Improved inference of chromosome conformation from images of labeled loci [version 3; peer review: 2 approved] by Brian C. Ross, James C. Costello

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ProstaMine: a bioinformatics tool for identifying subtype-specific co-alterations associated with aggressiveness in prostate cancer by Michael V. Orman, Varsha Sreekanth, Teemu D. Laajala, Teemu D. Laajala, Scott D. Cramer, Scott D. Cramer, James C. Costello, James C. Costello

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Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes by Josh Lewis Stern, Richard D. Paucek, Franklin W. Huang, Mahmoud Ghandi, Ronald Nwumeh, James C. Costello, Thomas R. Cech

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SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses by Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene

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KDM3A/Ets1 epigenetic axis contributes to PAX3/FOXO1‐driven and independent disease‐promoting gene expression in fusion‐positive Rhabdomyosarcoma by Lays M. Sobral, Hannah M. Hicks, Janet K. Parrish, Tyler S. McCann, Joseph Hsieh, Andrew Goodspeed, James C. Costello, Joshua C. Black, Paul Jedlicka

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A harmonized resource of integrated prostate cancer clinical, -omic, and signature features by Teemu D. Laajala, Varsha Sreekanth, Alex C. Soupir, Jordan H. Creed, Anni S. Halkola, Federico C. F. Calboli, Kalaimathy Singaravelu, Michael V. Orman, Christelle Colin-Leitzinger, Travis Gerke, Brooke L. Fridley, Svitlana Tyekucheva, James C. Costello

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SIX1 and EWS/FLI1 co-regulate an anti-metastatic gene network in Ewing Sarcoma by Connor J. Hughes, Kaiah M. Fields, Etienne P. Danis, Jessica Y. Hsu, Deepika Neelakantan, Melanie Y. Vincent, Annika L. Gustafson, Michael J. Oliphant, Varsha Sreekanth, Vadym Zaberezhnyy, James C. Costello, Paul Jedlicka, Heide L. Ford

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

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Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth by Adi L. Tarca, Bálint Ármin Pataki, Roberto Romero, Marina Sirota, Yuanfang Guan, Rintu Kutum, Nardhy Gomez-Lopez, Bogdan Done, Gaurav Bhatti, Thomas Yu, Gaia Andreoletti, Tinnakorn Chaiworapongsa, Sonia S. Hassan, Chaur-Dong Hsu, Nima Aghaeepour, Gustavo Stolovitzky, Istvan Csabai, James C. Costello

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Trisomy 21 activates the kynurenine pathway via increased dosage of interferon receptors by Rani K. Powers, Rachel Culp-Hill, Michael P. Ludwig, Keith P. Smith, Katherine A. Waugh, Ross Minter, Kathryn D. Tuttle, Hannah C. Lewis, Angela L. Rachubinski, Ross E. Granrath, María Carmona-Iragui, Rebecca B. Wilkerson, Darcy E. Kahn, Molishree Joshi, Alberto Lleó, Rafael Blesa, Juan Fortea, Angelo D’Alessandro, James C. Costello, Kelly D. Sullivan, Joaquin M. Espinosa

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