InstitutionMD Anderson
DepartmentBioinformatics & Computational Biology
Address1400 Pressler St
Houston TX 77030-4008
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Nagaraja AS, Dood RL, Armaiz-Pena G, Kang Y, Wu SY, Allen JK, Jennings NB, Mangala LS, Pradeep S, Lyons Y, Haemmerle M, Gharpure KM, Sadaoui NC, Rodriguez-Aguayo C, Ivan C, Wang Y, Baggerly K, Ram P, Lopez-Berestein G, Liu J, Mok SC, Cohen L, Lutgendorf SK, Cole SW, Sood AK. Adrenergic-mediated increases in INHBA drive CAF phenotype and collagens. JCI Insight. 2021 Apr 08; 6(7). PMID: 33793425.
    2. Siedel JH, Ring KL, Hu W, Dood RL, Wang Y, Baggerly K, Darcy KM, Conrads TP, Gallagher S, Tshiaba P, Neff C, Timms KM, Mangala S, Westin SN, Broaddus R, Lopez-Berestein G, Lu KH, Coleman RL, Maxwell GL, Sood AK. Clinical significance of homologous recombination deficiency score testing in endometrial Cancer. Gynecol Oncol. 2021 Mar; 160(3):777-785. PMID: 33563487.
      Citations: 1     Fields:    
    3. Wen Y, Wang Y, Chelariu-Raicu A, Stur E, Liu Y, Corvigno S, Bartsch F, Redfern L, Zand B, Kang Y, Liu J, Baggerly K, Sood AK. Blockade of the Short Form of Prolactin Receptor Induces FOXO3a/EIF-4EBP1-Mediated Cell Death in Uterine Cancer. Mol Cancer Ther. 2020 09; 19(9):1943-1954. PMID: 32737156.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    4. Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK. Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer. Cell Rep. 2020 04 14; 31(2):107502. PMID: 32294438.
      Citations: 6     Fields:    
    5. Zeng Z, Liu W, Benton CB, Konoplev S, Lu H, Wang RY, Chen J, Shpall E, Baggerly KA, Champlin R, Konopleva M. Proteomic Profiling of Signaling Networks Modulated by G-CSF/Plerixafor/Busulfan-Fludarabine Conditioning in Acute Myeloid Leukemia Patients in Remission or with Active Disease prior to Allogeneic Stem Cell Transplantation. Acta Haematol. 2019; 142(3):176-184. PMID: 31112940.
      Citations: 1     Fields:    Translation:HumansCellsCTClinical Trials
    6. Guo CC, Majewski T, Zhang L, Yao H, Bondaruk J, Wang Y, Zhang S, Wang Z, Lee JG, Lee S, Cogdell D, Zhang M, Wei P, Grossman HB, Kamat A, Duplisea JJ, Ferguson JE, Huang H, Dadhania V, Gao J, Dinney C, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer. Cell Rep. 2019 05 07; 27(6):1781-1793.e4. PMID: 31067463.
      Citations: 13     Fields:    Translation:HumansCells
    7. McGuire MH, Herbrich SM, Dasari SK, Wu SY, Wang Y, Rupaimoole R, Lopez-Berestein G, Baggerly KA, Sood AK. Pan-cancer genomic analysis links 3'UTR DNA methylation with increased gene expression in T cells. EBioMedicine. 2019 May; 43:127-137. PMID: 31056473.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    8. Simmons AR, Fourkala EO, Gentry-Maharaj A, Ryan A, Sutton MN, Baggerly K, Zheng H, Lu KH, Jacobs I, Skates S, Menon U, Bast RC. Complementary Longitudinal Serum Biomarkers to CA125 for Early Detection of Ovarian Cancer. Cancer Prev Res (Phila). 2019 06; 12(6):391-400. PMID: 30967390.
      Citations: 4     Fields:    Translation:Humans
    9. Ragon BK, Odenike O, Baer MR, Stock W, Borthakur G, Patel K, Han L, Chen H, Ma H, Joseph L, Zhao Y, Baggerly K, Konopleva M, Jain N. Oral MEK 1/2 Inhibitor Trametinib in Combination With AKT Inhibitor GSK2141795 in Patients With Acute Myeloid Leukemia With RAS Mutations: A Phase II Study. Clin Lymphoma Myeloma Leuk. 2019 07; 19(7):431-440.e13. PMID: 31056348.
      Citations: 13     Fields:    Translation:HumansCTClinical Trials
    10. Majewski T, Yao H, Bondaruk J, Chung W, Lee S, Lee JG, Zhang S, Cogdell D, Yang G, Choi W, Dinney C, Grossman HB, Logothetis C, Scherer SE, Guo CC, Zhang L, Wei P, Weinstein JN, Issa JP, Baggerly K, McConkey DJ, Czerniak B. Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis. Cell Rep. 2019 02 19; 26(8):2241-2256.e4. PMID: 30784602.
      Citations: 8     Fields:    Translation:HumansCells
    11. Herbrich SM, Baggerly KA, Konopleva M. Refining statistics clarifies leukaemic stem cell genomics. Br J Haematol. 2019 06; 185(5):1005-1007. PMID: 30474856.
      Citations:    Fields:    Translation:HumansAnimals
    12. Villar-Prados A, Wu SY, Court KA, Ma S, LaFargue C, Chowdhury MA, Engelhardt MI, Ivan C, Ram PT, Wang Y, Baggerly K, Rodriguez-Aguayo C, Lopez-Berestein G, Ming-Yang S, Maloney DJ, Yoshioka M, Strovel JW, Roszik J, Sood AK. Predicting Novel Therapies and Targets: Regulation of Notch3 by the Bromodomain Protein BRD4. Mol Cancer Ther. 2019 02; 18(2):421-436. PMID: 30420565.
      Citations: 2     Translation:HumansAnimalsCells
    13. Dood RL, Zhao Y, Armbruster SD, Coleman RL, Tworoger S, Sood AK, Baggerly KA. Defining Survivorship Trajectories Across Patients With Solid Tumors: An Evidence-Based Approach. JAMA Oncol. 2018 11 01; 4(11):1519-1526. PMID: 29860375.
      Citations: 7     Fields:    Translation:Humans
    14. Gharpure KM, Pradeep S, Sans M, Rupaimoole R, Ivan C, Wu SY, Bayraktar E, Nagaraja AS, Mangala LS, Zhang X, Haemmerle M, Hu W, Rodriguez-Aguayo C, McGuire M, Mak CSL, Chen X, Tran MA, Villar-Prados A, Pena GA, Kondetimmanahalli R, Nini R, Koppula P, Ram P, Liu J, Lopez-Berestein G, Baggerly K, S Eberlin L, Sood AK. FABP4 as a key determinant of metastatic potential of ovarian cancer. Nat Commun. 2018 07 26; 9(1):2923. PMID: 30050129.
      Citations: 29     Fields:    Translation:HumansAnimalsCells
    15. Nagaraja AS, Dood RL, Armaiz-Pena G, Kang Y, Wu SY, Allen JK, Jennings NB, Mangala LS, Pradeep S, Lyons Y, Haemmerle M, Gharpure KM, Sadaoui NC, Rodriguez-Aguayo C, Ivan C, Wang Y, Baggerly K, Ram P, Lopez-Berestein G, Liu J, Mok SC, Cohen L, Lutgendorf SK, Cole SW, Sood AK. Adrenergic-mediated increases in INHBA drive CAF phenotype and collagens. JCI Insight. 2018 Jun 07; 3(11). PMID: 29889660.
      Citations:    Fields:    
    16. Baggerly K. Experimental Design, Randomization, and Validation. Clin Chem. 2018 10; 64(10):1534-1535. PMID: 29776951.
