Publications

 

 

  1. Huber, C.G., Premstaller, A., Xiao, W., Oberacher, H., Bonn, G.K., and Oefner, P.J. (2001). Mutation detection by capillary denaturing high-performance liquid chromatography using monolithic columns. J Biochem Biophys Methods 47, 5-19.
  2. Premstaller, A., Xiao, W., Oberacher, H., O’Keefe, M., Stern, D., Willis, T., Huber, C.G., and Oefner, P.J. (2001). Temperature-modulated array high-performance liquid chromatography. Genome Res 11, 1944-1951.
  3. Xiao, W., and Oefner, P.J. (2001). Denaturing high-performance liquid chromatography: A review. Hum Mutat 17, 439-474.
  4. Xiao, W., Stern, D., Jain, M., Huber, C.G., and Oefner, P.J. (2001). Multiplex capillary denaturing high-performance liquid chromatography with laser-induced fluorescence detection. Biotechniques 30, 1332-1338.
  5. Wang, Q.T., Xiao, W., Mindrinos, M., and Davis, R.W. (2002). Yeast tRNA as carrier in the isolation of microscale RNA for global amplification and expression profiling. Biotechniques 33, 788, 790, 792 passim.
  6. Lau, G.W., Goumnerov, B.C., Walendziewicz, C.L., Hewitson, J., Xiao, W., Mahajan-Miklos, S., Tompkins, R.G., Perkins, L.A., and Rahme, L.G. (2003). The Drosophila melanogaster toll pathway participates in resistance to infection by the gram-negative human pathogen Pseudomonas aeruginosa. Infect Immun 71, 4059-4066.
  7. Blonder, J., Goshe, M.B., Xiao, W., Camp, D.G., 2nd, Wingerd, M., Davis, R.W., and Smith, R.D. (2004). Global analysis of the membrane subproteome of Pseudomonas aeruginosa using liquid chromatography-tandem mass spectrometry. J Proteome Res 3, 434-444.
  8. Feezor, R.J., Baker, H.V., Mindrinos, M., Hayden, D., Tannahill, C.L., Brownstein, B.H., Fay, A., MacMillan, S., Laramie, J., Xiao, W., et al. (2004). Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol Genomics 19, 247-254.
  9. Feezor, R.J., Baker, H.V., Xiao, W., Lee, W.A., Huber, T.S., Mindrinos, M., Kim, R.A., Ruiz-Taylor, L., Moldawer, L.L., Davis, R.W., et al. (2004). Genomic and proteomic determinants of outcome in patients undergoing thoracoabdominal aortic aneurysm repair. J Immunol 172, 7103-7109.
  10. Prokisch, H.*, Scharfe, C.*, Camp, D.G., 2nd*, Xiao, W.*, David, L., Andreoli, C., Monroe, M.E., Moore, R.J., Gritsenko, M.A., Kozany, C., et al. (2004). Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol 2, e160.
  11. Rodwell, G.E., Sonu, R., Zahn, J.M., Lund, J., Wilhelmy, J., Wang, L., Xiao, W., Mindrinos, M., Crane, E., Segal, E., et al. (2004). A transcriptional profile of aging in the human kidney. PLoS Biol 2, e427.
  12. Shen, Y., Jacobs, J.M., Camp, D.G., 2nd, Fang, R., Moore, R.J., Smith, R.D., Xiao, W., Davis, R.W., and Tompkins, R.G. (2004). Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal Chem 76, 1134-1144.
  13. The Tumor Analysis Best Practices Working Group (2004). Expression profiling–best practices for data generation and interpretation in clinical trials. Nat Rev Genet 5, 229-237.
  14. Apidianakis, Y., Mindrinos, M.N., Xiao, W., Lau, G.W., Baldini, R.L., Davis, R.W., and Rahme, L.G. (2005). Profiling early infection responses: Pseudomonas aeruginosa eludes host defenses by suppressing antimicrobial peptide gene expression. Proc Natl Acad Sci U S A 102, 2573-2578.
