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Since August 3rd, 2009
Book Chapters
  1. Hong JY, Allegood JC, Kelly S, Wang E, Merrill AH Jr., and Wang MD. Computer visualization models for the de novo sphingolipid biosynthetic pathway. In: Hirabayashi B, Igarashi Y, Merrill AH Jr., editors. Sphingolipid biology. Tokyo: Springer-Verlag; 2006. p. 493-508.
  2. Phan JH, Quo CF, and Wang MD. Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics. Prog Brain Res. 2006; 158: 83-108.
  3. Schmelz EM, Wang MD, Merrill AH Jr. Genomics, proteomics, metabolomics and systems biology approach to nutrition. In: Bowman BA and Russell RM, editors. Present Knowledge in Nutrition. 9th ed. Washington, D.C.: ILSI Press; 2006. p. 3-19.
  4. Moffitt RA and Wang MD. Microarray data analysis. In: Metin A, editor. Wiley Encyclopedia of Biomedical Engineering. John Wiley & Sons, Inc.; 2006 Apr 14. p. 2270-9.
  5. Agrawal A, Wang MD, and Nie SM. Bioconjugated nanoparticles for ultrasensitive detection of molecular biomarkers and infectious agents. In: Gonsalves K, Halberstadt C, Laurencin CT, and Nair LS, editors. Biomedical nanostructures. Hoboken, NJ: John Wiley & Sons, Inc.; 2007 Apr 11. p. 205-20.
  6. Wang MD, Simons JW, and Nie SM. Cancer nanotechnology for molecular profiling and individualized therapy. In: Leyland-Jones B, editor. Pharmacogenetics of breast cancer: towards the individualization of therapy. 1st ed. Informa Healthcare; 2008 May 1. p.143-56.
  7. Quo CF and Wang MD. Incorporating problem-based learning (PBL) in medical image processing education. In: Transform Science: Computational Education for Scientists. Microsoft Research; 2009. p. 176-94.
Journal Articles
  1. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, and Weinstein JN. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 2003 Mar 25; 4(4):R28.
  2. *Pardo SJ, *Patel MJ (equal contributing authors), Sykes MC, Platt MO, Boyd NO, Sorescu GP, Xu M, van Loon JJ, Wang MD, and Jo H. Simulated microgravity using the random positioning machine inhibits differentiation and alters gene expression profiles of 2T3 pre-osteoblasts. Am J Physiol Cell Physiol. 2005 Jun; 288(6): C1211-21.
  3. *Wang MD, *Simons JW, and *Nie SM (co-corresponding senior authors). Nanotechnology in personalized and predictive oncology. US Oncol. 2006; 1(2): 92-5.
  4. Yin-Goen Q, Dale J, Yang WL, Phan JH, Moffitt RA, Petros JA, Datta MW, Amin MB, Wang MD, and Young AN. Advances in molecular classification of renal neoplasms. Histol Histopathol. 2006 Mar; 21(3): 325-39.
  5. Young AN, Dale J, Yin-Goen Q, Harris WB, Petros JA, Datta MW, Wang MD, Marshall FF, Amin MB. Current trends in molecular classification of adult renal tumors. Urology. 2006 May; 67(5):873-80.
  6. Xing Y, Chaudry Q, Shen C, Kong KY, Zhau HE, Chung LW, Petros JA, O.Regan RM, Yezhelyev MV, Simons JW, *Wang MD, and *Nie SM (co-corresponding senior authors). Bioconjugated quantum dots for multiplexed and quantitative immunohistochemistry. Nat Protoc. 2007 May 3; 2(5):1152-65.
  7. *Stokes TH, *Moffitt RA (equal contributing authors), Phan JH, and Wang MD. chip artifact CORRECTion (caCORRECT): A bioinformatics system for quality assurance of genomics and proteomics array data. Ann Biomed Eng. 2007 Jun; 35(6): 1068-80.
  8. Wang MD, Shin DM, Simons JW, and Nie SM. Nanotechnology for targeted cancer therapy. Expert Rev Anticancer Ther. 2007 Jun; 7(6): 833-7.
  9. *Wang MD, *Simons JW, and *Nie SM (co-corresponding senior authors). Biomedical nanotechnology with bioinformatics.the promise and current progress. Proc IEEE. 2007 Jul; 95(7): 1386-9.
  10. Merrill AH Jr., Wang MD, Park M, and Sullards MC. (Glyco)sphingolipidology: an amazing challenge and opportunity for systems biology. Trends Biochem Sci. 2007 Oct; 32(10): 457-68.
