Pan Du

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Research Assistant Professor

Biomedical Informatics Center, NUCATS
Robert H. Lurie Comprehensive Cancer Center
Feinberg School of Medicine
Northwestern University

750 N Lake Shore, 11-176
Chicago IL 60611
Phone: 312-503-2360
email


Pan Du joined the Bioinformatics group at the end of 2005 after receiving his Ph.D. from Iowa State University with co-majors in Bioinformatics and Computational Biology and Electrical Engineering. He was the Research Assistant Professor at the Biomedical Informatics Center of Northwestern University. His job responsibilities include consulting, data analysis, new methodology development and pipeline implementation in Bioinformatics and Computational Biology. His research experience includes all kinds of microarray data analysis (including mRNA, DNA methylation, SNP, CNV and LOH analysis), classification and biomarker identification, NGS analysis (including ChIP, DNA and RNA-seq), multi-level data integration, ontology analysis, proteomics and systems biology. He has developed and maintains three Bioconductor packages: lumi (for Illumina Methylation and Expression microarray data analysis), GeneAnswers (for gene functional analysis and visualization) and MassSpecWavelet (for mass spectrometry based proteomics data analysis). In March 2011, he moved to Genentech as a Senior Computational Biologist.


EDUCATION

• Ph.D. (Dec. 2005), in Bioinformatics and Computational Biology, with co-major in Electrical Engineering, Iowa State University, Ames, IA

• M.S. (Apr. 1998) and B.S. (Jul. 1995), in Electrical Engineering, National University of Defense Technology, China


PROFESSIONAL EXPERIENCE

• Northwestern University, Chicago, IL

11/2007 – 03/2011, Research Assistant Professor,

Biomedical Informatics Center / Robert H. Lurie Comprehensive Cancer Center

12/2005 – 10/2007, Research Associate / Senior Bioinformatics Analyst,

The Robert H. Lurie Comprehensive Cancer Center


• Iowa State University, Ames, IA

2000-2005, Research Assistant, Department of Electrical and Computer Engineering


• National University of Defense Technology, Changsha, China

1995 - 2000, Research Assistant, The Automatic Target Recognition National Lab


PUBLICATIONS

Recent peer reviewed journal publications:

1. Gallant-Behm CL, Du P, Lin SM, Marucha PT, DiPietro LA, and Mustoe TA, “Epithelial regulation of mesenchymal tissue behavior”, accepted by Journal of Investigative Dermatology (Nature Publishing Group)

2. Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, and Lin SM: “Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis”, BMC Bioinformatics 2010, 11:587

3. Desai J, Flatow JM, Song J, Zhu L, Du P, Huang CC, Lu H, Lin SM, and Kibbe WA: “Visual Presentation as a Welcome Alternative to Textual Presentation of Gene Annotation Information”, Adv Exp Med Biol. 2010;680:709-715

4. Co-author (one of the major participants and contributors): “The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.” Nature Biotechnology. 2010 Aug;28 (8):827-38.

5. Benavides MA, Hagen KL, Fang W, Du P, Lin S, Moyer MP, Yang W, Bland KI, Grizzle WE, Bosland MC: “Suppression by L-methionine of cell cycle progression in LNCaP and MCF-7 cells but not benign cells.” Anticancer Res 2010, 30(6):1881-1885.

6. Benavides MA, Hu D, Baraoidan MK, Bruno A, Du P, Lin S, Yang W, Bland KI, Grizzle WE, Bosland MC: “L-methionine-induced alterations in molecular signatures in MCF-7 and LNCaP cancer cells.” J Cancer Res Clin Oncol, 2010.

7. Feng G, Du P, Krett NL, Tessel M, Rosen S, Kibbe WA, Lin SM: “A collection of bioconductor methods to visualize gene-list annotations.” BMC Res Notes 2010, 3:10. (co-first author)

8. Xu F, Du P, Shen H, Hu H, Xie J, Yu L: “Correlated Mutation Analysis on the Catalytic Domains of Serine/Threonine Protein Kinases”, PLoS ONE 4(6): e5913. doi:10.1371

9. Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM: “From Disease Ontology (DO) to Disease-Ontology Lite (DOLite): statistical methods to adapt a general-purpose ontology for the test of gene-disease associations”, Bioinformatics, 2009 Jun 15;25(12):i63-8

10. Shi C, Awad IA, Jafari N, Lin SM, Du P, Hage ZA, Shenkar R, Getch CC, Bredel M, Batjer HH, Bendok BR: “Genomics of human intracranial aneurysm wall”, STROKE 2009 Apr;40(4):1252-61.

11. Lin SM, Du P, Jafari N, and Ouchi T: “Using Free and Open-source Bioconductor Packages to Analyze Array Comparative Genomics Hybridization (aCGH) Data”, Current Genomics, 2009 Vol. 10 (1) pp. 60-63

12. Du P, Lin SM, Yang MQ, Yang JY: “2009 and beyond: the decade of personalized Medicine” International Journal of Computational Biology and Drug Design, 2008, Vol 1 (4): 329-333

13. Lee C, Fu D, Du P, Lin SM, Jiang H, and Kibbe WA: “A Divide-and-conquer Strategy to Solve the Out-of-memory Problem of Processing Thousands of Affymetrix Micorarrays”, International Journal of Computational Biology and Drug Design, 2008, Vol 1(4):396-405

14. Fang F, Flegler AJ, Whitehead JL, Du P, Lin SM, Clevenger CV: “Expression of Cyclophilin B is Associated with Malignant Progression and Regulation of Genes Implicated in the Pathogenesis of Breast Cancer”, The American Journal of Pathology, 2008 Dec 4.

