Publications

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2024

• Integrated analysis of immunometabolic interactions in Down syndrome Lucas A Gillenwater, Matthew D Galbraith, Angela L Rachubinski, Neetha Paul Eduthan, Kelly D Sullivan, Joaquin M Espinosa, James C Costello. Science Advances 10,eadq3073(2024). DOI:10.1126/sciadv.adq3073

• Regulation of volume-regulated anion channels alters sensitivity to platinum chemotherapy Lily Elizabeth R. Feldman, Saswat Mohapatra, Mathijs Scholtes, Charlene B. Tilton, Michael V. Orman, Molishree Joshi, Cailin S. Deiter, Travis P. Broneske, Fangyuan Qu, Corazon Gutierrez, Huihui Ye, Eric T. Clambey, Sarah Parker, Tokameh Mahmoudi, Tahlita Zuiverloon, James C. Costello, and Dan Theodorescu. Science  Advances,10,eadr9364(2024),  DOI: 10.1126/sciadv.adr9364

• A Pathway-Level Information ExtractoR (PLIER) framework to gain mechanistic insights into obesity in Down syndrome, Sutanu Nandi, Yuehua Zhu, Lucas A Gillenwater, Marc Subirana-Granés, Haoyu Zhang, Negar Janani, Casey Greene, Milton Pividori, Maria Chikina, James C Costello,  Biocomputing 2025, 412-425, doi: 10.1142/9789819807024_0030

• E-cadherin expression and gene expression profiles in corticotroph pituitary neuroendocrine tumor subtypes, Katja Kiseljak-Vassiliades, Kristin Lipe, Christie G Turin, Lauren Fishbein, James C Costello, Janice M Kerr, Tessa B Holmstoen, A Samy Youssef, Kevin O Lillehei, Bette K Kleinschmidt-DeMasters, Margaret E Wierman, Journal of Neuropathology & Experimental Neurology, Volume 83, Issue 7, July 2024, Pages 586–595, https://doi.org/10.1093/jnen/nlae034

• NPEPPS Is a Druggable Driver of Platinum Resistance. Robert T. Jones, Mathijs Scholtes, Andrew Goodspeed, Maryam Akbarzadeh, Saswat Mohapatra, Lily Elizabeth Feldman, Hedvig Vekony, Annie Jean, Charlene B. Tilton, Michael V. Orman, Shahla Romal, Cailin Deiter, Tsung Wai Kan, Nathaniel Xander, Stephanie P. Araki, Molishree Joshi, Mahmood Javaid, Eric T. Clambey, Ryan Layer, Teemu D. Laajala, Sarah J. Parker, Tokameh Mahmoudi, Tahlita C.M. Zuiverloon, Dan Theodorescu, James C. Costello;  Cancer Res 15 May 2024; 84 (10): 1699–1718. https://doi.org/10.1158/0008-5472.CAN-23-1976

• ProstaMine: a bioinformatics tool for identifying subtype-specific co-alterations associated with aggressiveness in prostate cancer. Orman MV, Sreekanth V, Laajala TD, Cramer SD and Costello JC (2024), Front. Pharmacol. 15:1360352. doi: 10.3389/fphar.2024.1360352

• Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research Jonathan L Golob, Tomiko T Oskotsky, Alice S Tang, Alennie Roldan, Verena Chung, Connie WY Ha, Ronald J Wong, Kaitlin J Flynn, Antonio Parraga-Leo, Camilla Wibrand, Samuel S Minot, Boris Oskotsky, Gaia Andreoletti, Idit Kosti, Julie Bletz, Amber Nelson, Jifan Gao, Zhoujingpeng Wei, Guanhua Chen, Zheng-Zheng Tang, Pierfrancesco Novielli, Donato Romano, Ester Pantaleo, Nicola Amoroso, Alfonso Monaco, Mirco Vacca, Maria De Angelis, Roberto Bellotti, Sabina Tangaro, Abigail Kuntzleman, Isaac Bigcraft, Stephen Techtmann, Daehun Bae, Eunyoung Kim, Jongbum Jeon, Soobok Joe, Kevin R Theis, Sherrianne Ng, Yun S Lee, Patricia Diaz-Gimeno, Phillip R Bennett, David A MacIntyre, Gustavo Stolovitzky, Susan V Lynch, Jake Albrecht, Nardhy Gomez-Lopez, Roberto Romero, David K Stevenson, Nima Aghaeepour, Adi L Tarca, James C Costello, Marina Sirota. Cell Reports Medicine, https://doi.org/10.1016/j.xcrm.2023.101350