  15. Calvano, S.E.*, Xiao, W.*, Richards, D.R., Felciano, R.M., Baker, H.V., Cho, R.J., Chen, R.O., Brownstein, B.H., Cobb, J.P., Tschoeke, S.K., et al. (2005). A network-based analysis of systemic inflammation in humans. Nature 437, 1032-1037.
  16. Cobb, J.P., Mindrinos, M.N., Miller-Graziano, C., Calvano, S.E., Baker, H.V., Xiao, W., Laudanski, K., Brownstein, B.H., Elson, C.M., Hayden, D.L., et al. (2005). Application of genome-wide expression analysis to human health and disease. Proc Natl Acad Sci U S A 102, 4801-4806.
  17. Qian, W.J., Jacobs, J.M., Camp, D.G., 2nd, Monroe, M.E., Moore, R.J., Gritsenko, M.A., Calvano, S.E., Lowry, S.F., Xiao, W., Moldawer, L.L., et al. (2005). Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. Proteomics 5, 572-584.
  18. Qian, W.J., Monroe, M.E., Liu, T., Jacobs, J.M., Anderson, G.A., Shen, Y., Moore, R.J., Anderson, D.J., Zhang, R., Calvano, S.E., et al. (2005). Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Mol Cell Proteomics 4, 700-709.
  19. Storey, J.D., Xiao, W., Leek, J.T., Tompkins, R.G., and Davis, R.W. (2005). Significance analysis of time course microarray experiments. Proc Natl Acad Sci U S A 102, 12837-12842.
  20. Laudanski, K.*, Miller-Graziano, C.*, Xiao, W.*, Mindrinos, M.N., Richards, D.R., De, A., Moldawer, L.L., Maier, R.V., Bankey, P., Baker, H.V., et al. (2006). Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways. Proc Natl Acad Sci U S A 103, 15564-15569.
  21. Brownstein BH, Logvinenko T, Lederer JA, Cobb JP, Hubbard WJ, Chaudry IH, Remick DG, Baker HV, Xiao W, Mannick JA. Commonality and differences in leukocyte gene expression patterns among three models of inflammation and injury. Physiol Genomics 2006;24:298-309.
  22. Liu, T., Qian, W.J., Gritsenko, M.A., Xiao, W., Moldawer, L.L., Kaushal, A., Monroe, M.E., Varnum, S.M., Moore, R.J., Purvine, S.O., et al. (2006). High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics 5, 1899-1913.
  23. Apidianakis, Y., Mindrinos, M.N., Xiao, W., Tegos, G.P., Papisov, M.I., Hamblin, M.R., Davis, R.W., Tompkins, R.G., and Rahme, L.G. (2007). Involvement of skeletal muscle gene regulatory network in susceptibility to wound infection following trauma. PLoS One 2, e1356.
  24. Dairkee, S.H., Seok, J., Champion, S., Sayeed, A., Mindrinos, M., Xiao, W., Davis, R.W., and Goodson, W.H. (2008). Bisphenol A induces a profile of tumor aggressiveness in high-risk cells from breast cancer patients. Cancer Res 68, 2076-2080.
  25. Lederer, J.A., Brownstein, B.H., Lopez, M.C., Macmillan, S., Delisle, A.J., Macconmara, M.P., Choudhry, M.A., Xiao, W., Lekousi, S., Cobb, J.P., et al. (2008). Comparison of longitudinal leukocyte gene expression after burn injury or trauma-hemorrhage in mice. Physiol Genomics 32, 299-310.
  26. Li, L., Ying, L., Naesens, M., Xiao, W., Sigdel, T., Hsieh, S., Martin, J., Chen, R., Liu, K., Mindrinos, M., et al. (2008). Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples. Physiol Genomics 32, 190-197.
