Peer-Reviewed Journal Papers

48. Melchior JT, Street SE, Andraski AB, Furtado JD, Sacks FM, Shute RL, Greve EI, Swertfeger DK, Li H, Shah AS, Lu LJ, and Davdison WS (2017). Apolipoprotein A-II alters the proteome of human lipoproteins and enhances cholesterol efflux from ABCA1. Journal of Lipid Research. in press. [PDF]

47. Swertfeger DK, Li H, Rebholz S, Zhu X, Shah AS, Davidson WS, and Lu LJ (2017). Mapping atheroprotective functions and related proteins/lipoproteins in size fractionated human plasma. Molecular & Cellular Proteomics. 16(4): 680-693 [PDF]

46. Li L, Fang Z, Zhou J, Chen H, Hu Z, Gao L, Chen L, Ren S, Ma H, Lu L, Zhang W, and Peng H (2017). An accurate and efficient method for large-scale SSR genotyping and applications. Nucleic Acids Research. in press [PDF]

45. Gordon SM, Li H, Zhu X, Tso P, Reardon CA, Shah AS, Lu LJ, and Davidson WS (2016). Impact of genetic deletion of platform apolipoproteins on the size distribution of the murine lipoproteome. Journal of Proteomics. 146:184-94. [PDF]

44. Deshpande AK, Tan L, Lu LJ, Altaye M, and Holland SK (2016). fMRI as a Preimplant Objective Tool to Predict Postimplant Oral Language Outcomes in Children with Cochlear Implants. Ear and Hearing. 37(4):e263-72. [PDF]

43. Chen Y, Mazlack L, Minai AA, and Lu LJ (2015). Inferring causal networks using Fuzzy Cognitive Maps and evolutionary algorithms with application to gene regulatory network reconstruction. Applied Soft Computing. 37: 667-679. [PDF]

42. Tan L, Holland S, Deshpande A, Chen Y, Choo D, and Lu LJ (2015). A semi-supervised SVM model for predicting the language outcomes following cochlear implantation based on pre-implant brain fMRI imaging. Brain and Behavior. 5(12):e00391. [PDF] [NPR News] [Science Daily]

41. Cai WF, Liu GS, Lam CK, Florea S, Qian J, Zhao W, Pritchard T, Haghighi K, Lebeche D, Lu LJ, Deng J, Fan GC, Hajjar RJ, Kranias EG. (2015) Up-regulation of micro-RNA765 in human failing hearts is associated with post-transcriptional regulation of protein phosphatase inhibitor-1 and depressed contractility. European Journal of Heart Failure. 17(8): 782-793. [PDF]

40. Ren S, Hinzman AA, Kang EL, Szczesniak RD and Lu LJ (2015) Computational and statistical analysis of metabolomics data. Metabolomics. 11(6): 1492-1513. [PDF] [2016 Best Review Award]

39. Li H, Gordon S, Zhu X, Deng J, Swertfeger D, Davidson WS, and Lu LJ (2015) Network-based analysis on orthogonal separation of human plasma uncovers distinct high density lipoprotein complexes. Journal of Proteome Research. 14(8): 3082-3094. [PDF] [Pediatric Insights Newsletter] [Research Horizons]

38. Heink A, Davidson WS, Swertfeger D, Lu LJ, and Shah A (2015) A Comparison of Methods to Enhance Protein Detection of Lipoproteins by Mass Spectrometry. Journal of Proteome Research. 14(7): 2943-2950. [PDF]

37. Lu Y, Lu Y, Deng J, Peng H, Lu H, and Lu LJ (2015) A novel essential domain perspective for exploring gene essentiality. Bioinformatics. 31(18): 2921-9. [PDF]

36. Gordon S, Li H, Zhu X, Shah A, Lu LJ, Davidson WS (2015) A comparison of the mouse and human lipoproteome: Suitability of the mouse model for studies of human lipoproteins. Journal of Proteome Research. 14(6): 2686-2695. [PDF]

35. DeFranco E, Hall E, Hossain M, Chen A, Haynes EN, Jones D, Ren S, Lu LJ and Muglia L (2015) Air pollution and stillbirth risk: exposure to airborne particulate matter during pregnancy is associated with fetal death. PLoS One. 10(3):e0120594. [PDF]

34. Lu Y, Deng J, Rhodes J, Lu H, and Lu LJ (2014). Predicting essential genes for identifying potential drug targetsin Aspergillus fumigatus. Computational Biology and Chemistry. 50:29-40 [PDF]

33. Krishnan K, Ren Z, Losada L, Nierman WC, Lu LJ and Askew DS (2014). Polysome profiling reveals broad translatome remodeling during endoplasmic reticulum (ER) stress in the pathogenic fungus Aspergillus fumigatus. BMC Genomics. 15:159 [PDF]

32. Tan L, Chen Y, Maloney TC, Care MM, Holland SK and Lu LJ (2013). Combined analysis of sMRI and fMRI imaging data provides accurate disease markers for hearing impairment. NeuroImage: Clinical. 3:416-28. [PDF]

