New Algorithms and Computational Methods

• 6888 · PDF scDeBussy：队列水平的伪时间对齐揭示组织学转化中反复出现的动态基因程序 scDeBussy: Cohort-level pseudotime alignment reveals recurrent dynamic gene programs in histological transformation Meng Wang, Jose Meza-Llamosas, Xinjun Wang, Joseph Chan
• 6889 · PDF AI赋能的虚拟免疫肽组学揭示新肿瘤抗原免疫原性的新型调控因子 AI-empowered virtual immunopeptidomics uncovers novel regulators of neoantigen immunogenicity Yuhao Tan, Ziqi Yang, Julia Fleming, Hailong Hu, Bo Li
• 6890 · PDF CDH1突变型弥漫性胃癌的亚细胞三维多组学模型改善了对肿瘤微环境结构的重现并揭示了癌前特征龛 Subcellular 3D multi-omic models of CDH1-mutant diffuse gastric cancer improve recapitulation of tumor microenvironment structure and reveal precancer signature niches Jean R. Clemenceau, Yunhe Liu, Idania Carolina Lubo Julio, Soyoung Im, Seock-Jin Chung, Sam C. Wang, Paul F. Mansfield, Luisa Maren Solis Soto, Linghua Wang, Tae Hyun Hwang
• 6891 · PDF 癌症中情境依赖性的功能性非整倍体 Context dependent functional aneuploidy in cancer Polly L. S. Hung, Stephanie S. Liu, Tina N. Wei, Lesley S. K. Lau, Kui Liu, Karen K. L. Chan, Haonan Lu
• 6892 · PDF 组织和血浆游离DNA中端粒长度的泛癌图谱 A pan-cancer atlas of telomere length in tissues and plasma cell-free DNA Junming Shi, Leslie Espinoza, Mengran Zhang, Mohammad Shahrokh Esfahani
• 6893 · PDF MambaSV：利用深度序列模型从长读长中准确进行种系和体细胞结构变异检测 MambaSV: Accurate germline and somatic structural variant calling from long-reads with deep sequence model Zhihan Zhou, Tong Zhu, Pankaj Vats
• 6894 · PDF 预测、扰动与处理：一个用于识别合成致死的系统生物学流程 Predict, perturb, and process: A systems biology pipeline for identifying synthetic lethality Juihsuan Chou, Chenchu Lin, Iulia Veronica Gheorghe, Sabriyeh Alibai, Subin Kim, Lori Wilson, Xingdi Ma, Junjie Chen, Glen Traver Hart
• 6895 · PDF DISSECT整合细胞学图像与空间转录组学以实现细胞分割 DISSECT integrates cytological images and spatial transcriptomics for cell segmentation Yufeng He, Yanping Zhao, Rui Zhang, Heli Yang, Zhaode Bu, Yuan Luo, Deng Pan, Zexian Zeng
• 6896 · PDF ELEVATE：单细胞转录组数据中共变基因程序的轴耦合映射 ELEVATE: Axis-coupled mapping of co-varying gene programs in single-cell transcriptomic data Kourosh Kouhmareh, Richard L. Klemke
• 6897 · PDF 一种用于评估单细胞测序数据中推断亚克隆结构的二分划分函数算法 A bi-partition function algorithm to evaluate inferred subclonal structures in single-cell sequencing data Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, John D. Bridgers, Teresa M. Przytycka, Salem Malikic, Funda Ergun, Cenk Sahinalp
• 6898 · PDF 通过肿瘤进展树比对识别稳健的亚克隆结构 Identifying robust subclonal structures through tumor progression tree alignment Jacob Gilbert, Chih Hao Wu, Marina Knittel, Alejandro Schaffer, Salem Malikić, S. Cenk Sahinalp
• 6900 · PDF Wakhan：利用长读长测序重建肿瘤基因组染色体尺度的拷贝数图谱 Wakhan: Reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing Tanveer Ahmad, Ayse Keskus, Mikhail Kolmogorov, Sergey Aganezov, Michael C. Dean, Midhat S. Farooqi, S. Cenk Sahinalp, Benedict Paten, Karen H. Miga, Salem Malikić, Yuelin Liu, Byunggil Yoo, Ataberk Ataberk Donmez, Anton Goretsky
• 6901 6901 用于稳健的通路感知特征选择的分层Dorfman筛选识别NSCLC中MEK抑制剂响应的预测因子 Hierarchical Dorfman screening for robust pathway-aware feature selection identifies predictors of MEK-inhibitor response in NSCLC Wanru Guo, Juan Xie
