2019
2018
R Liu, JA Dickerson, “Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq,” PLoS Computational Biology, 13(11), e1005851.
D Mistry, RP Wise, JA Dickerson, “DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network,” PloS One, 12(11), e0187091.
2017
JR Walsh, ML Schaeffer, P Zhang, SY Rhee, JA Dickerson, TZ Sen, “The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize,” BMC Systems Biology, 10(1), 1292016.
2016
E Whigham, S Qi, D Mistry, P Surana, R Xu, G Fuerst, C Pliego, LV Bindschedler, PD Spanu, JA Dickerson, D Nettleton, AJ Bogdanove, RP Wise, “Broadly conserved fungal effector BEC1019 suppresses host cell death and enhances pathogen virulence in powdery mildew of barley (Hordeum vulgare L.),” Molecular Plant-Microbe Interactions, Vol 28(9), 968-983; 2015.
2015
R Liu, AE Loraine, JA Dickerson, “Comparisons of computational methods for alternative splicing detection using RNA-seq in plant systems,” BMC Bioinformatics, 15:364, DOI: 10.1186/s12859-014-0364-4.(Google scholar citation count: 29)
JR Walsh, TZ Sen, JA Dickerson, “A Computational Platform to Maintain and Migrate Manual Functional Annotations for Model Organism Databases,” BMC Systems Biology, 8:115, doi:10.1186/s12918-014-0115-1,2014.
2014
E. Marsh, J. Kelly, JA Dickerson, JH Oliver, “Fuzzy Navigation Engine: Mitigating the Cognitive Demands of Semi-Natural Locomotion", Presence: Teleoperators and Virtual Environments,MIT Press, 23(3):300-319 (Special Section: Robots, Virtual Reality and Brain Computer Interfaces in Telepresence), doi:10.1162/PRES_a_00195; 2014.
RP Wise, P Surana, G Fuerst, R Xu, D Mistry, JA Dickerson, D Nettleton, “Flor Revisited (again) eQTL and Mutational Analysis of NB-LRR Mediated Immunity to Powdery Mildew in Barley,” Journal of Integrative Agriculture, 13(2):237-243, 2014, http://dx.doi.org/10.1016/S2095-3119(13)60651-6.
Zhou WG, Dickerson JA, “A novel class dependent feature selection method for cancer biomarker discovery,” Computers in Biology and Medicine, 47(1), 66-75, 2014, http://dx.doi.org/10.1016/j.compbiomed.2014.01.014.
Royce, L, E Boggess, Y. Fu, P. Liu, JV Shanks, J.A. Dickerson, L Jarboe, “Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage,” PLoS ONE, 2014.
2013
P Liu, A Chernyshov, T Najdi, Y Fu, JDickerson, S. Sandmeyer, L Jarboe, “Membrane stress caused by octanoic acid in Saccharomyces cerevisiae,” Applied Microbiology Biotechnology, 97:3239-3251, Springer, 2013, DOI: 10.1007/s00253-013-4773-5.
2012
Blake, V.C., Kling, J.G., Hayes, P.M., Jannink, J., Jillella, S.R.+, Lee, J., Matthews, D.E., Chao, S., Close, T.J., Muehlbauer, G.J., Smith, K.P., Wise, R.P., Dickerson, J.A. 2012. The hordeum toolbox - the barley CAP genotype and phenotype resource. The Plant Genome. DOI: 10.385/plantgenome2012.03.0002.
Grimplet, J., Van Hemert, JL+, Carbonell-Bejerano, P, Diaz-Riquelme, J, Dickerson, JA, Fennell, A, Pezzotti, M., Martinez-Zapater JM, “Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences,” BMC Research Notes, 5:213, 2012; doi:10.1186/1756-0500-5-213.
Xia, T., JS. Tong, SS Rathore, X Gu, JA Dickerson, “Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis,” BMC Systems Biology, 6:19, 2012, doi:10.1186/1752-0509-6-19.
Van Hemert, J.L., J.A. Dickerson, "Discriminating response groups in metabolic and regulatory pathway networks", Bioinformatics, 2012, doi: 10.1093/bioinformatics/bts039.
P. Bais, S.M. Moon-Quanbeck, B.J. Nikolau, J.A. Dickerson, “Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics,” Nucleic Acids Research, 2012 Database Issue, doi: 10.1093/nar/gkr1006.
