2(6):365-77, 2016. Cover Highly Accessed

4. Kramer DM, Chen J, Ostendorf E, Xu L, Cruz J, Brodersen J. Methods for Estimating Photosynthetic Characteristics in Plant Canopies and Systems and Apparatus Related Thereto, US Patent. WO 2016176612 A1. 2016.

5. Peng J, Bai K, Shang X, Wang G, Jin S, Cheng L, Wang Y*, Chen J*, Predicting Disease-related Genes using Integrated Biomedical Networks, BMC Genomics, in press, 2016 Oral Presentation at GIW2016

6. Yin X, Liu X, Chen J, Kramer DM. Jointly Multi-Leaf Segmentation, Alignment, and Tracking from Fluorescence Plant Videos, in revision, 2016

7. Peng J*, Xue H, Shao Y, Shang X, Wang Y*, Chen J*, Measuring Phenotype Semantic Similarity using Human Phenotype Ontology, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, 2016

8. Peng J, Li H, Liu Y, Juan L, Jiang Q, Wang Y*, Chen J*. InteGO2: a Web Tool for Measuring and Visualizing Gene Semantic Similarities using Gene Ontology. BMC Genomics, 17(S5):530, 2016. PDF (InteGO2 website) Oral Presentation at ISBRA2015

9. Peng J, Wang T, Hu J, Wang Y*, Chen J*, Constructing Networks of Organelle Functional Modules in Arabidopsis, Current Genomics, 17(5):427-38, 2016 Editor's choice

10. Morris D, Imran S, Chen J, Kramer DM. Depth Image Superpixels for Foliage Modeling, proceedings of the 13th Conference on Computer and Robot Vision (CRV 2016), Victoria, Canada, 2016


2015

11. Gao Q^, Ostendorf E^, Cruz JA, Jin R*, Kramer DM*, Chen J*. Inter-functional analysis of high-throughput phenotype data by nonparametric clustering and its application in photosynthesis. Bioinformatics, 32(1):67-76, 2015 PDF Highly Accessed

12. Xu L, Cruz JA, Savage L, Kramer DM* and Chen J*. Plant Photosynthesis Phenomics Data Quality Control. Bioinformatics, 31(11):1796-1804, 2015. PDF (DynamicFilter website) Highlighted at ACM BCB 2015 Highly Accessed

13. Dutta S, Cruz JA, Jiao Y, Chen J, Kramer DM, Osteryoung KW. Non-invasive, whole-plant imaging of chloroplast movements and chlorophyll fluorescence reveals photosynthetic phenotypes independent of chloroplast photorelocation defects in chloroplast division mutants. Plant Journal, 2015, 84(2):428-442 Featured Article

14. Cruz JA, Yin X, Liu X, Imran S, Morris D, Kramer DM, Chen J. Multi-modality Imagery Database for Plant Phenotyping, Machine Vision and Applications, 27(5):735-749, 2015

15. Ji S, Tian X, Chen J*. Improving biological significance of gene expression biclusters with key missing genes. proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology (ACM BCB 2015), 2015, pp. 268-277 PDF

16. Peng J, Li H, Wang Y*, Chen J*. A web tool for measuring gene semantic similarities by combining Gene Ontology and gene co-function networks. proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology (ACM BCB 2015), 2015, pp. 678-679 (demo paper) PDF

17. Xu X, Wang W, Lu J, Chen J*. Incremental Distributed Weighted Class Discriminant Analysis on Interval-Valued Emitter Parameters. Lecture Notes in Computer Science, 2015, 9403:619-624. Oral Presentation at KSEM2015

18. Xin XF, Nomura K, Ding X, Aung K, Chen X, Wang K, Aung K, Uribe F, Yao J, Chen J, He S-Y, Pseudomonas syringae Effector Avirulence Protein E Localizes to the Host Plasma Membrane and Down-Regulates the Expression of the NONRACE-SPECIFIC DISEASE RESISTANCE1/HARPIN-INDUCED1-LIKE13 Gene Required for Antibacterial Immunity in Arabidopsis., Plant Physiology, pp.00547.2015 PDF

19. Peng J, Uygun S, Kim T, Wang Y*, Rhee SY* and Chen J*. Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. BMC Bioinformatics, 2015, 16:44. PDF (NETSIM website) Highly Accessed

20. Weraduwage SM, Chen J, Anozie FC, Morales A, Weise SE, Sharkey TD, The Relationship between Leaf Area Growth and Biomass Accumulation in Arabidopsis thaliana, Frontiers in Plant Science, 2015, 6:167. PDF



2014

21. Peng J, Li X, Jiang Q, Wang Y* and Chen J*. An Integrative Approach for Measuring Semantic Similarities using Gene Ontology, BMC Systems Biology, 2014, 8(Suppl 5): S8 (InteGO2 website) PDF Oral Presentation at GIW 2014 Highly Accessed

