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James C. Costello

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-PHARM General Operations
Phone303/724-8619

    Collapse Research 
    Collapse research activities and funding
    R13CA291000     (COSTELLO, JAMES CHRISTOPHER)Jul 11, 2024 - Jun 30, 2025
    NIH
    Systems Approaches to Cancer Biology Meeting
    Role: Principal Investigator
    R01CA268055     (THEODORESCU, DAN)Aug 1, 2022 - Jul 31, 2027
    NIH
    NPEPPS is a novel and druggable determinant of chemotherapy resistance in bladder cancer
    Role: Co-Principal Investigator
    R21CA241647     (TYEKUCHEVA, SVITLANA)Mar 1, 2020 - Feb 28, 2022
    NIH
    Curated prostate cancer data for novel and reproducible prognostic modeling
    Role: Co-Principal Investigator
    U01CA231978     (COSTELLO, JAMES CHRISTOPHER)Sep 1, 2019 - Aug 31, 2024
    NIH
    Systems analysis of aggressive prostate cancer pathology
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    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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    1. Jeong D, Morse B, Polk SL, Chen DT, Li J, Hodul P, Centeno BA, Costello J, Jiang K, Machado S, El Naqa I, Farah PT, Huynh T, Raghunand N, Mok S, Dam A, Malafa M, Qayyum A, Fleming JB, Permuth JB. Pancreatic Cyst Size Measurement on Magnetic Resonance Imaging Compared to Pathology. Cancers (Basel). 2024 Jan 01; 16(1). PMID: 38201633.
      View in: PubMed
    2. Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Rep Med. 2024 01 16; 5(1):101350. PMID: 38134931.
      View in: PubMed
    3. Taniguchi CM, Frakes JM, Aguilera TA, Palta M, Czito B, Bhutani MS, Colbert LE, Abi Jaoude J, Bernard V, Pant S, Tzeng CD, Kim DW, Malafa M, Costello J, Mathew G, Rebueno N, Koay EJ, Das P, Ludmir EB, Katz MHG, Wolff RA, Beddar S, Sawakuchi GO, Moningi S, Slack Tidwell RS, Yuan Y, Thall PF, Beardsley RA, Holmlund J, Herman JM, Hoffe SE. Stereotactic body radiotherapy with or without selective dismutase mimetic in pancreatic adenocarcinoma: an adaptive, randomised, double-blind, placebo-controlled, phase 1b/2 trial. Lancet Oncol. 2023 12; 24(12):1387-1398. PMID: 38039992.
      View in: PubMed
    4. Hughes CJ, Fields KM, Danis EP, Hsu JY, Neelakantan D, Vincent MY, Gustafson AL, Oliphant MJ, Sreekanth V, Zaberezhnyy V, Costello JC, Jedlicka P, Ford HL. SIX1 and EWS/FLI1 co-regulate an anti-metastatic gene network in Ewing Sarcoma. Nat Commun. 2023 07 19; 14(1):4357. PMID: 37468459.
      View in: PubMed
    5. Thomas SN, Niemeyer BF, Jimenez-Valdes RJ, Kaiser AJ, Espinosa JM, Sullivan KD, Goodspeed A, Costello JC, Alder JK, Ca?as-Arranz R, Garc?a-Sastre A, Benam KH. Down syndrome is associated with altered frequency and functioning of tracheal multiciliated cells, and response to influenza virus infection. iScience. 2023 Aug 18; 26(8):107361. PMID: 37554445.
      View in: PubMed
    6. Laajala TD, Sreekanth V, Soupir AC, Creed JH, Halkola AS, Calboli FCF, Singaravelu K, Orman MV, Colin-Leitzinger C, Gerke T, Fridley BL, Tyekucheva S, Costello JC. A harmonized resource of integrated prostate cancer clinical, -omic, and signature features. Sci Data. 2023 07 05; 10(1):430. PMID: 37407670.
      View in: PubMed
    7. de Jong FC, Laajala TD, Hoedemaeker RF, Jordan KR, van der Made ACJ, Boev? ER, van der Schoot DKE, Nieuwkamer B, Janssen EAM, Mahmoudi T, Boormans JL, Theodorescu D, Costello JC, Zuiverloon TCM. Non-muscle-invasive bladder cancer molecular subtypes predict differential response to intravesical Bacillus Calmette-Gu?rin. Sci Transl Med. 2023 05 24; 15(697):eabn4118. PMID: 37224225.