Quanbeck SMM ,Brachova L ,Campbell AA ,Guan X ,Perera A ,He K ,Rhee SY. ,Bais P , Dickerson J ,Dixon P ,Wohlgemuth G ,Fiehn O ,Barkan L ,Lange BM ,Lee I ,Cortes D ,Salazar C ,Shuman J ,Shulaev V ,Huhman D ,Sumner LW. ,Roth MR. ,Welti R ,Ilarslan H ,Wurtele ES. ,Nikolau BJ. , “Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”,Frontiers in Plant Science, 3:00015, 2012, doi: 10.3389/fpls.2012.00015.
Dash, S., J. Van Hemert, L. Hong, R.P. Wise, J.A. Dickerson, “PLEXdb: gene expression resources for plants and plant pathogens,” Nucleic Acids Research, 2012 Database Issue, Early doi: 10.1093/nar/gkr938.
W.G. Zhou, J.A. Dickerson, “StruLocPred : structure-based Protein Subcellular Localization Prediction Multi-class Support Vector Machine,” International Journal of Data Mining and Bioinformatics, 6(2), 130-143, 2012.
2011
Fu, Y., L.R. Jarboe, J.A. Dickerson, “Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities,” BMC Bioinformatics,12:233, 2011, doi:10.1186/1471-2105-12-233.
Xia, T, Van Hemert, J.L., Dickerson, J.A., “CytoModeler: A tool for bridging large-scale network analysis and dynamic quantitative modeling,” Bioinformatics,doi: 10.1093/bioinformatics/btr150, March, 2011.
2010
Xia, T., Van Hemert, J.L., Dickerson, J.A., “OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data,” Bioinformatics26(23): 2995-2996, doi:10.1093/bioinformatics/btq583, 2010.
Ming J., D. Reiners, E.S. Wurtele, J.A. Dickerson, “MetNetGE: Visualizing Biological Networks in Hierarchical Views and 3D Tiered Layouts,” BMC Bioinformatics2010, 11:469 doi:10.1186/1471-2105-11-469, 2010.
J. Van Hemert, J.A. Dickerson, “PathwayAccess: CellDesigner Plugins for Pathway Datasources,” Bioinformatics, 26 (18): 2345-2346. doi: 10.1093/bioinformatics/btq423, 2010.
J. Van Hemert, J.A. Dickerson, “Monte Carlo Randomization Tests for Large-Scale Abundance Datasets on the GPU,” Computer Methods and Programs in Biomedicine,101(1) 80-86, June 9, 2010.
Preeti Bais, Stephanie M. Moon, Kun He, Ricardo Leitao, Kate Dreher, Tom Walk, Yves Sucaet, Lenore Barkan, Gert Wohlgemuth, Mary R. Roth, Eve Syrkin Wurtele, Philip Dixon, Oliver Fiehn, B. Markus Lange, Vladimir Shulaev, Lloyd W. Sumner, Ruth Welti, Basil J. Nikolau, Seung Rhee, and Julie A. Dickerson, “PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments,” Plant Physiology, pp. 109,DOI:10.1104/pp.109.151027,Feb. 10, 2010. .
Lekha Sreekantan, Kathy Mathiason, Jérôme Grimplet, Karen Schlauch, Julie A. Dickersonand Anne Y. Fennell, ” Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning,” Plant Molecular Biology, E-pub date: 12 Feb, DOI 10.1007/s11103-010-9611-x, 2010. (
2009
Grimplet, J., Cramer, G.R., Dickerson, J.A., Mathiason, K., Van Hemert, J. and Fennell, A.Y.(2009) VitisNet: "Omics" Integration through Grapevine Molecular Networks. PLoS One, 4, e8365.(Google scholar citation count: 76)
Mao, L., Van Hemert, J., Dash, S. and Dickerson, J. (2009) Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics, 10, 346.
El Kaissi, M., Jia, M., Reiners, D., Dickerson, J.and Wurtele, E. (2009) Visualization of Gene Regulatory Networks Lecture Notes in Computer Science, 5876, 909-918.
El Kaissi, M., Jia, M., Dickerson, J., Wurtele, E. and Reiners, D. (2009) Reaction centric layout for metabolic networks. Lecture Notes in Computer Science, 5876, 81-91.
2008
Xia, T., Dickerson, J.A., OmicsViz: Cytoscape plug-in for visualizing omics data across species,” Bioinformatics, 24, 21, 2557-2558, 2008. (Google scholar citation count: 11)
2007
Fiehn O, Sumner LW, Rhee SY, Ward J, Dickerson J, Lange BM, Lane G, Roessner U, Last R, Nikolau B (2007) Minimum reporting standards for plant biology context information in metabolomics studies. Metabolomics 3: 195-201.