31. Chen Y, Storrs J, Tan L, Mazlack LJ, Lee JH and Lu LJ (2014). Detecting brain structural changes as biomarker from Magnetic Resonance images using a local feature based SVM approach. Journal of Neuroscience Methods. 221C:22-31 [PDF]

30. Gordon SM, Deng J, Tomann AB, Shah AS, Lu LJ and Davidson WS (2013). Multi-dimensional co-separation analysis reveals protein-protein interactions defining plasma lipoprotein subspecies. Molecular & Cellular Proteomics. 12(11):3123-34. [PDF]

29. Green JV, Orsborn KI, Zhang M, Tan QKG, Greis KD, Porollo A, Andes DR, Lu LJ and Hostetter MK (2013). Heparin binding motifs and biofilm formation by Candida albicans. Journal of Infectious Diseases. 208(10):1695-704 [PDF]

28. Gordon SM, Davidson WS, Urbina EM, Dolan LM, Heink A, Zang H, Lu LJ and Shah AS (2013). The effects of type 2 diabetes on lipoprotein composition and arterial stiffness in male youth. Diabetes. 62(8):2958-67. [PDF]

27. Shah AS, Tan L, Long JL and Davidson WS (2013). The proteomic diversity of high density lipoproteins: Our emerging understanding of its importance in lipid transport and beyond. Journal of Lipid Research. 54(10):2575-85. [PDF]

26. Deng J, Su S, Lin X, Hassett DJ and Lu LJ (2013). A statistical framework for improving genomic annotations of prokaryotic essential genes. PLoS One. 8(3):e58178. [PDF]

25. Lu Y, Deng J, Carson MB, Lu H and Lu LJ (2013). Computational methods for the prediction of microbial essential genes. Current Bioinformatics. [Link]

24. Zhang M, Su S, Bhatnagar RK, Hassett DJ and Lu LJ (2012). Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PLoS One. 7(7):e41202. [PDF]

23. Deng JTan L, Lin X, Lu Y and Lu LJ (2012). Exploring the optimal strategy to predict essential genes in microbes. Biomolecules. 2:1-22. [PDF]

22. 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 and Askew DS (2011). HacA-independent functions of the ER stress sensor IreA synergize with the canonical UPR to influence virulence traits in Aspergillus fumigatusPLoS Pathogens. 7(10):e1002330. [PDF]

21. Ren J, Jegga AG, Zhang MDeng J, Liu J, Gordon CB, Aronow BJ, Lu LJ, Zhang B and Ma J (2011). A Drosophila model of the neurodegenerative disease SCA17 reveals a role of RBP-J/Su(H) in modulating the pathological outcome.  Human Molecular Genetics. 20(17):3424-36. [PDF]

20. Zhang M, Zhu C, Lu LJ and Jegga AG (2011). The orphan disease networks.  The American Journal of Human Genetics.  88(6):755-66 [PDF] [News]

19. Zhang M and Lu LJ (2010). Investigating the validity of current network analysis on static conglomerate networks by protein network stratification.  BMC Bioinformatics. 11:466. [PDF]

18. Deng JDeng L, Su S, Zhang M, Lin X, Wei L,L, Minai A, Hassett DJ and Lu LJ (2010). Investigating the predictability of essential genes across distantly related organisms using an integrative approach.  Nucleic Acids Research. 39(3):795-807. [PDF]

17. Gordon SM, Deng JLu LJ and Davidson SW (2010). Proteomic characterization of human plasma high density lipoprotein fractionated by gel filtration chromatography.  Journal of Proteome Research. 9(10): 5239-5249. [PDF]

16. He F, Wen Y, Cheung D, Deng JLu LJ, Jiao R and Ma J (2010). Distance measurements via the morphogen gradient ofBicoid in Drosophila embryos.  BMC Developmental Biology. 10:80. [PDF]

15. Xu Y, Zhang M, Wang Y, Dave V, Kadambi P, Lu LJ and Whitsett J (2010). A systems approach to mapping transcriptional networks controlling surfactant homeostasis.  BMC Genomics. 11:451. [PDF]

14. Deng J, Wang W, Lu LJ and Ma J (2010). A two-dimensional simulation model of the Bicoid gradient in DrosophilaPLoS One. 5(4): e10275. [PDF]

13. Gordon S, Durairaj A, Lu LJ and Davidson WS (2010). HDL proteomics: Identifying new drug targets and biomarkers by understanding functionality.  Current Cardiovascular Risk Report. 4:1-8. [PDF]

12. He F, Wen Y, Deng J, Lin X, Lu LJ, Jiao R and Ma J (2008). Probing intrinsic properties of a robust morphogen gradient inDrosophilaDevelopmental Cell. 15(4):558-67. [PDF]

11. Huang YJ, Hang D, Lu LJ, Gerstein MB, Montelione GT (2008). Targeting the human cancer pathway protein interaction network by structural genomics. Molecular & Cellular Proteomics. 7(10):2048-60. [PDF]