      View in: PubMed
    8. Romano G, Paradiso F, Li P, Shukla P, Barger LN, El Naggar O, Miller JP, Liang RJ, Helms TL, Lazar AJ, Wargo JA, Taraballi F, Costello JC, Kwong LN. Microparticle-Delivered Cxcl9 Prolongs Braf Inhibitor Efficacy in Melanoma. Cancer Immunol Res. 2023 05 03; 11(5):558-569. PMID: 36820825.
      View in: PubMed
    9. Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv. 2023 Apr 11. PMID: 36945505.
      View in: PubMed
    10. Laajala TD, Sreekanth V, Soupir A, Creed J, Calboli FC, Singaravelu K, Orman M, Colin-Leitzinger C, Gerke T, Fidley BL, Tyekucheva S, Costello JC. curatedPCaData: Integration of clinical, genomic, and signature features in a curated and harmonized prostate cancer data resource. bioRxiv. 2023 Jan 19. PMID: 36711769.
      View in: PubMed
    11. Lee AJ, Mould DL, Crawford J, Hu D, Powers RK, Doing G, Costello JC, Hogan DA, Greene CS. SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. Genomics Proteomics Bioinformatics. 2022 10; 20(5):912-927. PMID: 36216026.
      View in: PubMed
    12. Rinaldetti S, Zhou Q, Abbott JM, de Jong FC, Esquer H, Costello JC, Theodorescu D, LaBarbera DV. High-Content Drug Discovery Targeting Molecular Bladder Cancer Subtypes. Int J Mol Sci. 2022 Sep 14; 23(18). PMID: 36142576.
      View in: PubMed
    13. Camp FA, Brunetti TM, Williams MM, Christenson JL, Sreekanth V, Costello JC, Hay ZLZ, Kedl RM, Richer JK, Slansky JE. Antigens Expressed by Breast Cancer Cells Undergoing EMT Stimulate Cytotoxic CD8+ T Cell Immunity. Cancers (Basel). 2022 Sep 09; 14(18). PMID: 36139558.
      View in: PubMed
    14. Sun D, Nguyen TM, Allaway RJ, Wang J, Chung V, Yu TV, Mason M, Dimitrovsky I, Ericson L, Li H, Guan Y, Israel A, Olar A, Pataki BA, Stolovitzky G, Guinney J, Gulko PS, Frazier MB, Chen JY, Costello JC, Bridges SL. A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis. JAMA Netw Open. 2022 08 01; 5(8):e2227423. PMID: 36036935.
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    15. Shull LC, Lencer ES, Kim HM, Goyama S, Kurokawa M, Costello JC, Jones K, Artinger KB. PRDM paralogs antagonistically balance Wnt/?-catenin activity during craniofacial chondrocyte differentiation. Development. 2022 02 15; 149(4). PMID: 35132438.
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    16. Hsu JY, Danis EP, Nance S, O'Brien JH, Gustafson AL, Wessells VM, Goodspeed AE, Talbot JC, Amacher SL, Jedlicka P, Black JC, Costello JC, Durbin AD, Artinger KB, Ford HL. SIX1 reprograms myogenic transcription factors to maintain the rhabdomyosarcoma undifferentiated state. Cell Rep. 2022 02 01; 38(5):110323. PMID: 35108532.
      View in: PubMed
    17. M?rquez-Ortiz RA, Contreras-Z?rate MJ, Tesic V, Alvarez-Eraso KLF, Kwak G, Littrell Z, Costello JC, Sreekanth V, Ormond DR, Karam SD, Kabos P, Cittelly DM. IL13Ra2 Promotes Proliferation and Outgrowth of Breast Cancer Brain Metastases. Clin Cancer Res. 2021 11 15; 27(22):6209-6221. PMID: 34544797.
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    18. Jillson LK, Yette GA, Laajala TD, Tilley WD, Costello JC, Cramer SD. Androgen Receptor Signaling in Prostate Cancer Genomic Subtypes. Cancers (Basel). 2021 Jun 30; 13(13). PMID: 34208794.