2023

• Down syndrome is associated with altered frequency and functioning of tracheal multiciliated cells, and response to influenza virus infection Samantha N. Thomas, Brian F. Niemeyer, Alexander J. Kaiser, Joaquin M. Espinosa, Kelly D. Sullivan, Andrew Goodspeed, James C. Costello, Rodrigo Cañas-Arranz, Adolfo García-Sastre, Kambez H. Benam. iScience (Accepted)

• A harmonized resource of integrated prostate cancer clinical, -omic, and signature features Teemu D Laajala, Varsha Sreekanth, Alex C. Soupir, Jordan H. Creed, Anni S. Halkola, Federico CFG Calboli, Kalaimathy Singarvelu, Michael V. Orman, Christelle Colin-Leitzinger, Travis Gerke, Brooke L Fidley, Svitlana Tyekucheva, James Costello. Scientific Data 10(1):430.

• Non-muscle invasive bladder cancer molecular subtypes predict differential response to intravesical Bacillus Calmette-Guerin
  Florus C De Jong, Teemu Daniel Laajala, Robert F Hoedemaeker, Kimberly R Jordan, Angelique CJ van der Made, Egbert R Boeve, Deric KE van der Schoot, Bart B Nieuwkamer, Emiel AM Janssen, Tokameh Mahmoudi, Joost L Boormans, Dan Theodorescu, James C Costello, Tahlita CM Zuiverloon. Science Translational Medicine 15(697):abn4118

• Microparticle-delivered Cxcl9 delays the relapse of BRAF inhibitor-treated melanoma  Gabriele Romano, Francesca Paradisco, John P. Miller, Roger J. Liang, Jennifer A. Wargo, Francesca Tarballi, James C. Costello, Lawrence Kwong. Cacner Immunology Research 23; CIR-22-0224.

2022

• Antigens expressed by breast cancer cells undergoing EMT stimulate cytotoxic CD8+ T cell immunity Faye A. Camp, Tonya M. Brunetti, Michelle M. Williams, Jessica L. Christenson, Varsha Sreekanth, James C. Costello, Zachary L.Z. Hay, Ross M. Kedl, Jennifer K Richer, Jill E Slansky. Cancers 14(8):4397.

• High-content drug discovery targeting molecular bladder cancer subtypes Sébastien Rinaldetti, Qiong Zhou, Joshua M. Abbott, Florus C. DeJong, Hector Esquer, James C. Costello, Dan Theodorescu, Daniel V. LaBarbera. International Journal of Molecular Sciences 23(18):10605.

• A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis Dongmei Sun, Thanh M. Nguyen, Robert J. Allaway, Jelai Wang, Verena Chung, Thomas V Yu, Michael Mason, Isaac Dimitrovsky, Lars Ericson, Hongyang Li, Yuanfang Guan, Ariel Israel, Alex Olar, Balint Armin Pataki, RA2 DREAM Challenge Community, Gustavo Stolovitzky, Justin Guinney, Percio S. Gulko, Mason B. Frazier, Jake Y. Chen*, James C. Costello*, S. Louis Bridges, Jr. JAMA Network Open 5(8):e2227423.

• SOPHIE: Generative neural networks separate common and specific transcriptional responses. Alexandra J Lee, Dallas L Mould, Jake Crawford, Dongbo Hu, Rani K Powers, Georgia Doing, James C Costello, Deborah A Hogan, Casey S Greene. Genomics, Proteomics, and Bioinformatics 20(5):912-927.

• Six1 is a master regulator of the Rhabdomyosarcoma undifferentiated state 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. Cell Reports 38(5):110323.

• PRDM proteins control Wnt/B-catenin activity to regulate craniofacial chondrocyte differentiation Lomeli C Shull, Hyun Min Kim, Ezra S Lencer, Susumu Goyama, Mineo Kurokawa, James C Costello, Kenneth Jones, Kristin B Artinger. Development 149(4):dev200082.

