Rezultati - Joshua M. Stuart

Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. od Vladislav Uzunangelov, Christopher K Wong, Joshua M Stuart

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Computational integration of homolog and pathway gene module expression reveals general stemness signatures. od Martina Koeva, E Camilla Forsberg, Joshua M Stuart

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Associating transcription factors to single-cell trajectories with DREAMIT od Nathan D. Maulding, Lucas Seninge, Joshua M. Stuart

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Biological process activity transformation of single cell gene expression for cross-species alignment od Hongxu Ding, Andrew Blair, Ying Yang, Joshua M. Stuart

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Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression od Nathan D. Maulding, Spencer Seiler, Alexander Pearson, Nicholas Kreusser, Joshua M. Stuart

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Pathway-Based Genomics Prediction using Generalized Elastic Net. od Artem Sokolov, Daniel E Carlin, Evan O Paull, Robert Baertsch, Joshua M Stuart

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The manatee variational autoencoder model for predicting gene expression alterations caused by transcription factor perturbations od Ying Yang, Lucas Seninge, Ziyuan Wang, Anthony Oro, Joshua M. Stuart, Hongxu Ding

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Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer od Nathan D Maulding, Jun Zou, Wei Zhou, Ciara Metcalfe, Joshua M Stuart, Xin Ye, Marc Hafner

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Prioritizing transcriptional factors in gene regulatory networks with PageRank od Hongxu Ding, Ying Yang, Yuanqing Xue, Lucas Seninge, Henry Gong, Rojin Safavi, Andrea Califano, Joshua M. Stuart

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RADIA: RNA and DNA integrated analysis for somatic mutation detection. od Amie J Radenbaugh, Singer Ma, Adam Ewing, Joshua M Stuart, Eric A Collisson, Jingchun Zhu, David Haussler

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A factor graph nested effects model to identify networks from genetic perturbations. od Charles J Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H Lee, Joshua M Stuart

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Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells. od E Camilla Forsberg, Emmanuelle Passegué, Susan S Prohaska, Amy J Wagers, Martina Koeva, Joshua M Stuart, Irving L Weissman

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Revealing cancer subtypes with higher-order correlations applied to imaging and omics data od Kiley Graim, Tiffany Ting Liu, Achal S. Achrol, Evan O. Paull, Yulia Newton, Steven D. Chang, Griffith R. Harsh, Sergio P. Cordero, Daniel L. Rubin, Joshua M. Stuart

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Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling od Mario Niepel, Marc Hafner, Qiaonan Duan, Zichen Wang, Evan O. Paull, Mirra Chung, Xiaodong Lu, Joshua M. Stuart, Todd R. Golub, Aravind Subramanian, Avi Ma’ayan, Peter K. Sorger

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Germline contamination and leakage in whole genome somatic single nucleotide variant detection od Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros

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Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges od Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros, Justin Guinney

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Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. od Peter H Waltman, Jian Guo, Emily Nahas Reistetter, Samuel Purvine, Charles K Ansong, Marijke J van Baren, Chee-Hong Wong, Chia-Lin Wei, Richard D Smith, Stephen J Callister, Joshua M Stuart, Alexandra Z Worden

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Valection: design optimization for validation and verification studies od Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P’ng, Kathleen E Houlahan, Cristian Caloian, Michael Fraser, SMC-DNA Challenge Participants, Kyle Ellrott, Adam A Margolin, Robert G Bristow, Joshua M Stuart, Paul C Boutros

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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection od Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros

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Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes od Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium

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