Network Biology and Precision Medicine

• 6858 · PDF Single-cell elucidation of molecularly distinct states and therapeutic vulnerabilities in IDH-mutant glioma Luca Zanella, Patrick M. Kerwin, Mikko Turunen, Peter A. Sims, Peter D. Canoll, Andrea Califano
• 6859 · PDF Targeting master regulators to reprogram neutrophils and enhance PD-1 blockade efficacy in castration-resistant prostate cancer Melania Franchini, Florencia Picech, Cory Abate-Shen, Andrea Califano
• 6860 · PDF Ensemble somatic variant calling and transcript reconstruction for high-fidelity neoantigen discovery in mRNA cancer vaccine design Po-Yuan Chen, Mi-Hua Tao, Tai-Ming Ko
• 6861 · PDF NeonDisco: A Nextflow orchestration framework for in silico discovery and prioritization of recurrent neoantigen candidates Mohd Suffian Azizan, Min Hui Tan, Jia Wern Pan, Sok Ching Cheong
• 6862 · PDF A scalable workflow for in silico TMA construction and groupwise comparison of spatial transcriptomic data for analyzing tumor microenvironment Dongjoo Lee, Sungwoo Bae, Yeonjae Jung, Kwon Joong Na, Hongyoon Choi
• 6863 · PDF Integrating computational and experimental approaches to optimize RNA fusion identification in BRCA associated breast cancer Janvi Sandhu, Anjana Bhardwaj, Chathurani Ranathunge, Dilshan C. Adhikari, Shiyanth Thevasagayampillai, Jamal Hill, Abhijit Mazumdar, Preethi H. Gunaratne, Isabelle Bedrosian
• 6865 · PDF A knowledge graph screen of innovative versus incremental lung cancer trials for need-aligned designs Mahitha Simhambhatla, Maya Ylagan, Praneeth Sajja, Daruka Mahadevan, Erik S. Ferlanti, James Carson, Boone Goodgame, Ehsan Irajizad, Samir M. Hanash, Jeanne Kowalski
• 6866 · PDF Mapping cancer-relevant genetic interactions with functional module prediction and in4mer enCas12a platform Chenchu Lin, Veronica Gheorghe, Juihsuan Rosalind Chou, Sabriyeh Alibai, Subin Kim, Nazanin Esmaeili Anvar, Yixin Xu, Xingdi Ma, Lori L. Wilson, Russell Moser, Junjie Chen, Christopher J. Kemp, Scott Kopetz, Glen Traver Hart
• 6867 · PDF Uncovering the systems-level mutational landscape of intrinsically disordered regions in cancer Kivilcim Ozturk, Hannah K. Carter
• 6868 · PDF Understanding molecular mechanisms of prostate cancer via transcriptome-wide causal gene regulatory networks Min Zhang, Zhongli Jiang, Xiaolin Zi, Danni Liu, Yan Li, Dabao Zhang
• 6869 · PDF Multi-omic profiling identified three molecular clusters in urothelial carcinoma: A path towards clinical precision Nils Cornelis Hendricus van Creij, Piotr Tymoszuk, Florian Handle, Andreas Seeber, Teresa Sellemond, Agnieszka Martowicz, Eva Compérat, Hamed Wafa, Steffen Ormanns, Michael Günther, Walther Parson, Maxim Noeparast, Frederic Romain Santer, Jose Daniel Subiela, Petros Grivas, Roger Li, Zoran Culig, Renate Pichler
• 6870 · PDF Quartet: A database of robust somatic mutations in tumor cell lines Daniel Halmos, Trey Ideker
• 6871 · PDF Real-world analytical concordance of four next-generation sequencing assays: Impact of assay methodology and bioinformatics on clinical decision-making Liudmila Zhukova, Sergei Smolin, Svetlana Smolina, Nikolai Karnaukhov
