New Software Tools for Data Analysis

• 5496 · PDF 从转录本到细胞：剖析Xenium空间转录组学中的灵敏度、信号污染与特异性 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 用于癌症研究的AI增强沉浸式3D和4D空间分析界面 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 利用集成机器学习框架SPACEMAP解决表型分型不一致问题 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在黑色素瘤3D多重成像中探索肿瘤生态系统 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 利用变分自编码器对高度多重化组织图像进行形态学感知的分析 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 一种量子驱动的图谱规模资源，用于研究癌症TME中的代谢图景与异质性 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：一个应用于修复后FFPE、血液全基因组及临床靶向检测的整合分子肿瘤学解读框架 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 CEDAR中的癌症表位预测工具与分析流程 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：一个用于探索里程碑式CoMMpass观察性研究中新诊断多发性骨髓瘤患者临床与基因组数据的交互式平台 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 一个用于跨平台空间组学分析和深度空间分析的统一框架 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 一种用于ALT检测的集成机器学习方法揭示了缺乏可成药靶点的儿童癌症中的治疗脆弱性 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 一款用户友好、无需编程、符合HIPAA规范的大规模表格数据自动化分析应用 A user-friendly, no-code, application for HIPAA-compliant automated analysis of tabular data at scale Paraic A. Kenny
• 5508 · PDF 利用外显子组测序数据检测微拷贝数变异的生物信息学方法 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 用于癌症药物筛选数据可重复分析的计算框架 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 利用Owl在长读长数据中搜寻微卫星不稳定性 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：利用整合性长读长测序准确识别突变蛋白型和新抗原 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：从转录组高保真推断蛋白质组 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：从空间组学数据预测具有生物学意义的转录调控因子 BART-spatial: Predicting biologically significant transcriptional regulators from spatial omics data Jingyi Wang, Hongpan Zhang, Zhenjia Wang, Chongzhi Zang
• 5515 · PDF 利用NVIDIA Parabricks通过GPU加速基因组分析来加速微小残留病（MRD）检测 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 基于学习的不变特征工程揭示癌症的对称性编码指纹以促进药物发现 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 采用可配置、技术驱动的监督模式，规范全球肿瘤学试验中的患者安全与研究中心合规性 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 迈向用于预测癌细胞动力学的精准量子支持向量模块 Towards an accurate quantum support vector module for predicting cancer cell dynamics Amit Prakash
• 5519 · PDF SOMaC：一个可解释、可泛化的框架，用于整合与聚类多模态空间组学以解析癌症中的细胞状态和免疫生态位 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 NetFlow 框架中的多模态整合，用于全面的探索性数据分析 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：用于揭示肥胖相关癌症之间代谢关联的知识库 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：在细胞分辨率下对临床癌症队列数据进行单细胞生存分析 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：面向肿瘤学靶点发现的分期解析与泛癌转录组分析 TNMplot 2.0: Stage-resolved and pan-cancer transcriptomic analytics for target discovery in oncology Aron Baratha, Balazs Gyorffy
• 5524 · PDF 使用 UCSC Xena 对癌症基因组学数据进行可视化和分析 Visualization and analysis of cancer genomics data using UCSC Xena Mary Goldman, Brian Craft, Cally Lin, Jingchun Zhu, David Haussler
• 5525 · PDF 空间维度上的非整倍体预测 Aneuploidy prediction in the spatial domain Calogero Carlino, Valentina Giansanti, Giovanni Petri, Davide Cittaro

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