Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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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
    U01CA231978     (COSTELLO, JAMES CHRISTOPHER)Sep 1, 2019 - Aug 31, 2024
    NIH
    Systems analysis of aggressive prostate cancer pathology
    Role: 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

    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. 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
    2. Tarca AL, Pataki BÁ, 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 Jun 15; 2(6):100323. PMID: 34195686.
      View in: PubMed
    3. 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 Aug; 19(8):1270-1282. PMID: 33947745.
      View in: PubMed
    4. 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
    5. Mueller AC, Piper M, Goodspeed A, Bhuvane S, Williams JS, Bhatia S, Phan AV, Van Court B, Zolman KL, Peña 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, Chiaro MD, 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 Jun 15; 81(12):3255-3269. PMID: 33526513.
      View in: PubMed
    6. 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.
      View in: PubMed
    7. 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
    8. 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.
      View in: PubMed
    9. 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
    10. 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.
      View in: PubMed
    11. 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.
      View in: PubMed
    12. 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
    13. 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.
      View in: PubMed
    14. 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.
      View in: PubMed
    15. 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.
      View in: PubMed
    16. 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, Lleó 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.
      View in: PubMed
    17. 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
    18. 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.
      View in: PubMed
    19. 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
    20. 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.
      View in: PubMed
    21. Ross BC, Costello JC. Improved inference of chromosome conformation from images of labeled loci. F1000Res. 2018; 7. PMID: 31363407.
      View in: PubMed
    22. 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.
      View in: PubMed
    23. 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.
      View in: PubMed
    24. 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.
      View in: PubMed
    25. 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.
      View in: PubMed
    26. 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.
      View in: PubMed
    27. 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.
      View in: PubMed
    28. 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
    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. 2017 12 26; 21(13):3700-3707. PMID: 29281820.
      View in: PubMed
    30. 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.
      View in: PubMed
    31. Zhou H, Costello JC. All Paths Lead to TRIM25. Trends Cancer. 2017 10; 3(10):673-675. PMID: 28958384.
      View in: PubMed
    32. Laajala TD, Guinney J, Costello JC. Community mining of open clinical trial data. Oncotarget. 2017 Oct 10; 8(47):81721-81722. PMID: 29137211.
      View in: PubMed
    33. 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.
      View in: PubMed
    34. 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.
      View in: PubMed
    35. 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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    36. 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.
      View in: PubMed
    37. 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.
      View in: PubMed
    38. 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.
      View in: PubMed
    39. Cokelaer T, Bansal M, Bare C, Bilal E, Bot BM, Chaibub Neto E, Eduati F, Gönen M, Hill SM, Hoff B, Karr JR, Küffner 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.
      View in: PubMed
    40. 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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    41. 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.
      View in: PubMed
    42. 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.
      View in: PubMed
    43. 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.
      View in: PubMed
    44. 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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    45. 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.
      View in: PubMed
    46. 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.
      View in: PubMed
    47. 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.
      View in: PubMed
    48. Costello JC, Heiser LM, Georgii E, Gönen 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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    49. 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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    50. 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.
      View in: PubMed
    51. 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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    52. 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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    53. 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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    54. 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.
      View in: PubMed
    55. 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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    56. Marbach D, Costello JC, Küffner 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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    57. 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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    58. 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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    59. 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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    60. Costello JC, Schrider D, Gehlhausen J, Dalkilic M. Data-driven ontologies. Pac Symp Biocomput. 2009; 15-26. PMID: 19213131.
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    61. 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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    62. 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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    63. 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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