New Algorithms and Computational Methods

• 6888 · PDF 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-empowered virtual immunopeptidomics uncovers novel regulators of neoantigen immunogenicity Yuhao Tan, Ziqi Yang, Julia Fleming, Hailong Hu, Bo Li
• 6890 · PDF 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 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 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: Accurate germline and somatic structural variant calling from long-reads with deep sequence model Zhihan Zhou, Tong Zhu, Pankaj Vats
• 6894 · PDF 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 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: Axis-coupled mapping of co-varying gene programs in single-cell transcriptomic data Kourosh Kouhmareh, Richard L. Klemke
• 6897 · PDF 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 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: 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 Hierarchical Dorfman screening for robust pathway-aware feature selection identifies predictors of MEK-inhibitor response in NSCLC Wanru Guo, Juan Xie
• 6902 · PDF 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 A transcript-only framework for pseudocell boundary inference in high-resolution spatial transcriptomics Sungwoo Bae, Hongyoon Choi, Dongjoo Lee, Daeseung Lee
• 6904 · PDF OTTER: Optimal transport-based transcriptomics and genomics representation fusion for T-ALL subtyping Lusheng Li, Jieqiong Wang, Shibiao Wan
• 6905 · PDF 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 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: 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 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 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 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 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 Phasing tumor clones by timing point mutations using bulk long-read sequencing Ataberk Donmez, Mikhail Kolmogorov
• 6913 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: 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 Investigating the role of the conserved notch pathway in glioblastoma cells Larissa Barroso, Megan E. Keniry

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