      View in: PubMed
    19. Tarca AL, Pataki B?, Romero R, Sirota M, Guan Y, Kutum R, Gomez-Lopez N, Done B, Bhatti G, Yu T, Andreoletti G, Chaiworapongsa T, Hassan SS, Hsu CD, Aghaeepour N, Stolovitzky G, Csabai I, Costello JC. Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. Cell Rep Med. 2021 06 15; 2(6):100323. PMID: 34195686.
      View in: PubMed
    20. Sottnik JL, Bordeaux EK, Mehrotra S, Ferrara SE, Goodspeed AE, Costello JC, Sikora MJ. Mediator of DNA Damage Checkpoint 1 (MDC1) Is a Novel Estrogen Receptor Coregulator in Invasive Lobular Carcinoma of the Breast. Mol Cancer Res. 2021 08; 19(8):1270-1282. PMID: 33947745.
      View in: PubMed
    21. Jillson LK, Rider LC, Rodrigues LU, Romero L, Karimpour-Fard A, Nieto C, Gillette C, Torkko K, Danis E, Smith EE, Nolley R, Peehl DM, Lucia MS, Costello JC, Cramer SD. MAP3K7 Loss Drives Enhanced Androgen Signaling and Independently Confers Risk of Recurrence in Prostate Cancer with Joint Loss of CHD1. Mol Cancer Res. 2021 07; 19(7):1123-1136. PMID: 33846123.
      View in: PubMed
    22. Mueller AC, Piper M, Goodspeed A, Bhuvane S, Williams JS, Bhatia S, Phan AV, Van Court B, Zolman KL, Pe?a B, Oweida AJ, Zakem S, Meguid C, Knitz MW, Darragh L, Bickett TE, Gadwa J, Mestroni L, Taylor MRG, Jordan KR, Dempsey P, Lucia MS, McCarter MD, Del Chiaro M, Messersmith WA, Schulick RD, Goodman KA, Gough MJ, Greene CS, Costello JC, Neto AG, Lagares D, Hansen KC, Van Bokhoven A, Karam SD. Induction of ADAM10 by Radiation Therapy Drives Fibrosis, Resistance, and Epithelial-to-Mesenchyal Transition in Pancreatic Cancer. Cancer Res. 2021 06 15; 81(12):3255-3269. PMID: 33526513.
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    23. Tu MM, Abdel-Hafiz HA, Jones RT, Jean A, Hoff KJ, Duex JE, Chauca-Diaz A, Costello JC, Dancik GM, Tamburini BAJ, Czerniak B, Kaye J, Theodorescu D. Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy. Commun Biol. 2020 11 27; 3(1):720. PMID: 33247183.
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    24. Joshi M, Kim J, D'Alessandro A, Monk E, Bruce K, Elajaili H, Nozik-Grayck E, Goodspeed A, Costello JC, Schlaepfer IR. CPT1A Over-Expression Increases Reactive Oxygen Species in the Mitochondria and Promotes Antioxidant Defenses in Prostate Cancer. Cancers (Basel). 2020 Nov 18; 12(11). PMID: 33218188.
      View in: PubMed
    25. McCann TS, Parrish JK, Hsieh J, Sechler M, Sobral LM, Self C, Jones KL, Goodspeed A, Costello JC, Jedlicka P. KDM5A and PHF2 positively control expression of pro-metastatic genes repressed by EWS/Fli1, and promote growth and metastatic properties in Ewing sarcoma. Oncotarget. 2020 Oct 27; 11(43):3818-3831. PMID: 33196691.
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    26. Greene CS, Costello JC. Biologically Informed Neural Networks Predict Drug Responses. Cancer Cell. 2020 11 09; 38(5):613-615. PMID: 33096022.
      View in: PubMed
    27. Jordan KR, Sikora MJ, Slansky JE, Minic A, Richer JK, Moroney MR, Hu J, Wolsky RJ, Watson ZL, Yamamoto TM, Costello JC, Clauset A, Behbakht K, Kumar TR, Bitler BG. The Capacity of the Ovarian Cancer Tumor Microenvironment to Integrate Inflammation Signaling Conveys a Shorter Disease-free Interval. Clin Cancer Res. 2020 12 01; 26(23):6362-6373. PMID: 32928797.