• 6902 · PDF 化疗对癌细胞结构的重塑 Remodeling of cancer cell architecture by chemotherapy Gege Qian, Xiaoyu Zhao, Leah V. Schaffer, Kyung-Mee Moon, Jiahao Gao, Emma Lundberg, Leonard Foster, Trey Ideker
• 6903 · PDF 用于高分辨率空间转录组学中伪细胞边界推断的仅基于转录本的框架 A transcript-only framework for pseudocell boundary inference in high-resolution spatial transcriptomics Sungwoo Bae, Hongyoon Choi, Dongjoo Lee, Daeseung Lee
• 6904 · PDF OTTER：基于最优传输的转录组学与基因组学表征融合用于T-ALL分型 OTTER: Optimal transport-based transcriptomics and genomics representation fusion for T-ALL subtyping Lusheng Li, Jieqiong Wang, Shibiao Wan
• 6905 · PDF 通过整合式组合优化利用多样本批量测序数据重建肿瘤克隆树 Reconstruction of Tumor Clonal Trees with Multi-Sample Bulk Sequencing Data by Integrative Combinatorial Optimization Salem Malikic, Hamza Iseric, Chih Hao Wu, Erin Molloy, S. Cenk Sahinalp
• 6906 · PDF 利用转录组学的测试时计算对儿童T细胞急性淋巴细胞白血病进行亚型分类 Test-time compute for subtype classification in pediatric T-cell acute lymphoblastic leukemia using transcriptomics Tarun Karthik Kumar Mamidi, Irina Pushel, Byunggil Yoo, Midhat S. Farooqi, Keith J. August
• 6907 · PDF ecSegCls：基于深度学习的方法用于在间期和中期癌细胞中检测染色体外DNA ecSegCls: Deep learning-based method for detecting extrachromosomal DNAs in both interphase and metaphase cancer cells Se Young Chun, Hoigi Seo, Yoonjoo Nam, Dong Un Kang, Hyewon Bae, Ruda Lee, Hoon Kim
• 6908 · PDF 通过新型贝叶斯迁移学习框架整合大规模患者队列以识别AML中稳健的药物反应特征 Large-scale patient cohorts integration via a novel Bayesian transfer learning framework identifies robust drug response signatures in AML Dharani Thirumalaisamy, Evan F. Lind, Elie Traer, Jeffrey W. Tyner, Mehmet Gönen, Olga Nikolova
• 6909 · PDF 来自Xenium RNA和蛋白质的无量纲、零校准空间指数用于乳腺IDC和肺腺癌 Dimensionless, null-calibrated spatial indices from Xenium RNA and protein in breast IDC and lung adenocarcinoma Jinghao Tian, Tommy Tran, Elim Cheung, Rikita Gakhar, Vidyodhaya Sundaram
• 6910 · PDF 一致性引导的扩散重建增强磁粒子成像中肝周肿瘤的可见性 Consistency-guided diffusion reconstruction enhances peri-hepatic tumor visibility in magnetic particle imaging Gen Shi, Ziwei Chen, Yimeng Li, Zeyu Zhang, Xin Feng, Jie Tian
• 6911 · PDF 频域信号分离网络改善磁粒子成像中动脉瘤区域的双示踪剂检测 Frequency-domain signal separation network improves dual-tracer detection of aneurysm regions in magnetic particle imaging Ziwei Chen, Yimeng Li, Gen Shi, Jian'an Ye, Zeyu Zhang, Xin Feng, Yu An, Jie Tian
• 6912 · PDF 利用批量长读长测序对点突变进行时序分析以实现肿瘤克隆定相 Phasing tumor clones by timing point mutations using bulk long-read sequencing Ataberk Donmez, Mikhail Kolmogorov
• 6913 6913 空间分子数据的无偏细胞类型鉴定与生物学解读 Unbiased cell type identification and biological interpretation of spatial molecular data Filippo Pullara, Raymond Yan, Brian Falkenstein, A. Burak Tosun, S. Chakra Chennubhotla
• 6914 · PDF STCS：空间转录组学细胞分割在多张切片上优于现有方法 STCS: Spatial transcriptomics cell segmentation outperforms existing methods on multiple slides Xinyu Hu, Fengwei Zhan, Lixia C. Wu, Jose Gonzalez, Chuhanwen Sun, Rachel Ofer, Tyler Tran, Michael Verzi, Jiekun Yang
• 6915 · PDF 研究保守的 Notch 通路在胶质母细胞瘤细胞中的作用 Investigating the role of the conserved notch pathway in glioblastoma cells Larissa Barroso, Megan E. Keniry

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