  27. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, Xing Y,  Lubischer JL, Krieg PA, Krupenko SA, Thompson WJ, Barres BA. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci. 2008 Jan 2;28(1):264-78.
  28. Russom A, Sethu P, Irimia D, et al, and the Inflammation and the Host Response to Injury Large Scale Collaborative Research.. Microfluidic leukocyte isolation for gene expression analysis in critically ill hospitalized patients. Clin Chem 2008:54(5):891-900
  29. Hiller, D., Jiang, H., Xu, W., and Wong, W.H. (2009). Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics 25, 3056-3059.
  30. Irimia, D., Mindrinos, M., Russom, A., Xiao, W., Wilhelmy, J., Wang, S., Heath, J.D., Kurn, N., Tompkins, R.G., Davis, R.W., et al. (2009). Genome-wide transcriptome analysis of 150 cell samples. Integr Biol (Camb) 1, 99-107.
  31. Lin, L., Liu, S., Brockway, H., Seok, J., Jiang, P., Wong, W.H., and Xing, Y. (2009). Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Res 37, e90.
  32. Qian, W.J., Liu, T., Petyuk, V.A., Gritsenko, M.A., Petritis, B.O., Polpitiya, A.D., Kaushal, A., Xiao, W., Finnerty, C.C., Jeschke, M.G., et al. (2009). Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled “universal” reference sample. J Proteome Res 8, 290-299.
  33. Seok, J., Xiao, W., Moldawer, L.L., Davis, R.W., and Covert, M.W. (2009). A dynamic network of transcription in LPS-treated human subjects. BMC Syst Biol 3, 78.
  34. Talasaz, A.H., Powell, A.A., Huber, D.E., Berbee, J.G., Roh, K.H., Yu, W., Xiao, W., Davis, M.M., Pease, R.F., Mindrinos, M.N., et al. (2009). Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device. Proc Natl Acad Sci U S A 106, 3970-3975.
  35. Sigdel T, Kaushal A, Gritsenko M, Norbeck A, Xiao W, Qian W, Camp D, Smith RD, Sarwal M, (2009) Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection, Proteomics 4: 32 – 47.
  36. Hoover, S.E., Xu, W., Xiao, W., and Burkholder, W.F. (2010). Changes in DnaA-dependent gene expression contribute to the transcriptional and developmental response of Bacillus subtilis to manganese limitation in Luria-Bertani medium. J Bacteriol 192, 3915-3924.
  37. Kotz, K.T., Xiao, W., Miller-Graziano, C., Qian, W.J., Russom, A., Warner, E.A., Moldawer, L.L., De, A., Bankey, P.E., Petritis, B.O., et al. (2010). Clinical microfluidics for neutrophil genomics and proteomics. Nature Medicine 16, 1042-1047.
  38. Qian, W.J., Petritis, B.O., Kaushal, A., Finnerty, C.C., Jeschke, M.G., Monroe, M.E., Moore, R.J., Schepmoes, A.A., Xiao, W., Moldawer, L.L., et al. (2010). Plasma proteome response to severe burn injury revealed by 18O-labeled “universal” reference-based quantitative proteomics. J Proteome Res 9, 4779-4789.
  39. Seok, J., Kaushal, A., Davis, R.W., and Xiao, W#. (2010). Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships. BMC Bioinformatics 11 Suppl 1, S8.
  40. Zhou, B., Xu, W., Herndon, D., Tompkins, R., Davis, R., Xiao, W.#, Wong, W.H.# (2010). Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Proc Natl Acad Sci U S A 107, 9923-9928.
  41. Srinivasan BS, Evans EA, Flannick J, Patterson AS, Chang CC, Pham T, Young S, Kaushal A, Lee J, Jacobson JL, Patrizio P. A universal carrier test for the long tail of Mendelian disease. Reprod Biomed Online. 2010 Oct;21(4):537-51.
