Integrative Computational Approaches 2

• 4174 · PDF hla2vec: Developing a HLA embedding space using probabilistic cross-reactive groups Isabel Quesada, Jordan Tagle, Kyle Ellrott
• 4175 Neoantigen-guided TCR discovery pipeline to improve specificity and reduce off-target toxicity in AML Pamella Borges, Martiela Freitas, Samee Ullah, Hussein A. Abbas, Dinler Antunes
• 4176 · PDF DAG-guided kernel learning framework to mitigate racial disparities in breast cancer Min-jeong Baek, Jieqiong Wang, Vimla Band, Shibiao Wan
• 4177 · PDF Integrated meta-clustering reveals subtype-specific transcriptomic heterogeneity of pediatric low-grade glioma Bulidierxin Tuerhanbayi, Jieqiong Wang, Shibiao Wan
• 4178 · PDF Mapping the imputation-augmented somatic mutation landscape of 2,551 NSCLC patients highlights contrasting patterns across histologic subtype, smoking status, and ancestry Isam Mohd-Ibrahim, Zhuokun Feng, Yu Chen, Lauren Higa, Youping Deng
• 4179 · PDF Three-dimensional spatial multi-omics of gastric tumor sections reveal hidden features beyond 2D analyses Inyeop Jang, Soyoung Im, Minji Kim, Seok-Jin Chung, Minsoo Lee, Soonyoung Lee, Jongseong Jang, Tae Hyun Hwang
• 4180 · PDF Protocol-specific and coverage-based RNA-seq metrics characterize RNA integrity signatures across cohorts Miyeon Yeon, Wonyoung Choi, Jin Young Lee, David Neil Hayes, Hyo Young Choi
• 4181 · PDF De-risk targets through mechanism-enabled simulations in the Virtual Lab Krishna Bulusu, Katalin Szégner, László Mérő, Eszter Szarka, Iván Fekete, María Victoria Ruiz Perez, Csilla Hegedűs, Imre Gáspár, Gábor Kovács, Kristóf Szalay, Daniel Veres
• 4182 Pan-cancer landscapes of transcriptional heterogeneity in metastatic tumors Ramyar Molania, Himisha Beltran
• 4183 · PDF Finding Goldilocks: How AI-powered covalent drug discovery removes the “un” from “undruggable” Johannes C. Hermann, Robert Everley, Han Wool Yoon, Rohan Varma, Karsten Krug, Daniel Erlanson, Chris Varma, Kevin R. Webster
• 4184 · PDF Multimodal deep learning framework for predicting clinically significant phenotypes in prostate cancer Priyanka Vasanthakumari, Mohamed Omar
• 4185 · PDF A modular in silico triage pipeline for multi omic evaluation of surface protein targets across indications Satyajit Rajapurkar, Lena Eismann, Mariana Pereira, Theodore Groth, Mugdha Khaladkar, Kathrin Jansen, Edward Curry, Marica Speranza
• 4186 · PDF A novel integrated AI ML and COSMIC signature profiling approach resolving blast crisis CML heterogeneity into single patient level pan cancer actionable programs enabling repurposable therapies for relapsed refractory and metastasized cancers Zafar Iqbal, Abdulkareem AlGarni, Lubna Alnuaim, Sahrish Khan, Sohail Rao, Yaqob Taleb, Nasser Mohammed AlQahtani, Muhammad Alshuaibi, Essa Al Mansour, Mashael AlShuker, Azfar Athar Ishaqui, Giuseppe Saglio, Kaleem Ahmed, Rizwan Naeem, Masood A. Shammas, Muhammad Farooq Sabar
• 4187 scOncoNet: Dual-graph attention network for program-aware in-silico gene perturbation in single-cell cancer data Tingyi Li, Yuanyuan Shen, Bin Baek, Xiaoqing Yu, Xuefeng Wang