      Citations:    Fields:    Translation:Humans
    17. Gharpure KM, Lara OD, Wen Y, Pradeep S, LaFargue C, Ivan C, Rupaimoole R, Hu W, Mangala LS, Wu SY, Nagaraja AS, Baggerly K, Sood AK. ADH1B promotes mesothelial clearance and ovarian cancer infiltration. Oncotarget. 2018 May 18; 9(38):25115-25126. PMID: 29861857.
      Citations: 5     Fields:    
    18. Boulbes DR, Costello T, Baggerly K, Fan F, Wang R, Bhattacharya R, Ye X, Ellis LM. A Survey on Data Reproducibility and the Effect of Publication Process on the Ethical Reporting of Laboratory Research. Clin Cancer Res. 2018 07 15; 24(14):3447-3455. PMID: 29643062.
      Citations: 2     Fields:    Translation:Humans
    19. Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 04 09; 33(4):690-705.e9. PMID: 29622464.
      Citations: 101     Fields:    Translation:Humans
    20. Zhang S, Wang Y, Bondaruk J, Majewski T, Yao H, Lee S, Lee JG, Cogdell D, Lotan Y, Dinney C, Wei P, Baggerly K, Czerniak B. Detection of Bladder Cancer in Urine Sediments by a Novel Multicolor Fluorescence In Situ Hybridization (Quartet) Test. Eur Urol Focus. 2019 07; 5(4):664-675. PMID: 29428551.
      Citations: 1     Fields:    Translation:Humans
    21. Jiao J, Niu W, Wang Y, Baggerly K, Ye Y, Wu X, Davenport D, Almeda JL, Betancourt-Garcia MM, Forse RA, Stevenson HL, Watt GP, McCormick JB, Fisher-Hoch SP, Beretta L. Prevalence of Aflatoxin-Associated TP53R249S Mutation in Hepatocellular Carcinoma in Hispanics in South Texas. Cancer Prev Res (Phila). 2018 02; 11(2):103-112. PMID: 29089331.
      Citations: 6     Fields:    Translation:Humans
    22. Assel MJ, Li F, Wang Y, Allen AS, Baggerly KA, Vickers AJ. Genetic Polymorphisms of CFH and ARMS2 Do Not Predict Response to Antioxidants and Zinc in Patients with Age-Related Macular Degeneration: Independent Statistical Evaluations of Data from the Age-Related Eye Disease Study. Ophthalmology. 2018 03; 125(3):391-397. PMID: 29032853.
      Citations: 9     Fields:    Translation:Humans
    23. Jinesh GG, Manyam GC, Mmeje CO, Baggerly KA, Kamat AM. Surface PD-L1, E-cadherin, CD24, and VEGFR2 as markers of epithelial cancer stem cells associated with rapid tumorigenesis. Sci Rep. 2017 08 29; 7(1):9602. PMID: 28851898.
      Citations: 14     Fields:    Translation:HumansCells
    24. Lyons YA, Pradeep S, Wu SY, Haemmerle M, Hansen JM, Wagner MJ, Villar-Prados A, Nagaraja AS, Dood RL, Previs RA, Hu W, Zhao Y, Mak DH, Xiao Z, Melendez BD, Lizee GA, Mercado-Uribe I, Baggerly KA, Hwu P, Liu J, Overwijk WW, Coleman RL, Sood AK. Macrophage depletion through colony stimulating factor 1 receptor pathway blockade overcomes adaptive resistance to anti-VEGF therapy. Oncotarget. 2017 Nov 14; 8(57):96496-96505. PMID: 29228548.
      Citations: 16     Fields:    
    25. Zhang M, Adeniran AJ, Vikram R, Tamboli P, Pettaway C, Bondaruk J, Liu J, Baggerly K, Czerniak B. Carcinoma of the urethra. Hum Pathol. 2018 02; 72:35-44. PMID: 28827100.
      Citations: 3     Fields:    Translation:HumansCells
    26. Nagaraja AS, Dood RL, Armaiz-Pena G, Kang Y, Wu SY, Allen JK, Jennings NB, Mangala LS, Pradeep S, Lyons Y, Haemmerle M, Gharpure KM, Sadaoui NC, Rodriguez-Aguayo C, Ivan C, Wang Y, Baggerly K, Ram P, Lopez-Berestein G, Liu J, Mok SC, Cohen L, Lutgendorf SK, Cole SW, Sood AK. Adrenergic-mediated increases in INHBA drive CAF phenotype and collagens. JCI Insight. 2017 Aug 17; 2(16). PMID: 28814667.
      Citations: 11     Fields:    
    27. Lyons YA, Wu SY, Overwijk WW, Baggerly KA, Sood AK. Immune cell profiling in cancer: molecular approaches to cell-specific identification. NPJ Precis Oncol. 2017; 1(1):26. PMID: 29872708.
      Citations: 22     
    28. McDonnell SL, Baggerly KA, Baggerly CA, Aliano JL, French CB, Baggerly LL, Ebeling MD, Rittenberg CS, Goodier CG, Mateus Niño JF, Wineland RJ, Newman RB, Hollis BW, Wagner CL. Maternal 25(OH)D concentrations =40 ng/mL associated with 60% lower preterm birth risk among general obstetrical patients at an urban medical center. PLoS One. 2017; 12(7):e0180483. PMID: 28738090.
      Citations: 26     Fields:    Translation:Humans
    29. Wang Z, Kim TB, Peng B, Karam J, Creighton C, Joon A, Kawakami F, Trevisan P, Jonasch E, Chow CW, Canales JR, Tamboli P, Tannir N, Wood C, Monzon F, Baggerly K, Varella-Garcia M, Czerniak B, Wistuba I, Mills G, Shaw K, Chen K, Sircar K. Sarcomatoid Renal Cell Carcinoma Has a Distinct Molecular Pathogenesis, Driver Mutation Profile, and Transcriptional Landscape. Clin Cancer Res. 2017 Nov 01; 23(21):6686-6696. PMID: 28710314.
      Citations: 15     Fields:    Translation:Humans
    30. Zeng Z, Liu W, Tsao T, Qiu Y, Zhao Y, Samudio I, Sarbassov DD, Kornblau SM, Baggerly KA, Kantarjian HM, Konopleva M, Andreeff M. High-throughput profiling of signaling networks identifies mechanism-based combination therapy to eliminate microenvironmental resistance in acute myeloid leukemia. Haematologica. 2017 09; 102(9):1537-1548. PMID: 28659338.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    31. Yang WL, Gentry-Maharaj A, Simmons A, Ryan A, Fourkala EO, Lu Z, Baggerly KA, Zhao Y, Lu KH, Bowtell D, Jacobs I, Skates SJ, He WW, Menon U, Bast RC. Elevation of TP53 Autoantibody Before CA125 in Preclinical Invasive Epithelial Ovarian Cancer. Clin Cancer Res. 2017 Oct 01; 23(19):5912-5922. PMID: 28637689.
      Citations: 17     Fields:    Translation:Humans
    32. Lutgendorf SK, Shinn E, Carter J, Leighton S, Baggerly K, Guindani M, Fellman B, Matzo M, Slavich GM, Goodman MT, Tew W, Lester J, Moore KM, Karlan BY, Levine DA, Sood AK. Quality of life among long-term survivors of advanced stage ovarian cancer: A cross-sectional approach. Gynecol Oncol. 2017 07; 146(1):101-108. PMID: 28527672.
      Citations: 1     Fields:    Translation:Humans
    33. Lappe J, Watson P, Travers-Gustafson D, Recker R, Garland C, Gorham E, Baggerly K, McDonnell SL. Effect of Vitamin D and Calcium Supplementation on Cancer Incidence in Older Women: A Randomized Clinical Trial. JAMA. 2017 03 28; 317(12):1234-1243. PMID: 28350929.
      Citations: 51     Fields:    Translation:Humans
    34. Bottai G, Diao L, Baggerly KA, Paladini L, Gyorffy B, Raschioni C, Pusztai L, Calin GA, Santarpia L. Integrated MicroRNA-mRNA Profiling Identifies Oncostatin M as a Marker of Mesenchymal-Like ER-Negative/HER2-Negative Breast Cancer. Int J Mol Sci. 2017 Jan 19; 18(1). PMID: 28106823.
