Complete List of Published Work: https://www.ncbi.nlm.nih.gov/myncbi/brooke.fridley.1/bibliography/public/

--2023—

  1. Wang X, Fridley BL. Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications. Methods in molecular biology. 2023;2629:1-9. doi: 10.1007/978-1-0716-2986-4_1. PubMed PMID: 36929070.
  2. Thomas M, Li J, King K, Persaud AK, Duah E, Vangundy Z, Hofmeister CC, Lamba JK, Tan AC, Fridley BL, Poi MJ, Seligson ND. PARP1 and POLD2 as prognostic biomarkers for multiple myeloma in autologous stem cell transplant. Haematologica. 2023. Epub 20230302. doi: 10.3324/haematol.2022.282399. PubMed PMID: 36861411.
  3. Skinner A, Buhlmann M, Fridley BL, Reed DR, Vicedo D, Mason NT. Pilot Study in Investigating Material Financial Toxicity Markers by Age in Cancer Patients. J Adolesc Young Adult Oncol. 2023;12(1):34-42. Epub 20220912. doi: 10.1089/jayao.2022.0011. PubMed PMID: 36094443; PMCID: PMC9968625.
  4. Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods in molecular biology. 2023;2629:115-40. doi: 10.1007/978-1-0716-2986-4_7. PubMed PMID: 36929076.
  5. Metts JL, Trucco M, Weiser DA, Thompson P, Sandler E, Smith T, Crimella J, Sansil S, Thapa R, Fridley BL, Llosa N, Badgett T, Gorlick R, Reed D, Gill J. A phase I trial of metformin in combination with vincristine, irinotecan, and temozolomide in children with relapsed or refractory solid and central nervous system tumors: A report from the national pediatric cancer foundation. Cancer Med. 2023;12(4):4270-81. Epub 20220923. doi: 10.1002/cam4.5297. PubMed PMID: 36151773; PMCID: PMC9972017.
  6. Hathaway CA, Wang T, Townsend MK, Vinci C, Jake-Schoffman DE, Saeed-Vafa D, Moran Segura C, Nguyen JV, Conejo-Garcia JR, Fridley BL, Tworoger SS. Lifetime Exposure to Cigarette Smoke and Risk of Ovarian Cancer by T-cell Tumor Immune Infiltration. Cancer Epidemiol Biomarkers Prev. 2023;32(1):66-73. doi: 10.1158/1055-9965.EPI-22-0877. PubMed PMID: 36318652; PMCID: PMC9839509.
  7. Hathaway CA, Conejo-Garcia JR, Fridley BL, Rosner B, Saeed-Vafa D, Moran Segura C, Nguyen JV, Hecht JL, Sasamoto N, Terry KL, Tworoger SS, Townsend MK. Measurement of ovarian tumor immune profiles by multiplex immunohistochemistry: implications for epidemiologic studies. Cancer Epidemiol Biomarkers Prev. 2023. Epub 20230320. doi: 10.1158/1055-9965.EPI-22-1285. PubMed PMID: 36940177.
  8. Fan S, Wilson CM, Fridley BL, Li Q. Statistics and Machine Learning in Mass Spectrometry-Based Metabolomics Analysis. Methods in molecular biology. 2023;2629:247-69. doi: 10.1007/978-1-0716-2986-4_12. PubMed PMID: 36929081.
  9. Chalise P, Kwon D, Fridley BL, Mo Q. Statistical Methods for Integrative Clustering of Multi-omics Data. Methods in molecular biology. 2023;2629:73-93. doi: 10.1007/978-1-0716-2986-4_5. PubMed PMID: 36929074.
  10. Abbas-Aghababazadeh F, Sasamoto N, Townsend MK, Huang T, Terry KL, Vitonis AF, Elias KM, Poole EM, Hecht JL, Tworoger SS, Fridley BL. Predictors of residual disease after debulking surgery in advanced stage ovarian cancer. Frontiers in oncology. 2023;13:1090092. Epub 20230124. doi: 10.3389/fonc.2023.1090092. PubMed PMID: 36761962; PMCID: PMC9902593. 

