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Our lab is focused on using quantitative approaches, from disciplines such as computer science and applied mathematics, to address fundamental questions in molecular biology.
In particular, we are interested in deciphering the human genetic blueprint, modeling complex biological systems such as biomolecular networks and pathways, and facilitating drug discovery and development. We have a special focus on developing computational tools to unravel the molecular mechanism of human diseases, especially pediatric cancer, cardiovascular and pulmonary diseases. We would welcome any suggestions on initiating collaborations.
Our research emphasizes the structural and functional aspects of biomolecules through modeling and simulation. We exploit diverse sources of genomic databases by integration and comparison.
For additional information visit Dr. Lu's externally hosted lab website.
Li H, Gordon S, Zhu X, Deng J, Swertfeger D, Davidson WS, Lu LJ. Network-based analysis on orthogonal separation of human plasma uncovers distinct high density lipoprotein complexes. J Proteome Res. 2015. In press.
Heink A, Davidson WS, Swertfeger D, Lu LJ, Shah A. A Comparison of Methods to Enhance Protein Detection of Lipoproteins by Mass Spectrometry. J Proteome Res. 2015 Jul 2;14(7):2943-50.
Lu Y, Lu Y, Deng J, Peng H, Lu H, Lu L. A novel essential domain perspective for exploring gene essentiality. Bioinformatics. 2015 May 22. [Epub ahead of print]
Gordon S, Li H, Zhu X, Shah A, Lu LJ, Davidson WS. A comparison of the mouse and human lipoproteome: Suitability of the mouse model for studies of human lipoproteins. J Proteome Res. 2015 Jun 5;14(6):2686-95.
DeFranco E, Hall E, Hossain M, Chen A, Haynes EN, Jones D, Ren S, Lu L, Muglia L. Air pollution and stillbirth risk: exposure to airborne particulate matter during pregnancy is associated with fetal death. PLoS One. 2015;10(3):e0120594.
Lu Y, Deng J, Rhodes J, Lu H, Lu LJ. Predicting essential genes for identifying potential drug targetsin Aspergillus fumigatus. Comput Biol Chem. 2014 Jun;50:29-40.
Krishnan K, Ren Z, Losada L, Nierman WC, Lu LJ, Askew DS. Polysome profiling reveals broad translatome remodeling during endoplasmic reticulum (ER) stress in the pathogenic fungus Aspergillus fumigatus. BMC Genomics. 2014 Feb 25;15:159.
Tan L, Chen Y, Maloney TC, Care MM, Holland SK, Lu LJ. Combined analysis of sMRI and fMRI imaging data provides accurate disease markers for hearing impairment. Neuroimage Clin. 2013 Oct 11;3:416-28.
Chen Y, Storrs J, Tan L, Mazlack LJ, Lee JH, Lu LJ. Detecting brain structural changes as biomarker from Magnetic Resonance images using a local feature based SVM approach. J Neurosci Methods. 2014 Jan 15;221:22-31.
Gordon SM, Deng J, Tomann AB, Shah AS, Lu LJ, Davidson WS. Multi-dimensional co-separation analysis reveals protein-protein interactions defining plasma lipoprotein subspecies. Mol Cell Proteomics. 2013 Nov;12(11):3123-34.
Green JV, Orsborn KI, Zhang M, Tan QKG, Greis KD, Porollo A, Andes DR, Lu LJ, Hostetter MK. Heparin binding motifs and biofilm formation by Candida albicans. J Infect Dis. 2013 Nov 15;208(10):1695-704.
Gordon SM, Davidson WS, Urbina EM, Dolan LM, Heink A, Zang H, Lu LJ, Shah AS. The effects of type 2 diabetes on lipoprotein composition and arterial stiffness in male youth. Diabetes. 2013 Aug;62(8):2958-67.
Shah AS, Tan L, Long JL, Davidson WS. The proteomic diversity of high density lipoproteins: Our emerging understanding of its importance in lipid transport and beyond. J Lipid Res. 2013 Oct;54(10):2575-85.
Deng J, Su S, Lin X, Hassett DJ, Lu LJ. A statistical framework for improving genomic annotations of prokaryotic essential genes. PLoS One. 2013;8(3):e58178.
Lu Y, Deng J, Carson MB, Lu H, Lu LJ. Computational methods for the prediction of microbial essential genes. Current Bioinformatics. 2013;9(2):89-101.
Zhang M, Su S,Bhatnagar RK,Hassett DJ, Lu LJ. Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PLoS One. 2012;7(7):e41202.
Deng J, Tan L, Lin X, Lu Y, Lu LJ. Exploring the optimal strategy to predict essential genes in microbes. Biomolecules. 2012;2:1-22.
Chen Y, Mazlack LJ, Lu LJ. Inferring fuzzy cognitive map models for gene regulatory networks from gene expression data. 2012 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2012). October 4-7, 2012, Philadelphia, USA. 598-601.
Chen Y, Mazlack LJ, Lu LJ. Fuzzy cognitive maps development using ant colony optimization with local search procedure. Proceedings of the 2012 Annual Meeting of the North American Fuzzy Information Processing Society (NAFIPS 2012). August 6-8, 2012, Berkeley, USA. 1-6. †Best student paper finalist
Chen Y, Mazlack LJ, Lu LJ. Learning fuzzy cognitive maps from data by Ant Colony Optimization. Proceedings of the 14th International Conference on Genetic and Evolutionary Computation (GECCO 2012). July 7-11, 2012, Philadelphia, USA.9-16. †Best paper award runner-up in ACO-SI track.
Zhang M, Deng J, Tan L, Chen Y, Lu LJ. Network analysis and applications in pediatric diseases. Pediatric Biomedical Informatics. Chapter 15: 265-285. 2012.
