Peer Reviewed Publications


1. 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, 2015, in press

2. 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) Highlight Talk at ACM BCB 2015

3. Peng J, Wang T, Hu J, Wang YD*, Chen J*, Constructing organelle association network in Arabidopsis thaliana, Current Genomics, 2015, in press

4. 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, in press

5. 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, 2015, in press

6. 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’15), 2015, in press PDF

7. 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’15), 2015, (demo paper) in press PDF

8. Xu X, Wang W, Lu J, Chen J*. Incremental Distributed Weighted Class Discriminant Analysis on Interval-Valued Emitter Parameters, proceedings of the 8th International Conference on Knowledge Science, Engineering and Management (KSEM’15), 2015, in press

9. 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 AvrE localizes to the host plasma membrane and down-regulates the expression of the NDR/HIN1-like 13 gene required for antibacterial immunity in Arabidopsis, Plant Physiology, pp.00547.2015 PDF

10. 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

11. 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, in press. PDF (InteGO2 website) Oral Presentation at ISBRA2015

12. 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


13. 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

14. 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

15. 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

16. 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

17 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

18. 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

19. 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

20. 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

21. 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

22. 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


23. 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 Highlight Talk at ACM BCB 2013

24. 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

25. 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

26. 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, 2013 PDF

27. 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


28. 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

29. 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

30. 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

31. 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

32. 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

33. 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’12), pp. 51-58, Arlington, VA, Aug. 2012 PDF


34. 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


35. 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, Loqué 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, Vol.1 Num 24, pp. 1-14, 2010 PDF

36. 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

2009 and older

37. 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

38. 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, Vol. 53, Num. 4, pp. 610-635, 2008 PDF

39. 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

40. 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 Paper

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

42. 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

43. 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, Vol. 35, Issue 1-2, pp. 37-47, 2005 PDF

44. 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

45. 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

Last edit on Aug 12 2015 by Jin Chen