New Software Tools for Data Analysis

• 5496 · PDF From transcripts to cells: Dissecting sensitivity, signal contamination, and specificity in Xenium spatial transcriptomics Mariia Bilous, Daria Buszta, Jonathan Bac, Senbai Kang, Yixing Dong, Stephanie Renaud-Tissot, Sylvie Andre, Marina Alexandre-Gaveta, Christel Voize, Solange Peters, Krisztian Homicsko, Raphael Gottardo
• 5497 · PDF AI-augmented immersive 3D and 4D spatial analysis interface for cancer research Jonathan S. Kim, Minji Kim, Seock-Jin Chung, Inyeop Jang, Young-Won Cho, Jiwon Kim, Soonyoung Lee, Jongseong Jang, Eunyoung Choi, Tae Hyun Hwang
• 5498 · PDF Resolving phenotyping discordance with SPACEMAP, an integrated machine learning framework Arely Perez Rodriguez, Bassel Dawod, Sebastian Diegeler, Eslam A. Elghonaimy, Megan Wachsmann, Purva Gopal, David Hein, Paul H. Acosta, Andrew Jamieson, Gaudenz Danuser, Robert Timmerman, Satwik Rajaram, Todd A. Aguilera
• 5499 · PDF SpatialTopic exploring tumor ecosystem in 3D multiplexed imaging of melanoma Xiyu Peng, James Smithy, Mohammad Yosofvand, Caroline Kostrzewa, Fiona Ehrich, MaryLena Bleile, Jasme Lee, Michael A. Postow, Margaret K. Callahan, Katherine Panageas, Ronglai Shen
• 5500 · PDF Morphology-aware profiling of highly multiplexed tissue images using variational autoencoders Gregory J. Baker, Edward Novikov, Shannon Coy, Yu-An Chen, Clemens Hug, Zergham Ahmed, Sebastian A. Cajas Ordonez, Siyu Huang, Clarence Yapp, Gaurav N. Joshi, Fumiki Yanagawa, Artem Sokolov, Hanspeter Pfister, Sandro Santagata, Peter K. Sorger
• 5501 · PDF A quantum-enabled atlas-scale resource to study metabolic landscapes and heterogeneity in cancer TME Yinuo Zhao, Jiahe Yu, Min Yang, Chi Zhang
• 5502 · PDF gOS: A total molecular oncology interpretation framework applied to repaired FFPE and heme whole genome and clinical targeted assays Kevin Hadi, Aditya Deshpande, Shihab Dider, Charalampos Xanthopoulakis, Johnathan Rafailov, Marcin Imielinski
• 5503 · PDF Cancer epitope prediction tools & analysis pipelines in CEDAR Ibel Carri, Jason Greenbaum, Zhen Yan, Kevin Kim, Haeuk Kim, Ashmitaa Logandha Ramamoorthy Premlal, Daniel Marrama, Nina Blazeska, Hannah K. Carter, Morten Nielsen, Alessandro Sette, Bjoern Peters, Zeynep Kosaloglu-Yalcin
• 5504 · PDF CoMMpass Explorer: An interactive platform to explore clinical and genomic data from newly diagnosed multiple myeloma patients from the landmark CoMMpass observational study Wanxing Zhang, Chaitanya R. Acharya, Steven M. Foltz, David E. Avigan, Samir Parekh, Ravi Vij, Shaji Kunnathu Kumar, Taxiarchis Kourelis, Sagar Lonial, Hearn Cho, Ioannis S. Vlachos, Sacha Gnjatic, Li Ding, Manoj Bhasin, George Mulligan
• 5505 · PDF A unified framework for cross-platform spatial omics analysis and deep spatial profiling Yunhe Liu, Edoardo L. Draetta, Kayla R. Caughlin, Alexandria Lau, Andre Fonseca, Tian Chu, Kyung Serk Cho, Yibo Dai, Yang Liu, Jun Wang, Jiahui Jiang, Yinyin Yuan, Futreal Andrew, Mingyao Li, Linghua Wang
• 5506 · PDF An ensemble machine learning approach to ALT detection revals therapeutic vulnerabilities in pediatric cancers lacking actionable drug targets Declan Bennett, Monika Weirdl, Lillian M. Guenther, Paul Geeleher
• 5507 · PDF A user-friendly, no-code, application for HIPAA-compliant automated analysis of tabular data at scale Paraic A. Kenny
