Integrative Computational Approaches 1

• 1462 · PDF Cell type-specific somatic variants captured from single-cell RNA sequencing underlie transcriptional programs in pre-malignant blood Jasmine Ryu Won Kang, Mawusse Agbessi, June Kim, Ido Nofech-Mozes, Marie-Julie Fave, Philip Awadalla
• 1463 DNA methylation driven clonal splicing neoantigens predict immunotherapy response in lung cancer Sadegh Saghafinia, Carla Castignani, Amirhossein Ghorbanpour, Carlos Marínez-Ruiz, Francisco Gimeno-Valiente, Ariana Huebner, Cristina Naceur-Lombardelli, Raju Veeriah, Mariam Jamal-Hanjani, Alan Hackshaw, Nnennaya Kanu, Charles Swanton, Crispin Hiley
• 1464 · PDF CELLama-Perturb: A virtual cell modeling approach for mapping drug sensitivity across spatial tumor heterogeneity Haenara Shin, Jeongbin Park, Dongjoo Lee, Hongyoon Choi
• 1465 · PDF Expression-based immune-phenotyping ML model predict ICI response and long-term clinic benefit in lung adenocarcinoma Ki Wook Lee, Hyun Woo Park, Han-En Lo, Sehhoon Park, Balachandran Manavalan, Young-Jun Jeon
• 1466 · PDF CellNeighbor: A transcriptional atlas of patient tumors and cell line models to inform preclinical model selection Caitlin M. A. Simopoulos, Gabrielle Persad, Otto Morris, Carlos A. Origel Marmolejo, Laura M. Richards, Kelly M. Biette
• 1467 · PDF Mechanism-aware cancer therapy planning with group-relative policy optimization on a multimodal oncology foundation model Eric E. Schadt, Jackson Stokes, Lihua Zhao, Jason Chin, Jonathan Tyler, Lijia Sun, Lauren Beck, Duo Xu, Aviva G. Beckmann, Iker Huerga
• 1468 · PDF Germline whole exome sequencing implicates homologous recombination repair pathway genes as risk factors in SMARCB1 deficient renal medullary phenotypes without sickle hemoglobinopathies Pankaj Kumar Chauhan, Panayiotis Kontoyiannis, Evan von Eschenbach, Jessica P. Cheng, Susan S. Thomas, Luigi Perelli, Christopher J. Logothetis, Daria Melikhova, Lev Bedniagin, Michael Hensley, Nizar M. Tannir, Pavlos Msaouel
• 1469 · PDF Multi-omics profiling of neuroblastoma identifies immunological biomarkers associated with higher risk of relapse: Results from the MICCHADO study Antonio Colaprico, Alexandra Saint-Charles, Stelly Ballet, Charles Bobin, Joffrey Alves-Gasnier, Valery Attignon, Nathalie Droin, Ana Lalanne, Doriane Gorret, Lydie Cassard, Imene Hezam, Yasmine Iddir, Anthony Ferrari, Elnaz Saberi Ansari, Gaëlle Pierron, Julien Masliah-Planchon, Angela Bellini, Nathalie Chaput, Charlotte Butterworth, Benoit Dumont, Olivier Lantz, Olivier Delattre, Nadège Corradini, Claudia Pasqualini, Gudrun Schleiermacher
• 1470 · PDF Selecting representative histologic sections for cost-efficient 3D spatial transcriptomics and tumor microenvironment reconstruction Minh-Khang Le, James Evans, Harsimran Kaur, Sojung Lee, Vivek Pujara, Alan Joey Simmons, Seungwoo Kang, Jai Mehta, Louis J. Vaickus, Ken Lau, Joshua Jay Levy
• 1471 · PDF Unsupervised learning with MORPHAEUS enhances conventional tissue spatial phenotyping Elias Pavlatos, Benjamin Tate, Gregory Joseph Baker, Joanna Pucilowska
• 1472 · PDF AI-derived nuclear morphometrics as a novel prognostic indicator in lung adenocarcinoma Bokyung Ahn, Hee Sang Hwang, Hyun-Jung Sung, Se Jin Jang, Pil-Jong Kim, Heounjeong Go
• 1473 · PDF Local indicators of spatial association bioinformatics analysis identifies animmunosuppressive zone at the liver tumor margin Yoshiki Nonaka, Kanae Echizen, Tomonori Kamiya, Maho Tsuda, Yoshimi Yukawa-Muto, Hideki Fujii, Ryo Takahashi, Takahiro Kodama, Naoko Ohtani