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    28. Sobral LM, Hicks HM, Parrish JK, McCann TS, Hsieh J, Goodspeed A, Costello JC, Black JC, Jedlicka P. KDM3A/Ets1 epigenetic axis contributes to PAX3/FOXO1-driven and independent disease-promoting gene expression in fusion-positive Rhabdomyosarcoma. Mol Oncol. 2020 10; 14(10):2471-2486. PMID: 32697014.
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    29. Stern JL, Paucek RD, Huang FW, Ghandi M, Nwumeh R, Costello JC, Cech TR. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes. Cell Rep. 2020 May 26; 31(8):107718. PMID: 32460014.
      View in: PubMed
    30. Zhou H, Blevins MA, Hsu JY, Kong D, Galbraith MD, Goodspeed A, Culp-Hill R, Oliphant MUJ, Ramirez D, Zhang L, Trinidad-Pineiro J, Mathews Griner L, King R, Barnaeva E, Hu X, Southall NT, Ferrer M, Gustafson DL, Regan DP, D'Alessandro A, Costello JC, Patnaik S, Marugan J, Zhao R, Ford HL. Identification of a Small-Molecule Inhibitor That Disrupts the SIX1/EYA2 Complex, EMT, and Metastasis. Cancer Res. 2020 06 15; 80(12):2689-2702. PMID: 32341035.
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    31. Stern JL, Hibshman G, Hu K, Ferrara SE, Costello JC, Kim W, Tamayo P, Cech TR, Huang FW. Mesenchymal and MAPK Expression Signatures Associate with Telomerase Promoter Mutations in Multiple Cancers. Mol Cancer Res. 2020 07; 18(7):1050-1062. PMID: 32276990.
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    32. Pei S, Pollyea DA, Gustafson A, Stevens BM, Minhajuddin M, Fu R, Riemondy KA, Gillen AE, Sheridan RM, Kim J, Costello JC, Amaya ML, Inguva A, Winters A, Ye H, Krug A, Jones CL, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers JR, Ashton JM, Nemkov T, D'Alessandro A, Gutman JA, Ramsey HE, Savona MR, Smith CA, Jordan CT. Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Patients with Acute Myeloid Leukemia. Cancer Discov. 2020 04; 10(4):536-551. PMID: 31974170.
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    33. Powers RK, Culp-Hill R, Ludwig MP, Smith KP, Waugh KA, Minter R, Tuttle KD, Lewis HC, Rachubinski AL, Granrath RE, Carmona-Iragui M, Wilkerson RB, Kahn DE, Joshi M, Lle? A, Blesa R, Fortea J, D'Alessandro A, Costello JC, Sullivan KD, Espinosa JM. Trisomy 21 activates the kynurenine pathway via increased dosage of interferon receptors. Nat Commun. 2019 10 18; 10(1):4766. PMID: 31628327.
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    34. Laajala TD, Gerke T, Tyekucheva S, Costello JC. Modeling genetic heterogeneity of drug response and resistance in cancer. Curr Opin Syst Biol. 2019 Oct; 17:8-14. PMID: 37736115.
      View in: PubMed
    35. Washino S, Rider LC, Romero L, Jillson LK, Affandi T, Ohm AM, Lam ET, Reyland ME, Costello JC, Cramer SD. Loss of MAP3K7 Sensitizes Prostate Cancer Cells to CDK1/2 Inhibition and DNA Damage by Disrupting Homologous Recombination. Mol Cancer Res. 2019 10; 17(10):1985-1998. PMID: 31300540.
      View in: PubMed
    36. Tu MM, Lee FYF, Jones RT, Kimball AK, Saravia E, Graziano RF, Coleman B, Menard K, Yan J, Michaud E, Chang H, Abdel-Hafiz HA, Rozhok AI, Duex JE, Agarwal N, Chauca-Diaz A, Johnson LK, Ng TL, Cambier JC, Clambey ET, Costello JC, Korman AJ, Theodorescu D. Targeting DDR2 enhances tumor response to anti-PD-1 immunotherapy. Sci Adv. 2019 02; 5(2):eaav2437. PMID: 30801016.
