| 2024 | Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. | Jack Freestone, Lukas Kll, William Stafford Noble, Uri Keich |
| 2024 | GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. | Yimin Fan, Yu Li, Jun Ding, Yue Li |
| 2024 | A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements. | C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford |
| 2024 | ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. | Yuxuan Du, Wenxuan Zuo, Fengzhu Sun |
| 2024 | Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks. | Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen |
| 2024 | Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. | Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael |
| 2024 | Haplotype-Aware Sequence Alignment to Pangenome Graphs. | Ghanshyam Chandra, Daniel Gibney, Chirag Jain |
| 2024 | MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies. | Myson C. Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas |
| 2024 | scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis. | Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei, Xuegong Zhang |
| 2024 | GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. | Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra |
| 2024 | Processing-Bias Correction with DEBIAS-M Improves Cross-Study Generalization of Microbiome-Based Prediction Models. | George I. Austin, Aya Brown Kav, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Tal Korem |
| 2024 | Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. | Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab |
| 2023 | DM-Net: A Dual-Model Network for Automated Biomedical Image Diagnosis. | Xiaogen Zhou, Zhiqiang Li, Tong Tong |
| 2023 | Translation Rate Prediction and Regulatory Motif Discovery with Multi-task Learning. | Weizhong Zheng, John H. C. Fong, Yuk Kei Wan, Athena H. Y. Chu, Yuanhua Huang, Alan S. L. Wong, Joshua W. K. Ho |
| 2023 | Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model. | Yasamin Tabatabaee, Sbastien Roch, Tandy J. Warnow |
| 2023 | Percolate: An Exponential Family JIVE Model to Design DNA-Based Predictors of Drug Response. | Soufiane Mourragui, Marco Loog, Mirrelijn M. van Nee, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels |
| 2023 | CDGCN: Conditional de novo Drug Generative Model Using Graph Convolution Networks. | Shikha Mallick, Sahely Bhadra |
| 2023 | VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction from Assembly Graphs. | Runpeng Luo, Yu Lin |
| 2023 | Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks. | Spencer Krieger, John D. Kececioglu |
| 2023 | Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing. | Jason Fan, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro |
| 2023 | MTGL-ADMET: A Novel Multi-task Graph Learning Framework for ADMET Prediction Enhanced by Status-Theory and Maximum Flow. | Bing-Xue Du, Yi Xu, Siu-Ming Yiu, Hui Yu, Jian-Yu Shi |
| 2023 | T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy. | Ziqi Chen, Martin Renqiang Min, Hongyu Guo, Chao Cheng, Trevor Clancy, Xia Ning |
| 2023 | Sequence to Graph Alignment Using Gap-Sensitive Co-linear Chaining. | Ghanshyam Chandra, Chirag Jain |
| 2022 | Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer. | Jingkang Zhao, Vincentius Martin, Raluca Gordn |
| 2022 | Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi. | Ruochi Zhang, Tianming Zhou, Jian Ma |