• 1475 · PDF An evidence-based tool to systematically identify potential adverse drug-drug interactions Meetali Sinha, Ansu Kumar, Rajeev K, Vandana Nair, Liptimayee Behura, Deepak Lala, James Wingrove
• 1476 · PDF Improve spatial transcriptomic data with integrated hybrid transformer and graph convolutional networks Steven Yan, Limin Jiang, Yan Guo
• 1477 · PDF Lysosomal routing geometry drives immunosuppressive secretion in triple negative breast cancer Sudhanshu Sharma, Manoj K. Mishra
• 1478 · PDF Unifying molecular structure and cellular morphology to enhance drug-target interaction modeling in cancer Ying-Ju Lai, Yu-Chiao Chiu
• 1479 CAB: A confidence-aware sequence model enabling high-throughput prediction of mutation-driven binding affinity change in antibody-based cancer therapeutics Yuanfei Sun, Bing Jiang, Huiping Liu
• 1480 · PDF Transcriptional condensates at super-enhancers mediate pH-dependent transcriptional control in innate immunity Shengyuan Wang, Zhongyang Wu, Zhe Zhong, Zhenjia Wang, Xu Zhou, Chongzhi Zang
• 1481 · PDF Integrative analysis identifies potential proteomic intermediates associated with renal cell carcinoma and its risk factors Ibrahim Hossain Sajal, Andrew J. Song, Kevin M. Brown, Mitchell J. Machiela, Peter Kraft, Stephen J. Chanock, Mark P. Purdue, Diptavo Dutta
• 1482 · PDF A deep learning-based multimodal integration framework for clinical outcome prediction Baoyi Zhang, Helen Tian, Thanh Bui, Yookyung Christy Choi, Mona H. Cai, Peter Ansell, Aditee Shrotre, Steven Chirieleison, Kevin Kolahi, Xi Zhao, Josue Samayoa, Weilong Zhao
• 1483 · PDF Cleaved ATP5A1 mediates a poly(ADP-ribose)-dependent regulatory axis for R-Loop homeostasis under oxidative stress Aniruddha Mukherjee, Kaveri Goel, Weiqi Lei, Nicholas Hill, Rory Greer, Yuhua Song, Neil Pfister
• 1484 · PDF p-EMT transitional hub and its DC2-macrophage niche define recurrence in oral squamous cell carcinoma Yongjoon Jin, Jeong-Yeon Ji, Hyojung Lee, Na-yeon Kim, Eun-Jae Chung, Jong-Il Kim
• 1485 · PDF Multimodal AI for patient subtype discovery in LUSC using real-world data Swati Kaushik, Mark Carty, Akul Singhania, Justin Guinney, Radia Johnson
• 1486 · PDF From animals to computational oncology: Digital twins as ethical enablers of next-generation bone metastasis research Luca Marsilio, Stefan Maksimovic, Elisa Serafini, Alice Maccarini, Sergio Barrios, Pietro Cerveri, Stefano Casarin, Eleonora Dondossola
• 1487 Spatial microdomains from histology reveal multi-omic biomarkers for enhanced idiopathic pulmonary fibrosis diagnosis Raymond Yan, Brian Falkenstein, A. Burak Tosun, Filippo Pullara, S. Chakra Chennubhotla
• 1488 · PDF Structure-guided dual targeting of EZH2 and dopamine D1 receptor suppresses TNBC growth and metastasis Francesco Drago, Libere Ndacayisaba, Xilal Y. Rima, Gautam Sarathy, Deborah Ramsey, Gwen Fewell, Senthil Saravanamuthu, Sanjay Gupta, Giovanni Nigita, Eduardo Reátegu, Pierre Giglio, Christian Rolfo, Eswar Shankar
• 1489 · PDF STniche: An approach to identify functional niches in the tumor microenvironment from spatial transcriptomics Sasi Arunachalam, Oscar Ospina, Alex C. Soupir, Xiaoqing Yu, Brooke L. Fridley
• 1490 · PDF A single cell-based protein activity landscape for human small cell lung cancer Lucas ZhongMing Hu, Anish Thomas, Andrea Califano
• 4875 · PDF Modeling GBM-vasculature interaction on chip Promise Emeh, Alan Fetah, Jade Admiraal, Marleen Bokkers, Kevin Jimenez-Cowell, Will Allen, Nienke Wevers, Martine Lamfers, Clemens M. Dirven, Todd Burton, Karla Queiroz

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