22. Peng J, Wang Y* and Chen J*. Towards Integrative Gene Functional Similarity Measurement, BMC Bioinformatics, 2014, 15(Suppl 2):S5 (InteGO website) PDF Oral Presentation at APBC 2014

23. Awad S and Chen J*. Inferring Transcription Factor Collaborations in Gene Regulatory Networks, BMC Systems Biology, 2014, 8(Suppl 1):S1 (mTRIM website) PDF Oral Presentation at APBC 2014

24. Jones AM, Lalonde S, Ho CH, Xu M, Wang RS, Xuan Y, You CH, Sardi MI, Parsa SA, Smith-Valle E, Su T, Frazer KA, Pilot G, Pratelli R, Grossmann G, Acharya BR, Hu HC, Engineer C, Villiers F, Ju C, Takeda K, Su Z, Dong Q, Assmann SM, Chen J, Kwak JM, Schroeder JI, Albert R, Rhee SY and Frommer WB. Border Control - A Membrane-linked Interactome of Arabidopsis. Science, 2014, 344(6185): 711-716 PDF Highly Accessed

25 Yin X, Liu X, Chen J and Kramer DM. Multi-leaf Tracking from Fluorescence Plant Videos, proceedings of IEEE International Conference on Image Processing (ICIP 2014), Paris, France, Oct. 2014. PDF Top Paper Award

26. Yin X, Liu X, Chen J, Kramer DM. Multi-leaf Alignment from Fluorescence Plant Images, proceedings of the IEEE Winter Conference on Applications of Computer Vision (WACV 2014), Steamboat Springs, March 2014. (LeafAlignment website) PDF Best Student Paper Award

27. Noble S, Wawrousek K, Korlach J, Chen J, Eckert C, Yu J and Maness PC. Genome annotation provides insight into the carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus. PLOS One 2014, DOI: 10.1371/journal.pone.0114551 PDF

28. Panchy N, Wu G, Newton L, Tsai CH, Chen J, Benning C, Farre E and Shui SH. Evolution of the Diurnal, Prevalence, Evolution, and cis-Regulation of Diel Transcription in Chlamydomonas reinhardtii, G3: Genes, Genomes, Genetics, 2014, 4(12): 2461-2471 PDF

29. Attaran E, Major IT, Cruz JA, Rosa BA, Koo AJK, Chen J, Kramer DM, He SY and Howe GA. Temporal Dynamics of Growth and Photosynthesis Suppression in Response to Jasmonate Signaling, Plant Physiology, 2014, 165(3): 1302-1314 PDF

30. Pattanaik B, Busch AUW, Hu P, Chen J, Montgomery BL. Responses to Iron Limitation are Impacted by Light Quality and Regulated by RcaE in the Chromatically Acclimating Cyanobacterium Fremyella diplosiphon, Microbiology, 160(5): 992-1005, 2014. PDF Editor's Choice

31. Jiao Y, Chen L and Chen J*. Data Acquisition and Preprocessing on Three Dimensional Medical Images. (Li X and Ng SK Eds.) Biological Data Mining and its Applications in Healthcare, World Scientific, ISBN: 978-981-4551-00-7, 2014 PDF



2013

32. Rosa BA, Zhang J, Major I, Qin W* and Chen J*. Knowledge-based Optimal Timepoint Sampling in High-Throughput Temporal Experiments. Bioinformatics, 2012, 28(21):2773-2781. (OTS website) PDF Highlighted at ACM BCB 2013 Highly Accessed

33. Tessmer OL^, Jiao Y^, Cruz JA, Kramer DM* and Chen J*. Functional Approach to High-throughput Plant Growth Analysis. BMC Systems Biology, 2013, 7(Suppl 6):S17 (HPGA website) PDF Oral Presentation at GIW 2013 Highly Accessed

34. Peng J, Chen J*, Wang Y*. Identifying Cross-category Relations in Gene Ontology and Constructing Genome-specific Term Association Networks. BMC Bioinformatics 2013, 14(Suppl 2):S15 (CroGO website) PDF Oral Presentation at APBC 2013

35. Huang P, Liu CJ, Xiao L, Chen J. Wireless Spectrum Occupancy Prediction with Partial Periodic Pattern Mining. IEEE Transactions on Parallel and Distributed Systems, 2013, (25): 1925-1934 PDF Highly Accessed



2012

36. Jiao Y^, Rosa BA^, Oh S, Montgomery B, Qin W*, Chen J*. Detection and Decomposition: Treatment-induced Cyclic Gene Expression Disruption in High-throughput Time-series Datasets. Journal of Bioinformatics and Computational Biology, 10(6): 1271002, 2012 PDF

37. Rosa BA^, Jiao Y^, Oh S, Montgomery B, Qin W*, Chen J*. Frequency-based time-series gene expression recomposition using PRIISM. BMC Systems Biology, 6:69, 2012 (PRIISM website) PDF