      Citations: 5     Fields:    Translation:HumansCells
    35. Mobley A, Zhang S, Bondaruk J, Wang Y, Majewski T, Caraway NP, Huang L, Shoshan E, Velazquez-Torres G, Nitti G, Lee S, Lee JG, Fuentes-Mattei E, Willis D, Zhang L, Guo CC, Yao H, Baggerly K, Lotan Y, Lerner SP, Dinney C, McConkey D, Bar-Eli M, Czerniak B. Aurora Kinase A is a Biomarker for Bladder Cancer Detection and Contributes to its Aggressive Behavior. Sci Rep. 2017 01 19; 7:40714. PMID: 28102366.
      Citations: 16     Fields:    Translation:HumansCells
    36. Doecke JD, Wang Y, Baggerly K. Co-localized genomic regulation of miRNA and mRNA via DNA methylation affects survival in multiple tumor types. Cancer Genet. 2016 Oct; 209(10):463-473. PMID: 27810075.
      Citations: 9     Fields:    Translation:HumansCells
    37. Dadhania V, Zhang M, Zhang L, Bondaruk J, Majewski T, Siefker-Radtke A, Guo CC, Dinney C, Cogdell DE, Zhang S, Lee S, Lee JG, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Meta-Analysis of the Luminal and Basal Subtypes of Bladder Cancer and the Identification of Signature Immunohistochemical Markers for Clinical Use. EBioMedicine. 2016 Oct; 12:105-117. PMID: 27612592.
      Citations: 69     Fields:    Translation:Humans
    38. Zhang L, Baladandayuthapani V, Zhu H, Baggerly KA, Majewski T, Czerniak BA, Morris JS. Functional CAR models for large spatially correlated functional datasets. J Am Stat Assoc. 2016; 111(514):772-786. PMID: 28018013.
      Citations: 4     
    39. Wu SY, Rupaimoole R, Shen F, Pradeep S, Pecot CV, Ivan C, Nagaraja AS, Gharpure KM, Pham E, Hatakeyama H, McGuire MH, Haemmerle M, Vidal-Anaya V, Olsen C, Rodriguez-Aguayo C, Filant J, Ehsanipour EA, Herbrich SM, Maiti SN, Huang L, Kim JH, Zhang X, Han HD, Armaiz-Pena GN, Seviour EG, Tucker S, Zhang M, Yang D, Cooper LJ, Ali-Fehmi R, Bar-Eli M, Lee JS, Ram PT, Baggerly KA, Lopez-Berestein G, Hung MC, Sood AK. A miR-192-EGR1-HOXB9 regulatory network controls the angiogenic switch in cancer. Nat Commun. 2016 Apr 04; 7:11169. PMID: 27041221.
      Citations: 47     Fields:    Translation:HumansAnimalsCells
    40. Misganaw B, Ahsen E, Singh N, Baggerly KA, Unruh A, White MA, Vidyasagar M. Optimized Prediction of Extreme Treatment Outcomes in Ovarian Cancer. Cancer Inform. 2015; 14(Suppl 5):45-55. PMID: 27034613.
    41. Guo CC, Dadhania V, Zhang L, Majewski T, Bondaruk J, Sykulski M, Wronowska W, Gambin A, Wang Y, Zhang S, Fuentes-Mattei E, Kamat AM, Dinney C, Siefker-Radtke A, Choi W, Baggerly KA, McConkey D, Weinstein JN, Czerniak B. Gene Expression Profile of the Clinically Aggressive Micropapillary Variant of Bladder Cancer. Eur Urol. 2016 10; 70(4):611-620. PMID: 26988609.
      Citations: 37     Fields:    Translation:HumansCells
    42. Zand B, Previs RA, Zacharias NM, Rupaimoole R, Mitamura T, Nagaraja AS, Guindani M, Dalton HJ, Yang L, Baddour J, Achreja A, Hu W, Pecot CV, Ivan C, Wu SY, McCullough CR, Gharpure KM, Shoshan E, Pradeep S, Mangala LS, Rodriguez-Aguayo C, Wang Y, Nick AM, Davies MA, Armaiz-Pena G, Liu J, Lutgendorf SK, Baggerly KA, Eli MB, Lopez-Berestein G, Nagrath D, Bhattacharya PK, Sood AK. Role of Increased n-acetylaspartate Levels in Cancer. J Natl Cancer Inst. 2016 Jan 26; 108(6):djv426. PMID: 26819345.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    43. Yang H, Das P, Yu Y, Mao W, Wang Y, Baggerly K, Wang Y, Marquez RT, Bedi A, Liu J, Fishman D, Lu Z, Bast RC. NDN is an imprinted tumor suppressor gene that is downregulated in ovarian cancers through genetic and epigenetic mechanisms. Oncotarget. 2016 Jan 19; 7(3):3018-32. PMID: 26689988.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    44. Shields BB, Pecot CV, Gao H, McMillan E, Potts M, Nagel C, Purinton S, Wang Y, Ivan C, Kim HS, Borkowski RJ, Khan S, Rodriguez-Aguayo C, Lopez-Berestein G, Lea J, Gazdar A, Baggerly KA, Sood AK, White MA. A genome-scale screen reveals context-dependent ovarian cancer sensitivity to miRNA overexpression. Mol Syst Biol. 2015 Dec 11; 11(12):842. PMID: 26655797.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    45. Wagner CL, Baggerly C, McDonnell S, Baggerly KA, French CB, Baggerly L, Hamilton SA, Hollis BW. Post-hoc analysis of vitamin D status and reduced risk of preterm birth in two vitamin D pregnancy cohorts compared with South Carolina March of Dimes 2009-2011 rates. J Steroid Biochem Mol Biol. 2016 Jan; 155(Pt B):245-51. PMID: 26554936.
      Citations: 39     Fields:    Translation:Humans
    46. Aparicio AM, Shen L, Tapia EL, Lu JF, Chen HC, Zhang J, Wu G, Wang X, Troncoso P, Corn P, Thompson TC, Broom B, Baggerly K, Maity SN, Logothetis CJ. Combined Tumor Suppressor Defects Characterize Clinically Defined Aggressive Variant Prostate Cancers. Clin Cancer Res. 2016 Mar 15; 22(6):1520-30. PMID: 26546618.
      Citations: 58     Fields:    Translation:HumansCells
    47. Boland GM, Piha-Paul SA, Subbiah V, Routbort M, Herbrich SM, Baggerly K, Patel KP, Brusco L, Horombe C, Naing A, Fu S, Hong DS, Janku F, Johnson A, Broaddus R, Luthra R, Shaw K, Mendelsohn J, Mills GB, Meric-Bernstam F. Clinical next generation sequencing to identify actionable aberrations in a phase I program. Oncotarget. 2015 Aug 21; 6(24):20099-110. PMID: 26015395.
      Citations: 22     Fields:    Translation:HumansCTClinical Trials
    48. Sircar K, Yoo SY, Majewski T, Wani K, Patel LR, Voicu H, Torres-Garcia W, Verhaak RG, Tannir N, Karam JA, Jonasch E, Wood CG, Tamboli P, Baggerly KA, Aldape KD, Czerniak B. Biphasic components of sarcomatoid clear cell renal cell carcinomas are molecularly similar to each other, but distinct from, non-sarcomatoid renal carcinomas. J Pathol Clin Res. 2015 Oct; 1(4):212-24. PMID: 27499906.
      Citations: 4     Fields:    
    49. Singh RR, Murugan P, Patel LR, Voicu H, Yoo SY, Majewski T, Mehrotra M, Wani K, Tannir N, Karam JA, Jonasch E, Wood CG, Creighton CJ, Medeiros LJ, Broaddus RR, Tamboli P, Baggerly KA, Aldape KD, Czerniak B, Luthra R, Sircar K. Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma: challenges for personalized therapy. Mod Pathol. 2015 Sep; 28(9):1225-35. PMID: 26111976.
