| 2022 | CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. | Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir |
| 2022 | Semi-supervised Single-Cell Cross-modality Translation Using Polarbear. | Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble |
| 2022 | CLMB: Deep Contrastive Learning for Robust Metagenomic Binning. | Pengfei Zhang, Zhengyuan Jiang, Yixuan Wang, Yu Li |
| 2022 | Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing. | Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma |
| 2022 | ProTranslator: Zero-Shot Protein Function Prediction Using Textual Description. | Hanwen Xu, Sheng Wang |
| 2022 | Learning Probabilistic Protein-DNA Recognition Codes from DNA-Binding Specificities Using Structural Mappings. | Joshua L. Wetzel, Kaiqian Zhang, Mona Singh |
| 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 | 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 | 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 | Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). | Amatur Rahman, Paul Medvedev |
| 2022 | Identifying Systematic Variation at the Single-Cell Level by Leveraging Low-Resolution Population-Level Data. | Elior Rahmani, Michael I. Jordan, Nir Yosef |
| 2022 | Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships. | Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab |
| 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 | MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. | Vijini Mallawaarachchi, Yu Lin |
| 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 | Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. | Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael |
| 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 | Single-Cell Multi-omic Velocity Infers Dynamic and Decoupled Gene Regulation. | Chen Li, Maria Virgilio, Kathleen L. Collins, Joshua D. Welch |
| 2022 | Unsupervised Cell Functional Annotation for Single-Cell RNA-Seq. | Dongshunyi Li, Jun Ding, Ziv Bar-Joseph |
| 2022 | Safety and Completeness in Flow Decompositions for RNA Assembly. | Shahbaz Khan, Milla Kortelainen, Manuel Cceres, Lucia Williams, Alexandru I. Tomescu |
| 2022 | Lossless Indexing with Counting de Bruijn Graphs. | Mikhail Karasikov, Harun Mustafa, Gunnar Rtsch, Andr Kahles |
| 2022 | Co-linear Chaining with Overlaps and Gap Costs. | Chirag Jain, Daniel Gibney, Sharma V. Thankachan |
| 2022 | Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds. | Pesho Ivanov, Benjamin Bichsel, Martin T. Vechev |
| 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 | DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes. | Minh Hoang, Hongyu Zheng, Carl Kingsford |