Feng X, Krishnan K, Richie DL, Aimanianda V, Hartl L, Grahl N, Powers-Fletcher MV, Zhang M, Fuller KK, Nierman WC,Lu LJ, Latge JP, Woollett L, Newman SL, Cramer RA Jr, Rhodes JC, Askew DS. HacA-independent functions of the ER stress sensor IreA synergize with the canonical UPR to influence virulence traits in Aspergillus fumigatus. PLoS Pathog. 2011 Oct;7(10):e1002330.
Ren J, Jegga AG, Zhang M, Deng J, Liu J, Gordon CB, Aronow BJ, Lu LJ, Zhang B, Ma J. A Drosophila model of the neurodegenerative disease SCA17 reveals a role of RBP-J/Su(H) in modulating the pathological outcome. Hum Mol Genet. 2011 Sep 1;20(17):3424-36.
Zhang M, Zhu C, Lu LJ, Jegga AG. The orphan disease networks. Am J Hum Genet. 2011 Jun 10;88(6):755-66.
Zhang M, Fang CV, Xu Y, Bhatnagar R, Lu LJ. An integrative scoring approach to identify transcriptional regulations controlling lung surfactant homeostasis. Proceedings of the 10th IEEE International Conference on Data Mining (ICDM) Workshops. December 2010, Sydney, Australia. 787-792.
Fang CV, Zhang M, Ralescu A, Lu LJ. Curve profiling feature: Novel compact representation for Drosophila embryonic gene expression pattern mining. Proceedings of the 10th IEEE International Conference on Data Mining (ICDM) Workshops. December 2010, Sydney, Australia. 695-702.
Zhang M, Deng J, Fang C, Zhang X, Lu LJ. Biomolecular network analysis and applications. Knowledge-Based Bioinformatics. 11: 253-288. 2010.
Zhang M, Lu LJ. Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics. 2010 Sep 16;11:466.
Deng J, Deng L, Su S, Zhang M, Lin X, Wei L, Minai A, Hassett DJ, Lu LJ. Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res. 2011 Feb;39(3):795-807.
Gordon SM, Deng J, Lu LJ, Davidson SW. Proteomic characterization of human plasma high density lipoprotein fractionated by gel filtration chromatography. J Proteome Res. 2010 Oct 1;9(10):5239-49.
He F, Wen Y, Cheung D, Deng J, Lu LJ, Jiao R, Ma J. Distance measurements via the morphogen gradient ofBicoid in Drosophila embryos. BMC Dev Biol. 2010 Aug 2;10:80.
Xu Y, Zhang M, Wang Y, Dave V, Kadambi P, Lu LJ, Whitsett J. A systems approach to mapping transcriptional networks controlling surfactant homeostasis. BMC Genomics. 2010 Jul 26;11:451.
Deng J, Wang W, Lu LJ, Ma J. A two-dimensional simulation model of the Bicoid gradient in Drosophila. PLoS One. 2010 Apr 21;5(4):e10275.
Gordon S, Durairaj A, Lu LJ, Davidson WS. High-Density Lipoprotein Proteomics: Identifying New Drug Targets and Biomarkers by Understanding Functionality. Curr Cardiovasc Risk Rep. 2010;4(1):1-8.
He F, Wen Y, Deng J, Lin X, Lu LJ, Jiao R, Ma J. Probing intrinsic properties of a robust morphogen gradient in Drosophila. Dev Cell. 2008 Oct;15(4):558-67.
Huang YJ, Hang D, Lu LJ, Gerstein MB, Montelione GT. Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics. 2008 Oct;7(10):2048-60.
Lu LJ, Sboner A, Huang YJ, Lu HX, et al. Comparing classical pathways and modern networks: Towards the development of an edge ontology. Trends Biochem Sci. 2007 Jul;32(7):320-31.
Wu L, Hwang S†, Rezaul K†, Lu LJ†, Mayya V, Gerstein M, Eng JK, Lundgren DH, Han DK. Global survey of human T leukemic cells by integrating proteomic and transcriptomic profiling. Mol Cell Proteomics. 2007 Aug;6(8):1343-53. † Contribute Equally
Flores SC, Lu LJ, Yang J, Carriero N, Gerstein MB. Hinge Atlas: Relating protein sequence to sites of structural flexibility. BMC Bioinformatics. 2007 May 22;8:167.
Kim PM, Lu LJ, Xia Y, Gerstein MB. Relating three-dimensional structures to protein networks provides evolutionary insights. Science. 2006 Dec 22;314(5807):1938-41.
Xia Y, Lu LJ, Gerstein MB. Integrated prediction of the helical membrane protein interactome in yeast. J Mol Biol. 2006 Mar 17;357(1):339-49.
Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu E, Thorpe M, Gerstein MB. The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D296-301.
Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein MB. Assessing the limits of genomic data integration for predicting protein networks. Genome Res. 2005 Jul;15(7):945-53.
Lu LJ, Xia Y, Yu H, Rives A, Lu H, Schubert F, Gerstein MB. Protein interaction prediction by integrating genomic features and protein interaction network analysis. Data Analysis and Visualization in Genomics and Proteomics. 2005;5: 61-81.
Lu L, Arakaki AK, Lu H, Skolnick J. Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae. Genome Res. 2003 Jun;13(6A):1146-54.
Lu H, Lu L, Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys J. 2003 Mar;84(3):1895-901.
Lu L, Lu H, Skolnick J. MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins. 2002 Nov 15;49(3):350-64.
Long “Jason” Lu, PhDDivision of Biomedical Informatics3333 Burnet Ave.MLC 7024Cincinnati, OH 45229-3039Phone: 513-636-8720Fax: 513-636-2056E-mail: firstname.lastname@example.org
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