Anson Call, Steven Herrnstadt, Eve Wurtele, Diane Bassham, J.A. Dickerson, “MetaBlast! Virtual Cell: A Pedagogical Convergence Between Game Design and Science Education,” Journal of Systemics, Cybernetics, and Informatics, 5(5), 27-31, December, 2007.
2006
Joset A. Etzel, Erica L. Johnsen,J.A. Dickerson, Ralph Adolphs, “Cardiovascular and Respiratory Responses during Musical Mood Induction,” International Journal of Psychophysiology, 2006.
S.Y. Rhee, J.A. Dickerson, D. Xu, “Bioinformatics and Its Applications in Plant Biology,”Annual Review of Plant Biology, 57, 335-359, 2006.
2005
C.M. Helgason, T.H. Jobe, J.A. Dickerson, “Introduction to the Special Section on Fuzzy Logic in Biologic Systems and Medicine,” Special issue of IEEE Transactions on Systems, Man and Cybernetics, Part B,35(6):1326-1327, 2005.
Pan Du+, Jian Gong, Eve Syrkin Wurtele, and J.A. Dickerson,“Modeling Gene Expression Networks using Fuzzy Logic,” Special issue of IEEE Transactions on Systems, Man and Cybernetics, Part B,35(6):1351-1359, 2005. (Google scholar citation count: 57)
Yuting Yang, Levent Engin, Eve Syrkin Wurtele, Carolina Cruz-Neira, J.A. Dickerson, “Integration of metabolic networks and gene expression in virtual reality,” Bioinformatics, 21: 3645-3650.
Ding, J., K. Viswanathan, D. Berleant, L. Hughes, E. S. Wurtele, D. Ashlock, J. A. Dickerson, A. Fulmer and P. S. Schnable (2005). "Using the biological taxonomy to access biological literature with PathBinderH." Bioinformatics21(10): 2560-2562.
2004
Lishuang Shen+, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, J.A. Dickerson, “Barleybase – An Expression Profiling Database For Plant Genomics,” Nucleic Acids Research,33(suppl_1): D614-618, 2004.
Tang, L. Shen,J.A. Dickerson, “BarleyExpress: a web-based submission tool for enriched microarray database annotations,” Bioinformatics,21(3): 399-401, 2005 (pub early access September, 2004).
Timothy J. Close, Steve Wanamaker, Rico A. Caldo, Stacy M. Turner, Daniel A. Ashlock, Julie A. Dickerson, Rod A. Wing, Gary J. Muehlbauer, Andris Kleinhofs, and Roger P. Wise, “A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age,” Plant Physiology, March 2004, Vol. 134, pp. 960-968.
2003
E. S. Wurtele, J. Li, L. Diao, H. Zhang, C. Foster, B. Fatland, J. A. Dickerson, A. Brown, Z. Cox, D. Cook, E.-K. Lee, and H. Hofmann, “MetNet: software to build and model the biogenetic lattice of Arabidopsis,” Comparative and Functional Genomics, vol. 4, pp.239-245, 2003.
2000
P. Sutherland, A. Rossini, T. Lumley, N. Lewin-Koh, J.A. Dickerson, Z. Cox, D. Cook, “Orca: A Visualization Toolkit for High-Dimensional Data,” Journal of Computational and Graphical Statistics, 9, 509-529, 2000.
J. Hong,J.A. Dickerson, “Autonomous Star Identification Using Fuzzy Neural Logic Networks,” Journal of Guidance, Control, and Dynamics. Volume 23, Number 4, 728-735, July-August, 2000.
1997
J. A. Dickerson, C.M. Helgason, “The Characterization of stroke subtype and science of evidence-based medicine using fuzzy logic,” Journal of Neurovascular Disease, Volume 2, Number 4, 138-144,1997.
1996
J. A. Dickerson, B. Kosko, “Fuzzy Function Approximation with Ellipsoidal Rules,” IEEE Transactions on Systems, Man, and Cybernetics, Volume 26, Number 4, 542-560, August 1996.
J. A. Dickerson, H.M. Kim, B. Kosko, “Fuzzy Throttle and brake control for platoons of smart cars,”Fuzzy Sets and Systems,Volume 84, Number 3, 209-234, 1996.
1994
J. A. Dickerson, B. Kosko, “Virtual Worlds as Fuzzy Cognitive Maps,” Presence, Volume 3, Number 2, 173-189, 1994.
J. A. Dickerson, B. Kosko, “Fuzzy Virtual Worlds,” AI Expert, Volume 3, Number 2, 173-189, 1994.