James Costello, PhD

Publications

• 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 3;5(192):192ra85. PubMed PMID: 23825301
• Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C, ImmGen Consortium. Differential splicing across immune system lineages. Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14324-9. PubMed PMID: 23934048
• 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. PubMed PMID: 24305501
• Gazit R, Garrison BS, Rao TN, Shay T, Costello J, Ericson J, Kim F, Collins JJ, Regev A, Wagers AJ, Rossi DJ, Immunological Genome Project Consortium. Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports. 2013;1(3):266-80. PubMed PMID: 24319662
• 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. PubMed PMID: 23549146
• A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology. Accepted Feb 15, 2014
• EPSLiM: Ensemble Predictor for Short Linear Motifs in nuclear hormone receptors. Molecular Endocrinology. Accepted Feb 17, 2014.
• 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. 2014 Dec 16. [Epub ahead of print] PubMed PMID: 25516960
• 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, NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A, NCI-DREAM Community. A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol. 2014 Dec;32(12):1213-22. PubMed PMID: 25419740
• 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, NCI DREAM Community, 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. PubMed PMID: 24880487
• 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. PubMed PMID: 25348955
• 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. PubMed PMID: 25225064
• Costello JC, Theodorescu D. Decade in review-bladder cancer: international progress: from cytology to genomics. Nat Rev Urol. 2014 Nov;11(11):609-10. PubMed PMID: 25179501
• 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. PubMed PMID: 24678734
• 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. PubMed PMID: 25770290
• 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. PubMed PMID: 25516960
• 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. PubMed PMID: 25722414
• Goodspeed A, Heiser LM, Gray JW, Costello JC. Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics. Mol Cancer Res. 2015 Aug 6. [Epub ahead of print] PubMed PMID: 26248648
• Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Saez-Rodriguez (2015) DREAMTools: a Python package for scoring collaborative challenges. F1000Research 2015, 4:1030 (doi: 10.12688/f1000research.7118.1)
• 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 Sep 20;16(12):3195-207. PubMed PMID: 27653685
• 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. PubMed PMID: 26248648
• 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 Jan 5;36(1):35-46. PubMed PMID: 27270441
• 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 Sep 1;76(17):5175-85. PubMed PMID: 27312530
• 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 Jul 15;17(8):470-86. PubMed PMID: 27418159
• Elias Chaibub Neto, Bruce R. Hoff, Chris Bare, Brian M. Bot, Thomas Yu, Lara Mangravite, Andrew D. Trister, Thea Norman, Pablo Meyer, Julio Saez-Rodriguez, James C. Costello, Justin Guinney, Gustavo Stolovitzky. Reducing overfitting in challenge-based competitions. arXiv:1607.00091
• Fatemeh Seyednasrollah, Devin C Koestler, Tao Wang, Stephen R Piccolo, Roberto Vega, Russ Greiner, Christiane Fuchs, Eyal Gofer, Luke Kumar, Russel D Wolfinger, Kimberly Kanigel Winner, Chris Bare, Elias Chaibub Neto, Thomas Yu, Liji Shen, Kald Abdallah, Thea Norman, Gustavo Stolovitzky, PCC-DREAM Community, Howard Soule, Chistopher J Sweeney, Charles J Ryan, Howard I Scher, Oliver Sartor, Laura L Elo, Fang L Zhou, Justin Guinney, James C. Costello. A community-based collaboration to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer patients. bioRxiv http://biorxiv.org/content/early/2016/11/15/087809
• 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 Dec 26;21(13):3700-3707. PubMed PMID: 29281820
• Laajala TD, Guinney J, Costello JC. Community mining of open clinical trial data. Oncotarget. 2017 Oct 10;8(47):81721-81722. PubMed PMID: 29137211
• Zhou H, Costello JC. All Paths Lead to TRIM25. Trends Cancer. 2017 Oct;3(10):673-675. PubMed PMID: 28958384
• 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 Jan 5;36(1):35-46. PubMed PMID: 27270441
• 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. PubMed PMID: 27897011
• 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 Jan;18(1):132-142. PubMed PMID: 27864015
• Laajala TD, Guinney J, Costello JC. Community mining of open clinical trial data. Oncotarget. 2017 Oct 10;8(47):81721-81722. PubMed PMID: 29137211
• Brian C Ross, Mayla Boguslav, Holly Weeks, James C. Costello. Modeling heterogeneous populations using Boolean networks. bioRxiv BIORXIV/2017/110817
• 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 Feb;75(2):242-250. PubMed PMID: 30414698
• 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 Jan 3. [Epub ahead of print] PubMed PMID: 30606720
• 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 Sep 4;115(36):E8479-E8488. PubMed PMID: 30127018
• 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. PubMed PMID: 30112438
• Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello JC. GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics. 2018 Jul 1;34(13):i555-i564. PubMed PMID: 29950010
• Camacho DM, Collins KM, Powers RK, Costello JC, Collins JJ. Next-Generation Machine Learning for Biological Networks. Cell. 2018 Jun 14;173(7):1581-1592. PubMed PMID: 29887378
• Ross BC, Boguslav M, Weeks H, Costello JC. Simulating heterogeneous populations using Boolean models. BMC Syst Biol. 2018 Jun 7;12(1):64. PubMed PMID: 29879983
• 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 Jun 1;128(6):2535-2550. PubMed PMID: 29757193
• 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. PubMed PMID: 29732388
• 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 Oct 18;10(1):4766. PubMed PMID: 31628327
• 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 Oct;17(10):1985-1998. PubMed PMID: 31300540
• 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 Feb;5(2):eaav2437. PubMed PMID: 30801016
• 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 Feb 15;79(4):720-734. PubMed PMID: 30606720
• 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 Feb;75(2):242-250. PubMed PMID: 30414698
• 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 Acute Myeloid Leukemia Patients. Cancer Discov. 2020 Jan 23. [Epub ahead of print] PubMed PMID: 31974170
• Teemu D Laajala, Travis Gerke, Svitlana Tyekucheva, James C Costello. Modeling genetic heterogeneity of drug response and resistance in cancer. Current Opinions in Systems Biology. 17: 8-14.