• 4188 · PDF Breaks in the cancer immunity cycle correlate with response-predictive HNSCC immune microenvironment phenotypes Sarah R. Harrington, Daniel Uralov, Sophia Linguiti, Hannah Kenny, Parvesh Kumar, Janvi J. Shukla, Marianna Nicodemi, Ian Argento, Emma J. Anisman, Eloise Freitag, Adam J. Luginbuhl, Larry Harshyne, Zhao Lin, Alban J. Linnenbach, Ubaldo E. Martinez-Outschoorn, Joseph M. Curry
• 4189 · PDF Quantifying uncertainty in virtual spatial transcriptomics using Bayesian neural networks Thanosan Prathifkumar, Nehan Mohamed, Anvith Kakkera, Zarif Azher, Xiaoying Liu, Fred Kolling, Laurent Perreard, Scott Palisoul, Louis J. Vaickus, Joshua Jay Levy
• 4190 · PDF A scalable, proteome-wide protein profiling platform with absolute quantification of 1000 proteins to power oncologic drug discovery pipelines Jerid Robinson, Nathaniel Robichaud, Grant Ongo, Kiran Edwardson, Alyssa Rosenbloom, Narges Rashidi, Arya Tavakoli, Jeff Munzar, Milad Dagher
• 4191 · PDF TP53 dysfunction drives immunometabolic rewiring via mTORC1 activation and autophagy suppression in colorectal cancer Eunseuk Lee, Dana Al-Assi, Randy Rueda-Rivera
• 4192 · PDF Coordinated miRNA regulation of AR-PI3K/MAPK crosstalk and EMT in prostate cancer Fabiana Buono, William Lautert-Dutra, Dan Dion, Camila Morais Melo, Cheryl Crozier, Fabiano Pinto Saggioro, Rodolfo Borges dos Reis, Jeremy Andrew Squire, Jane Bayani
• 4193 · PDF Heterogeneous graph neural network meta-analysis of lung cancer and tuberculosis transcriptomic datasets reveals convergent host response networks Andrew Triska, Selvakumar Subbian, Natarajan Ganesan
• 4195 · PDF OncoGraphDB: Rapid projections of patient-level multimodal graph database facilitates efficient exploration of tumor subtypes and identifies new combinatorial biomarkers of patient outcomes and gene essentiality Jacob Pfeil, Amber Tse, Severiano Villarruel, Emily Rossi, Liqian Ma, Xi Zhao, Josue Samayoa, Kyle Halliwill
• 4196 · PDF Predicting self-antigen recognition of TCRs derived from tumor infiltrating CD8+ T cells via contrastive learning and T cell phenotyping Brinda Vijaykumar, Qiaomu Tian, Jack Prazich, Preet Joshi, Neel Patel, John Abel, Anthony Coyle, Daniel Pregibon
• 4197 · PDF Multiomic dissection of KRAS signaling reveals targetable metabolic and DNA repair vulnerabilities in colorectal cancer Tom Cohen, Ashima Mehta, Adam Richardson, Monil Gandhi, Douglas Guzior, Kevin Cho, Ethan Stancliffe, Gary Patti
• 4198 · PDF Integrative single-cell transcriptomics and computational docking identify CCL18 as an immunomodulatory target in prostate cancer Edwige Flore Gouegni, Gebre-Eziagbher Kiros, Renee Reams, Diana J. Wilke, Fredenburg Kristianna, Bodour Salhia
• 4200 · PDF Exploring unrestricted antibiotic use gut microbiome imbalance and chemical carcinogens in liver and kidneys toxicity through computer modeling and in vivo study Solomon Owumi, Dooshima A. Bagu, Joseph Chimezie, Esther M. Pius, Uche O. Arunsi, Jesutosin O. Babalola, Ayomide P. Akomolafe, Chima Amadi, Chinedum Udekwu, Adegboyega K. Oyelere, E. Oluwabunmi Olapade-Olaopa, Olorunseun O. Ogunwobi
• 4201 · PDF Simulating trans-endothelial nanoparticle transport via macropinocytosis Marvin Skiba, Hae-gyung T. Han, Warren Chan

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