| 2022 | A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World. Agniva Chowdhury, Aritra Bose, Samson Zhou, David P. Woodruff, Petros Drineas |
| 2022 | A Novel Matrix Factorization Model for Interpreting Single-Cell Gene Expression from Biologically Heterogeneous Data. Kun Qian, Shiwei Fu, Hongwei Li, Wei Vivian Li |
| 2022 | AutoComplete: Deep Learning-Based Phenotype Imputation for Large-Scale Biomedical Data. Ulzee An, Na Cai, Andy Dahl, Sriram Sankararaman |
| 2022 | Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael |
| 2022 | CLMB: Deep Contrastive Learning for Robust Metagenomic Binning. Pengfei Zhang, Zhengyuan Jiang, Yixuan Wang, Yu Li |
| 2022 | CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir |
| 2022 | Co-linear Chaining with Overlaps and Gap Costs. Chirag Jain, Daniel Gibney, Sharma V. Thankachan |
| 2022 | Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing. Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma |
| 2022 | DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes. Minh Hoang, Hongyu Zheng, Carl Kingsford |
| 2022 | DiffDomain Enables Identification of Structurally Reorganized Topologically Associating Domains. Dunming Hua, Ming Gu, Yanyi Du, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian |
| 2022 | Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds. Pesho Ivanov, Benjamin Bichsel, Martin T. Vechev |
| 2022 | Fast, Flexible, and Exact Minimum Flow Decompositions via ILP. Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu |
| 2022 | Gene Set Priorization Guided by Regulatory Networks with p-values through Kernel Mixed Model. Haohan Wang, Oscar L. Lopez, Wei Wu, Eric P. Xing |
| 2022 | Identifying Systematic Variation at the Single-Cell Level by Leveraging Low-Resolution Population-Level Data. Elior Rahmani, Michael I. Jordan, Nir Yosef |
| 2022 | ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes Using Short Read Data. Michael K. B. 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 J. Chanock, Lindsey Rosen, Steven Holland, Helen Su, Luigi Notarangelo, Uzi Vishkin, Corey Watson, Süleyman Cenk Sahinalp |
| 2022 | Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees. Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel |
| 2022 | Learning Probabilistic Protein-DNA Recognition Codes from DNA-Binding Specificities Using Structural Mappings. Joshua L. Wetzel, Kaiqian Zhang, Mona Singh |
| 2022 | Lossless Indexing with Counting de Bruijn Graphs. Mikhail Karasikov, Harun Mustafa, Gunnar Rätsch, André Kahles |
| 2022 | Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel |
| 2022 | MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. Vijini Mallawaarachchi, Yu Lin |
| 2022 | Multi-modal Genotype and Phenotype Mutual Learning to Enhance Single-Modal Input Based Longitudinal Outcome Prediction. Alireza Ganjdanesh, Jipeng Zhang, Wei Chen, Heng Huang |
| 2022 | NetMix2: Unifying Network Propagation and Altered Subnetworks. Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael |
| 2022 | On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation. Max Hill, Sebastien Roch |
| 2022 | ProTranslator: Zero-Shot Protein Function Prediction Using Textual Description. Hanwen Xu, Sheng Wang |
| 2022 | QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data. Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M. Sohel Rahman, Md. Shamsuzzoha Bayzid |
| 2022 | Real-Valued Group Testing for Quantitative Molecular Assays. Seyran Saeedi, Myrna G. Serrano, Dennis G. Yang, J. Paul Brooks, Gregory A. Buck, Tomasz Arodz |
| 2022 | Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, San Diego, CA, USA, May 22-25, 2022, Proceedings Itsik Pe'er |
| 2022 | Resistor: An Algorithm for Predicting Resistance Mutations Using Pareto Optimization over Multistate Protein Design and Mutational Signatures. Nathan Guerin, Teresa Kaserer, Bruce Randall Donald |
| 2022 | SOPHIE: Viral Outbreak Investigation and Transmission History Reconstruction in a Joint Phylogenetic and Network Theory Framework. Pavel Skums, Fatemeh Mohebbi, Vyacheslav Tsyvina, Pelin Icer, Sumathi Ramachandran, Yury Khudyakov |
| 2022 | Safety and Completeness in Flow Decompositions for RNA Assembly. Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu |
| 2022 | Semi-supervised Single-Cell Cross-modality Translation Using Polarbear. Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble |
| 2022 | Single-Cell Multi-omic Velocity Infers Dynamic and Decoupled Gene Regulation. Chen Li, Maria Virgilio, Kathleen L. Collins, Joshua D. Welch |
| 2022 | The Complexity of Approximate Pattern Matching on de Bruijn Graphs. Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru |
| 2022 | Tractable and Expressive Generative Models of Genetic Variation Data. Meihua Dang, Anji Liu, Xinzhu Wei, Sriram Sankararaman, Guy Van den Broeck |
| 2022 | Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer. Jingkang Zhao, Vincentius Martin, Raluca Gordân |
| 2022 | Ultra High Diversity Factorizable Libraries for Efficient Therapeutic Discovery. Zheng Dai, Sachit D. Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert, David K. Gifford |
| 2022 | Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi. Ruochi Zhang, Tianming Zhou, Jian Ma |
| 2022 | Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab |
| 2022 | Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). Amatur Rahman, Paul Medvedev |
| 2022 | Unsupervised Cell Functional Annotation for Single-Cell RNA-Seq. Dongshunyi Li, Jun Ding, Ziv Bar-Joseph |
| 2022 | Unsupervised Integration of Single-Cell Multi-omics Datasets with Disproportionate Cell-Type Representation. Pinar Demetci, Rebecca Santorella, Björn Sandstede, Ritambhara Singh |