• Ross BC, Costello JC. Improved inference of chromosome conformation from images of labeled loci. F1000Res. 2018;7. PubMed PMID: 31363407
• Brian C Ross, Fabio Anaclerio, Nicola Lorusso, Mario Ventura, James C Costello. Measuring chromosome conformation by fluorescence microscopy. bioRxiv 10.1101/798512 (October 16, 2019).
• Rani K Powers, Anthony Sun, James C Costello. GSEA-InContext Explorer: An interactive visualization too for putting gene set enrichment analysis results into biological context. bioRxiv 10.1101/659847 (June 4, 2019).
• 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). PubMed PMID: 33218188
• 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 Nov 27;3(1):720. PubMed PMID: 33247183
• 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. PubMed PMID: 33196691
• Greene CS, Costello JC. Biologically Informed Neural Networks Predict Drug Responses. Cancer Cell. 2020 Nov 9;38(5):613-615. PubMed PMID: 33096022
• 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 Dec 1;26(23):6362-6373. PubMed PMID: 32928797
• 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 Oct;14(10):2471-2486. PubMed PMID: 32697014
• 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. PubMed PMID: 32460014
• 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 Jun 15;80(12):2689-2702. PubMed PMID: 32341035
• 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 Jul;18(7):1050-1062. PubMed PMID: 32276990
• 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 Apr;10(4):536-551. PubMed PMID: 31974170
• . ImmGen at 15. Nat Immunol. 2020 Jul;21(7):700-703. PubMed PMID: 32577013
• 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. PubMed PMID: 33526513
• 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 Jul;19(7):1123-1136. PubMed PMID: 33846123
• 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. PubMed PMID: 33947745
• 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. PubMed PMID: 34195686
• 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). PubMed PMID: 34208794
• Jessica Y Hsu, Stephanie Nance, Jenean O'Brien, Veronica M Wessells, Andrew E Goodspeed, Jared C Talbot, Sharon L Amacher, Paul Jedlicka, Joshua C Black, James C Costello, Adam D Durbin, Kristin B Artinger, Heide L Ford. Six1 is a master regulator of the Rhabdomyosarcoma undifferentiated state. Cell Reports (Accepted)
• Lomeli C Shull, Hyun Min Kim, Ezra S Lencer, Susumu Goyama, Mineo Kurokawa, James C Costello, Kenneth Jones, Kristin B Artinger. PRDM proteins control Wnt/B-catenin activity to regulate craniofacial chondrocyte differentiation. Development (Accepted)
• R Alejandro Marquez-Ortiz, Maria J Contreras-Zarate, Karen LF Alvarez-Eraso, Vesna Tesic, Gina Kwak, Zachary Littrell, James C Costello, Varsha Sreekanth, D Ryan Ormond, Sana D Karam, Peter Kabos, Diana M Cittelly. IL13TRa2 promotes proliferation and outgrowth of breast cancer brain metastasis. Clinical Cancer Research (accepted).
• 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 9;14(18). PubMed PMID: 36139558
• 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). PubMed PMID: 36142576
• 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 Jr. A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis. JAMA Netw Open. 2022 Aug 1;5(8):e2227423. PubMed PMID: 36036935
• 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 Oct 7. [Epub ahead of print] PubMed PMID: 36216026
• 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 Feb 1;38(5):110323. PubMed PMID: 35108532
• Shull LC, Lencer ES, Kim HM, Goyama S, Kurokawa M, Costello JC, Jones K, Artinger KB. PRDM paralogs antagonistically balance Wnt/ß-catenin activity during craniofacial chondrocyte differentiation. Development. 2022 Feb 15;149(4). PubMed PMID: 35132438
• 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. 2023 Dec 21;:101350. [Epub ahead of print] PubMed PMID: 38134931
• 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 Jul 19;14(1):4357. PubMed PMID: 37468459
• Thomas SN, Niemeyer BF, Jimenez-Valdes RJ, Kaiser AJ, Espinosa JM, Sullivan KD, Goodspeed A, Costello JC, Alder JK, Cañas-Arranz R, García-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. PubMed PMID: 37554445
• 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 Jul 5;10(1):430. PubMed PMID: 37407670
• de Jong FC, Laajala TD, Hoedemaeker RF, Jordan KR, van der Made ACJ, Boevé 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-Guérin. Sci Transl Med. 2023 May 24;15(697):eabn4118. PubMed PMID: 37224225
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