--2022--

  1. Wilson C, Soupir AC, Thapa R, Creed J, Nguyen J, Segura CM, Gerke T, Schildkraut JM, Peres LC, Fridley BL. Tumor immune cell clustering and its association with survival in African American women with ovarian cancer. PLoS Comput Biol. 2022;18(3):e1009900. Epub 20220302. doi: 10.1371/journal.pcbi.1009900. PubMed PMID: 35235563; PMCID: PMC8920290.
  2. Skinner A, Buhlmann M, Fridley BL, Reed DR, Vicedo D, Mason NT. Pilot Study in Investigating Material Financial Toxicity Markers by Age in Cancer Patients. J Adolesc Young Adult Oncol. 2022. Epub 20220912. doi: 10.1089/jayao.2022.0011. PubMed PMID: 36094443.
  3. Sasamoto N, Stewart PA, Wang T, Yoder SJ, Chellappan S, Hecht JL, Fridley BL, Terry KL, Tworoger SS. Lifetime ovulatory years and ovarian cancer gene expression profiles. J Ovarian Res. 2022;15(1):59. Epub 20220513. doi: 10.1186/s13048-022-00995-1. PubMed PMID: 35562768; PMCID: PMC9102743.
  4. Samanic CM, Teer JK, Thompson ZJ, Creed JH, Fridley BL, Burt Nabors L, Williams SL, Egan KM. Mitochondrial DNA sequence variation and risk of glioma. Mitochondrion. 2022;63:32-6. Epub 20220112. doi: 10.1016/j.mito.2022.01.002. PubMed PMID: 35032707; PMCID: PMC8885975.
  5. Peres LC, Colin-Leitzinger C, Sinha S, Marks JR, Conejo-Garcia JR, Alberg AJ, Bandera EV, Berchuck A, Bondy ML, Christensen BC, Cote ML, Doherty JA, Moorman PG, Peters ES, Moran Segura C, Nguyen JV, Schwartz AG, Terry PD, Wilson CM, Fridley BL, Schildkraut JM. Racial Differences in the Tumor Immune Landscape and Survival of Women with High-Grade Serous Ovarian Carcinoma. Cancer Epidemiol Biomarkers Prev. 2022;31(5):1006-16. doi: 10.1158/1055-9965.EPI-21-1334. PubMed PMID: 35244678; PMCID: PMC9081269.
  6. Ospina OE, Wilson CM, Soupir AC, Berglund A, Smalley I, Tsai KY, Fridley BL. spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics. Bioinformatics. 2022;38(9):2645-7. doi: 10.1093/bioinformatics/btac145. PubMed PMID: 35258565; PMCID: PMC9890305.
  7. Mitchell JR, Szepietowski P, Howard R, Reisman P, Jones JD, Lewis P, Fridley BL, Rollison DE. A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study. J Med Internet Res. 2022;24(3):e27210. Epub 20220323. doi: 10.2196/27210. PubMed PMID: 35319481; PMCID: PMC8987958.
  8. Metts JL, Trucco M, Weiser DA, Thompson P, Sandler E, Smith T, Crimella J, Sansil S, Thapa R, Fridley BL, Llosa N, Badgett T, Gorlick R, Reed D, Gill J. A phase I trial of metformin in combination with vincristine, irinotecan, and temozolomide in children with relapsed or refractory solid and central nervous system tumors: A report from the national pediatric cancer foundation. Cancer Med. 2022. Epub 20220923. doi: 10.1002/cam4.5297. PubMed PMID: 36151773.
  9. McLeod KL, Skinner AM, Beaupin LK, Vadaparampil ST, Fridley BL, Reed DR. Clinical Trial Availability by Location for 1000 Simulated AYA Patients. J Adolesc Young Adult Oncol. 2022;11(1):95-103. Epub 20210513. doi: 10.1089/jayao.2021.0014. PubMed PMID: 33983850; PMCID: PMC8864422.
  10. Liu X, Zhao B, Shaw TI, Fridley BL, Duckett DR, Tan AC, Teng M. Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. Nucleic Acids Res. 2022;50(6):3115-27. doi: 10.1093/nar/gkac141. PubMed PMID: 35234924; PMCID: PMC8989535.
  11. Kuznicki ML, Mallen A, Ha K, McClung EC, Castaneda AV, Cao B, Fridley BL, Chon HS, Chern JY, Hoffman M, Wenham RM, Matsuo K, Shahzad MMK. Prognostic features of endometrial cancer metastasis to the central nervous system. PLoS One. 2022;17(8):e0268794. Epub 20220826. doi: 10.1371/journal.pone.0268794. PubMed PMID: 36018828; PMCID: PMC9417007.
  12. Fasching PA, Liu D, Scully S, Ingle JN, Lyra PC, Rack B, Hein A, Ekici AB, Reis A, Schneeweiss A, Tesch H, Fehm TN, Heinrich G, Beckmann MW, Ruebner M, Huebner H, Lambrechts D, Madden E, Shen J, Romm J, Doheny K, Jenkins GD, Carlson EE, Li L, Fridley BL, Cunningham JM, Janni W, Monteiro ANA, Schaid DJ, Haberle L, Weinshilboum RM, Wang L. Identification of Two Genetic Loci Associated with Leukopenia after Chemotherapy in Patients with Breast Cancer. Clin Cancer Res. 2022;28(15):3342-55. doi: 10.1158/1078-0432.CCR-20-4774. PubMed PMID: 35653140; PMCID: PMC9357161.
  13. Buras AL, Wang T, Whiting J, Townsend MK, Fridley BL, Tworoger SS. Prospective Analyses of Sedentary Behavior in Relation to Risk of Ovarian Cancer. Am J Epidemiol. 2022;191(6):1021-9. doi: 10.1093/aje/kwac018. PubMed PMID: 35094053; PMCID: PMC9271222.