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    37. Oliphant MUJ, Vincent MY, Galbraith MD, Pandey A, Zaberezhnyy V, Rudra P, Johnson KR, Costello JC, Ghosh D, DeGregori J, Espinosa JM, Ford HL. SIX2 Mediates Late-Stage Metastasis via Direct Regulation of SOX2 and Induction of a Cancer Stem Cell Program. Cancer Res. 2019 02 15; 79(4):720-734. PMID: 30606720.
      View in: PubMed
    38. Goodspeed A, Jean A, Costello JC. A Whole-genome CRISPR Screen Identifies a Role of MSH2 in Cisplatin-mediated Cell Death in Muscle-invasive Bladder Cancer. Eur Urol. 2019 02; 75(2):242-250. PMID: 30414698.
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    39. Ross BC, Costello JC. Improved inference of chromosome conformation from images of labeled loci. F1000Res. 2018; 7. PMID: 31363407.
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    40. Morgan MJ, Fitzwalter BE, Owens CR, Powers RK, Sottnik JL, Gamez G, Costello JC, Theodorescu D, Thorburn A. Metastatic cells are preferentially vulnerable to lysosomal inhibition. Proc Natl Acad Sci U S A. 2018 09 04; 115(36):E8479-E8488. PMID: 30127018.
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    41. Goodspeed A, Jean A, Theodorescu D, Costello JC. A Gene Expression Signature Predicts Bladder Cancer Cell Line Sensitivity to EGFR Inhibition. Bladder Cancer. 2018 Jul 30; 4(3):269-282. PMID: 30112438.
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    42. Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello JC. GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics. 2018 07 01; 34(13):i555-i564. PMID: 29950010.
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    43. Ross BC, Boguslav M, Weeks H, Costello JC. Simulating heterogeneous populations using Boolean models. BMC Syst Biol. 2018 06 07; 12(1):64. PMID: 29879983.
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    44. Camacho DM, Collins KM, Powers RK, Costello JC, Collins JJ. Next-Generation Machine Learning for Biological Networks. Cell. 2018 06 14; 173(7):1581-1592. PMID: 29887378.
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    45. Vartuli RL, Zhou H, Zhang L, Powers RK, Klarquist J, Rudra P, Vincent MY, Ghosh D, Costello JC, Kedl RM, Slansky JE, Zhao R, Ford HL. Eya3 promotes breast tumor-associated immune suppression via threonine phosphatase-mediated PD-L1 upregulation. J Clin Invest. 2018 06 01; 128(6):2535-2550. PMID: 29757193.
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    46. Zuiverloon TCM, de Jong FC, Costello JC, Theodorescu D. Systematic Review: Characteristics and?Preclinical Uses of Bladder Cancer Cell?Lines. Bladder Cancer. 2018 Apr 26; 4(2):169-183. PMID: 29732388.
      View in: PubMed
    47. Stern JL, Paucek RD, Huang FW, Ghandi M, Nwumeh R, Costello JC, Cech TR. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes. Cell Rep. 2017 12 26; 21(13):3700-3707. PMID: 29281820.
      View in: PubMed
    48. Seyednasrollah F, Koestler DC, Wang T, Piccolo SR, Vega R, Greiner R, Fuchs C, Gofer E, Kumar L, Wolfinger RD, Kanigel Winner K, Bare C, Neto EC, Yu T, Shen L, Abdallah K, Norman T, Stolovitzky G, Soule HR, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Elo LL, Zhou FL, Guinney J, Costello JC. A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer. JCO Clin Cancer Inform. 2017 11; 1:1-15. PMID: 30657384.
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    49. Zhou H, Costello JC. All Paths Lead to TRIM25. Trends Cancer. 2017 10; 3(10):673-675. PMID: 28958384.
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    50. Laajala TD, Guinney J, Costello JC. Community mining of open clinical trial data. Oncotarget. 2017 Oct 10; 8(47):81721-81722. PMID: 29137211.
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    51. Kanigel Winner KR, Costello JC. A SPATIOTEMPORAL MODEL TO SIMULATE CHEMOTHERAPY REGIMENS FOR HETEROGENEOUS BLADDER CANCER METASTASES TO THE LUNG. Pac Symp Biocomput. 2017; 22:611-622. PMID: 27897011.