  42. Logan, A.C., Gao, H., Wang, C., Sahaf, B., Jones, C.D., Marshall, E.L., Buno, I., Armstrong, R., Fire, A.Z., Weinberg, K.I., et al. (2011). High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proc Natl Acad Sci U S A 108, 21194-21199.
  43. Luciani, M.G., Seok, J., Sayeed, A., Champion, S., Goodson, W.H., Jeffrey, S.S., Xiao, W., Mindrinos, M., Davis, R.W., and Dairkee, S.H. (2011). Distinctive responsiveness to stromal signaling accompanies histologic grade programming of cancer cells. PLoS One 6, e20016.
  44. Xiao, W.*, Mindrinos, M.N.*, Seok, J.*, Cuschieri, J., Cuenca, A.G., Gao, H., Hayden, D.L., Hennessy, L., Moore, E.E., Minei, J.P., et al. (2011). A genomic storm in critically injured humans. J Exp Med 208, 2581-2590.
  45. Xu, W.*, Seok, J.*, Mindrinos, M.N.*, Schweitzer, A.C., Jiang, H., Wilhelmy, J., Clark, T.A., Kapur, K., Xing, Y., Faham, M.Storey JD, Moldawer LL, Maier RV, Tompkins RG, Wong WH, Davis RW, Xiao W#. (2011). Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A 108, 3707-3712.
  46. Apidianakis, Y., Que, Y.A., Xu, W., Tegos, G.P., Zimniak, P., Hamblin, M.R., Tompkins, R.G., Xiao, W., and Rahme, L.G. (2012). Down-regulation of glutatione S-transferase alpha 4 (hGSTA4) in the muscle of thermally injured patients is indicative of susceptibility to bacterial infection. FASEB J 26, 730-737.
  47. Cuschieri, J., Johnson, J.L., Sperry, J., West, M.A., Moore, E.E., Minei, J.P., Bankey, P.E., Nathens, A.B., Cuenca, A.G., Efron, P.A., Hennessy L, Xiao W, et al. (2012). Benchmarking outcomes in the critically injured trauma patient and the effect of implementing standard operating procedures. Ann Surg 255, 993-999.
  48. Li, L., Khatri, P., Sigdel, T.K., Tran, T., Ying, L., Vitalone, M.J., Chen, A., Hsieh, S., Dai, H., Zhang, M., et al. (2012). A peripheral blood diagnostic test for acute rejection in renal transplantation. Am J Transplant 12, 2710-2718.
  49. Seok J*, Xu W*, Jiang H, Davis RW, Xiao W#.(2012) Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research. PLoS One. 7(2):e31440. Epub 2012 Feb 1.
  50. Seok, J., Xu, W., Gao, H., Davis, R.W., and Xiao, W#. (2012). JETTA: junction and exon toolkits for transcriptome analysis. Bioinformatics 28, 1274-1275.
  51. Xu, W., Gao, H., Seok, J., Wilhelmy, J., Mindrinos, M.N., Davis, R.W., and Xiao, W#. (2012). Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies. Biotechniques 52, 386-388.
  52. Cuenca AG*, Gentile LF*, Lopez MC, Ungaro R, Liu H, Xiao W, Mindrinos MN, et al., (2013) Development of a genomic metric that can be rapidly used to predict clinical outcome in severely injured trauma patients. Crit Care Med, 41(5):1175-85
  53. Seok J*, Warren S*, Cuenca AG*, Mindrinos MN, Baker HV, Xu W, Richards DR, McDonald-Smith GP, Gao H,  Hennessy L,  Finnerty CC, López C, Honari S, Moore EE, Minei JP, Cuschieri J, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Jeschke MG, Klein MB, Gamelli RL, Gibran NS, Brownstein BH, Miller-Graziano C, Calvano SE, Mason PH, Storey JD, Cobb P, Rahme LG, Lowry SF, Maier RV, Moldawer LL, Herndon DN, Davis RW#, Xiao W#, Tompkins RG (2013) Gene response in mouse models poorly mimics severe human inflammatory diseases. Proc Natl Acad Sci U S A 110(9):3507-12.
