Table of Contents

• Orientation-Aware Networks for Protein Structure Representation LearningJiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng 0001, Jianzhu Ma. 1-16 [doi]
• Active Learning for Protein Structure PredictionZexin Xue, Michael Bailey, Abhinav Gupta, Ruijiang Li, Alejandro Corrochano-Navarro, Sizhen Li, Lorenzo Kogler-Anele, Qui Yu, Ziv Bar-Joseph, Sven Jager. 17-33 [doi]
• Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language ModelsChiho Im, Ryan Zhao, Scott D. Boyd, Anshul Kundaje. 34-48 [doi]
• DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated ProteinsShaojun Wang, Hancheng Liu, Weiqi Zhai, Shanfeng Zhu. 49-67 [doi]
• Detecting Antimicrobial Resistance Through MALDI-TOF Mass Spectrometry with Statistical Guarantees Using Conformal PredictionNina Corvelo Benz, Lucas Miranda 0002, Dexiong Chen, Janko Sattler, Karsten M. Borgwardt. 68-85 [doi]
• Hierarchical Spatio-Temporal State-Space Modeling for fMRI AnalysisYuxiang Wei 0004, Anees Abrol, Vince D. Calhoun. 86-98 [doi]
• A Phylogenetic Approach to Genomic Language ModelingCarlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song. 99-117 [doi]
• Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing DataJunyan Dai, Erin K. Molloy. 118-133 [doi]
• Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design PerformancesThéo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao. 134-152 [doi]
• Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational InvarianceTianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang 0001. 153-174 [doi]
• An Exact and Fast SAT Formulation for the DCJ DistanceAaryan M. Sarnaik, Ke Chen 0011, Austin Diaz, Mingfu Shao. 175-189 [doi]
• Improved Pangenomic Classification Accuracy with Chain StatisticsNathaniel K. Brown, Vikram Shivakumar, Ben Langmead. 190-208 [doi]
• Dynamic μ-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale DataPramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang. 209-226 [doi]
• Prokrustean Graph: A Substring Index for Rapid K-Mer Size AnalysisAdam Park, David Koslicki. 227-249 [doi]
• Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented GenerationPeidong Zhang, Xingang Peng, Rong Han, Ting Chen 0006, Jianzhu Ma. 250-254 [doi]
• Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability PredictionZiang Li, Yunan Luo. 255-259 [doi]
• Learning a CoNCISE Language for Small-Molecule BindingMert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh 0001. 260-263 [doi]
• An Adversarial Scheme for Integrating Multi-modal Data on Protein FunctionRami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan. 264-267 [doi]
• Decoding the Functional Interactome of Non-model Organisms with PHILHARMONICSamuel Sledzieski, Charlotte Versavel, Rohit Singh 0001, Faith Ocitti, Kapil Devkota, Lokender Kumar, Polina Shpilker, Liza Roger, Jinkyu Yang, Nastassja Lewinski, Hollie Putnam, Bonnie Berger, Judith Klein-Seetharaman, Lenore Cowen. 268-272 [doi]
• The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction ProblemsHenri Schmidt, Benjamin J. Raphael. 273-276 [doi]
• ScisTree2: An Improved Method for Large-Scale Inference of Cell Lineage Trees and Genotype Calling from Noisy Single Cell DataHaotian Zhang, Yiming Zhang 0007, Teng Gao, Yufeng Wu. 277-280 [doi]
• OMKar: Optical Map Based Automated Karyotyping of Genomes to Identify Constitutional DisordersSiavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Naz Güleray-Lafci, Jürgen Neesen, Alex Hastie, Andy Wing Chun Pang, Paul Dremsek, Vineet Bafna. 281-284 [doi]
• TarDis: Achieving Robust and Structured Disentanglement of Multiple CovariatesKemal Inecik, Aleyna Kara, Antony Rose, Muzlifah Haniffa, Fabian J. Theis. 285-289 [doi]
• Devider: Long-Read Reconstruction of Many Diverse HaplotypesJim Shaw, Christina Boucher 0001, Yun William Yu, Noelle R. Noyes, Heng Li. 290-293 [doi]
• Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of TumorsLeah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir. 294-298 [doi]
• GEM-Finder: Dissecting GWAS Variants via Long-Range Interacting Cis-Regulatory Elements with Differentiationspecific GenesGyeongsik Park, Andrew J. Lee, Inkyung Jung. 299-302 [doi]
• Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease StatesTianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang 0002, Minsheng Hao, Héctor Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg. 303-306 [doi]
• cfDecon: Accurate and Interpretable Methylation-Based Cell Type Deconvolution for Cell-Free DNAYixuan Wang, Jiayi Li, Jingqi Li, Shen Yang, Yuhan Huang, Xinyuan Liu, Yimin Fan, Irwin King, Yumei Li 0019, Yu Li 0006. 307-311 [doi]