      Citations: 10     Fields:    Translation:HumansCells
    50. Aslan B, Monroig P, Hsu MC, Pena GA, Rodriguez-Aguayo C, Gonzalez-Villasana V, Rupaimoole R, Nagaraja AS, Mangala S, Han HD, Yuca E, Wu SY, Ivan C, Moss TJ, Ram PT, Wang H, Gol-Chambers A, Ozkayar O, Kanlikilicer P, Fuentes-Mattei E, Kahraman N, Pradeep S, Ozpolat B, Tucker S, Hung MC, Baggerly K, Bartholomeusz G, Calin G, Sood AK, Lopez-Berestein G. The ZNF304-integrin axis protects against anoikis in cancer. Nat Commun. 2015 Jun 17; 6:7351. PMID: 26081979.
      Citations: 16     Fields:    Translation:HumansCells
    51. Choi HH, Guma S, Fang L, Phan L, Ivan C, Baggerly K, Sood A, Lee MH. Regulating the stability and localization of CDK inhibitor p27(Kip1) via CSN6-COP1 axis. Cell Cycle. 2015; 14(14):2265-73. PMID: 25945542.
      Citations: 11     Translation:HumansAnimalsCells
    52. Daver N, Boumber Y, Kantarjian H, Ravandi F, Cortes J, Rytting ME, Kawedia JD, Basnett J, Culotta KS, Zeng Z, Lu H, Richie MA, Garris R, Xiao L, Liu W, Baggerly KA, Jabbour E, O'Brien S, Burger J, Bendall LJ, Thomas D, Konopleva M. A Phase I/II Study of the mTOR Inhibitor Everolimus in Combination with HyperCVAD Chemotherapy in Patients with Relapsed/Refractory Acute Lymphoblastic Leukemia. Clin Cancer Res. 2015 Jun 15; 21(12):2704-14. PMID: 25724525.
      Citations: 17     Fields:    Translation:HumansCellsCTClinical Trials
    53. Huang X, Cao M, Wang L, Wu S, Liu X, Li H, Zhang H, Wang RY, Sun X, Wei C, Baggerly KA, Roth JA, Wang M, Swisher SG, Fang B. Expression of sulfotransferase SULT1A1 in cancer cells predicts susceptibility to the novel anticancer agent NSC-743380. Oncotarget. 2015 Jan 01; 6(1):345-54. PMID: 25514600.
      Citations: 5     Fields:    Translation:HumansCells
    54. Zhang S, Lu Z, Unruh AK, Ivan C, Baggerly KA, Calin GA, Li Z, Bast RC, Le XF. Clinically relevant microRNAs in ovarian cancer. Mol Cancer Res. 2015 Mar; 13(3):393-401. PMID: 25304686.
      Citations: 38     Fields:    Translation:Humans
    55. Hayashi N, Manyam GC, Gonzalez-Angulo AM, Niikura N, Yamauchi H, Nakamura S, Hortobágyi GN, Baggerly KA, Ueno NT. Reverse-phase protein array for prediction of patients at low risk of developing bone metastasis from breast cancer. Oncologist. 2014 Sep; 19(9):909-14. PMID: 25117064.
      Citations: 6     Fields:    Translation:Humans
    56. Rytelewski M, Tong JG, Buensuceso A, Leong HS, Maleki Vareki S, Figueredo R, Di Cresce C, Wu SY, Herbrich SM, Baggerly KA, Romanow L, Shepherd T, Deroo BJ, Sood AK, Chambers AF, Vincent M, Ferguson PJ, Koropatnick J. BRCA2 inhibition enhances cisplatin-mediated alterations in tumor cell proliferation, metabolism, and metastasis. Mol Oncol. 2014 Dec; 8(8):1429-40. PMID: 24974076.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    57. Stone RL, Baggerly KA, Armaiz-Pena GN, Kang Y, Sanguino AM, Thanapprapasr D, Dalton HJ, Bottsford-Miller J, Zand B, Akbani R, Diao L, Nick AM, DeGeest K, Lopez-Berestein G, Coleman RL, Lutgendorf S, Sood AK. Focal adhesion kinase: an alternative focus for anti-angiogenesis therapy in ovarian cancer. Cancer Biol Ther. 2014 Jul; 15(7):919-29. PMID: 24755674.
      Citations: 12     Translation:HumansAnimalsCells
    58. Tucker SL, Gharpure K, Herbrich SM, Unruh AK, Nick AM, Crane EK, Coleman RL, Guenthoer J, Dalton HJ, Wu SY, Rupaimoole R, Lopez-Berestein G, Ozpolat B, Ivan C, Hu W, Baggerly KA, Sood AK. Molecular biomarkers of residual disease after surgical debulking of high-grade serous ovarian cancer. Clin Cancer Res. 2014 Jun 15; 20(12):3280-8. PMID: 24756370.
      Citations: 25     Fields:    Translation:Humans
    59. Hu W, Liu T, Ivan C, Sun Y, Huang J, Mangala LS, Miyake T, Dalton HJ, Pradeep S, Rupaimoole R, Previs RA, Han HD, Bottsford-Miller J, Zand B, Kang Y, Pecot CV, Nick AM, Wu SY, Lee JS, Sehgal V, Ram P, Liu J, Tucker SL, Lopez-Berestein G, Baggerly KA, Coleman RL, Sood AK. Notch3 pathway alterations in ovarian cancer. Cancer Res. 2014 Jun 15; 74(12):3282-93. PMID: 24743243.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    60. Wu SY, Yang X, Gharpure KM, Hatakeyama H, Egli M, McGuire MH, Nagaraja AS, Miyake TM, Rupaimoole R, Pecot CV, Taylor M, Pradeep S, Sierant M, Rodriguez-Aguayo C, Choi HJ, Previs RA, Armaiz-Pena GN, Huang L, Martinez C, Hassell T, Ivan C, Sehgal V, Singhania R, Han HD, Su C, Kim JH, Dalton HJ, Kovvali C, Keyomarsi K, McMillan NA, Overwijk WW, Liu J, Lee JS, Baggerly KA, Lopez-Berestein G, Ram PT, Nawrot B, Sood AK. 2'-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity. Nat Commun. 2014 Mar 12; 5:3459. PMID: 24619206.
      Citations: 35     Fields:    Translation:HumansAnimalsCells
    61. Cho MS, Vasquez HG, Rupaimoole R, Pradeep S, Wu S, Zand B, Han HD, Rodriguez-Aguayo C, Bottsford-Miller J, Huang J, Miyake T, Choi HJ, Dalton HJ, Ivan C, Baggerly K, Lopez-Berestein G, Sood AK, Afshar-Kharghan V. Autocrine effects of tumor-derived complement. Cell Rep. 2014 Mar 27; 6(6):1085-1095. PMID: 24613353.
      Citations: 67     Fields:    Translation:HumansAnimalsCells
    62. Konopleva MY, Walter RB, Faderl SH, Jabbour EJ, Zeng Z, Borthakur G, Huang X, Kadia TM, Ruvolo PP, Feliu JB, Lu H, Debose L, Burger JA, Andreeff M, Liu W, Baggerly KA, Kornblau SM, Doyle LA, Estey EH, Kantarjian HM. Preclinical and early clinical evaluation of the oral AKT inhibitor, MK-2206, for the treatment of acute myelogenous leukemia. Clin Cancer Res. 2014 Apr 15; 20(8):2226-35. PMID: 24583795.
      Citations: 30     Fields:    Translation:HumansCellsCTClinical Trials
    63. Choi W, Porten S, Kim S, Willis D, Plimack ER, Hoffman-Censits J, Roth B, Cheng T, Tran M, Lee IL, Melquist J, Bondaruk J, Majewski T, Zhang S, Pretzsch S, Baggerly K, Siefker-Radtke A, Czerniak B, Dinney CP, McConkey DJ. Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. Cancer Cell. 2014 Feb 10; 25(2):152-65. PMID: 24525232.