2021

• IL13TRa2 promotes proliferation and outgrowth of breast cancer brain metastasis 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. Clinical Cancer Research 27(22):6209-6221.

• Androgen receptor signaling in prostate cancer genomics subtypes Lauren K Jillson, Gabriel A Yette, Teemu D Laajala, Wayne D Tilley, James C Costello, Scott D Cramer. Cancers 13(13):3272.

• Mediator of DNA damage checkpoint 1 (MDC1) is a novel estrogen receptor co-regulator in invasive lobular carcinoma of the breast Joseph L Sottnik, Evelyn K Bordeaux, Sanjana Mehrotra, Sarah E Ferrara, Andrew Goodspeed, James C Costello, Matthew J Sikora. Molecular Cancer Research 10.1158/1541-7789.MCR-21-0025.

• MAP3K7 loss drives enhanced androgen signaling and independently confers risk of recurrence in prostate cancer with join loss of CHD1 Lauren K Jillson, Leah C Rider, Lindsey U Rodrigues, Lina Romero, Anis Karimpour-Fard, Cera Nieto, Claire Gillette, Kathleen Torkko, Etienne Danis, Elizabeth E Smith, Rosalie Nolley, Donna M Peehl, M Scott Lucia, James C Costello, Scott D Cramer. Molecular Cancer Research 10.1158/1541-7786.MCR-20-0913.

• Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth Adi L Tarca, Balint Armin Pataki, Roberto Romero, Marina Sirota, Yuanfang Guan, Rintu Kuntum, Nardhy Gomez-Lopez, Bogdan Done, Gaurav Bhatti, Thomas Yu, Gaia Andrioletti, Tinnakorn Chaiworapongsa, The DREAM Preterm Birth Prediction Challenge Consortium, Sonia S Hassan, Caur-Dong Hsu, Nima Aghaeepour, Gustavo Stolovitzky, Istvan Csabai, James C Costello Cell Reports Medicine 2(6):100323.

• The M1 aminopeptidase NPEPPS is a novel regulator of cisplatin sensitivity  Robert T Jones, Andrew Goodspeed, Maryam C Akbarkzadeh, Mathijs Scholtes, Hedvig Vokony, Annie Jean, Charlene B Tilton, Michael V Orman, Molishree Joshi, Teemu D Laajala, Mahmood Javaid, Eric T Clambey, Ryan Layer, Sarah Parker, Tokameh Mahmoudi, Tahlita Zuiverloon, Dan Theodorescu, James C Costello. bioRxiv 10.1101/2021.03.04.433676.

• Induction of ADAM10 by RT drives fibrosis, resistance, and EMT in pancreatic cancer Adam Mueller, Miles Piper, Andrew Goodspeed, Shiv Bhuvane, Jason Williams, Shilpa Bhatia, Andy Phan, Benjamin Van Court, Kathryn Zolman, Brisa Peña, Ayman Oweida, Sara Zakem, Cheryl Meguid, Michael Knitz, Laurel Darragh, Thomas Bickett, Jacob Gadwa, Luisa Mestroni, Matthew Taylor, Kimberly Jordan, Peter Dempsey, M. Lucia, Martin McCarter, Marco Del Chiaro, Wells Messersmith, Richard Schulick, Karyn Goodman, Michael Gough, Casey Greene, James C Costello, Antonio Galvao Neto, David Lagares, Kirk Hansen, Adrie van Bokhoven, and Sana Karam. Cancer Research canres.CAN-20-3892-A.2020.

2020

• KDM5A and PHF2 positively control expression of pro-metastatic genes repressed by EWS/Fli1, and promoter growth and metastatic properties in Ewing sarcoma Tyler S McCann, Janet K Parrish, Joseph Hsieh, Marybeth Sechler, Lays M Sobral, Chelsea Self, Kenneth L Jones, Andrew Goodspeed, James C Costello, Paul Jedlicka. Oncotarget 11(43):3818-3831.

• CPT1A Over-expression Increases Reactive Oxygen Species in the Mitochondria and Promotes Antioxidant Defenses in Prostate Cance rMolishree Joshi, Jihye Kim, Angelo D'Alessandro, Emily Monk, Kimberley Bruce, Hanan Elajaili, Eva Nozik, Andrew Goodspeed, James C Costello, Isabel Schlaepfer. Cancers 12(11):3431.

• Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy Megan M Tu , Hany A Abdel-Hafiz, Robert T Jones, Annie Jean, Katelyn J Hoff, Jason E Duex, Ana Chauca-Diaz, James C Costello, Garrett M Dancik, Beth A Jirón Tamburini, Bogdan Czerniak, Jonathan Kaye, and Dan Theodorescu. Communications Biology 3(1):720.

• Biologically informed neural networks predict drug responses Casey Greene, James C Costello. Cancer Cell 10.1016/j.ccell.2020.10.014.

• The capacity of the ovarian cancer tumor microenvironment to integrate inflammation signaling conveys a shorter disease-free interval Kimberly R. Jordan, Matthew J. Sikora, Jill E. Slansky, Angela Minic, Jennifer K Richer, Marisa R Moroney, Junxiao Hu, Rebecca J Wolsky, Zachary L Watson, Tomoni M Yamamoto, James C Costello, Aaron Clauset, Kian Behbakht, T Rajendra Kumar, Benjamin G Bitler. Clinical Cancer Research 10.1158/1078-0432.CCR-20-1762.

• KDM3A/Ets1 epigenetic axis contributes to PAX3/FOXO1-driven and independent disease-promoting gene expression in fusion-positive Rhabdomyosarcoma Martin Sobral, Hannah Hicks, Janet Parrish, Tyler McCann, Joseph Hsieh, Andrew Goodspeed, James C Costello,  Joshua Black, Paul Jedlicka. Molecular Oncology 14(10):2471-2486.

• ImmGen at 15 The Immunological Genome Project (consortium member). Nature Immunology 21(7):700-703.

• Identification of a small-molecule inhibitor that disrupts the SIX1/EYA2 complex, EMT, and metastasis Hengbo Zhou, Melanie A Blevins, Jessica Y Hsu, Deguang Kong, Matthew D Galbraith, Andrew Goodspeed, Rachel Culp-Hill, Michael UJ Oliphant, Dominique Ramirez, Lingdi Zhang, Jennyvette T Pineiro, Lesley Matthews Griner, Rebecca King, Elena Barnaeva, Xin Hu, Noel T Southall, Marc Ferrer, Daniel L Gustafson, Daniel P Regan, Angelo D'Alessandro, James C Costello, Samarjit Patnaik, Juan Marugan, Rui Zhao, Heide L Ford. Cancer Research 80(12):2689-2702.

• Mesenchymal and MAPK expression signatures associated with telomerase promoter mutations in multiple cancers Josh L Stern, Grave Hibsham, Kevin Hu, Sarah E Ferrara, James C Costello, William Kim, Pablo Tamayo, Thomas R Cech, Franklin W Huang. Molecular Cancer Research 18(7):1050-1062.

• Monocytic subclones confer resistance to Venetoclax-based therapy in acute myeloid leukemia patients Shanshan Pei, Daniel A Pollyea, Annika Gustafson, Brett M Stevens, Mohammad Minhajuddin, Rui Fu, Kent A Riemondy, Austin E Gillen, Ryan M Sheridan, Jihye Kim, James C Costello, Maria L Amaya, Anagha Inguva, Amanda Winters, Haobin Ye, Anna Krug, Courtney L Jones, Biniam Adane, Nabilah Khan, Jessica Ponder, Jeffrey Schowinsky, Diana Abbott, Andrew Hammes, Jason R Myers, John M Ashton, Travis Nemkov, Angelo D'Alessandro, Jonathan A Gutman, Haley E Ramsey, Michael R Savona, Clayton A Smith, Craig T Jordan. Cancer Discovery 10:536–51.

2019

• Measuring chromosome conformation by fluorescence microscopy Brian C Ross, Fabio Anaclerio, Nicola Lorusso, Mario Ventura, James C Costello. bioRxiv 10.1101/798512 (October 16, 2019).

• GSEA-InContext Explorer: An interactive visualization tool for putting gene set enrichment analysis results into biological context Rani K Powers, Anthony Sun, James C Costello. bioRxiv 10.1101/659847v1 (June 4, 2019).