• 5508 · PDF Bioinformatic method for the detection of micro copy number variations with exome sequencing data Jin Young Lee, Hyo Young Choi, D. Neil Hayes
• 5509 · PDF A computational framework for reproducible analysis of cancer drug screening data Huiyi Yang, Jax Lubkowitz, Xiaomeng Huang, Gabor Marth, Samuel Cheshier, Philip Moos, Yi Qiao
• 5510 · PDF Hunting for microsatellite instability in long-read data with Owl Zev Kronenberg, Khi Pin Chua, Mark J. P. Chaisson, Byunggil Yoo, Lisa Lansdon, William J. Rowell, Egor Dolzhenko, Kie Kyon Huang, Patrick Tan, Shruti S. Bhise, Everett Fan, Mark Mendoza, Emily O'donnell, Tomi Pastinen, Elizabeth R. Lawlor, Scott N. Furlan, Midhat S. Farooqi, Michael A. Eberle
• 5511 · PDF Exacto: Accurate identification of mutant proteoforms and neoantigens using integrative long-read sequencing Jin Seok Lee, Maria J. Sambade, Jeremy Wang, Alex Rubinsteyn, Benjamin G. Vincent
• 5512 · PDF ProteoRon: High-fidelity proteome inference from transcriptomes Kaiqiang Hu, Wanyu Tao, Ye Yuan, Zhe Li, Yuxin Zhang, Pengwei Pan, Fang He
• 5514 · PDF BART-spatial: Predicting biologically significant transcriptional regulators from spatial omics data Jingyi Wang, Hongpan Zhang, Zhenjia Wang, Chongzhi Zang
• 5515 · PDF Accelerating minimal residual disease (MRD) detection through GPU-accelerated genomic analysis using NVIDIA Parabricks Zhuosheng Gu, Adam Harmon, Maciej Pacula, Megan Rivera, Zachary Costliow, Ashley Tellis, Seka Lazare, Xiaomin Zhao, Wendy Winckler
• 5516 · PDF Learning-based invariant feature engineering reveals symmetry-encoded fingerprints of cancers that facilitate drug discovery Cristina Correia, Choong-Yong Ung, Cheng Zhang, Shizhen Zhu, Hu Li
• 5517 · PDF Standardizing global patient safety and site compliance in oncology trials using a configurable, technology-driven oversight model Ashley Herrick, Dmitri Berman, Elaina Haeuber, Sandy Shah, Salini Naidu
• 5518 · PDF Towards an accurate quantum support vector module for predicting cancer cell dynamics Amit Prakash
• 5519 · PDF SOMaC: An interpretable and generalizable framework for integrating and clustering multimodal spatial omics to resolve cell states and immune niches in cancer Junming Shi, Md Tauhidul Islam
• 5520 · PDF Multi-modal integration in the NetFlow framework for comprehensive exploratory data analysis Rena Elkin, Jung Hun Oh, Anish K. Simhal, Joseph O. Deasy
• 5521 · PDF MeDOC-KB: Knowledge base for unraveling the metabolic links between obesity-related cancers Madhan Subramanian, Sam Rosin, Stephanie Hall, Nisha Grover-Fairchild, Kim Robien, Loretta DiPietro, Marinella Temprosa
• 5522 · PDF scSurvival: Single-cell survival analysis of clinical cancer cohort data at cellular resolution Tao Ren, Faming Zhao, Canping Chen, Lingyun Wu, Gordon B. Mills, Lisa M. Coussens, Zheng Xia
• 5523 · PDF TNMplot 2.0: Stage-resolved and pan-cancer transcriptomic analytics for target discovery in oncology Aron Baratha, Balazs Gyorffy
• 5524 · PDF Visualization and analysis of cancer genomics data using UCSC Xena Mary Goldman, Brian Craft, Cally Lin, Jingchun Zhu, David Haussler
• 5525 · PDF Aneuploidy prediction in the spatial domain Calogero Carlino, Valentina Giansanti, Giovanni Petri, Davide Cittaro

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