      Citations: 440     Fields:    Translation:Humans
    64. Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD. illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000Res. 2013; 2:264. PMID: 24701342.
      Citations: 16     Fields:    
    65. Masuda H, Baggerly KA, Wang Y, Iwamoto T, Brewer T, Pusztai L, Kai K, Kogawa T, Finetti P, Birnbaum D, Dirix L, Woodward WA, Reuben JM, Krishnamurthy S, Symmans W, Van Laere SJ, Bertucci F, Hortobagyi GN, Ueno NT. Comparison of molecular subtype distribution in triple-negative inflammatory and non-inflammatory breast cancers. Breast Cancer Res. 2013 Nov 25; 15(6):R112. PMID: 24274653.
      Citations: 18     Fields:    Translation:Humans
    66. Bachinski LL, Baggerly KA, Neubauer VL, Nixon TJ, Raheem O, Sirito M, Unruh AK, Zhang J, Nagarajan L, Timchenko LT, Bassez G, Eymard B, Gamez J, Ashizawa T, Mendell JR, Udd B, Krahe R. Most expression and splicing changes in myotonic dystrophy type 1 and type 2 skeletal muscle are shared with other muscular dystrophies. Neuromuscul Disord. 2014 Mar; 24(3):227-40. PMID: 24332166.
      Citations: 15     Fields:    Translation:HumansCells
    67. Liu T, Hu W, Dalton HJ, Choi HJ, Huang J, Kang Y, Pradeep S, Miyake T, Song JH, Wen Y, Lu C, Pecot CV, Bottsford-Miller J, Zand B, Jennings NB, Ivan C, Gallick GE, Baggerly KA, Hangauer DG, Coleman RL, Frumovitz M, Sood AK. Targeting SRC and tubulin in mucinous ovarian carcinoma. Clin Cancer Res. 2013 Dec 01; 19(23):6532-43. PMID: 24100628.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    68. Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID: 24071849.
      Citations: 1694     Fields:    Translation:Humans
    69. Wang W, Baggerly KA, Knudsen S, Askaa J, Mazin W, Coombes KR. Independent validation of a model using cell line chemosensitivity to predict response to therapy. J Natl Cancer Inst. 2013 Sep 04; 105(17):1284-91. PMID: 23964133.
      Citations: 9     Fields:    Translation:HumansCells
    70. Masuda H, Baggerly KA, Wang Y, Zhang Y, Gonzalez-Angulo AM, Meric-Bernstam F, Valero V, Lehmann BD, Pietenpol JA, Hortobagyi GN, Symmans WF, Ueno NT. Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes. Clin Cancer Res. 2013 Oct 01; 19(19):5533-40. PMID: 23948975.
      Citations: 206     Fields:    Translation:Humans
    71. Simmons AR, Baggerly K, Bast RC. The emerging role of HE4 in the evaluation of epithelial ovarian and endometrial carcinomas. Oncology (Williston Park). 2013 Jun; 27(6):548-56. PMID: 23909069.
      Citations: 21     Fields:    Translation:Humans
    72. Sankaranarayanapillai M, Zhang N, Baggerly KA, Gelovani JG. Metabolic shifts induced by fatty acid synthase inhibitor orlistat in non-small cell lung carcinoma cells provide novel pharmacodynamic biomarkers for positron emission tomography and magnetic resonance spectroscopy. Mol Imaging Biol. 2013 Apr; 15(2):136-47. PMID: 22886728.
      Citations: 7     Fields:    Translation:HumansCells
    73. Xie X, Bartholomeusz C, Ahmed AA, Kazansky A, Diao L, Baggerly KA, Hortobagyi GN, Ueno NT. Bisphosphorylated PEA-15 sensitizes ovarian cancer cells to paclitaxel by impairing the microtubule-destabilizing effect of SCLIP. Mol Cancer Ther. 2013 Jun; 12(6):1099-111. PMID: 23543364.
      Citations: 10     Translation:HumansCells
    74. Baggerly K. More data, please! Clin Chem. 2013 Mar; 59(3):459-61. PMID: 23340443.
      Citations: 2     Fields:    Translation:Humans
    75. Pecot CV, Rupaimoole R, Yang D, Akbani R, Ivan C, Lu C, Wu S, Han HD, Shah MY, Rodriguez-Aguayo C, Bottsford-Miller J, Liu Y, Kim SB, Unruh A, Gonzalez-Villasana V, Huang L, Zand B, Moreno-Smith M, Mangala LS, Taylor M, Dalton HJ, Sehgal V, Wen Y, Kang Y, Baggerly KA, Lee JS, Ram PT, Ravoori MK, Kundra V, Zhang X, Ali-Fehmi R, Gonzalez-Angulo AM, Massion PP, Calin GA, Lopez-Berestein G, Zhang W, Sood AK. Tumour angiogenesis regulation by the miR-200 family. Nat Commun. 2013; 4:2427. PMID: 24018975.
      Citations: 155     Fields:    Translation:HumansCells
    76. Ivan C, Hu W, Bottsford-Miller J, Zand B, Dalton HJ, Liu T, Huang J, Nick AM, Lopez-Berestein G, Coleman RL, Baggerly KA, Sood AK. Epigenetic analysis of the Notch superfamily in high-grade serous ovarian cancer. Gynecol Oncol. 2013 Mar; 128(3):506-11. PMID: 23200915.
      Citations: 12     Fields:    Translation:HumansCells
    77. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27; 489(7417):519-25. PMID: 22960745.
      Citations: 1419     Fields:    Translation:HumansCells
    78. Zeng Z, Shi YX, Tsao T, Qiu Y, Kornblau SM, Baggerly KA, Liu W, Jessen K, Liu Y, Kantarjian H, Rommel C, Fruman DA, Andreeff M, Konopleva M. Targeting of mTORC1/2 by the mTOR kinase inhibitor PP242 induces apoptosis in AML cells under conditions mimicking the bone marrow microenvironment. Blood. 2012 Sep 27; 120(13):2679-89. PMID: 22826565.
      Citations: 55     Fields:    Translation:HumansAnimalsCells
    79. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487(7407):330-7. PMID: 22810696.
      Citations: 2908     Fields:    Translation:HumansCells
    80. Neeley ES, Baggerly KA, Kornblau SM. Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots. Cancer Inform. 2012; 11:77-86. PMID: 22550399.
      Citations: 21     
    81. Levin VA, Panchabhai S, Shen L, Baggerly KA. Protein and phosphoprotein levels in glioma and adenocarcinoma cell lines grown in normoxia and hypoxia in monolayer and three-dimensional cultures. Proteome Sci. 2012 Jan 25; 10(1):5. PMID: 22276931.
      Citations: 9     
    82. Nick AM, Stone RL, Armaiz-Pena G, Ozpolat B, Tekedereli I, Graybill WS, Landen CN, Villares G, Vivas-Mejia P, Bottsford-Miller J, Kim HS, Lee JS, Kim SM, Baggerly KA, Ram PT, Deavers MT, Coleman RL, Lopez-Berestein G, Sood AK. Silencing of p130cas in ovarian carcinoma: a novel mechanism for tumor cell death. J Natl Cancer Inst. 2011 Nov 02; 103(21):1596-612. PMID: 21957230.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    83. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15. PMID: 21720365.
      Citations: 2657     Fields:    Translation:HumansCells
    84. Baggerly KA, Coombes KR. What information should be required to support clinical "omics" publications? Clin Chem. 2011 May; 57(5):688-90. PMID: 21364027.
      Citations: 18     Fields:    Translation:Humans
    85. Diao L, Clarke CH, Coombes KR, Hamilton SR, Roth J, Mao L, Czerniak B, Baggerly KA, Morris JS, Fung ET, Bast RC. Reproducibility of SELDI Spectra Across Time and Laboratories. Cancer Inform. 2011 Mar 14; 10:45-64. PMID: 21552492.