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    52. Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T, Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. Lancet Oncol. 2017 01; 18(1):132-142. PMID: 27864015.
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    53. Andrews FH, Tong Q, Sullivan KD, Cornett EM, Zhang Y, Ali M, Ahn J, Pandey A, Guo AH, Strahl BD, Costello JC, Espinosa JM, Rothbart SB, Kutateladze TG. Multivalent Chromatin Engagement and Inter-domain Crosstalk Regulate MORC3 ATPase. Cell Rep. 2016 09 20; 16(12):3195-3207. PMID: 27653685.
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    54. Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G. Crowdsourcing biomedical research: leveraging communities as innovation engines. Nat Rev Genet. 2016 07 15; 17(8):470-86. PMID: 27418159.
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    55. Agarwal N, Dancik GM, Goodspeed A, Costello JC, Owens C, Duex JE, Theodorescu D. GON4L Drives Cancer Growth through a YY1-Androgen Receptor-CD24 Axis. Cancer Res. 2016 09 01; 76(17):5175-85. PMID: 27312530.
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    56. Nickerson ML, Witte N, Im KM, Turan S, Owens C, Misner K, Tsang SX, Cai Z, Wu S, Dean M, Costello JC, Theodorescu D. Molecular analysis of urothelial cancer cell lines for modeling tumor biology and drug response. Oncogene. 2017 01 05; 36(1):35-46. PMID: 27270441.
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    57. Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, G?nen M, Hill SM, Hoff B, Karr JR, K?ffner R, Menden MP, Meyer P, Norel R, Pratap A, Prill RJ, Weirauch MT, Costello JC, Stolovitzky G, Saez-Rodriguez J. DREAMTools: a Python package for scoring collaborative challenges. F1000Res. 2015; 4:1030. PMID: 27134723.
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    58. Goodspeed A, Heiser LM, Gray JW, Costello JC. Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics. Mol Cancer Res. 2016 Jan; 14(1):3-13. PMID: 26248648.
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    59. Rodrigues LU, Rider L, Nieto C, Romero L, Karimpour-Fard A, Loda M, Lucia MS, Wu M, Shi L, Cimic A, Sirintrapun SJ, Nolley R, Pac C, Chen H, Peehl DM, Xu J, Liu W, Costello JC, Cramer SD. Coordinate loss of MAP3K7 and CHD1 promotes aggressive prostate cancer. Cancer Res. 2015 Mar 15; 75(6):1021-34. PMID: 25770290.
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    60. Borah S, Xi L, Zaug AJ, Powell NM, Dancik GM, Cohen SB, Costello JC, Theodorescu D, Cech TR. Cancer. TERT promoter mutations and telomerase reactivation in urothelial cancer. Science. 2015 Feb 27; 347(6225):1006-10. PMID: 25722414.
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    61. Griner EM, Dancik GM, Costello JC, Owens C, Guin S, Edwards MG, Brautigan DL, Theodorescu D. RhoC Is an Unexpected Target of RhoGDI2 in Prevention of Lung Colonization of Bladder Cancer. Mol Cancer Res. 2015 Mar; 13(3):483-92. PMID: 25516960.
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    62. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A. A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol. 2014 Dec; 32(12):1213-22. PMID: 25419740.
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    63. Wang CA, Drasin D, Pham C, Jedlicka P, Zaberezhnyy V, Guney M, Li H, Nemenoff R, Costello JC, Tan AC, Ford HL. Homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression. Cancer Res. 2014 Dec 15; 74(24):7357-70. PMID: 25348955.
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    64. Nickerson ML, Dancik GM, Im KM, Edwards MG, Turan S, Brown J, Ruiz-Rodriguez C, Owens C, Costello JC, Guo G, Tsang SX, Li Y, Zhou Q, Cai Z, Moore LE, Lucia MS, Dean M, Theodorescu D. Concurrent alterations in TERT, KDM6A, and the BRCA pathway in bladder cancer. Clin Cancer Res. 2014 Sep 15; 20(18):4935-48. PMID: 25225064.
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    65. Costello JC, Theodorescu D. Decade in review-bladder cancer: international progress: from cytology to genomics. Nat Rev Urol. 2014 11; 11(11):609-10. PMID: 25179501.
