Abstract is missing.
- Unsupervised Integration of Single-Cell Multi-omics Datasets with Disproportionate Cell-Type RepresentationPinar Demetci, Rebecca Santorella, Björn Sandstede, Ritambhara Singh. 3-19 [doi]
- Semi-supervised Single-Cell Cross-modality Translation Using PolarbearRan Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble. 20-35 [doi]
- Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in CancerJingkang Zhao, Vincentius Martin, Raluca Gordân. 36-51 [doi]
- DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer SchemesMinh Hoang, Hongyu Zheng, Carl Kingsford. 52-69 [doi]
- MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly GraphsVijini Mallawaarachchi, Yu Lin 0001. 70-85 [doi]
- A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the WorldAgniva Chowdhury, Aritra Bose, Samson Zhou, David P. Woodruff, Petros Drineas. 86-106 [doi]
- Gene Set Priorization Guided by Regulatory Networks with p-values through Kernel Mixed ModelHaohan Wang, Oscar L. Lopez, Wei Wu 0023, Eric P. Xing. 107-125 [doi]
- Real-Valued Group Testing for Quantitative Molecular AssaysSeyran Saeedi, Myrna G. Serrano, Dennis G. Yang, J. Paul Brooks, Gregory A. Buck, Tomasz Arodz. 126-142 [doi]
- On the Effect of Intralocus Recombination on Triplet-Based Species Tree EstimationMax Hill, Sebastien Roch. 143-158 [doi]
- QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing DataSazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M. Sohel Rahman, Md. Shamsuzzoha Bayzid. 159-176 [doi]
- Safety and Completeness in Flow Decompositions for RNA AssemblyShahbaz Khan 0004, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu. 177-192 [doi]
- NetMix2: Unifying Network Propagation and Altered SubnetworksUthsav Chitra, Tae-Yoon Park, Benjamin J. Raphael. 193-208 [doi]
- Multi-modal Genotype and Phenotype Mutual Learning to Enhance Single-Modal Input Based Longitudinal Outcome PredictionAlireza Ganjdanesh, Jipeng Zhang, Wei Chen, Heng Huang. 209-229 [doi]
- Fast, Flexible, and Exact Minimum Flow Decompositions via ILPFernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu. 230-245 [doi]
- Co-linear Chaining with Overlaps and Gap CostsChirag Jain, Daniel Gibney, Sharma V. Thankachan. 246-262 [doi]
- The Complexity of Approximate Pattern Matching on de Bruijn GraphsDaniel Gibney, Sharma V. Thankachan, Srinivas Aluru. 263-278 [doi]
- ProTranslator: Zero-Shot Protein Function Prediction Using Textual DescriptionHanwen Xu, Sheng Wang. 279-294 [doi]
- Single-Cell Multi-omic Velocity Infers Dynamic and Decoupled Gene RegulationChen Li, Maria Virgilio, Kathleen L. Collins, Joshua D. Welch. 297-299 [doi]
- Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-HigashiRuochi Zhang, Tianming Zhou, Jian Ma 0004. 300-301 [doi]
- DiffDomain Enables Identification of Structurally Reorganized Topologically Associating DomainsDunming Hua, Ming Gu, Yanyi Du, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian. 302-303 [doi]
- Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation TreesXiang Ge Luo, Jack Kuipers, Niko Beerenwinkel. 304-305 [doi]
- Fast and Optimal Sequence-to-Graph Alignment Guided by SeedsPesho Ivanov, Benjamin Bichsel, Martin T. Vechev. 306-325 [doi]
- CLMB: Deep Contrastive Learning for Robust Metagenomic BinningPengfei Zhang, Zhengyuan Jiang, Yixuan Wang, Yu Li. 326-348 [doi]
- Unsupervised Cell Functional Annotation for Single-Cell RNA-SeqDongshunyi Li, Jun Ding, Ziv Bar-Joseph. 349-352 [doi]
- A Novel Matrix Factorization Model for Interpreting Single-Cell Gene Expression from Biologically Heterogeneous DataKun Qian, Shiwei Fu, Hongwei Li, Wei Vivian Li. 353-355 [doi]
- Tractable and Expressive Generative Models of Genetic Variation DataMeihua Dang, Anji Liu, Xinzhu Wei, Sriram Sankararaman, Guy Van den Broeck. 356-357 [doi]
- Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication TimingYang Yang 0094, Yuchuan Wang, Yang Zhang 0042, Jian Ma. 358-359 [doi]
- CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in CoronavirusesChuanyi Zhang, Palash Sashittal, Mohammed El-Kebir. 360-362 [doi]
- Learning Probabilistic Protein-DNA Recognition Codes from DNA-Binding Specificities Using Structural MappingsJoshua L. Wetzel, Kaiqian Zhang, Mona Singh 0001. 363-365 [doi]
- Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic RelationshipsEleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab. 366-368 [doi]
- SOPHIE: Viral Outbreak Investigation and Transmission History Reconstruction in a Joint Phylogenetic and Network Theory FrameworkPavel Skums, Fatemeh Mohebbi, Vyacheslav Tsyvina, Pelin Icer, Sumathi Ramachandran, Yury Khudyakov. 369-370 [doi]
- Identifying Systematic Variation at the Single-Cell Level by Leveraging Low-Resolution Population-Level DataElior Rahmani, Michael I. Jordan, Nir Yosef. 371 [doi]
- Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved TranscriptomicsCong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael. 372-373 [doi]
- Lossless Indexing with Counting de Bruijn GraphsMikhail Karasikov, Harun Mustafa, Gunnar Rätsch, André Kahles. 374-376 [doi]
- Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT)Amatur Rahman, Paul Medvedev. 377-379 [doi]
- Mapping Single-Cell Transcriptomes to Copy Number Evolutionary TreesPedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel. 380-381 [doi]
- ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes Using Short Read DataMichael Ford, Ananth Hari, Oscar Rodriguez, Junyan Xu, Justin Lack, Cihan Oguz, Yu Zhang, Sarah Weber, Mary Magliocco, Jason Barnett, Sandhya Xirasagar, Smilee Samuel, Luisa Imberti, Paolo Bonfanti, Andrea Biondi, Clifton L. Dalgard, Stephen Chanock, Lindsey Rosen, Steven Holland, Helen Su, Luigi Notarangelo, Uzi Vishkin, Corey Watson, Süleyman Cenk Sahinalp. 382-384 [doi]
- AutoComplete: Deep Learning-Based Phenotype Imputation for Large-Scale Biomedical DataUlzee An, Na Cai, Andy Dahl, Sriram Sankararaman. 385-386 [doi]
- Resistor: An Algorithm for Predicting Resistance Mutations Using Pareto Optimization over Multistate Protein Design and Mutational SignaturesNathan Guerin, Teresa Kaserer, Bruce R. Donald. 387-389 [doi]
- Ultra High Diversity Factorizable Libraries for Efficient Therapeutic DiscoveryZheng Dai, Sachit D. Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert, David K. Gifford. 390-392 [doi]