--2021--

  1. Yu X, Abbas-Aghababazadeh F, Chen YA, Fridley BL. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments. Methods in molecular biology. 2021;2194:143-75. Epub 2020/09/15. doi: 10.1007/978-1-0716-0849-4_9. PubMed PMID: 32926366; PMCID: PMC7771369.
  2. Mills M, Liveringhouse C, Lee F, Nanda RH, Ahmed KA, Washington IR, Thapa R, Fridley BL, Blumencranz P, Extermann M, Loftus L, Balducci L, Diaz R. The prevalence of luminal B subtype is higher in older postmenopausal women with ER+/HER2- breast cancer and is associated with inferior outcomes. J Geriatr Oncol. 2021;12(2):219-26. Epub 2020/08/30. doi: 10.1016/j.jgo.2020.08.007. PubMed PMID: 32859560; PMCID: PMC7907245.
  3. Mallen AR, Conley CC, Fuzzell L, Ketcher D, Augusto BM, McIntyre M, Barton LV, Townsend MK, Fridley BL, Tworoger SS, Wenham RM, Vadaparampil ST. "I think that a brief conversation from their provider can go a very long way": Patient and provider perspectives on barriers and facilitators of genetic testing after ovarian cancer. Support Care Cancer. 2021;29(5):2663-77. Epub 2020/09/26. doi: 10.1007/s00520-020-05779-1. PubMed PMID: 32975643; PMCID: PMC7981241.
  4. Kho PF, Amant F, Annibali D, Ashton K, Attia J, Auer PL, Beckmann MW, Black A, Brinton L, Buchanan DD, Chanock SJ, Chen C, Chen MM, Cheng THT, Cook LS, Crous-Bous M, Czene K, De Vivo I, Dennis J, Dork T, Dowdy SC, Dunning AM, Durst M, Easton DF, Ekici AB, Fasching PA, Fridley BL, Friedenreich CM, Garcia-Closas M, Gaudet MM, Giles GG, Goode EL, Gorman M, Haiman CA, Hall P, Hankinson SE, Hein A, Hillemanns P, Hodgson S, Hoivik EA, Holliday EG, Hunter DJ, Jones A, Kraft P, Krakstad C, Lambrechts D, Le Marchand L, Liang X, Lindblom A, Lissowska J, Long J, Lu L, Magliocco AM, Martin L, McEvoy M, Milne RL, Mints M, Nassir R, Otton G, Palles C, Pooler L, Proietto T, Rebbeck TR, Renner SP, Risch HA, Rubner M, Runnebaum I, Sacerdote C, Sarto GE, Schumacher F, Scott RJ, Setiawan VW, Shah M, Sheng X, Shu XO, Southey MC, Tham E, Tomlinson I, Trovik J, Turman C, Tyrer JP, Van Den Berg D, Wang Z, Wentzensen N, Xia L, Xiang YB, Yang HP, Yu H, Zheng W, Webb PM, Thompson DJ, Spurdle AB, Glubb DM, O'Mara TA. Mendelian randomization analyses suggest a role for cholesterol in the development of endometrial cancer. Int J Cancer. 2021;148(2):307-19. Epub 2020/08/28. doi: 10.1002/ijc.33206. PubMed PMID: 32851660; PMCID: PMC7757859.
  5. Wilson CM, Fridley BL, Conejo-Garcia JR, Wang X, Yu X. Wide and deep learning for automatic cell type identification. Comput Struct Biotechnol J. 2021;19:1052-62. Epub 2021/02/23. doi: 10.1016/j.csbj.2021.01.027. PubMed PMID: 33613870; PMCID: PMC7878986.
  6. Ward GA, McGraw KL, Abbas-Aghababazadeh F, Meyer BS, McLemore AF, Vincelette ND, Lam NB, Aldrich AL, Al Ali NH, Padron E, Pinilla-Ibarz J, Masala E, Santini V, Kosmider O, Fontenay M, Fenaux P, Johnson J, Fridley BL, List AF. Oxidized mitochondrial DNA released after inflammasome activation is a disease biomarker for myelodysplastic syndromes. Blood Adv. 2021;5(8):2216-28. Epub 2021/04/24. doi: 10.1182/bloodadvances.2020003475. PubMed PMID: 33890980.
  7. Damaghi M, West J, Robertson-Tessi M, Xu L, Ferrall-Fairbanks MC, Stewart PA, Persi E, Fridley BL, Altrock PM, Gatenby RA, Sims PA, Anderson ARA, Gillies RJ. The harsh microenvironment in early breast cancer selects for a Warburg phenotype. Proc Natl Acad Sci U S A. 2021;118(3). Epub 2021/01/17. doi: 10.1073/pnas.2011342118. PubMed PMID: 33452133; PMCID: PMC7826394.

