Lu Lab Publications

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2007 – Present: CCHMC/UC

Deng J, Deng L, Su S, Zhang M, Lin X, Wei 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. (in press)

Gordon SM, Deng J, Lu LJ and Davidson SW (2010) Proteomic Characterization of Human Plasma High Density Lipoprotein Fractionated by Gel Filtration Chromatography. Journal of Proteome Research. (in press) [PDF]

He F, Wen Y, Cheung D, Deng J, Lu LJ, Jiao R and Ma J (2010) Distance Measurements Via the Morphogen Gradient of Bicoid in Drosophila Embryos. BMC Developmental Biology. 10:80 [PDF]

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]

Zhang M, Deng J, Fang C, Zhang X and Lu LJ (2010) Biomolecular Network Analysis and Applications. Knowledge-Based Bioinformatics. 11: 253-288 [PDF][Book Contents].

Deng J, Wang W, Lu LJ and Ma J (2010) A Two-Dimensional Simulation Model of the Bicoid Gradient in Drosophila. PLoS One. 5(4): e10275 [PDF]

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]

He F, Wen Y, Deng J, Lin X, Lu LJ, Jiao R and Ma J (2008) Probing Intrinsic Properties of a Robust Morphogen Gradient in Drosophila. Developmental Cell. 15(4):558-67 [PDF]

2003 – 2007: Yale University

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]

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]

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

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]

Kim PM, Lu LJ, Xia Y and Gerstein M. (2006) Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights. Science. 314(5807): 1938-41 [PDF][Perspective][Faculty of 1000]

Xia Y, Lu LJ and Gerstein M. (2006) Integrated Prediction of Membrane Helical Protein Interactions in Yeast. Journal of Molecular Biology. 357(1): 339-349 [PDF]

Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu E, Thorpe M, and Gerstein M. (2006) The Database of Macromolecular Motions: New Features Added at the Decade Mark. Nucleic Acids Research. 34:D296-301. [PDF]

Lu LJ, Xia Y, Paccanaro A, Yu H and Gerstein M. (2005) Assessing the Limits of Genomic Integration for Predicting Protein-Protein Interactions. Genome Research. 15: 945-53. [PDF] [Faculty of 1000]

Lu LJ, Xia Y, Yu H, Rives A, Lu H, Schubert F and Gerstein M. (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]

Before 2003: Washington University in St. Louis

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 cerevisiae. Genome Research. 13:1146-1154 [PDF] [Press] [Faculty of 1000]

Lu H, Lu L and Skolnick J. (2003) Development of Unified Statistical Potentials Describing Protein-Protein Interactions. Biophysical Journal. 84 (3): 1895-901 [PDF]

Lu L, Lu H and Skolnick J. (2002) MULTIPROSPECTOR: An Algorithm for the Prediction of Protein-Protein Interactions by Multimeric Threading. Proteins: Structure, Functions, Genetics. 49:350-364 [PDF] [Cover] [Press] [Faculty of 1000]

* 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.

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

* The names of my students are underscored.