      Citations: 7     
    86. Suominen T, Bachinski LL, Auvinen S, Hackman P, Baggerly KA, Angelini C, Peltonen L, Krahe R, Udd B. Population frequency of myotonic dystrophy: higher than expected frequency of myotonic dystrophy type 2 (DM2) mutation in Finland. Eur J Hum Genet. 2011 Jul; 19(7):776-82. PMID: 21364698.
      Citations: 38     Fields:    Translation:Humans
    87. Chumbalkar V, Latha K, Hwang Y, Maywald R, Hawley L, Sawaya R, Diao L, Baggerly K, Cavenee WK, Furnari FB, Bogler O. Analysis of phosphotyrosine signaling in glioblastoma identifies STAT5 as a novel downstream target of ?EGFR. J Proteome Res. 2011 Mar 04; 10(3):1343-52. PMID: 21214269.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    88. Bachinski LL, Sirito M, Böhme M, Baggerly KA, Udd B, Krahe R. Altered MEF2 isoforms in myotonic dystrophy and other neuromuscular disorders. Muscle Nerve. 2010 Dec; 42(6):856-63. PMID: 21104860.
      Citations: 14     Fields:    Translation:HumansCells
    89. 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. 2011 Mar 17; 30(11):1329-40. PMID: 21057542.
      Citations: 18     Fields:    Translation:HumansCells
    90. Wang J, Byers LA, Yordy JS, Liu W, Shen L, Baggerly KA, Giri U, Myers JN, Ang KK, Story MD, Girard L, Minna JD, Heymach JV, Coombes KR. Blasted cell line names. Cancer Inform. 2010 Oct 14; 9:251-5. PMID: 21082038.
    91. 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. 2011 Feb 01; 117(3):606-17. PMID: 20945327.
      Citations: 36     Fields:    Translation:HumansCells
    92. Mazouni C, Baggerly K, Hawke D, Tsavachidis S, André 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.
      Citations: 6     Fields:    Translation:Humans
    93. Baggerly K. Disclose all data in publications. Nature. 2010 Sep 23; 467(7314):401. PMID: 20864982.
      Citations: 21     Fields:    Translation:Humans
    94. 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 10; 11(10):733-9. PMID: 20838408.
      Citations: 596     Fields:    
    95. 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. PMID: 20068086.
      Citations: 36     Fields:    Translation:Humans
    96. 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, Edström 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. PMID: 20066428.
      Citations: 22     Fields:    Translation:HumansCells
    97. 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.
      Citations: 28     Fields:    Translation:HumansCells
    98. Morris JS, Baggerly KA, Gutstein HB, Coombes KR. Statistical contributions to proteomic research. Methods Mol Biol. 2010; 641:143-66. PMID: 20407946.
      Citations: 2     Fields:    Translation:Humans
    99. 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. PMID: 19603265.
      Citations: 21     Fields:    Translation:HumansCells
    100. 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. PMID: 19395869.
      Citations: 30     Translation:HumansAnimals
    101. 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. PMID: 19506066.
      Citations: 57     Fields:    Translation:HumansCells
    102. 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. PMID: 19435916.
      Citations: 342     Fields:    Translation:HumansCells
    103. Neeley ES, Kornblau SM, Coombes KR, Baggerly KA. Variable slope normalization of reverse phase protein arrays. Bioinformatics. 2009 Jun 01; 25(11):1384-9. PMID: 19336447.
      Citations: 44     Fields:    
    104. 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. PMID: 19293934.
      Citations: 51     Fields:    Translation:HumansCells
    105. Colella S, Richards KL, Bachinski LL, Baggerly KA, Tsavachidis S, Lang JC, Schuller DE, Krahe R. Molecular signatures of metastasis in head and neck cancer. Head Neck. 2008 Oct; 30(10):1273-83. PMID: 18642293.
      Citations: 14     Fields:    Translation:HumansCells
    106. Park HS, Park WS, Bondaruk J, Tanaka N, Katayama H, Lee S, Spiess PE, Steinberg JR, Wang Z, Katz RL, Dinney C, Elias KJ, Lotan Y, Naeem RC, Baggerly K, Sen S, Grossman HB, Czerniak B. Quantitation of Aurora kinase A gene copy number in urine sediments and bladder cancer detection. J Natl Cancer Inst. 2008 Oct 01; 100(19):1401-11. PMID: 18812553.
      Citations: 31     Fields:    Translation:HumansCells
    107. Cheung HC, Baggerly KA, Tsavachidis S, Bachinski LL, Neubauer VL, Nixon TJ, Aldape KD, Cote GJ, Krahe R. Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays. BMC Genomics. 2008 May 12; 9:216. PMID: 18474104.
      Citations: 36     Fields:    Translation:HumansCells
    108. Majewski T, Lee S, Jeong J, Yoon DS, Kram A, Kim MS, Tuziak T, Bondaruk J, Lee S, Park WS, Tang KS, Chung W, Shen L, Ahmed SS, Johnston DA, Grossman HB, Dinney CP, Zhou JH, Harris RA, Snyder C, Filipek S, Narod SA, Watson P, Lynch HT, Gazdar A, Bar-Eli M, Wu XF, McConkey DJ, Baggerly K, Issa JP, Benedict WF, Scherer SE, Czerniak B. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy. Lab Invest. 2008 Jul; 88(7):694-721. PMID: 18458673.
      Citations: 17     Fields:    Translation:HumansCells
    109. Baggerly KA, Coombes KR, Neeley ES. Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer. J Clin Oncol. 2008 Mar 01; 26(7):1186-7; author reply 1187-8. PMID: 18309960.
      Citations: 26     Fields:    Translation:Humans
    110. Kassouf W, Black PC, Tuziak T, Bondaruk J, Lee S, Brown GA, Adam L, Wei C, Baggerly K, Bar-Eli M, McConkey D, Czerniak B, Dinney CP. Distinctive expression pattern of ErbB family receptors signifies an aggressive variant of bladder cancer. J Urol. 2008 Jan; 179(1):353-8. PMID: 18006009.
      Citations: 27     Fields:    Translation:Humans
    111. Coombes KR, Wang J, Baggerly KA. Microarrays: retracing steps. Nat Med. 2007 Nov; 13(11):1276-7; author reply 1277-8. PMID: 17987014.
      Citations: 45     Fields:    Translation:HumansCells
    112. Morris JS, Brown PJ, Herrick RC, Baggerly KA, Coombes KR. Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models. Biometrics. 2008 Jun; 64(2):479-89. PMID: 17888041.
      Citations: 37     Fields:    Translation:Cells
    113. Lee S, Jeong J, Majewski T, Scherer SE, Kim MS, Tuziak T, Tang KS, Baggerly K, Grossman HB, Zhou JH, Shen L, Bondaruk J, Ahmed SS, Samanta S, Spiess P, Wu X, Filipek S, McConkey D, Bar-Eli M, Issa JP, Benedict WF, Czerniak B. Forerunner genes contiguous to RB1 contribute to the development of in situ neoplasia. Proc Natl Acad Sci U S A. 2007 Aug 21; 104(34):13732-7. PMID: 17702869.
      Citations: 15     Fields:    Translation:HumansCells
    114. Hu J, He X, Baggerly KA, Coombes KR, Hennessy BT, Mills GB. Non-parametric quantification of protein lysate arrays. Bioinformatics. 2007 Aug 01; 23(15):1986-94. PMID: 17599930.
      Citations: 114     Fields:    
    115. Wu C, Zhao H, Baggerly K, Carta R, Zhang L. Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays. Bioinformatics. 2007 Oct 01; 23(19):2566-72. PMID: 17537749.
