| 2022 | On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation. | Max Hill, Sebastien Roch |
| 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 | The Complexity of Approximate Pattern Matching on de Bruijn Graphs. | Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru |
| 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 | 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, Sleyman Cenk Sahinalp |
| 2022 | Mapping Single-Cell Transcriptomes to Copy Number Evolutionary Trees. | Pedro F. Ferreira, Jack Kuipers, Niko Beerenwinkel |
| 2022 | Fast, Flexible, and Exact Minimum Flow Decompositions via ILP. | Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu |
| 2022 | Unsupervised Integration of Single-Cell Multi-omics Datasets with Disproportionate Cell-Type Representation. | Pinar Demetci, Rebecca Santorella, Bjrn Sandstede, Ritambhara Singh |
| 2022 | Tractable and Expressive Generative Models of Genetic Variation Data. | Meihua Dang, Anji Liu, Xinzhu Wei, Sriram Sankararaman, Guy Van den Broeck |
| 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 | 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 | NetMix2: Unifying Network Propagation and Altered Subnetworks. | Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael |
| 2022 | AutoComplete: Deep Learning-Based Phenotype Imputation for Large-Scale Biomedical Data. | Ulzee An, Na Cai, Andy Dahl, Sriram Sankararaman |
| 2020 | Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length. | Hongyu Zheng, Carl Kingsford, Guillaume Marais |
| 2020 | Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning. | Ruochi Zhang, Jian Ma |
| 2020 | Reconstruction of Gene Regulatory Networks by Integrating Biological Model and a Recommendation System. | Yijie Wang, Justin M. Fear, Isabelle Berger, Hangnoh Lee, Brian Oliver, Teresa M. Przytycka |
| 2020 | Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. | Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael |
| 2020 | A Mixture Model for Signature Discovery from Sparse Mutation Data. | Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan |
| 2020 | Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. | Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jrme Waldisphl |
| 2020 | d-PBWT: Dynamic Positional Burrows-Wheeler Transform. | Ahsan Sanaullah, Degui Zhi, Shaojie Zhang |
| 2020 | NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. | Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael |
| 2020 | Representation of k-mer Sets Using Spectrum-Preserving String Sets. | Amatur Rahman, Paul Medvedev |
| 2020 | Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores. | Brooks Paige, James Bell, Aurlien Bellet, Adri Gascn, Daphne Ezer |
| 2020 | RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. | Sneha Mitra, Jianling Zhong, David M. MacAlpine, Alexander J. Hartemink |
| 2020 | Log Transformation Improves Dating of Phylogenies. | Uyen Mai, Siavash Mirarab |