• Modeling genetic heterogeneity of drug response and resistance in cancer Teemu D Laajala, Travis Gerke, Svitlana Tyekucheva, James C Costello. Current Opinions in Systems Biology 17:8-14.

• Trisomy 21 drives production of neurotoxic tryptophan catabolites via the interferon-inducible kynurenine pathway Rani K Powers, Rachel Culp-Hill, Michael P Ludwig, Keith P Smith, Katherine A Waugh, Ross Minter, Kathryn D Tuttle, Angela L Rachubinski, Ross E Granrath, Rebecca B Wilkerson, Angelo D'Alessandro,  James C Costello, Kelly D Sullivan, Joaquin M Espinosa. Nature Communications 10(1):4766.

• Loss of MAP3K7 sensitizes prostate cells to CDK1/2 inhibition and DNA damage by disruption of homologous recombination Satoshi Washino, Leah C Rider, Lina Romero, Lauren Jillson, Trisiani Affandi, Angela M Ohm, Elaine T Lam, Mary E Reyland,  James C Costello, Scott D Cramer. Molecular Cancer Research 17(10):1985-1998.

• A Whole-genome CRISPR Screen Identifies a Role of MSH2 in Cisplatin-mediated Cell Death in Muscle-invasive Bladder Cancer Andrew Goodspeed, Annie Jean, James C Costello European Urology 75(2):242-250.

• Targeting DDR2 enhances tumor response to anti-PD-1 inmmunotherapy Megan M Tu, Francis YF Lee, Robert T Jones, Abigail K Kimball, Elizabeth Saravia, Robert F. Granziano, Briane Coleman, Krista Menard, Jun Yan, Erin Michaud, Han Chang, Hany A Abdel-Hafiz, Andrii Rozhok, Jason E Duex, Neeraj Agarwal, Ana Chaucau-Diaz, Linda K Johnson, Terry L Ng, John C Cambier, Erick T Clambey, James C Costello, Alan J Korman, Dan Theodorescu. Science Advances 5(2):eaav2437.

• Six2 mediates late-stage metastasis via direct regulation of Sox2 and induction of a cancer stem cell program Michael Oliphant,  Melanie Y Vincent, Matthew D Galbraith, Ahwan Pandey, Wadym Zaberezhnyy, Pratyaydipta Rudra, Katherine R Johnson, James C Costello, Debashis Ghosh, James Degregori, Joaquin M Espinosa, Heide Ford. Cancer Research 79(4):720-734.

2018

• Improved inference of chromosome conformation from images of labeled loci Brian C Ross,  James C Costello. F1000Research 2018, 7(ISCB Comm J):1521 (doi: 10.12688/f1000research.16252.1).

• Metastatic cells are preferentially vulnerable to lysosomal inhibition Michael Morgan, Brent Fitzwalter, Rani K Powers, Charles R. Owens, Graciela Gamez, James C Costello, Dan Theodorescu, Andrew Thorburn. PNAS 10.1073/pnas.1706526115.

• GSEA-InContext: Identifying novel and common patterns in expression experiments Rani K Powers, Andrew Goodspeed, Harrison Pielke-Lombardo, Aik-Choon Tan, James C Costello. Bioinformatics 34(13):i555-64.

• A gene expression signature predicts bladder cancer cell line sensitive to EGFR inhibition Andrew Goodspeed, Annie Jean, Dan Theodorescu, James C Costello. Bladder Cancer 4(3):269-82.

• Next-generation machine learning for biological networks Diogo Camacho, Katherine Collins, Rani K Powers, James C Costello, James J Collins. Cell 17(7):1581-92.

• Modeling heterogeneous populations using Boolean networks Brian C Ross, Mayla Boguslav, Holly Weeks, James C Costello. BMC Systems Biology 12:64.

• Eya3 Enhances Breast Cancer Progression via Threonine Phosphatase Mediated Upregulation of PD-L1 and Resultant Immune Suppression Rebecca L Vartuli, Hengbo Zhou, Lingdi Zhang Rani K Powers, Jared Klarquist, Pratyaydipta Rudra, Melanie Y Vincent. Debashis Ghosh, James C Costello, Ross M Kedl, Jill E Slansky, Rui Zhao, Heide L Ford. Journal of Clinical Investigation 10.1172/JCI96784.