      Citations: 12     Fields:    Translation:Cells
    116. Karpievitch YV, Hill EG, Smolka AJ, Morris JS, Coombes KR, Baggerly KA, Almeida JS. PrepMS: TOF MS data graphical preprocessing tool. Bioinformatics. 2007 Jan 15; 23(2):264-5. PMID: 17121773.
      Citations: 14     Fields:    
    117. Kolonin MG, Sun J, Do KA, Vidal CI, Ji Y, Baggerly KA, Pasqualini R, Arap W. Synchronous selection of homing peptides for multiple tissues by in vivo phage display. FASEB J. 2006 May; 20(7):979-81. PMID: 16581960.
      Citations: 47     Fields:    Translation:AnimalsCells
    118. Bast RC, Badgwell D, Lu Z, Marquez R, Rosen D, Liu J, Baggerly KA, Atkinson EN, Skates S, Zhang Z, Lokshin A, Menon U, Jacobs I, Lu K. New tumor markers: CA125 and beyond. Int J Gynecol Cancer. 2005 Nov-Dec; 15 Suppl 3:274-81. PMID: 16343244.
      Citations: 144     Fields:    Translation:Humans
    119. Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, Hung MC, Kuerer HM. Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics. 2005 Nov; 5(16):4107-17. PMID: 16254928.
      Citations: 68     Fields:    Translation:Humans
    120. Marquez RT, Baggerly KA, Patterson AP, Liu J, Broaddus R, Frumovitz M, Atkinson EN, Smith DI, Hartmann L, Fishman D, Berchuck A, Whitaker R, Gershenson DM, Mills GB, Bast RC, Lu KH. Patterns of gene expression in different histotypes of epithelial ovarian cancer correlate with those in normal fallopian tube, endometrium, and colon. Clin Cancer Res. 2005 Sep 01; 11(17):6116-26. PMID: 16144910.
      Citations: 107     Fields:    Translation:Humans
    121. Tuziak T, Jeong J, Majewski T, Kim MS, Steinberg J, Wang Z, Yoon DS, Kuang TC, Baggerly K, Johnston D, Czerniak B. High-resolution whole-organ mapping with SNPs and its significance to early events of carcinogenesis. Lab Invest. 2005 May; 85(5):689-701. PMID: 15908911.
      Citations: 5     Fields:    Translation:HumansCells
    122. Kim JH, Tuziak T, Hu L, Wang Z, Bondaruk J, Kim M, Fuller G, Dinney C, Grossman HB, Baggerly K, Zhang W, Czerniak B. Alterations in transcription clusters underlie development of bladder cancer along papillary and nonpapillary pathways. Lab Invest. 2005 Apr; 85(4):532-49. PMID: 15778693.
      Citations: 17     Fields:    Translation:HumansCells
    123. Abba MC, Hu Y, Sun H, Drake JA, Gaddis S, Baggerly K, Sahin A, Aldaz CM. Gene expression signature of estrogen receptor alpha status in breast cancer. BMC Genomics. 2005 Mar 11; 6:37. PMID: 15762987.
      Citations: 61     Fields:    Translation:HumansCells
    124. Coombes KR, Morris JS, Hu J, Edmonson SR, Baggerly KA. Serum proteomics profiling--a young technology begins to mature. Nat Biotechnol. 2005 Mar; 23(3):291-2. PMID: 15765078.
      Citations: 43     Fields:    
    125. Baggerly KA, Morris JS, Edmonson SR, Coombes KR. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst. 2005 Feb 16; 97(4):307-9. PMID: 15713966.
      Citations: 55     Fields:    Translation:Humans
    126. Hu J, Coombes KR, Morris JS, Baggerly KA. The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic. 2005 Feb; 3(4):322-31. PMID: 15814023.
      Citations: 36     Fields:    Translation:Humans
    127. Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics. 2005 May 01; 21(9):1764-75. PMID: 15673564.
      Citations: 80     Fields:    Translation:HumansCTClinical Trials
    128. Koomen JM, Zhao H, Li D, Nasser W, Hawke DH, Abbruzzese JL, Baggerly KA, Kobayashi R. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Rapid Commun Mass Spectrom. 2005; 19(12):1624-36. PMID: 15915451.
      Citations: 1     Fields:    Translation:HumansCells
    129. Baggerly KA, Coombes KR, Morris JS. Bias, randomization, and ovarian proteomic data: a reply to "producers and consumers". Cancer Inform. 2005; 1:9-14. PMID: 19305627.
      Citations: 10     
    130. Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R. Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Inform. 2005; 1:41-52. PMID: 19305631.
      Citations: 24     
    131. Baggerly KA, Edmonson SR, Morris JS, Coombes KR. High-resolution serum proteomic patterns for ovarian cancer detection. Endocr Relat Cancer. 2004 Dec; 11(4):583-4; author reply 585-7. PMID: 15613439.
      Citations: 17     Fields:    Translation:Humans
    132. Hu Y, Sun H, Drake J, Kittrell F, Abba MC, Deng L, Gaddis S, Sahin A, Baggerly K, Medina D, Aldaz CM. From mice to humans: identification of commonly deregulated genes in mammary cancer via comparative SAGE studies. Cancer Res. 2004 Nov 01; 64(21):7748-55. PMID: 15520179.
      Citations: 26     Fields:    Translation:HumansAnimals
    133. Baggerly KA, Deng L, Morris JS, Aldaz CM. Overdispersed logistic regression for SAGE: modelling multiple groups and covariates. BMC Bioinformatics. 2004 Oct 06; 5:144. PMID: 15469612.
      Citations: 24     Fields:    Translation:HumansCells
    134. Abba MC, Drake JA, Hawkins KA, Hu Y, Sun H, Notcovich C, Gaddis S, Sahin A, Baggerly K, Aldaz CM. Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression. Breast Cancer Res. 2004; 6(5):R499-513. PMID: 15318932.
      Citations: 50     Fields:    Translation:HumansCells
    135. Wu Z, Irizarry RA. Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004 Jun; 22(6):656-8; author reply 658. PMID: 15175677.
      Citations: 174     Fields:    Translation:Cells
    136. Zhang L, Wu C, Carta R, Baggerly K, Coombes KR. Response to Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004 Jun; 22(6):658. PMID: 15175679.
      Citations: 3     Fields:    Translation:Cells
    137. Lu KH, Patterson AP, Wang L, Marquez RT, Atkinson EN, Baggerly KA, Ramoth LR, Rosen DG, Liu J, Hellstrom I, Smith D, Hartmann L, Fishman D, Berchuck A, Schmandt R, Whitaker R, Gershenson DM, Mills GB, Bast RC. Selection of potential markers for epithelial ovarian cancer with gene expression arrays and recursive descent partition analysis. Clin Cancer Res. 2004 May 15; 10(10):3291-300. PMID: 15161682.
      Citations: 150     Fields:    Translation:HumansCells
    138. Pusztai L, Gregory BW, Baggerly KA, Peng B, Koomen J, Kuerer HM, Esteva FJ, Symmans WF, Wagner P, Hortobagyi GN, Laronga C, Semmes OJ, Wright GL, Drake RR, Vlahou A. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer. 2004 May 01; 100(9):1814-22. PMID: 15112261.
      Citations: 22     Fields:    Translation:Humans
    139. Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics. 2004 Mar 22; 20(5):777-85. PMID: 14751995.
      Citations: 127     Fields:    Translation:Humans
    140. Koomen JM, Zhao H, Li D, Abbruzzese J, Baggerly K, Kobayashi R. Diagnostic protein discovery using proteolytic peptide targeting and identification. Rapid Commun Mass Spectrom. 2004; 18(21):2537-48. PMID: 15468157.
      Citations: 2     Fields:    Translation:Humans
    141. Coombes KR, Fritsche HA, Clarke C, Chen JN, Baggerly KA, Morris JS, Xiao LC, Hung MC, Kuerer HM. Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin Chem. 2003 Oct; 49(10):1615-23. PMID: 14500586.