15. Du P, Kibbe WA and Lin SM: “lumi: a Bioconductor package for processing Illumina microarray” Bioinformatics 2008 24(13):1547-1548

16. Maio H, Chen L, Riordan SM, Li W, Juarez S, Crabb AM, Lukas TJ, Du P, Lin SM, Wise A, Agapova OA, Yang P, Gu CC, Hernandez MR: “Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donors”, PLoS ONE. 2008 Aug 6;3(8):e2847

17. Lukas TJ, Miao H, Chen L, Riordan SM, Li W, Juarez S, Crabb AM, Wise A, Du P, Lin SM, Agapova OA, Yang P, Gu CC, Hernandez MR: “Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors.” Genome Biol, 2008. 9(7): p. R111.

18. Lin SM, Du P and Kibbe WA: “Model-based Variance-stabilizing Transformation for Illumina Microarray Data”, Nucleic Acids Res. 2008 36(2):e11 (co-first author)

19. Du P, Kibbe WA and Lin SM: “nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays”, Biology Direct. (2007, 2:16)

20. Du P, Kibbe WA and Lin SM: “Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching”, Bioinformatics, 22, p.p. 2059-2065.

21. Du P, Gong J, Wurtele ES and Dickerson JA: “Modeling gene expression networks using fuzzy logic”, IEEE Trans. on Systems, Man, and Cybernetics, Part B, Vol.35, NO.6, pp. 1351-1359, Dec.2005. (Invited paper)


Recent peer reviewed conference proceeding papers:

• Wang H, Chang Y, Du P, “Application of Framelet Transform to the MS-based Proteomics Data Preprocessing”. BIOCOMP 2008: 379-382

• Lin SM, Du P and Kibbe WA “Large-scale GO analysis reveals gene expression level and variation are functional and location related”, CAMDA 2007, Valencia, Spain, Dec. 13-14, 2007

Du P, Wang H, Lin SM, Kibbe WA (2007), Application of Wavelet Transform to the MS-based Proteomics Data Preprocessing, IEEE 7th International Symposium on BioInformatics and BioEngineering - Proceedings, Cambridge - Boston, Massachusetts, USA, October 14-17, 2007

• Lin SM, Du P and Kibbe WA (2006) QA/QC of Clinical SELDI-TOF Data with Wavelets, Critical Assessment of Microarray Data Analysis 2006, Durham, NC, June 8-9, 2006

• Dickerson JA, Du P, Wurtele ES and Li J, “Fuzzy modeling of metabolic maps in MetNetDB”, Fuzzy Information, 2004. Processing NAFIPS '04. IEEE Annual Meeting, Volume 1, 27-30 June 2004 Page(s):175 - 179 Vol.1

• Yu W, Hu W, Du P, Yuan N: “Modulation characteristics of periodic moving objects” IEEE International Radar Conference - Proceedings, 1999, p.p. 291-294


Book Chapters

• Dickerson JA, Berleant D, Du P, Ding J, Foster C, Li L and Wurtele ES, book chapter of “Medical informatics: knowledge management and data mining in biomedicine”, published by Springer, 2005, ISBN:038724381x, p.p.491-518


Major conference presentations (first author only)

Du P, Huang CC, Zhang X, Navarro A, Jafari N, Bulun S, Kibbe WA, Lin SM: “An open-source pipeline of analyzing Illumina methylation microarray”, ISMB 2010, Boston, MA, July 11-13, 2010

Du P, Lin SM, Feng G, Kibbe WA: “GeneRIFcompendiate: Ranked gene annotations using collective GeneRIF associations and ontology terms”, ISMB 2010, Boston, MA, July 11-13, 2010

Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM, “From Disease Ontology (DO) to Disease-Ontology Lite (DOLite): statistical methods to adapt a general-purpose ontology for the test of gene-disease associations”, ISMB 2009, Stockholm, Sweden, June 27-July 2, 2009 (Oral presentation with paper)

Du P, Lin SM, “Dynamic update and quality assessment of probe-to-gene mapping and its application to Illumina microarrays”, BioC2008 (Bioconductor 2008), Seattle, WA, July 28-29, 2008 (Oral presentation)

Du P, Wang H, Lin SM, Kibbe WA (2007), Application of Wavelet Transform to the MS-based Proteomics Data Preprocessing, IEEE 7th International Symposium on BioInformatics and BioEngineering - Proceedings, Cambridge - Boston, Massachusetts, USA, October 14-17, 2007 (oral presentation with paper)

Du P, Lin SM “Cross-site and cross-platform concordance improved by variance stabilization” at the Quantitative PCR, Microarrays, and Biological Validation conference, in Providence, RI, USA, October 15-17 (oral presentation)

Du P, Lin SM, Kibbe WA, “Towards an Optimized Illumina Microarray Data Analysis Pipeline”, Midwest Symposium on Computational Biology & Bioinformatics 2007, Evanston, IL, October 6, 2007

Du P, Lin SM “Analysis of Illumina Data: The lumi package and the nuID naming scheme for oligonucleotides” BioC2007, Seattle, WA, Aug 6-7, 2007 (oral presentation)

Du P, Lin SM, Zhu J, and Kibbe WA, “Object Model and Analysis of Mass Spectra Data”, BioC2006, Seattle, WA, Aug 3-4, 2006

Du P, “Adopting caGRID Enabled Bioconductor”, caBIG ICR F2F meeting, Boston, MA, Sept 18-19, 2006 (Oral presentation)

Du P, Dickerson JA, “Multi-scale genetic network inference based on time series expression profiles”, ICSB (International Conference of Systems Biology) 2005, Boston, MA, Oct 19-23, 2005

Du P, Dickerson JA, Wurtele ES, Li J, “Genetic network inference and integration with metabolic networks”, at GSAC XVI (16th International Genome Sequence and Analysis Conference), Washington, DC, Sept. 27-30, 2004

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