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    66. Costello JC, Heiser LM, Georgii E, G?nen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. A community effort to assess and improve drug sensitivity prediction algorithms. Nat Biotechnol. 2014 Dec; 32(12):1202-12. PMID: 24880487.
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    67. Xue R, Zakharov MN, Xia Y, Bhasin S, Costello JC, Jasuja R. Research resource: EPSLiM: ensemble predictor for short linear motifs in nuclear hormone receptors. Mol Endocrinol. 2014 May; 28(5):768-77. PMID: 24678734.
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    68. Jasuja R, Costello JC, Singh R, Gupta V, Spina CS, Toraldo G, Jang H, Li H, Serra C, Guo W, Chauhan P, Narula NS, Guarneri T, Ergun A, Travison TG, Collins JJ, Bhasin S. Combined administration of testosterone plus an ornithine decarboxylase inhibitor as a selective prostate-sparing anabolic therapy. Aging Cell. 2014 Apr; 13(2):303-10. PMID: 24305501.
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    69. Gazit R, Garrison BS, Rao TN, Shay T, Costello J, Ericson J, Kim F, Collins JJ, Regev A, Wagers AJ, Rossi DJ. Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports. 2013; 1(3):266-80. PMID: 24319662.
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    70. Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C. Differential splicing across immune system lineages. Proc Natl Acad Sci U S A. 2013 Aug 27; 110(35):14324-9. PMID: 23934048.
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    71. Kalghatgi S, Spina CS, Costello JC, Liesa M, Morones-Ramirez JR, Slomovic S, Molina A, Shirihai OS, Collins JJ. Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in Mammalian cells. Sci Transl Med. 2013 Jul 03; 5(192):192ra85. PMID: 23825301.
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    72. Costello JC, Stolovitzky G. Seeking the wisdom of crowds through challenge-based competitions in biomedical research. Clin Pharmacol Ther. 2013 May; 93(5):396-8. PMID: 23549146.
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    73. Kwong LN, Costello JC, Liu H, Jiang S, Helms TL, Langsdorf AE, Jakubosky D, Genovese G, Muller FL, Jeong JH, Bender RP, Chu GC, Flaherty KT, Wargo JA, Collins JJ, Chin L. Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma. Nat Med. 2012 Oct; 18(10):1503-10. PMID: 22983396.
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    74. Marbach D, Costello JC, K?ffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. Nat Methods. 2012 Jul 15; 9(8):796-804. PMID: 22796662.
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    75. Kijimoto T, Costello J, Tang Z, Moczek AP, Andrews J. EST and microarray analysis of horn development in Onthophagus beetles. BMC Genomics. 2009 Oct 30; 10:504. PMID: 19878565.
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    76. Schrider DR, Costello JC, Hahn MW. All human-specific gene losses are present in the genome as pseudogenes. J Comput Biol. 2009 Oct; 16(10):1419-27. PMID: 19754271.
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    77. Costello JC, Dalkilic MM, Beason SM, Gehlhausen JR, Patwardhan R, Middha S, Eads BD, Andrews JR. Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. Genome Biol. 2009; 10(9):R97. PMID: 19758432.
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    78. Costello JC, Schrider D, Gehlhausen J, Dalkilic M. Data-driven ontologies. Pac Symp Biocomput. 2009; 15-26. PMID: 19213131.
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    79. Li YF, Costello JC, Holloway AK, Hahn MW. "Reverse ecology" and the power of population genomics. Evolution. 2008 Dec; 62(12):2984-94. PMID: 18752601.
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    80. Dalkilic MM, Costello JC, Clark WT, Radivojac P. From protein-disease associations to disease informatics. Front Biosci. 2008 May 01; 13:3391-407. PMID: 18508441.
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    81. Costello J, Cash AC, Dalkilic MM, Andrews J. Data pushing: a fly-centric guide to bioinformatics tools. Fly (Austin). 2008 Jan-Feb; 2(1):1-18. PMID: 18849648.
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    82. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. PMID: 17994087.
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    83. Eads B, Cash A, Bogart K, Costello J, Andrews J. Troubleshooting microarray hybridizations. Methods Enzymol. 2006; 411:34-49. PMID: 16939784.
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