      Citations: 31     Fields:    Translation:Humans
    142. Morris JS, Baggerly KA, Coombes KR. Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE. Biometrics. 2003 Sep; 59(3):476-86. PMID: 14601748.
      Citations: 9     Fields:    Translation:Humans
    143. Baggerly KA, Morris JS, Wang J, Gold D, Xiao LC, Coombes KR. A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics. 2003 Sep; 3(9):1667-72. PMID: 12973722.
      Citations: 35     Fields:    Translation:Humans
    144. Baggerly KA, Deng L, Morris JS, Aldaz CM. Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics. 2003 Aug 12; 19(12):1477-83. PMID: 12912827.
      Citations: 141     Fields:    
    145. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques. 2003 Jul; 35(1):146-50. PMID: 12866414.
      Citations: 199     Fields:    Translation:Cells
    146. Hu L, Wang J, Baggerly K, Wang H, Fuller GN, Hamilton SR, Coombes KR, Zhang W. Obtaining reliable information from minute amounts of RNA using cDNA microarrays. BMC Genomics. 2002 Jun 21; 3:16. PMID: 12086591.
      Citations: 28     Fields:    
    147. Coombes KR, Highsmith WE, Krogmann TA, Baggerly KA, Stivers DN, Abruzzo LV. Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. J Comput Biol. 2002; 9(4):655-69. PMID: 12323099.
      Citations: 12     Fields:    Translation:HumansCells
    148. Hess KR, Zhang W, Baggerly KA, Stivers DN, Coombes KR. Microarrays: handling the deluge of data and extracting reliable information. Trends Biotechnol. 2001 Nov; 19(11):463-8. PMID: 11602311.
      Citations: 28     Fields:    Translation:Humans
    149. Ramdas L, Coombes KR, Baggerly K, Abruzzo L, Highsmith WE, Krogmann T, Hamilton SR, Zhang W. Sources of nonlinearity in cDNA microarray expression measurements. Genome Biol. 2001; 2(11):RESEARCH0047. PMID: 11737946.
      Citations: 25     Fields:    Translation:Cells
    150. Baggerly KA. Probability binning and testing agreement between multivariate immunofluorescence histograms: extending the chi-squared test. Cytometry. 2001 Oct 01; 45(2):141-50. PMID: 11590626.
      Citations: 1     Fields:    
    151. Baggerly KA, Coombes KR, Hess KR, Stivers DN, Abruzzo LV, Zhang W. Identifying differentially expressed genes in cDNA microarray experiments. J Comput Biol. 2001; 8(6):639-59. PMID: 11747617.
      Citations: 19     Fields:    Translation:HumansCells
    152. Johnson DH, Gruner CM, Baggerly K, Seshagiri C. Information-theoretic analysis of neural coding. J Comput Neurosci. 2001 Jan-Feb; 10(1):47-69. PMID: 11316339.
      Citations: 21     Fields:    
    153. Zera EM, Molloy DP, Angleson JK, Lamture JB, Wensel TG, Malinski JA. Low affinity interactions of GDPbetaS and ribose- or phosphoryl-substituted GTP analogues with the heterotrimeric G protein, transducin. J Biol Chem. 1996 May 31; 271(22):12925-31. PMID: 11821895.
      Citations: 153     Fields:    Translation:HumansCells
    154. Axelrod DE, Baggerly KA, Kimmel M. Gene amplification by unequal sister chromatid exchange: probabilistic modeling and analysis of drug resistance data. J Theor Biol. 1994 May 21; 168(2):151-9. PMID: 8022195.
      Citations: 3     Fields:    Translation:AnimalsCells
    155. White RA, Terry NH, Baggerly KA, Meistrich ML. Measuring cell proliferation by relative movement. I. Introduction and in vitro studies. Cell Prolif. 1991 May; 24(3):257-70. PMID: 2039802.
      Citations: 1     Fields:    Translation:AnimalsCells
    156. NDN is an imprinted tumor suppressor gene that is downregulated in ovarian cancers through genetic and epigenetic mechanisms. Oncotarget. 7:3018-3032.
    157. illuminaio. F1000Research. 2.
    158. Statistical considerations in the assessment of cDNA microarray data obtained using amplification. 21-36.
    159. Empirical likelihood as a goodness-of-fit measure. Biometrika. 85:535-547.
    160. Creating synthetic baseline populations. Transportation Research Part A: Policy and Practice. 30:415-429.
    161. Co-localized genomic regulation of miRNA and mRNA via DNA methylation affects survival in multiple tumor types. Cancer genetics. 209:463-473.
    162. Bias, randomization, and ovarian proteomic data. Cancer Informatics. 1:9-14.
    163. Deriving chemosensitivity from cell lines. Annals of Applied Statistics. 3:1309-1334.
    164. Optimized prediction of extreme treatment outcomes in ovarian cancer. Cancer Informatics. 15:45-55.
    165. Comparison of sample-labeling techniques in DNA microarray experiments. Analytica Chimica Acta. 506:117-125.
    166. Adaptive importance sampling on discrete Markov chains. Annals of Applied Probability. 9:391-412.
    167. Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Informatics. 1:41-52.
    168. A miR-192-EGR1-HOXB9 regulatory network controls the angiogenic switch in cancer. Nature Communications. 7.
    169. The ZNF304-integrin axis protects against anoikis in cancer. Nature Communications. 6.
    170. Clinically relevant microRNAs in ovarian cancer. Molecular Cancer Research. 13:393-401.
    171. Obtaining reliable information from minute amounts of RNA using cDNA microarrays. BMC Genomics. 3.
    172. Combined tumor suppressor defects characterize clinically defined aggressive variant prostate cancers. Clinical Cancer Research. 22:1520-1530.
    173. The emerging role of HE4 in the evaluation of epithelial Ovarian and endometrial carcinomas. ONCOLOGY (United States). 27.
    174. Expression of sulfotransferase SULT1A1 in cancer cells predicts susceptibility to the novel anticancer agent NSC-743380. Oncotarget. 6:345-354.
    175. Role of Increased n-acetylaspartate Levels in Cancer. Journal of the National Cancer Institute. 108.
    176. Meta-Analysis of the Luminal and Basal Subtypes of Bladder Cancer and the Identification of Signature Immunohistochemical Markers for Clinical Use. EBioMedicine. 12:105-117.
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    179. Gene expression signature of estrogen receptor α status in breast cancer. BMC Genomics. 6.
    180. Regulating the stability and localization of CDK inhibitor p27Kip1 via CSN6-COP1 axis. Cell Cycle. 14:2265-2273.
    181. A genome-scale screen reveals context-dependent ovarian cancer sensitivity to miRNA overexpression. Molecular Systems Biology. 11:1-17.
    182. Studentizing microarray data. 49-59.
    183. Erratum. Breast Cancer Research. 7:32.
    184. Functional CAR Models for Large Spatially Correlated Functional Datasets. Journal of the American Statistical Association. 111:772-786.
    185. Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma. Modern Pathology. 28:1225-1235.
    186. Bayesian reliability analysis of high-reliability systems of binomial and poisson subsystems. International Journal of Reliability, Quality and Safety Engineering. 4:283-307.
    187. Clinical next generation sequencing to identify actionable aberrations in a phase I program. Oncotarget. 6:20099-20110.
    188. Cross-validation of multivariate densities. Journal of the American Statistical Association. 89:807-817.
    189. A phase I/II study of the mTOR inhibitor everolimus in combination with hyperCVAD chemotherapy in patients with relapsed/refractory acute lymphoblastic leukemia. Clinical Cancer Research. 21:2704-2714.
    190. Gene Expression Profile of the Clinically Aggressive Micropapillary Variant of Bladder Cancer. European Urology.
    191. Exponential convergence of adaptive importance sampling for Markov chains. Journal of Applied Probability. 37:342-358.
    192. Comprehensive molecular portraits of human breast tumours. Nature. 490:61-70.
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