• Systematic Review: Characteristics and preclinical uses of bladder cancer cell lines Tahlita Zulverloon, Florus C de Jong, James C Costello, Dan Theodorescu. Bladder Cancer 4(2):169-183.

2017

• Allele-specific DNA methylation and its interplay with repressive histone marks at promoter-mutant TERT genes Josh L Stern, Richard D Paucek, Franklin W Huang, Mahmoud Ghandi, Ronald Nwumeh, James C Costello, Thomas R Cech. Cell Reports 21(13):3700-3707.

• Community mining of open clinical trial data Teemu D. Laajala, Justin Guinney, James C Costello. Oncotarget 8(47):81721-2.

• All paths lead to TRIM25 Hengbo Zhou, James C Costello. Trends in Cancer 3(10):673-5.

• A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration-resistant prostate cancer patients 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. JCO Clinical Cancer Informatics 1(August 2017)1-15.

• 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 Justin Guinney, Tao Wang, Teemu D Laajala, The Prostate Cancer Challenge DREAM Community, Kimberly Kanigel Winner, J Christopher Bare, Elias Chaibub Neto, Suleiman A Khan, Gopalacharyulu Peddinti, Antti Airola, Tapio Pahikkala, Tuomas Mirtti, Thomas Yu, Brian M. Bot, Liji Shen, Kald Abdallah, Thea Norman, Stephen Friend, Gustavo Stolovitzky, Howard Soule, Christopher J Sweeney, Charles J Ryan, Howard I Scher, Oliver Sartor, Yang Xie, Tero Aittokallio, Fang Liz Zhou, James C Costello. The Lancet Oncology 18(1):132-142.

• A spatiotemporal model to simulate chemotherapy regimens for heterogeneous bladder cancer metastases to the lung Kimberly Kanigel Winner and James C Costello. Pacific Symposium for Biocomputing 22:611-622.

• Molecular analysis of urothelial cancer cell lines for modeling tumor biology and  drug response Michael L Nickerson, Nicolle Witte, Kate M Im, Sevilay Turan, Charles Owen, Kevin Misner, Shirley X Tsang, Zhiming Cai, Song Wu, Michael Dean, James C Costello, Dan Theodorescu. Oncogene 36(1):35-46.

2016

• Multivalent chromatin engagement and inter-domain crosstalk regulate MORC3 ATPase Forest H Andrews, Qiong Tong, D Fonseca, Evan Cornett, Yi Zhang, Muzaffar Ali, JaeWoo Ahn, James C Costello, Brian D Strahl, A Garcia-Sastre, Scott B Rothbart, Tatiana G Kutateladze. Cell Reports 16:3195-3207.

• Reducing overfitting in challenge-based competitions 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. arXiv 1607.00091.

• Crowdsourcing biomedical research: leveraging communities as innovation engineers Julio Saez-Rodriguez, James C Costello, Stephen H Friend, Michael R Kellen, Lara Mangravite, Pablo Meyer, Thea Norman, Gustavo Stolovitzky. Nature Reviews Genetics 17:470-486

• GON4L drives cancer growth through a YY1-androgen receptor-CD24 axis Neeraj Agarawal, Garrett M.Dancik, Andrew Goodspeed, James C Costello, Charles Owens, Jason E Duex, Dan Theodorescu. Cancer Research 76(17):5175-5185.

• Tumor-derived cell lines as molecular models of cancer pharmacogenomics Andrew Goodspeed, Laura M Heiser, Joe W Gray, James C Costello
  Molecular Cancer Research 14(1):3-13.

2015

• DREAMTools: a Python package for scoring collaborative challenges 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 .F1000Research , 4:1030 (doi: 10.12688/f1000research.7118.1).

• RhoC is an unexpected target of RhoGDI2 in prevention of lung colonization of bladder cancer Erin M. Griner, Garrett M. Dancik, James C. Costello, Charles Owens, Sunny Guin, Michael G. Edwards, David L. Brautigan, Dan Theodorescu. Molecular Cancer Research 13(3):483-92.