 

--2020--

  1. Wilson CM, Li Q, Gaedigk R, Bi C, de Wildt SN, Leeder JS, Fridley BL. Ontogeny Related Changes in the Pediatric Liver Metabolome. Front Pediatr. 2020;8:549. Epub 2020/10/30. doi: 10.3389/fped.2020.00549. PubMed PMID: 33117761; PMCID: PMC7550739.
  2. Reed DR, Metts J, Pressley M, Fridley BL, Hayashi M, Isakoff MS, Loeb DM, Makanji R, Roberts RD, Trucco M, Wagner LM, Alexandrow MG, Gatenby RA, Brown JS. An evolutionary framework for treating pediatric sarcomas. Cancer. 2020;126(11):2577-87. Epub 2020/03/17. doi: 10.1002/cncr.32777. PubMed PMID: 32176331; PMCID: PMC7318114.
  3. Oesterheld JE, Reed DR, Setty BA, Isakoff MS, Thompson P, Yin H, Hayashi M, Loeb DM, Smith T, Makanji R, Fridley BL, Wagner LM. Phase II trial of gemcitabine and nab-paclitaxel in patients with recurrent Ewing sarcoma: A report from the National Pediatric Cancer Foundation. Pediatr Blood Cancer. 2020;67(7):e28370. Epub 2020/05/10. doi: 10.1002/pbc.28370. PubMed PMID: 32386107; PMCID: PMC7771264.
  4. Li Q, Fisher K, Meng W, Fang B, Welsh E, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen YA. GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics. 2020;36(1):257-63. Epub 2019/06/15. doi: 10.1093/bioinformatics/btz488. PubMed PMID: 31199438; PMCID: PMC6956786.
  5. Hicks JK, Quilitz RE, Komrokji RS, Kubal TE, Lancet JE, Pasikhova Y, Qin D, So W, Caceres G, Kelly K, Salchert YS, Shahbazian K, Abbas-Aghababazadeh F, Fridley BL, Velez AP, McLeod HL, Greene JN. Prospective CYP2C19-Guided Voriconazole Prophylaxis in Patients With Neutropenic Acute Myeloid Leukemia Reduces the Incidence of Subtherapeutic Antifungal Plasma Concentrations. Clin Pharmacol Ther. 2020;107(3):563-70. Epub 2019/09/25. doi: 10.1002/cpt.1641. PubMed PMID: 31549389; PMCID: PMC7018540.
  6. Chalise P, Ni Y, Fridley BL. Network-based integrative clustering of multiple types of genomic data using non-negative matrix factorization. Comput Biol Med. 2020;118:103625. Epub 2020/01/31. doi: 10.1016/j.compbiomed.2020.103625. PubMed PMID: 31999549; PMCID: PMC7078030.
  7. Abbas-Aghababazadeh F, Mo Q, Fridley BL. Statistical genomics in rare cancer. Semin Cancer Biol. 2020;61:1-10. Epub 2019/08/23. doi: 10.1016/j.semcancer.2019.08.021. PubMed PMID: 31437624; PMCID: PMC7771546.
  8. Reid BM, Fridley BL. DNA Methylation in Ovarian Cancer Susceptibility. Cancers (Basel). 2020;13(1). Epub 2021/01/06. doi: 10.3390/cancers13010108. PubMed PMID: 33396385; PMCID: PMC7795210.