38. Awad S, Panchy N, Ng SK, Chen J*. Inferring the Regulatory Interaction Models of Transcription Factors in Transcriptional Regulatory Networks. Journal of Bioinformatics and Computational Biology. 10(5):1250012, 2012 (TRIM website) PDF

39. Chen J*, Lalonde S, Obrdlik P, Vatani AN, Parsa SA, Vilarino V, Revuelta JL, Frommer WB, Rhee SY*. Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. Frontiers in Plant Physiology, 3:124, 2012 PDF Highly Accessed

40. Hu P, Lang J, Wawrousek K, Yu J, Maness P, Chen J*. Draft genome sequence of Rubrivivax gelatinosus CBS. Journal of Bacteriology, 194(12):3262. 2012 (SEQUENCES) PDF

41. Huang P, Liu CJ, Xiao L, Chen J. Wireless Spectrum Occupancy Prediction with Partial Periodic Pattern Mining. proceedings of 20th IEEE International Symposium on Modelling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS 2012), pp. 51-58, Arlington, VA, Aug. 2012 PDF



2011 and older

42. Kramer D, Cruz J, Hall C, Kovac W, Chen J, Jiao Y, Zegarac R. Plant Phenometrics Platform (PPP) Dynamic, Developmental and Environmental Plant Phenometrics. 2011, States, U., Ed. PDF

43. Lalonde S, Sero A, Pratelli R, Pilot G, Chen J, Sardi M, Parsa S, Kim DY, Acharya B, Stein E, Hu HC, Villiers F, Takeda K, Yang Y, Han Y, Schwacke R, Chiang W, Kato N, Loque D, Assmann S, Kwak J, Schroeder J, Rhee S, Frommer W. A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2. Frontiers in Plant Physiology, 1(24):1-14, 2010 PDF

44. Rosa, BA, Oh, S, Montgomery, BL, Chen, J*, Qin, W*. Computing gene expression data with a knowledge-based gene clustering approach. International Journal of Biochemistry and Molecular Biology 1(1):51-68. 2010 PDF

45. Chen J, Ji LP, Hsu W, Tan KL, Rhee S. Exploiting domain knowledge to improve biological significance of bi-clusters with key missing genes, proceedings of 25th IEEE Intl Conf Data Engineering (ICDE 2009), pp. 1219-1222, Shanghai, China, Mar. 2009 PDF

46. Lalonde S, Ehrhardt D, Loque D, Chen J, Rhee S, Frommer W. Molecular and cellular approaches for the detection of protein-protein interactions: Latest Techniques and Current Limitations Plant Journal, 53(4):610-635, 2008 PDF Highly Accessed

47. Chen J, Hsu W, Lee ML, Ng SK. Labeling network motifs in protein interactomes for protein function prediction, proceedings of 23rd IEEE Intl Conf Data Engineering (ICDE 2007), pp. 546-555, Istanbul, Turkey, Apr. 2007 PDF Highly Accessed

48. Chen J, Chua HN, Hsu W, Lee ML, Ng SK, Saito R, Sung WK, Wong L. Increasing confidence of protein-protein interactomes. Proceedings of 17th Intl Conf Genome Informatics (GIW 2006), pp. 284-297, Yokohama, Japan, Dec.2006 PDF Keynote

49. Chen J, Hsu W, Lee ML, Ng SK. Increasing confidence of protein interactomes using network topological metrics, Bioinformatics 22(16):1998-2004, 2006 (IRAP* website) PDF Highly Accessed

50. Chen J, Hsu W, Lee ML, Ng SK. NeMoFinder: Dissecting genome-wide protein-protein interactions with meso-scale network motifs, proceedings of 12th ACM SIGKDD Intel Conf Knowledge Discovery and Data Mining (SIGKDD 2006), pp. 106-115, Philadelphia, Aug. 2006 PDF Highly Accessed

51. Chen J, Hsu W, Lee ML, Ng SK. Discovering reliable protein interactions from high-throughput experimental data using network topology, Artificial Intelligence in Medicine, Special Issue on Computational Intelligence Techniques in Bioinformatics, 35(1-2):37-47, 2005 PDF

52. Chen J, Hsu W, Lee ML, Ng SK. Systematic assessment of high-throughput experimental data for reliable protein interactions using network topology, proceedings of 16th IEEE Intl Conf Tools with Artificial Intelligence (ICTAI 2004), pp. 368-372, Boca Raton, Nov. 2004 PDF

53. Chen J, Hsu W, Lee ML. Order-sensitive clustering for remote homologous protein detection, proceedings of 15th IEEE Intl Conf Tools with Artificial Intelligence (ICTAI 2003), pp. 26-30, Sacramento, Nov. 2003 PDF

54. Chen J. Distributed digital libraries, Jiangsu Electrical Engineering, 2001 (in Chinese)

55. Chen J. Lotus Domino server management, Official Automation, (1):47-49, 1999 (in Chinese) PDF


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