| 2024 | Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching. | Paolo Pellizzoni, Carlos G. Oliver, Karsten M. Borgwardt |
| 2024 | DIISCO: A Bayesian Framework for Inferring Dynamic Intercellular Interactions from Time-Series Single-Cell Data. | Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Satyen Gohil, Shuqiang Li, Teddy Huang, David A. Knowles, Catherine J. Wu, Elham Azizi |
| 2024 | Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes. | Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums |
| 2024 | VICTree - A Variational Inference Method for Clonal Tree Reconstruction. | Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren |
| 2024 | Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. | Uyen Mai, Gillian Chu, Benjamin J. Raphael |
| 2024 | Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. | Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael |
| 2024 | PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. | Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang |
| 2024 | Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach. | Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao |
| 2024 | Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography. | Alexander T. Leighton, Yun William Yu |
| 2024 | regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models. | Avantika Lal, David Garfield, Tommaso Biancalani, Gkcen Eraslan |
| 2024 | Computing Robust Optimal Factories in Metabolic Reaction Networks. | Spencer Krieger, John D. Kececioglu |
| 2024 | CELL-E: A Text-to-Image Transformer for Protein Image Prediction. | Emaad Khwaja, Yun S. Song, Bo Huang |
| 2024 | Scalable Summary Statistics-Based Heritability Estimation Method with Individual Genotype Level Accuracy. | Moonseong Jeong, Ali Pazokitoroudi, Zhengtong Liu, Sriram Sankararaman |
| 2024 | An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. | Shani Jacobson, Roded Sharan |
| 2024 | Protein Domain Embeddings for Fast and Accurate Similarity Search. | Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye |
| 2024 | Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors. | Kexin Huang, Romain Lopez, Jan-Christian Htter, Takamasa Kudo, Antonio Rios, Aviv Regev |
| 2024 | Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets. | Matthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho |
| 2024 | DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. | Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael |
| 2024 | Mapping Cell Fate Transition in Space and Time. | Yichen Gu, Jialin Liu, Chen Li, Joshua D. Welch |
| 2024 | DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors. | Nathan Guerin, Henry Childs, Pei Zhou, Bruce Randall Donald |
| 2024 | Disease Risk Predictions with Differentiable Mendelian Randomization. | Ludwig Grf, Daniel Sens, Liubov Shilova, Francesco Paolo Casale |
| 2024 | Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency. | Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia |
| 2024 | Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. | Madalina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Roco Chamorro Gonzlez, Lotte Brckner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Philipp Euskirchen, Richard P. Koche, Kerstin Haase, Knut Reinert, Anton G. Henssen |
| 2024 | Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. | Askar Gafurov, Toms Vinar, Paul Medvedev, Brona Brejov |
| 2024 | A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits. | Boyang Fu, Prateek Anand, Aakarsh Anand, Joel Mefford, Sriram Sankararaman |