  9. Mills M, Liveringhouse C, Lee F, Nanda RH, Ahmed KA, Washington IR, Thapa R, Fridley BL, Blumencranz P, Extermann M, Loftus L, Balducci L, Diaz R. The prevalence of luminal B subtype is higher in older postmenopausal women with ER+/HER2- breast cancer and is associated with inferior outcomes. J Geriatr Oncol. 2020. Epub 2020/08/30. doi: 10.1016/j.jgo.2020.08.007. PubMed PMID: 32859560.
  10. Kho PF, Amant F, Annibali D, Ashton K, Attia J, Auer PL, Beckmann MW, Black A, Brinton L, Buchanan DD, Chanock SJ, Chen C, Chen MM, Cheng THT, Cook LS, Crous-Bous M, Czene K, De Vivo I, Dennis J, Dork T, Dowdy SC, Dunning AM, Durst M, Easton DF, Ekici AB, Fasching PA, Fridley BL, Friedenreich CM, Garcia-Closas M, Gaudet MM, Giles GG, Goode EL, Gorman M, Haiman CA, Hall P, Hankinson SE, Hein A, Hillemanns P, Hodgson S, Hoivik EA, Holliday EG, Hunter DJ, Jones A, Kraft P, Krakstad C, Lambrechts D, Le Marchand L, Liang X, Lindblom A, Lissowska J, Long J, Lu L, Magliocco AM, Martin L, McEvoy M, Milne RL, Mints M, Nassir R, Otton G, Palles C, Pooler L, Proietto T, Rebbeck TR, Renner SP, Risch HA, Rubner M, Runnebaum I, Sacerdote C, Sarto GE, Schumacher F, Scott RJ, Setiawan VW, Shah M, Sheng X, Shu XO, Southey MC, Tham E, Tomlinson I, Trovik J, Turman C, Tyrer JP, Van Den Berg D, Wang Z, Wentzensen N, Xia L, Xiang YB, Yang HP, Yu H, Zheng W, Webb PM, Thompson DJ, Spurdle AB, Glubb DM, O'Mara TA. Mendelian randomization analyses suggest a role for cholesterol in the development of endometrial cancer. Int J Cancer. 2020. Epub 2020/08/28. doi: 10.1002/ijc.33206. PubMed PMID: 32851660.
  11. Broman KK, Joya L, Sun W, Zhou JM, Fridley B, Javedan K, Diaz R, Laronga C. Utility of Taking Additional Margins When Performing Breast-Conserving Surgery with Intraoperative Radiation Therapy for Early Breast Cancer. World J Surg. 2020;44(10):3410-6. Epub 2020/07/23. doi: 10.1007/s00268-020-05490-6. PubMed PMID: 32696098.
  12. Peres LC, Sinha S, Townsend MK, Fridley BL, Karlan BY, Lutgendorf SK, Shinn E, Sood AK, Tworoger SS. Predictors of survival trajectories among women with epithelial ovarian cancer. Gynecol Oncol. 2020;156(2):459-66. Epub 2019/12/17. doi: 10.1016/j.ygyno.2019.12.011. PubMed PMID: 31839342.
  13. Mallen AR, Conley CC, Townsend MK, Wells A, Boac BM, Todd S, Gandhi A, Kuznicki M, Augusto BM, McIntyre M, Fridley BL, Tworoger SS, Wenham RM, Vadaparampil ST. Patterns and predictors of genetic referral among ovarian cancer patients at a National Cancer Institute-Comprehensive Cancer Center. Clin Genet. 2020;97(2):370-5. Epub 2019/10/11. doi: 10.1111/cge.13654. PubMed PMID: 31600840.