• TERT promoter mutations and telomerase reactivation in Urothelial Cancer Sumit Borah, Linghe Xi, Arthur J. Zaug, Natasha M. Powell, Garrett M. Dancik, Scott Cohen, James C. Costello, Dan Theodorescu, Thomas R. Cech. Science 347(6225):1006-10.

• Coordinate loss of MAP3K7 and CHD1 promotes aggressive prostate cancer Lindsey Ulkus Rodrigues, Leah Rider, Cera Nieto, Lina Romero, Anis Karimpour-Fard, Massimo Loda, M. Scott Lucia, Min Wu, Lihong Shi, Adela Cimic, S. Joseph Sirintrapun, Rosalie Nolley, Colton Pac, Haitao Chen, Donna M. Peehl, Jianfeng Xu, Wennuan Liu, James C. Costello, Scott D. Cramer. Cancer Research 75(6):1021-1034.

2014

• Decade in review-bladder cancer: international progress, from cytology to genomics James C. Costello, Dan Theodorescu. Nature Reviews Urology 11(11):609-10.

• A community computational challenge to predict the activity of pairs of compounds Mukesh Bansal, Jichen Yang, Charles Karan, Michael P Menden, James C. Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffery Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura Heiser, Ronald Realubit, Michela Mattioli, Mariano Alvarez, Yao Shen, NCI-DREAM Community, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky,  Andrea Califano. Nature Biotechnology 32:1213-22.

• A community effort to assess and improve drug sensitivity prediction algorithms James C. Costello, Laura M. Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P. Menden, Nicholas J. Wang, Mukesh Bansal, Muhammad Ammad-ud-din, Petteri Hintsanen, Suleiman A. Khan, John-Patrick Mpindi, NCI DREAM Community, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, James J. Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W. Gray, Gustavo Stolovitzky. Nature Biotechnology 32:1202-12. 

• Homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression Chu-An Wang,  David Drasin,  Catherine Pham,  Paul Jedlicka, Vadym Zaberezhnvv,  Michelle Guney,  Howard Li,  Raphael Nemenoff,  James C. Costello,  Aik-Choon Tan,  Heide Ford. Clinical Cancer Research 74(24):7357-70.

• Concurrent Alterations in TERT, KDM6A, and the BRCA Pathway in Bladder Cancer Michael L. Nickerson, Garrett M. Dancik, Kate M. Im, Michael G. Edwards, Sevilay Turan, Joseph Brown, Christina Ruiz-Rodriguez, Charles Owens, James C. Costello, Guangwu Guo, Shirley X. Tsang, Yingrui Li, Quan Zhou, Zhiming Cai, Lee E. Moore, M. Scott Lucia, Michael Dean, Dan Theodorescu Clinical Cancer Research 20:4935-48.

• EPSLiM: Ensemble Predictor for Short Linear Motifs in Nuclear Hormone Receptors Ran Xue, Mikhail N Zakharov, Yu Xia, Shalender Bhasin, James C. Costello, Ravi Jasuja. Molecular Endocrinology 28(5):768-77.

2013

• Seeking the wisdom of crowds through challenge-based competitions in biomedical research James C. Costello, Gustavo Stolovitzky. Clinical Pharmacology & Therapeutics 93:396-98.

• Combined administration of testosterone plus an ornithine decarboxylase inhibitor as a selective prostate-sparing anabolic therapy Ravi Jasuja, James C. Costello, Samudra Gangopadhyay, Rajan Singh, Vandana Gupta, Gianluca Toraldo, Hyeran Jang, Hu Li, Carlo Serra, Wen Guo, Pritibha Chauhan, Navjot S. Narula, Ayla Ergun, Katie Spina, Thomas G. Travison, James J. Collins, Shalender Bhasin. Aging Cell 13(2):303-10.

• Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells Roi Gazit, Brian S. Garrison, Tata N. Rao, Tal Shay, James C. Costello, Jeff Ericson, Francis Kim, James J. Collins, Aviv Regev, Amy J. Wagers, Derrick J. Rossi,  ImmGen Consortium. Stem Cell Reports 1:266-80.

• Differential splicing across immune system lineages Ayla Ergun, Graeme Doran, James C. Costello, Henry H. Paik, James J. Collins, Diane Mathis, Christophe Benoist, and ImmGen Consortium. Proceedings of the National Academy of Sciences 110:14324-29.

• Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in mammalian cells Sameer Kalghatgi, Catherine Spina, James C. Costello, Marc Liesa, Jose Ruben Morones-Ramirez, Shimyn Slomovic, Anthony Molina, Orian Shirihai, James J. Collins Science Translational Medicine 5:190ra81.

2012

• Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma Lawrence Kwong, James C. Costello, Huiyun Liu, Giannicola Genovese, Shan Jiang, Joseph H. Jeong, Ryan P. Bender, James J. Collins, Lynda Chin. Nature Medicine 18:1503-10.

• Wisdom of crowds for robust gene network inference Daniel Marbach, James C. Costello, Robert Kueffner, Nicci Vega, Robert Prill, Diogo M. Camacho, Kyle R. Allison, the DREAM5 Consortium, Manolis Kellis, James J. Collins, Gustavo Stolovitzky. Nature Methods 9(8):796-804.

Before 2012

• Gene networks in Drosophila melanogaster: Integrating experimental data to predict gene function James C. Costello, Mehmet M. Dalkilic, Scott M. Beason, Jeff R. Gehlhausen, Rupali Patwardhan, Sumit Middha, Brian D. Eads, Justen R. Andrews. Genome Biology 10:R97. 2009.

• EST and microarray analysis of horn development in Onthophagus beetles Teiya Kijimoto, James C. Costello, Zuojian Tang, Armin P. Moczek, Justen R. Andrews. BMC Genomics 10:504. 2009.

• All human-specific gene losses are present in the genome as pseudogenes Daniel R. Schrider, James C. Costello, Matthew W. Hahn. Journal of Computational Biology 16:1419-27. 2009.

• Data-driven ontologies James C. Costello, Daniel R. Schrider, Jeff R. Gehlhausen, Mehmet M. Dalkilic. The Pacific Symposium on Biocomputing 14:15-26. 2009.

• Reverse ecology and the power of population genomics Yong Li, James C. Costello, Alisha K. Holloway, Matthew W. Hahn. Evolution 62:2984-94. 2008.

• Limitations of pseudogenes in identifying gene losses James C. Costello, Mira V. Han, Matthew W. Hahn. In Proceedings of Recomb-CG. Paris, France. 2008.

• Data Pushing: a Fly-centric guide to Bioinformatics tools James C. Costello, Amy Cash, Mehmet M. Dalkilic, Justen R. Andrews. Fly 2(1):1-18. 2008.

• From protein-disease associations to disease informatics Mehmet M. Dalkilic, James C. Costello, Wyatt Clark, Predrag Radivojac. Frontiers in Bioscience 13:3391-3407. 2008.

• Evolution of genes and genomes on the Drosophila phylogeny Drosophila 12 Genomes Consortium.* (*Consortium member). Nature 450(7167):203-18. 2007.

• Integrating Drosophila data to discover disease-related protein interactions in human James C. Costello, Jade Buchannan-Carter, Mehmet M. Dalkilic, Justen R. Andrews. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology Honolulu, HI. 2007.

• Using compression to identify classes of inauthentic texts Mehmet M. Dalkilic, Wyatt Clark, James C. Costello, Predrag Radivojac. In Proceedings SIAM Conference on Data Mining Bethesda, MD. 603-07. 2006.

• Troubleshooting microarray hybridizations Brian Eads, Amy Cash, Kevin Bogart, James C. Costello, Justen R. Andrews. Methods in Enzymology 411:34-49. 2006

• BioKnOT: Biological Knowledge through Ontologies and TFIDF Mehmet M. Dalkilic, James C. Costello. In Proceedings ACM SIGIR Workshop: Search and Discovery in Bioinformatics Sheffield, UK. 2004.

• Semantic Thumbnails: A novel method for summarizing document collections Mehmet M. Dalkilic, James C. Costello, Arjjit Sengupta. In Proceedings ACM SIGDOC Memphis, TN. 2004.

• TREC 2004 genomic track experiments Kazuhiro Seki, James C. Costello, Vasanth Singhan, Javed Mostafa. In Proceedings of TREC 2004; Genomics Track 2004.