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James C. Costello, Ph.D. - Publications

Affiliations: 
2009 Informatics Indiana University, Bloomington, Bloomington, IN, United States 
Area:
Bioinformatics Biology, Information Science
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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. Molecular Oncology. PMID 32697014 DOI: 10.1002/1878-0261.12769  0.342
2020 Zhou H, Blevins MA, Hsu JY, Kong D, Galbraith MD, Goodspeed A, Culp-Hill R, Oliphant MU, Ramirez D, Zhang L, Pineiro JT, Mathews Griner L, King R, Barnaeva E, Hu X, ... ... Costello JC, et al. A SIX1/EYA2 small molecule inhibitor disrupts EMT and metastasis. Cancer Research. PMID 32341035 DOI: 10.1158/0008-5472.Can-20-0435  0.307
2020 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. Molecular Cancer Research : McR. PMID 32276990 DOI: 10.1158/1541-7786.Mcr-19-1244  0.335
2020 Goodspeed AE, Jean A, Costello JC. Abstract B08: MSH2 downregulation induces chemoresistance in bladder cancer Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Bladder19-B08  0.328
2019 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. Molecular Cancer Research : McR. PMID 31300540 DOI: 10.1158/1541-7786.Mcr-18-1335  0.317
2019 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 Research. PMID 30606720 DOI: 10.1158/0008-5472.Can-18-1791  0.309
2019 Jones RT, Zuiverloon TC, Vekony H, Goodspeed A, Laajala TD, Joshi M, Sempeck C, Tu M, Costello JC, Theodorescu D. Abstract 2107: Integrative molecular and functional genomic analysis of chemotherapy resistant bladder cancer cell lines identifies novel mediators of therapeutic response Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-2107  0.326
2019 Laajala TD, Gerke T, Tyekucheva S, Costello JC. Modeling genetic heterogeneity of drug response and resistance in cancer Current Opinion in Systems Biology. 17: 8-14. DOI: 10.1016/J.Coisb.2019.09.003  0.314
2018 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 30127018 DOI: 10.1073/Pnas.1706526115  0.321
2018 Oliphant MU, Pandey A, Johnson K, Powers R, Galbraith M, Costello J, Ford HL. Abstract 5001: Identification of a Six2/Sox2/Nanog stem cell axis that promotes breast cancer metastatic colonization Cancer Research. 78: 5001-5001. DOI: 10.1158/1538-7445.Am2018-5001  0.328
2017 Zhou H, Costello JC. All Paths Lead to TRIM25. Trends in Cancer. 3: 673-675. PMID 28958384 DOI: 10.1016/J.Trecan.2017.08.005  0.331
2016 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, ... ... Costello JC, et al. 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. The Lancet. Oncology. PMID 27864015 DOI: 10.1016/S1470-2045(16)30560-5  0.318
2016 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. Nature Reviews. Genetics. 17: 470-86. PMID 27418159 DOI: 10.1038/Nrg.2016.69  0.304
2016 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 Research. PMID 27312530 DOI: 10.1158/0008-5472.Can-16-1099  0.313
2016 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. PMID 27270441 DOI: 10.1038/Onc.2016.172  0.373
2016 Zhou FL, Guinney J, Wang T, Bare JC, Norman TC, Bot B, Shen L, Winner KK, Friend SH, Abdallah K, Stolovitzky GA, Xie Y, Costello J. Use of crowdsourced research to develop a prognostic model for first-line metastatic castrate resistant prostate cancer (mCRPC). Journal of Clinical Oncology. 34: 180-180. DOI: 10.1200/Jco.2016.34.2_Suppl.180  0.307
2016 Nickerson M, Im KM, Guo G, Gui Y, Turan S, Costello JC, Zhou Q, Cai Z, Wu S, Lucia MS, Moore LE, Dean M, Theodorescu D. Abstract A52: Gene alterations associated with clinical characteristics of bladder cancer Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-A52  0.363
2016 Hernandez B, Cronise K, Costello JC, Page R, Lana S, Jones KL, Duval DL. Abstract 617: Canine transitional cell carcinoma of the bladder expresses activated BRAF, but is not sensitive to vemurafenib Cancer Research. 76: 617-617. DOI: 10.1158/1538-7445.Am2016-617  0.351
2015 Goodspeed A, Heiser LM, Gray JW, Costello JC. Tumor-derived Cell Lines as Molecular Models of Cancer Pharmacogenomics. Molecular Cancer Research : McR. PMID 26248648 DOI: 10.1158/1541-7786.Mcr-15-0189  0.343
2015 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 (New York, N.Y.). 347: 1006-10. PMID 25722414 DOI: 10.1126/Science.1260200  0.306
