Keith Baggerly's Papers


  1. Yang L, Wang H, Kornblau SM, Graber DA, Zhang N, Matthews JA, Wang M, Weber DM, Thomas SK, Shah JJ, Zhang L, Lu G, Zhao M, Muddasani R, Yoo SY, Baggerly KA, Orlowski RZ. "Evidence of a role for the novel zinc-finger transcription factor ZKSCAN3 in modulating Cyclin D2 expression in multiple myeloma." Oncogene. 2010 Nov 8. [Epub ahead of print] PMID: 21057542
  2. Richards KL, Zhang B, Sun M, Dong W, Churchill J, Bachinski LL, Wilson CD, Baggerly KA, Yin G, Hayes DN, Wistuba II, Krahe R. "Methylation of the candidate biomarker TCF21 is very frequent across a spectrum of early-stage nonsmall cell lung cancers." Cancer. 2010 Oct 13. [Epub ahead of print] PMID: 20945327
  3. Baggerly K. "Disclose all data in publications." Nature. 2010 Sep 23;467(7314):401. PMID: 20864982
  4. Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. "Tackling the widespread and critical impact of batch effects in high-throughput data." Nat Rev Genet. 2010 Oct;11(10):733-9. Epub 2010 Sep 14. PMID: 20838408
  5. Mazouni C, Baggerly K, Hawke D, Tsavachidis S, Andre F, Buzdar AU, Martin PM, Kobayashi R, Pusztai L. "Evaluation of changes in serum protein profiles during neoadjuvant chemotherapy in HER2-positive breast cancer using an LC-MALDI-TOF/MS procedure." Proteomics. 2010 Oct;10(19):3525-32. PMID: 20827732
  6. Morris JS, Baggerly KA, Gutstein HB, Coombes KR. "Statistical contributions to proteomic research." Methods Mol Biol. 2010;641:143-66. PMID: 20407946
  7. Lee JK, Coutant C, Kim YC, Qi Y, Theodorescu D, Symmans WF, Baggerly K, Rouzier R, Pusztai L. "Prospective comparison of clinical and genomic multivariate predictors of response to neoadjuvant chemotherapy in breast cancer." Clin Cancer Res. 2010 Jan 15;16(2):711-8. Epub 2010 Jan 12. PMID: 20068086
  8. Vihola A, Bachinski LL, Sirito M, Olufemi SE, Hajibashi S, Baggerly KA, Raheem O, Haapasalo H, Suominen T, Holmlund-Hampf J, Paetau A, Cardani R, Meola G, Kalimo H, Edstrom L, Krahe R, Udd B. "Differences in aberrant expression and splicing of sarcomeric proteins in the myotonic dystrophies DM1 and DM2." Acta Neuropathol. 2010 Apr;119(4):465-79. Epub 2010 Jan 12. PMID: 20066428
  9. Levin VA, Panchabhai SC, Shen L, Kornblau SM, Qiu Y, Baggerly KA. "Different changes in protein and phosphoprotein levels result from serum starvation of high-grade glioma and adenocarcinoma cell lines." J Proteome Res. 2010 Jan;9(1):179-91. PMID: 19894763
  10. Liedtke C, Wang J, Tordai A, Symmans WF, Hortobagyi GN, Kiesel L, Hess K, Baggerly KA, Coombes KR, Pusztai L. "Clinical evaluation of chemotherapy response predictors developed from breast cancer cell lines." Breast Cancer Res Treat. 2010 Jun;121(2):301-9. Epub 2009 Jul 15. PMID: 19603265


  1. Baggerly KA, Coombes KR. "Deriving Chemosensitivity from Cell Lines: Forensic Bioinformatics and Reproducible Research in High-Throughput Biology." Ann App Statist, 2009;3(4):1309-34.
  2. Cheung HC, Hai T, Zhu W, Baggerly KA, Tsavachidis S, Krahe R, Cote GJ. "Splicing factors PTBP1 and PTBP2 promote proliferation and migration of glioma cell lines." Brain. 2009 Aug;132(Pt 8):2277-88. Epub 2009 Jun 8. PMID: 19506066
  3. Hennessy BT, Gonzalez-Angulo AM, Stemke-Hale K, Gilcrease MZ, Krishnamurthy S, Lee JS, Fridlyand J, Sahin A, Agarwal R, Joy C, Liu W, Stivers D, Baggerly K, Carey M, Lluch A, Monteagudo C, He X, Weigman V, Fan C, Palazzo J, Hortobagyi GN, Nolden LK, Wang NJ, Valero V, Gray JW, Perou CM, Mills GB. "Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics." Cancer Res. 2009 May 15;69(10):4116-24. Epub 2009 May 12. PMID: 19435916
  4. Shahzad MM, Lu C, Lee JW, Stone RL, Mitra R, Mangala LS, Lu Y, Baggerly KA, Danes CG, Nick AM, Halder J, Kim HS, Vivas-Mejia P, Landen CN, Lopez-Berestein G, Coleman RL, Sood AK. "Dual targeting of EphA2 and FAK in ovarian carcinoma." Cancer Biol Ther. 2009 Jun;8(11):1027-34. Epub 2009 Jun 24. PMID: 19395869
  5. Neeley ES, Kornblau SM, Coombes KR, Baggerly KA. "Variable slope normalization of reverse phase protein arrays." Bioinformatics. 2009 Jun 1;25(11):1384-9. Epub 2009 Mar 31. PMID: 19336447
  6. Richards KL, Zhang B, Baggerly KA, Colella S, Lang JC, Schuller DE, Krahe R. "Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability." PLoS One. 2009;4(3):e4941. Epub 2009 Mar 18. PMID: 19293934
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