James A. Eddy - Publications

Affiliations: 
2007-2012 Bioengineering University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 

23 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Samal A, Craig JP, Coradetti ST, Benz JP, Eddy JA, Price ND, Glass NL. Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa. Biotechnology For Biofuels. 10: 225. PMID 28947916 DOI: 10.1186/s13068-017-0901-2  0.72
2016 Allen M, Carrasquillo MM, Funk C, Heavner BD, Zou F, Younkin CS, Burgess JD, Chai HS, Crook J, Eddy JA, Li H, Logsdon B, Peters MA, Dang KK, Wang X, et al. Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases. Scientific Data. 3: 160089. PMID 27727239 DOI: 10.1038/sdata.2016.89  0.72
2015 Eddy JA, Funk CC, Price ND. Fostering synergy between cell biology and systems biology. Trends in Cell Biology. PMID 26013981 DOI: 10.1016/j.tcb.2015.04.005  0.72
2015 Chakrabarty P, Li A, Ceballos-Diaz C, Eddy JA, Funk CC, Moore B, DiNunno N, Rosario AM, Cruz PE, Verbeeck C, Sacino A, Nix S, Janus C, Price ND, Das P, et al. IL-10 alters immunoproteostasis in APP mice, increasing plaque burden and worsening cognitive behavior. Neuron. 85: 519-33. PMID 25619653 DOI: 10.1016/j.neuron.2014.11.020  0.72
2013 Wang C, Funk CC, Eddy JA, Price ND. Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas. Plos One. 8: e76694. PMID 24146911 DOI: 10.1371/journal.pone.0076694  0.72
2013 Earls JC, Eddy JA, Funk CC, Ko Y, Magis AT, Price ND. AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. Bmc Bioinformatics. 14: 78. PMID 23496976 DOI: 10.1186/1471-2105-14-78  0.72
2013 Ko Y, Ament SA, Eddy JA, Caballero J, Earls JC, Hood L, Price ND. Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. 110: 3095-100. PMID 23386717 DOI: 10.1073/pnas.1222897110  0.72
2012 Wang Y, Eddy JA, Price ND. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. Bmc Systems Biology. 6: 153. PMID 23234303 DOI: 10.1186/1752-0509-6-153  0.72
2012 Sangar V, Eddy JA, Simeonidis E, Price ND. Mechanistic modeling of aberrant energy metabolism in human disease. Frontiers in Physiology. 3: 404. PMID 23112774 DOI: 10.3389/fphys.2012.00404  0.72
2012 Yang JL, Cogdell D, Eddy J, Trent J, Price N, Zhang W. [Expression of PRUNE2 mRNA and its positive correlation with non-coding RNA PCA3 in leiomyosarcoma]. Zhonghua Zhong Liu Za Zhi [Chinese Journal of Oncology]. 34: 497-500. PMID 22967466 DOI: 10.3760/cma.j.issn.0253-3766.2012.07.005  0.72
2011 Chandrasekaran S, Ament SA, Eddy JA, Rodriguez-Zas SL, Schatz BR, Price ND, Robinson GE. Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states. Proceedings of the National Academy of Sciences of the United States of America. 108: 18020-5. PMID 21960440 DOI: 10.1073/pnas.1114093108  0.72
2011 Milne CB, Eddy JA, Raju R, Ardekani S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. Bmc Systems Biology. 5: 130. PMID 21846360 DOI: 10.1186/1752-0509-5-130  0.96
2011 Magis AT, Earls JC, Ko YH, Eddy JA, Price ND. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics (Oxford, England). 27: 872-3. PMID 21257608 DOI: 10.1093/bioinformatics/btr033  0.72
2010 Edelman LB, Eddy JA, Price ND. In silico models of cancer. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 438-59. PMID 20836040 DOI: 10.1002/wsbm.75  0.72
2010 Yang J, Eddy JA, Pan Y, Hategan A, Tabus I, Wang Y, Cogdell D, Price ND, Pollock RE, Lazar AJ, Hunt KK, Trent JC, Zhang W. Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug. Molecular & Cellular Proteomics : McP. 9: 2405-13. PMID 20651304 DOI: 10.1074/mcp.M110.000240  0.72
2010 Eddy JA, Hood L, Price ND, Geman D. Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). Plos Computational Biology. 6: e1000792. PMID 20523739 DOI: 10.1371/journal.pcbi.1000792  0.72
2010 Eddy JA, Sung J, Geman D, Price ND. Relative expression analysis for molecular cancer diagnosis and prognosis. Technology in Cancer Research & Treatment. 9: 149-59. PMID 20218737 DOI: c4306/Relative-Expression-Analysis-for-Molecular-Cancer-Diagnosis-and-Prognosis-149-160-p17776.html  0.72
2009 Eddy JA, Geman D, Price ND. Relative expression analysis for identifying perturbed pathways. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 5456-9. PMID 19964680 DOI: 10.1109/IEMBS.2009.5334063  0.72
2009 Milne CB, Kim PJ, Eddy JA, Price ND. Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnology Journal. 4: 1653-70. PMID 19946878 DOI: 10.1002/biot.200900234  0.72
2008 Lee JM, Min Lee J, Gianchandani EP, Eddy JA, Papin JA. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. Plos Computational Biology. 4: e1000086. PMID 18483615 DOI: 10.1371/journal.pcbi.1000086  0.72
2008 Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA. Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Molecular Systems Biology. 4: 177. PMID 18364711 DOI: 10.1038/msb.2008.15  0.72
2008 Lee JM, Gianchandani EP, Eddy JA, Papin JA. Application of a novel optimization-based approach to characterize integrated signalling, regulatory Ifac Proceedings Volumes (Ifac-Papersonline). 17. DOI: 10.3182/20080706-5-KR-1001.2567  0.72
2008 Eddy JA, Geman D, Price ND. Pathway expression rank analysis (p-xray): A novel tool for gene set expression analysis Aiche Annual Meeting, Conference Proceedings 0.72
Show low-probability matches.