2015 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. Molecular Cancer Research : McR. 13: 483-92. PMID 25516960 DOI: 10.1158/1541-7786.Mcr-14-0420  0.314
2015 Kothari S, Gustafson D, Killian K, Costello J, Edelman DC, Walling J, Meltzer PS, Theodorescu D, Apolo AB. COXEN prediction of antineoplastic drug sensitivity in bladder cancer patients. Journal of Clinical Oncology. 33: 365-365. DOI: 10.1200/Jco.2016.34.2_Suppl.365  0.337
2015 Zhou FL, Guinney J, Abdallah K, Norman TC, Bot B, Costello J, Shen L, Wang T, Xie Y, Stolovitzky GA. Building a crowd-sourced challenge using clinical trial data. Journal of Clinical Oncology. 33: e16047-e16047. DOI: 10.1200/Jco.2015.33.15_Suppl.E16047  0.324
2015 Guinney J, Wang T, Bare C, Norman T, Bot B, Shen L, Winner K, Friend S, Abdallah K, Stolovitzky G, Xie Y, Zhou FL, Costello JC. Abstract B204: A DREAM Challenge to improve prognostic models in patients with metastatic castrate-resistant prostate cancer Molecular Cancer Therapeutics. 14. DOI: 10.1158/1535-7163.Targ-15-B204  0.336
2014 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 Research. 74: 7357-70. PMID 25348955 DOI: 10.1158/0008-5472.Can-14-0666  0.309
2014 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, et al. Concurrent alterations in TERT, KDM6A, and the BRCA pathway in bladder cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 4935-48. PMID 25225064 DOI: 10.1158/1078-0432.Ccr-14-0330  0.346
2014 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. Molecular Endocrinology (Baltimore, Md.). 28: 768-77. PMID 24678734 DOI: 10.1210/Me.2014-1006  0.322
2013 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. 1: 266-80. PMID 24319662 DOI: 10.1016/J.Stemcr.2013.07.004  0.303
2013 Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C. Differential splicing across immune system lineages. Proceedings of the National Academy of Sciences of the United States of America. 110: 14324-9. PMID 23934048 DOI: 10.1073/Pnas.1311839110  0.328
2012 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. Nature Methods. 9: 796-804. PMID 22796662 DOI: 10.1038/Nmeth.2016  0.364
2009 Kijimoto T, Costello J, Tang Z, Moczek AP, Andrews J. EST and microarray analysis of horn development in Onthophagus beetles. Bmc Genomics. 10: 504. PMID 19878565 DOI: 10.1186/1471-2164-10-504  0.358
2009 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 Biology. 10: R97. PMID 19758432 DOI: 10.1186/Gb-2009-10-9-R97  0.686
2009 Schrider DR, Costello JC, Hahn MW. All human-specific gene losses are present in the genome as pseudogenes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1419-27. PMID 19754271 DOI: 10.1089/Cmb.2009.0085  0.35
2009 Costello JC, Schrider D, Gehlhausen J, Dalkilic M. Data-driven ontologies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 15-26. PMID 19213131  0.67
2008 Costello J, Cash AC, Dalkilic MM, Andrews J. Data pushing: a fly-centric guide to bioinformatics tools. Fly. 2: 1-18. PMID 18849648 DOI: 10.4161/Fly.5864  0.676
2008 Li YF, Costello JC, Holloway AK, Hahn MW. "Reverse ecology" and the power of population genomics. Evolution; International Journal of Organic Evolution. 62: 2984-94. PMID 18752601 DOI: 10.1111/J.1558-5646.2008.00486.X  0.329
2008 Dalkilic MM, Costello JC, Clark WT, Radivojac P. From protein-disease associations to disease informatics. Frontiers in Bioscience : a Journal and Virtual Library. 13: 3391-407. PMID 18508441 DOI: 10.2741/2934  0.662
2007 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, ... ... Costello JC, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.332
2007 Costello JC, Buchanan-Carter JE, Dalkilic MM, Andrews J. Using drosophila melanogaster data to discover disease-related protein interactions in humans 2007 Ieee Symposium On Computational Intelligence and Bioinformatics and Computational Biology, Cibcb 2007. 469-475.  0.639
2006 Costello J, Andrews J. Re-Annotation of DGRC-1 Amplicon Microarrays from Drosophila melanogaster Annotation version 3.1 to version 4.1 Cgb Technical Report. 2006. DOI: 10.2506/Cgbtr-200607  0.323
2006 Dalkilic MM, Clark WT, Costello JC, Radivojac P. Using compression to identify classes of inauthentic texts Proceedings of the Sixth Siam International Conference On Data Mining. 2006: 604-608.  0.612
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