• 6872 · PDF Assessing the Impact of Variant Calling Pipelines on De Novo SBS Mutational Signature Extraction Zichen Jiang, Jessica Nghi Au, Mariya Kazachkova, Marcos Díaz-Gay, Raviteja Vangara, Ludmil B. Alexandrov
• 6873 · PDF Knowledge graph driven insights and drug repurposing opportunities for neuroendocrine prostate cancer Pawan Verma, Prasanna Kumar Sekar Sekar, Dharani Dadi, Manimala Sen, Nobal Dhruw, Abhishek Jha
• 6874 · PDF A transcriptome-based AI meta-model for immunotherapy response classification in hepatocellular carcinoma Jimin Seo, Na Young Kwon, Ki Wook Lee, Han-En Lo, Young-Jun Jeon
• 6875 · PDF Mapping convergent neurodegenerative and oncogenic pathways in ALS using a multi-scale knowledge-graph framework Vasileios Alevizos, Sabrina Edralin, Clark Xu, George A. Papakostas, Zongliang Yue
• 6877 · PDF Chromatin networks inform the development of prognostic gene expression signatures in human cancers Lucio R. Queiroz, Shreyas Rajaram, Karnika Singh, Angelo Corso Faini, Erika Minonne, Nicola Barbaro, Scarfó Federico, Pushpita Roy, Wikum Dinalankara, Luigi Marchionni
• 6878 · PDF AI-driven structural variant annotation expands therapeutic stratification in breast cancer Kriti Shukla, Yue Wang, Philip M. Spanheimer, Elizabeth Brunk
• 6879 · PDF Integrating omics-driven digital avatars with patient-derived experimental models to accelerate precision oncology Bulak Arpat, Amel Bekkar, Michelle Barnard, Mark Eccleston, Ioannis Xenarios, Kevin Buyens, Michael Prosser
• 6880 · PDF Optimization of a urine based NGS assay for detecting minimal residual disease in bladder cancer Yujia Zheng, Philip H. Abbosh, Muhammed Murtaza, Rhea Arya
• 6881 · PDF Fast and cost-effective cloud-based pipelines to analyze cancer sequencing data Sam Wiseman, Samantha Van Seters, Saveliy Belkin, David I. Heiman, Vasuki Narasimha Swamy, Antonia Kowalewski, Scott Ritterbush, Zachary Everton, Ron Solan, Chip Stewart, David Lehotzky, Luis Antonio Corchete Sanchez, Xavi Loinaz, Haruna Tomono, Andrew D. Cherniack, Gengchao Wang, Brian P. Danysh, Young Seok Ju, Esther Rheinbay, Gad Getz
• 6882 · PDF Mechanism-concordant cell-line selection: Bridging real-world tumor drivers and in vitro models for target validation Aviva G. Beckmann, Phillip Comella, Qi Pan, Jonathan Tyler, Enrique Podaza, Veronica Calvo-Vidal, Mark Fereshteh, Iker Huerga, Eric E. Schadt
• 6883 · PDF An RNA-based survival model predicting real-world response to trastuzumab deruxtecan Klemen Žiberna, Anže Lovše, Žan Kuralt, Janez Kokošar, Marcel Levstek, Luka Ausec, Miha Štajdohar, Rafael Rosengarten, Mark Uhlik, Joshua Wheeler
• 6884 · PDF Quantum mechanics-based multi-tensor AI/ML correctly predicts - glioblastoma patients' overall survival, gene targets to sensitize the tumors, and the tumors' response to their targeting - from their whole genomes Orly Alter, Sri Priya Ponnapalli, Marissa Coppola, Angela C. Gushue, Tessa O. House, Penelope L. Miron, Kristy L. S. Miskimen, Kristin A. Waite, Sarah Pollock, David Bogumil, Nika Iremadze, Samantha Hernandez, Nadiya Sosonkina, Sara E. Coppens, Anthony C. Bryan, Estevan P. Kiernan, Huanming Yang, Jay Bowen, Ghunwa A. Nakouzi, Doron Lipson, Jill S. Barnholtz-Sloan, Andrew E. Sloan, Tiffany R. Hodges, Asaf Zviran, Jessica W. Tsai

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