10. Lu LJ, Sboner A, Huang YJ, Lu HX et al. (2007). Comparing classical pathways and modern networks: Towards the development of an edge ontology. Trends in Biochemical Science. 32(7): 320-331. [PDF]

9. Wu L, Hwang S†, Rezaul K†, Lu LJ†, Mayya V, Gerstein M, Eng JK, Lundgren DH and Han DK (2007). Global survey of human T leukemic cells by integrating proteomic and transcriptomic profiling. Molecular & Cellular Proteomics. 6(8): 1343-53. [PDF]           † Contribute Equally

8. Flores SC, Lu LJ, Yang J, Carriero N and Gerstein MB (2007). Hinge Atlas: Relating protein sequence to sites of structural flexibility. BMC Bioinformatics. 8:167. [PDF]

7. Kim PM, Lu LJ, Xia Y and Gerstein MB (2006). Relating three-dimensional structures to protein networks provides evolutionary insights. Science. 314(5807): 1938-41. [PDF][Perspective][Faculty of 1000]  

6. Xia Y, Lu LJ and Gerstein MB (2006). Integrated prediction of membrane helical protein interactions in yeast. Journal of Molecular Biology. 357(1): 339-349. [PDF

5. Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu E, Thorpe M, and Gerstein MB (2006). The database of macromolecular motions: New features added at the decade mark. Nucleic Acids Research. 34:D296-301. [PDF]

4. Lu LJ, Xia Y, Paccanaro A, Yu H and Gerstein MB (2005). Assessing the limits of genomic integration for predicting protein-protein interactions. Genome Research. 15: 945-53. [PDF] [Faculty of 1000

3. Lu L, Arakaki AK, Lu H and Skolnick J (2003). Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiaeGenome Research. 13:1146-1154 [PDF] [Press] [Faculty of 1000] 

2. Lu H, Lu L and Skolnick J (2003). Development of unified statistical potentials describing protein-protein interactions.Biophysical Journal. 84 (3): 1895-901 [PDF]

1. Lu L, Lu H and Skolnick J (2002). MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions bymultimeric threading. Proteins: Structure, Functions, Genetics. 49:350-364 [PDF] [Cover] [Press] [Faculty of 1000]


Peer-reviewed Conference Papers

6. Guo X, Minai A and Lu L (2017). Feature selection using multiple Auto-Encoders. 2017 IEEE International Joint Conference on Neural Networks (IJCNN 2017). May 14-19, 2017, Anchorage, Alaska, USA. [PDF]

5. Chen Y, Mazlack LJ and Lu LJ (2012). 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. [PDF]

4. Chen Y, Mazlack LJ and Lu LJ (2012). 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. [PDF] † Best student paper finalist

3. Chen Y, Mazlack LJ and Lu LJ (2012). 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. [PDF] † Best paper award runner-up in ACO-SI track.

2. Zhang MFang CV, Xu Y, Bhatnagar R and Lu LJ (2010). 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. [PDF]

1. Fang CVZhang M, Ralescu A and Lu LJ (2010). Curve profiling feature: Novel compact representation for Drosophilaembryonic gene expression pattern mining. Proceedings of the 10th IEEE International Conference on Data Mining (ICDM) Workshops. December 2010, Sydney, Australia. 695-702. [PDF]


Book Chapters & Invited Reviews

6. Li H, Ren Z, Ren S, Guo X, Zhu X, and Lu LJ (2016). Network analysis and applications in pediatric diseases. Pediatric biomedical informatics: computer applications in pediatric research. Chapter 13: 251-274. Editor: Hutton, John J. [PDF].

5. Lu Y, Lu Y, Deng J, Lu H and Lu LJ (2015). Discovering essential domains in essential genes. Gene Essentiality. Chapter 15: 235-245. [PDF].

3. Zhang M, Deng J, Tan L, Chen Y and Lu LJ (2012). Network analysis and applications in pediatric diseases. Pediatric Biomedical Informatics. Chapter 15: 265-285. [PDF] [Book Contents]

2. Zhang MDeng JFang C, Zhang X and Lu LJ (2010). Biomolecular network analysis and applications.  Knowledge-Based Bioinformatics. 11: 253-288. [PDF][Book Contents

1. Lu LJ, Xia Y, Yu H, Rives A, Lu H, Schubert F and Gerstein MB (2005). Protein interaction prediction by integrating genomic features and protein interaction network analysis.  Data Analysis and Visualization in Genomics and Proteomics. 5: 61-81. [PDF]



1. Lu LJ (2015). Gene Essentiality. Springer, New York, U.S.A. [Book Contents]


* The average number of times being cited for all peer-reviewed papers that have been published for at least 6 months is 27.6 as of July, 2007. H-Index is 12 as of September 2011.

* Four have been selected among top 10 papers by Faculty of 1000 in the sub-fields of bioinformatics or structural biology.

* The name of my lab member is underscored.

Lu Lab, Division of Biomedical Informatics,Cincinnati Children's Hospital Medical Center