Table of Contents

• Fast Approximate IsoRank for Scalable Global Alignment of Biological NetworksKapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen. 1-16 [doi]
• Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal PriorsKexin Huang, Romain Lopez, Jan-Christian Hütter, Takamasa Kudo, Antonio Rios, Aviv Regev. 17-37 [doi]
• Efficient Analysis of Annotation Colocalization Accounting for Genomic ContextsAskar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová. 38-53 [doi]
• Secure Federated Boolean Count Queries Using Fully-Homomorphic CryptographyAlexander T. Leighton, Yun William Yu. 54-67 [doi]
• FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven InterpretationAli Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Özlem Özmen Garibay. 68-85 [doi]
• An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean NetworksShani Jacobson, Roded Sharan. 86-98 [doi]
• ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based ImputationYuxuan Du, Wenxuan Zuo, Fengzhu Sun. 99-114 [doi]
• Graph-Based Genome Inference from Hi-C DataYihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford. 115-130 [doi]
• Meta-colored Compacted de Bruijn GraphsGiulio Ermanno Pibiri, Jason Fan, Rob Patro. 131-146 [doi]
• Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAsTaher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty. 147-163 [doi]
• Automated Design of Efficient Search Schemes for Lossless Approximate Pattern MatchingLuca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier. 164-184 [doi]
• CELL-E: A Text-to-Image Transformer for Protein Image PredictionEmaad Khwaja, Yun S. Song, Bo Huang. 185-200 [doi]
• A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain MeasurementsC. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford. 201-216 [doi]
• Overcoming Observation Bias for Cancer Progression ModelingRudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel. 217-234 [doi]
• Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep LearningHolly R. Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew J. Hirn, Michael Perlmutter, Smita Krishnaswamy. 235-252 [doi]
• Computing Robust Optimal Factories in Metabolic Reaction NetworksSpencer Krieger, John D. Kececioglu. 253-269 [doi]
• Undesignable RNA Structure Identification via Rival Structure Generation and Structure DecompositionTianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang 0001. 270-287 [doi]
• Structure- and Function-Aware Substitution Matrices via Learnable Graph MatchingPaolo Pellizzoni, Carlos G. Oliver, Karsten M. Borgwardt. 288-307 [doi]
• Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic DatasetsMatthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho. 308-313 [doi]
• GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq ModelingYimin Fan, Yu Li 0006, Jun Ding, Yue Li. 314-319 [doi]
• SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and SubtypesJianyu Yang, Kuangyu Yen, Shaun Mahony. 320-323 [doi]
• Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence ClassificationLi Song, Ben Langmead. 324-327 [doi]
• BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics DataEnakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Kimberly Glass, Dawn L. DeMeo, Camila Miranda Lopes-Ramos, John Quackenbush. 328-331 [doi]
• regLM: Designing Realistic Regulatory DNA with Autoregressive Language ModelsAvantika Lal, David Garfield, Tommaso Biancalani, Gökcen Eraslan. 332-335 [doi]
• DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide InhibitorsNathan Guerin, Henry Childs, Pei Zhou 0001, Bruce Randall Donald. 336-339 [doi]
• Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference LibrariesAli Osman Berk Sapci, Siavash Mirarab. 340-343 [doi]
• SpaCeNet: Spatial Cellular Networks from Omics DataStefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer 0005, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger. 344-347 [doi]
• Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning ModelsZiting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang. 348-351 [doi]
• MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association StudiesMyson C. Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas. 352-355 [doi]
• Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered PhenotypesFatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums. 356-359 [doi]
• Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing DataUyen Mai, Gillian Chu, Benjamin J. Raphael. 360-363 [doi]
• TRIBAL: Tree Inference of B Cell Clonal LineagesLeah L. Weber, Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan. 364-367 [doi]
• Mapping the Topography of Spatial Gene Expression with Interpretable Deep LearningUthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael. 368-371 [doi]
• GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic AssemblyAli Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra. 372-376 [doi]
• PRS-Net: Interpretable Polygenic Risk Scores via Geometric LearningHan Li, Jianyang Zeng 0001, Michael P. Snyder, Sai Zhang. 377-380 [doi]
• Haplotype-Aware Sequence Alignment to Pangenome GraphsGhanshyam Chandra, Daniel Gibney, Chirag Jain. 381-384 [doi]
• Disease Risk Predictions with Differentiable Mendelian RandomizationLudwig Gräf, Daniel Sens, Liubov Shilova, Francesco Paolo Casale. 385-389 [doi]
• DIISCO: A Bayesian Framework for Inferring Dynamic Intercellular Interactions from Time-Series Single-Cell DataCameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Satyen Gohil, Shuqiang Li, Teddy Huang, David A. Knowles, Catherine J. Wu, Elham Azizi. 390-395 [doi]
• Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match ApproachLechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao. 396-399 [doi]
• Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide PredictionShuai Zeng, Duolin Wang, Lei Jiang, Dong Xu 0002. 400-405 [doi]
• Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing DataMadalina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocío Chamorro González, Lotte Brückner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Philipp Euskirchen, Richard P. Koche, Kerstin Haase, Knut Reinert, Anton G. Henssen. 406-411 [doi]
• Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved EfficiencyMeir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia. 412-416 [doi]
• Mapping Cell Fate Transition in Space and TimeYichen Gu, Jialin Liu, Chen Li, Joshua D. Welch. 417-420 [doi]
• Protein Domain Embeddings for Fast and Accurate Similarity SearchBenjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye. 421-424 [doi]
• Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction ModelsGeorge I. Austin, Aya Brown Kav, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Tal Korem. 425-428 [doi]
• VICTree - A Variational Inference Method for Clonal Tree ReconstructionHarald Melin, Vittorio Zampinetti, Andrew McPherson 0003, Jens Lagergren. 429-433 [doi]
• DeST-OT: Alignment of Spatiotemporal Transcriptomics DataPeter Halmos, Xinhao Liu 0009, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael. 434-437 [doi]
• Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression HistoryChih-Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic. 438-443 [doi]
• Accurate Assembly of Circular RNAs with TERRACETasfia Zahin, Qian Shi, Xiaofei Carl Zang, Mingfu Shao. 444-447 [doi]
• Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry AnalysisJack Freestone, Lukas Käll, William Stafford Noble, Uri Keich. 448-453 [doi]
• CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read SequencingKaiyuan Zhu, Matthew G. Jones, Jens Luebeck, Xinxin Bu, Hyerim Yi, King L. Hung, Ivy Tsz-Lo Wong, Shu Zhang, Paul S. Mischel, Howard Y. Chang, Vineet Bafna. 454-457 [doi]
• A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex TraitsBoyang Fu, Prateek Anand, Aakarsh Anand, Joel Mefford, Sriram Sankararaman. 458-461 [doi]
• Optimal Tree Metric Matching Enables Phylogenomic Branch Length EstimationShayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab. 462-465 [doi]
• Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved TranscriptomicsCong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael. 466-469 [doi]
• Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness LandscapeJunming Zhao, Chao Zhang, Yunan Luo. 470-474 [doi]
• Scalable Summary Statistics-Based Heritability Estimation Method with Individual Genotype Level AccuracyMoonseong Jeong, Ali Pazokitoroudi, Zhengtong Liu, Sriram Sankararaman. 475-478 [doi]
• scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell AnalysisHaiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei, Xuegong Zhang. 479-482 [doi]