Selected Peer-Reviewed Publications

1.    Piening, B.D., Wang, P., Subramanian, A., and Paulovich, A.G.  Radiation-Derived Gene Expression Signature Predicts Clinical Outcome for Breast Cancer Patients.  Piening BD, Wang P, Subramanian A, Patterson J, Paulovich AG.  Radiation Research (2008) In Press.

 

2.      Paulovich AG, Whiteaker JR, Hoofnagle AN, and Wang P.  The Interface between Biomarker Discovery and Clinical Validation: The Tar Pit of the Protein Biomarker Pipeline. Proteomics-Clinical Applications. (2008) In Press.

 

3.      Whiteaker JR, Zhang H, Zhao L, Wang P, Kelly-Spratt KS, Ivey RG, Piening BD, Feng LC, Kasarda E, Gurley KE, Eng JK, Chodosh LA, Kemp CJ, McIntosh MW, Paulovich AG.  Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer.  Journal of Proteome Research (2007) 6(10):3962-75.

 

4.      May D, Fitzgibbon M, Liu Y, Holzman T, Eng J, Kemp CJ, Whiteaker J, Paulovich A, McIntosh M.  A Platform for Accurate Mass and Time Analyses of Mass Spectrometry Data. Journal of Proteome Research (2007) 6(10):1741-1748.

 

5.      Miguel AC, Kearney-Fischer M, Keane JF, Whiteaker J, Feng L, Paulovich A, Near-Lossless Compression of Mass Spectra for Proteomics, Proceedings of the 2007 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP2007) (2007).

 

6.      Whiteaker JR, Zhao L, Zhang HY, Feng L, Piening BD, Anderson L, and Paulovich AG. Antibody-based enrichment of peptides on magnetic beads for mass spectrometry-based quantification of serum biomarkers. Analytical Biochemistry (2007) 362(1):44-54.

 

7.      Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng L, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T, Fitzgibbon M, Lin C, Zhang H, Cooke K, Liu T, Camp DG, Anderson L, Watts J, Smith RD, McIntosh MW, and Paulovich A.  Head-to-Head Comparison of Serum Fractionation Techniques. Journal of Proteome Research, (2007) 6(2):828-36.

 

8.      Hartwell LH, Mankoff D, Paulovich A, Ramsey S, and Swisher E (2006).  Cancer biomarkers: a systems approach. Nature Biotechnology (2006) 24(8):905-908.

 

9.      Piening BD, Wang P, Bangur CS, Whiteaker J, Zhang H, Feng L-C, Keane JF, Eng JK, Tang H, Prakash A, McIntosh MW, and Paulovich A. Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles. Journal of Proteome Research (2006) 5(7):1527-34.

 

10.  Miguel AC, Keane JF, Whiteaker J, Zhang H, and Paulovich A. (2006).  Compression of LC/MS Proteomic Data.  Proceedings of the 19th IEEE International Symposium on Computer-Based Medical Systems (CBMS2006).

 

11.  Haab BB, Paulovich AG, Anderson NL, Clark AM, Downing GJ, Hermjakob H, Labaer J, Uhlen M.  A reagent resource to identify proteins and peptides of interest to the cancer community: A workshop report.  Mol Cell Proteomics (2006) 5(10):1996-2007.

 

12.  Wang P, Tang H, Zhang H, Whiteaker J, Paulovich A, Mcintosh M.  (2006). Normalization regarding non-random missing values in high-throughput mass spectrometry data.  Proceedings of the Pacific Symposium, edited by Russ B Altman, Tiffany Murray, Teri E Klein (Stanford University, USA), A Keith Dunker (Indiana University, USA) & Lawrence Hunter (University of Colorado Health Sciences Center, USA).

 

13.  Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin C, Chen J, Goodlett D, Whiteaker J, Paulovich A, McIntosh M.  A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.  Bioinformatics (2006) 22(15):1902-1909.

 

14.  Rauch A, Bellew, M Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin C, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whitaker J, States D, Hanash S, Paulovich A, McIntosh M. Computational Proteomics Analysis System (CPAS): An extensible open source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. Journal of Proteome Research (2006) 5(1):112-21.

 

15.  Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette M A, Paulovich A, Pomeroy S L, Golub TR, Lander E S and Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 102(43):15545-50.

 

16.  Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R and Schwikowski B. Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomics  (2005) 5(3):423-32.

 

17.  Paulovich AG, Armour CD, and Hartwell LH. The Saccharomyces cerevisiae RAD9, RAD17, RAD24 and MEC3 genes are required for tolerating irreparable, ultraviolet-induced DNA damage. Genetics (1998) 150(1):75-93.

 

18.  Paulovich AG, Toczysk, DP, and Hartwell LH. When checkpoints fail. Cell (1997) 88(3):315-321.

 

19.  Paulovich AG, Margulies RU, Garvik BM, and Hartwell LH. RAD9, RAD17, and RAD24 are required for S phase regulation in Saccharomyces cerevisiae in response to DNA damage. Genetics (1997) 145(1):45-62.

 

20.  Paulovich AG, and Hartwell LH. A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage. Cell (1995) 82(5):841-847.

 

21.  Li Z, Paulovich AG, and Woolford JL Jr. Feedback inhibition of the yeast ribosomal protein gene CRY2 is mediated by the nucleotide sequence and secondary structure of CRY2 pre-mRNA. Mol-Cell-Biol. (1995) 15(11):6454-6464.

 

22.  Paulovich AG, Thompson JR, Larkin JC, Li Z, and Woolford JL Jr. Molecular genetics of cryptopleurine resistance in Saccharomyces cerevisiae: expression of a ribosomal protein gene family. Genetics (1993) 135(3):719-730.

 

23.  Paulovich A. Creativity and graduate education. Mol-Biol-Cell. (1993) 4(6):565-568.

 

24.  Deshmukh M, Tsay YF, Paulovich AG, and Woolford JL Jr. Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S subunits. Mol-Cell-Biol. (1993) 13(5):2835-2845.

 

25.  Sandgren EP, Quaife CJ, Paulovich AG, Palmiter RD, and Brinster RL. Pancreatic tumor pathogenesis reflects the causative genetic lesion. Proc-Natl-Acad-Sci-U-S-A. (1991) 88(1):93-97.

 

26.  Moritz M, Paulovich AG. Tsay YF, and Woolford JL Jr. Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly. J-Cell-Biol. (1990) 111(6 Pt 1):2261-2274.