• Inferring Cell Differentiation Maps from Lineage Tracing DataPalash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael. 312-315 [doi]
• Alignment-Free Estimation of Read to Genome Distances and Its ApplicationsAli Osman Berk Sapci, Siavash Mirarab. 316-320 [doi]
• ML-MAGES: A Machine Learning Framework for Multivariate Genetic Association Analyses with Genes and Effect Size ShrinkageXiran Liu, Lorin Crawford, Sohini Ramachandran. 321-324 [doi]
• TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution EnvironmentNatnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, Hyunghoon Cho. 325-329 [doi]
• Hyper-k-mers: Efficient Streaming k-mers RepresentationIgor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset. 330-335 [doi]
• Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2Mrinmoy Saha Roddur, Vikram Ramavarapu, Abigail Bunkum, Ariana Huebner, Roman Mineyev, Nicholas McGranahan, Simone Zaccaria, Mohammed El-Kebir. 336-339 [doi]
• Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual InferenceShaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan. 340-344 [doi]
• Integration and Querying of Multimodal Single-Cell Data with PoE-VAEAnastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, Fabian J. Theis. 345-348 [doi]
• ralphi: A Deep Reinforcement Learning Framework for Haplotype AssemblyEnzo Battistella, Anant Maheshwari, Baris Ekim, Bonnie Berger, Victoria Popic. 349-353 [doi]
• GeneCover: A Combinatorial Approach for Label-Free Marker Gene Selectionan Wang, Stephanie Hicks, Donald Geman, Laurent Younes. 354-357 [doi]
• Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics PlatformsHongyu Zheng, Hirak Sarkar, Benjamin J. Raphael. 358-361 [doi]
• ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-ReadsRashid Al-Abri, Gamze Gürsoy. 362-366 [doi]
• Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal TransportPeter Halmos, Julian Gold, Xinhao Liu 0009, Benjamin J. Raphael. 367-370 [doi]
• Unified Integration of Spatial Transcriptomics Across PlatformsEllie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger. 371-375 [doi]
• Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-JoiningSebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew G. Jones, Yun S. Song, Nir Yosef. 376-380 [doi]
• mcRigor: A Statistical Method to Enhance the Rigor of Metacell Partitioning in Single-Cell RNA-seq and ATAC-seq Data AnalysisPan Liu, Jingyi Jessica Li. 381-385 [doi]
• TissueMosaic Enables Cross-Sample Differential Analysis of Spatial Transcriptomics Datasets Through Self-supervised Representation LearningSandeep Kambhampati, Luca D'Alessio, Fedor Grab, Stephen Fleming, Fei Chen, Mehrtash Babadi. 386-389 [doi]
• Accurate Detection of Tandem Repeats from Error-Prone Sequences with EquiRepZhezheng Song, Tasfia Zahin, Xiang Li, Mingfu Shao. 390-394 [doi]
• ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing DataWei-Hao Lee, Lechuan Li, Ruth Dannenfelser, Vicky Yao. 395-399 [doi]
• Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data AnalysesDongyuan Song, Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge, Jingyi Jessica Li. 400-404 [doi]
• Integer Programming Framework for Pangenome-Based Genome InferenceGhanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain. 405-408 [doi]
• A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing DataFarid Rashidi Mehrabadi, Erfan Sadeqi Azer, John D. Bridgers, Eva Pérez-Guijarro, Kerrie Marie, Howard H. Yang, Charli Gruen, Chih-Hao Wu, Welles Robinson, Huaitian Liu, Can Kizilkale, Michael C. Kelly, Cari Smith, Sung Chin, Jessica Ebersole, Sandra Burkett, Aydin Buluç, Maxwell P. Lee, Erin K. Molloy, Teresa M. Przytycka, Glenn Merlino, Chi-Ping Day, Salem Malikic, Funda Ergün, S. Cenk Sahinalp. 409-413 [doi]
• Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic ApproachYoav Dvir, Sagi Snir. 414-419 [doi]
• Learning Maximally Spanning Representations Improves Protein Function AnnotationJiaqi Luo, Yunan Luo. 420-423 [doi]
• Optimal Marker Genes for c-Separated Cell TypesBartol Borozan, Luka Borozan, Domagoj Severdija, Domagoj Matijevic, Stefan Canzar. 424-427 [doi]
• Bayesian Aggregation of Multiple Annotations Enhances Rare Variant Association TestingAntonio Nappi, Na Cai, Francesco Paolo Casale. 428-431 [doi]
• Steamboat: Attention-Based Multiscale Delineation of Cellular Interactions in TissuesShaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma. 432-436 [doi]