  54. Tompkins RG, Warren HS, Mindrinos MN, Xiao W, Davis RW. (2013) To study human inflammatory diseases in humans  Proc Natl Acad Sci U S A. 110 (36):E3371.
  55. Warren HS, Tompkins RG, Mindrinos MN, Xiao W, Davis RW. (2013) Of men, not mice, and inflammation. Proc Natl Acad Sci U S A. 110 (34):E3151.
  56. Zhou J*, Krovvidi RK*, Qian W, Gao H, De A, Miller-Graziano C, Bankey PE, Petritis BO, Nicora CO, Clauss TR,  Moore RJ, Xiao W, Davis RW, Tompkins RG, Camp DG, Smith RD (2013) Trauma-associated Human Neutrophil Alterations Revealed by Proteomics and Genomics Analysis. Proteomics. 7(7-8):571-83
  57. Celeste C. Finnerty CC, Jeschke MG, Qian W, Kaushal A, Xiao W, et al., (2013) Determination of burn patient outcome by large-scale quantitative discovery proteomics. Crit Care Med, 41(6):1421-34
  58. Sinha S, Kaushal A, Xiao W. Inference for longitudinal data with nonignorable nonmonotone missing responses.Computational Statistics and Data Analysis. 2014, 72: 77–91.
  59. Sigdel TK, Salomonis N, Nicora CD, Ryu S, He J, Dinh V, Orton D, Moore RJ, Hsieh S, Dai H, Thien-Vu M, Xiao W, Smith RD, Qian W, Camp DG, Sarwal MM The Identification of Novel Potential Injury Mechanisms and Biomarkers in Renal Allograft Rejection by Quantitative Proteomics. Mol Cell Proteomics. 2014 Feb;13(2):621-31.
  60. Ryu, S. Y. Chapter one – bioinformatics tools to identify and quantify proteins using mass spectrometry data. volume 94 of Advances in Protein Chemistry and Structural Biology, pages 1 – 17. Academic Press. 2014
  61. Fu G, Xu W, Wilhelmy J, Mindrinos MN, Davis RW, Xiao W and Fodor SPA. Molecular indexing enables quantitative targeted RNA sequencing and reveals poor sampling efficiencies in standard library preparations. Proc Natl Acad Sci U S A 2014; 111(5):1891-6
  62. Schlecht U, Suresh S, Xu W, Aparicio AM, Chu A, Proctor MJ, Davis RW, Scharfe C, St Onge RP. A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. BMC Genomics. 2014; 15(1):263. 
  63. Ryu SY, Payne SH, Schaab C, Xiao W. Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013. Bioinformatics. 2014 Mar 13.
  64. Klein MB GJ, Hayden DL, Fagan SP, McDonald-Smith GP,  Alexander AK, Gamelli RL, Gibran NS, Finnerty CC, Jeschke MG, Arnoldo B, Wispelwey B, Mindrinos MN, Xiao W, Honari SE, Mason PH, Schoenfeld  DA, Herndon DN, Tompkins RG. Benchmarking outcomes in the critically injured burn patient. Ann Surg. 2014; in press
  65. Xu W, Krishnakumar S, Miranda M, Jensen MA, Fukushima M, Palm C, Fung E, Davis RW, St Onge RP and Hyman RW. Targeted and highly multiplexed detection of microorganisms employing an ensemble of molecular probes. Appl Environ Microbiol. 2014. accepted.
  66. The SEQC consortium, Power and Limitations of RNA-Seq: findings from the SEQC (MAQC-III) consortium. Nature Biotechnology. 2014 accepted 

     

     

     

    *authors contributed equally, #corresponding author

 

 

 

Leave a Reply

Your email address will not be published. Required fields are marked *