  11. Qian X, Peng XH, Ansari DO, Yin-Goen Q, Chen GZ, Shin DM, Yang L, Young AN, Wang MD, and Nie SM. In vivo tumor targeting and spectroscopic detection with surface-enhanced Raman nanoparticle tags. Nat Biotechnol. 2008 Jan; 26(1): 83-90.
  12. Young AN, Master VA, Paner GP, Wang MD, and Amin MB. Renal epithelial neoplasms: diagnostic applications of gene expression profiling. Adv Anat Pathol. 2008 Jan; 15(1): 28-38.
  13. Agrawal A., Deo R, Wang G, *Wang MD, and *Nie SM (co-corresponding senior authors). Nanometer-scale mapping and single molecule detection with color-coded nanoparticle probes. Proc Natl Acad Sci USA. 2008 Mar 4; 105(9): 3298-303.
  14. Quo CF and Wang MD. Quantitative analysis of numerical solvers for oscillatory biomolecular system models. BMC Bioinformatics. 2008 May 28; 9(Suppl 6):S17.
  15. Stokes TH, Torrance JT, Li H, and Wang MD. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics. 2008 May 28; 9(Suppl 6): S18.
  16. Chaudry Q, Raza SH, Young AN, and Wang MD. Automated renal cell carcinoma subtype classification using morphological, textural and wavelets based features. J Signal Process Syst. 2008 Jun 21; 55:15-23.
  17. Merrill AH Jr., Stokes TH, Momin A, Park H, Portz BJ, Kelly S, Wang E, Sullards MC, and Wang MD. Sphingolipidomics: a valuable tool for understanding the roles of sphingolipids in biology and disease. J Lipid Res. 2009 Apr; 50(Suppl): S97-S102.
  18. Lane AL, Nyadong L, Galhena A, Stout EP, Parry RM, Wang MD, Hay ME, Fernandez FM, and Kubanek J. Desorption electrospray ionization mass spectrometry reveals surface-mediated antifungal chemical defense of a tropical seaweed. Proc Natl Acad Sci (PNAS) USA. 2009 May 5; 106(18): 7314-9.
  19. Nyadong L, Harris GA, Belayssac S, Galhena AS, Malet-Martino M, Martino R, Parry RM, Wang MD, *Fernandez FM, and *Gilard V (co-corresponding senior authors). Combining two-dimensional diffusion-ordered nuclear magnetic resonance spectroscopy, imaging desorption electrospray ionization mass spectrometry and direct analysis in real time mass spectrometry for the integral investigation of counterfeit pharmaceuticals. Anal Chem. 2009 May 19; 81(12): 4803-12.
  20. Phan JH, Moffitt RA, Stokes TH, Liu J, Young AN, *Nie SM, and *Wang MD (co-corresponding senior authors). Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. Trends Biotechnol. 2009 Jun; 27(6):350-8.
  21. Osunkoya AO, Yin-Goen Q, Phan JH, Moffitt RA, Stokes TH, Wang MD, and Young AN. Diagnostic biomarkers for renal cell carcinoma: selection using novel bioinformatics systems for microarray data analysis. Hum Pathol. 2009 Dec; 40(12):1671-8.
  22. Smith AM, Wen MM, Wang MD, and Nie SM. .Size-minimized quantum dots for molecular and cellular imaging. Single Molecule Spectroscopy in Chemistry, Physics, and Biology. 2010; 96(4):187-201.
  23. Liu J, Lau SK, Varma VA, Moffitt RA, Caldwell M, Liu T, Young AN, Petros JA, Osunkoya AO, Krogstad T, Leyland-Jones B, Wang MD, and Nie SM. Molecular mapping of tumor heterogeneity on clinical tissue specimens with multiplexed quantum dots. ACS Nano. 2010 Apr 8; 4(5):2755-65.
  24. The Microarray Quality Control Consortium (MAQC) and Shi L et al. (Wang MD, Phan JH, Stokes TH, Parry RM, Moffitt RA, and 190 other authors). The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010 Aug; 28(8):827-38.
  25. Parry RM*, Jones W*, Stokes TH* (equal contributing authors), Phan JH, Moffitt RA, Fang H, Shi L, Oberthuer A, Fischer M, Tong W, and Wang MD. K-nearest neighbors (KNN) models for microarray gene-expression analysis and clinical outcome prediction. Pharmacogenomics J. 2010 Aug; 10(4):292-309.
  26. Singhal S, Nie SM, and Wang MD. Nanotechnology applications in surgical oncology. Annu Rev Med. 2010 Aug 2. 61:359-73.
  27. Quo CF, Moffitt RA, Merrill AH Jr., and Wang MD. Adaptive control model reveals systematic feedback and key molecules in metabolic pathway regulation. J Comput Biol. 2011 Feb; 18(2):169-82.
  28. Thomas DG, Klaessig F, Harper SL, Fritts M, Hoover MD, Gaheen S, Stokes TH, Reznik-Zellen R, Freund ET, Klemm JD, Paik DS, and Baker NA. Informatics and standards for nanomedicine technology. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2011 Jun 30; 3(5):511-32.
  29. Moffitt RA, Yin-Goen Q, Stokes TH, Parry RM, Torrance JH, Phan JH, Young AN, and Wang MD. caCORRECT2: improving accuracy and reliability of microarray data in the presence of artifacts. BMC Bioinformatics. 2011 Sep 29; 12:383.
  30. Sharma Y, Moffitt RA, Stokes TH, Chaudry Q, and Wang MD. Feasibility analysis of high resolution tissue image registration using 3-D synthetic data. J Pathol Inform. 2012 Jan 19; 2:6.
  31. Parry RM, Phan JH, and Wang MD. Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems. BMC Bioinformatics. 2012 Mar 21; 13(Suppl 3):S7. i
  32. Freimuth RR, Freund ET, Schick L, Sharma MK Stafford GA Suzek BE, Hernandez J, Hipp J, Kelley J, Rokicki K, Pan S, Buckler A, Stokes TH, Fernandez A, Fore I, Beutow K, Klemm J. Life sciences domain analysis model. J Am Med Inform Assoc. 2012 Jun 28; 19(6):1095-102.
  33. Quo CF, Kaddi C, Phan JH, Zollanvari A, Xu M, Wang MD, and Alterovitz G. Reverse engineering biomolecular systems using -omics data: challenges, progress, and opportunities. Brief Bioinformatics. 2012 Jul; 13(4):430-45.
  34. Phan JH, Quo CF, and Wang MD. Cardiovascular genomics: a biomarker identification pipeline. IEEE Trans Inf Technol Biomed. 2012 Sep; 16(5):809-22.
  35. Andras TD, Alexander TS, Gahlena A, Parry RM, Fernandez FM, Kubanek J, Wang MD, and Hay ME. Seaweed allelopathy against coral: surface distribution of a seaweed secondary metabolite by imaging mass spectrometry. J Chem Ecol. 2012 Oct; 38(10):1203-14.
  36. Phan JH, Quo CF, Cheng C, and Wang MD. Multi-scale integration of molecular, imaging, and clinical data in biomedical informatics. IEEE Rev Biomed Eng. 2012 Dec 10; 5:74-87.
  37. Kong KY, Marcus AI, Giaanakakou P, and Wang MD. Integrating image analysis algorithms in a web interface for the quantification of microtubule dynamics. Int J Comput Biol Drug Des. 2012 Sep; 5(3-4):298-313.
  38. Phan JH, Young AN, and Wang MD. Robust microarray meta-analysis identifies differentially expressed genes for clinical prediction. ScientificWorldJournal, Bioinformatics and Biomedical Informatics. 2012 Nov 28; 2012:989637.
  39. Parry RM and Wang MD. A fast least-squares algorithm for population inference in GWAS. BMC Bioinformatics. 2013 Jan 23; 14:28.
  40. Parry RM, Galhena AS, Gamage CM, Bennett RV, Wang MD, and Fernandez FM. OmniSpect: An open MATLAB-based tool for visualization and analysis of matrix-assisted laser desorption/ionization and desorption electrospray ionization mass spectrometry images. J Am Soc Mass Spectrom. 2013 Feb 26; 1-4.
  41. Kairdolf BA, Smith AM, Stokes TH, Wang MD, Young AN, and Nie S. Semiconductor quantum dots for bioimaging and biodiagnostic applications. Annu Rev Anal Chem. 2013 Mar 12; 6:143-62.
  42. Kothari S, Phan JH, Young AN, and Wang MD. Histological image classification using biologically interpretable shape-based features. BMC Med Imaging. 2013 Mar 13; 13:9.
  43. Phan JH, Young AN, and Wang MD. omniBiomarker: a web-based application for knowledge-driven biomarker identification. IEEE Trans Biomed Eng. In Press.
  44. Wu PY, Phan JH, and Wang MD. The effect of human genome annotation complexity on RNA-seq gene expression quantification. BMC Bioinformatics. In Press.
  45. Kaddi CD, Parry RM, and Wang MD. Multivariate hypergeometric similarity measure. IEEE/ACM Trans Comput Biol Bioinformatics. In Press.