| 2024 | A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits. Boyang Fu, Prateek Anand, Aakarsh Anand, Joel Mefford, Sriram Sankararaman |
| 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 | Accurate Assembly of Circular RNAs with TERRACE. Tasfia Zahin, Qian Shi, Xiaofei Carl Zang, Mingfu Shao |
| 2024 | An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. Shani Jacobson, Roded Sharan |
| 2024 | Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier |
| 2024 | BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data. Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Kimberly Glass, Dawn L. DeMeo, Camila Miranda Lopes-Ramos, John Quackenbush |
| 2024 | CELL-E: A Text-to-Image Transformer for Protein Image Prediction. Emaad Khwaja, Yun S. Song, Bo Huang |
| 2024 | Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification. Li Song, Ben Langmead |
| 2024 | CoRAL Accurately Resolves Extrachromosomal DNA Genome Structures with Long-Read Sequencing. Kaiyuan Zhu, Matthew G. Jones, Jens Luebeck, Xinxin Bu, Hyerim Yi, King L. Hung, Ivy Tsz-Lo Wong, Shu Zhang, Paul S. Mischel, Howard Y. Chang, Vineet Bafna |
| 2024 | Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty |
| 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 | Computing Robust Optimal Factories in Metabolic Reaction Networks. Spencer Krieger, John D. Kececioglu |
| 2024 | Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape. Junming Zhao, Chao Zhang, Yunan Luo |
| 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 | DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael |
| 2024 | Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data. Madalina Giurgiu, Nadine Wittstruck, Elias Rodriguez-Fos, Rocío Chamorro González, Lotte Brückner, Annabell Krienelke-Szymansky, Konstantin Helmsauer, Anne Hartebrodt, Philipp Euskirchen, Richard P. Koche, Kerstin Haase, Knut Reinert, Anton G. Henssen |
| 2024 | Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History. Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic |
| 2024 | DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors. Nathan Guerin, Henry Childs, Pei Zhou, Bruce Randall Donald |
| 2024 | Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models. Ziting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang |
| 2024 | Disease Risk Predictions with Differentiable Mendelian Randomization. Ludwig Gräf, Daniel Sens, Liubov Shilova, Francesco Paolo Casale |
| 2024 | Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová |
| 2024 | Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach. Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao |
| 2024 | Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks. Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen |
| 2024 | FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation. Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Özlem Özmen Garibay |
| 2024 | GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. Yimin Fan, Yu Li, Jun Ding, Yue Li |
| 2024 | GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra |
| 2024 | Graph-Based Genome Inference from Hi-C Data. Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford |
| 2024 | Haplotype-Aware Sequence Alignment to Pangenome Graphs. Ghanshyam Chandra, Daniel Gibney, Chirag Jain |
| 2024 | ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation. Yuxuan Du, Wenxuan Zuo, Fengzhu Sun |
| 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 | Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning. Holly R. Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew J. Hirn, Michael Perlmutter, Smita Krishnaswamy |
| 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 | Mapping Cell Fate Transition in Space and Time. Yichen Gu, Jialin Liu, Chen Li, Joshua D. Welch |
| 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 | Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. Uyen Mai, Gillian Chu, Benjamin J. Raphael |
| 2024 | Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries. Ali Osman Berk Sapci, Siavash Mirarab |
| 2024 | Meta-colored Compacted de Bruijn Graphs. Giulio Ermanno Pibiri, Jason Fan, Rob Patro |
| 2024 | Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation. Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab |
| 2024 | Overcoming Observation Bias for Cancer Progression Modeling. Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel |
| 2024 | PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang |
| 2024 | Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency. Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia |
| 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 | Prompt-Based Learning on Large Protein Language Models Improves Signal Peptide Prediction. Shuai Zeng, Duolin Wang, Lei Jiang, Dong Xu |
| 2024 | Protein Domain Embeddings for Fast and Accurate Similarity Search. Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye |
| 2024 | Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings Jian Ma |
| 2024 | SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. Jianyu Yang, Kuangyu Yen, Shaun Mahony |
| 2024 | Scalable Summary Statistics-Based Heritability Estimation Method with Individual Genotype Level Accuracy. Moonseong Jeong, Ali Pazokitoroudi, Zhengtong Liu, Sriram Sankararaman |
| 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 | Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography. Alexander T. Leighton, Yun William Yu |
| 2024 | Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich |
| 2024 | Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors. Kexin Huang, Romain Lopez, Jan-Christian Hütter, Takamasa Kudo, Antonio Rios, Aviv Regev |
| 2024 | SpaCeNet: Spatial Cellular Networks from Omics Data. Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger |
| 2024 | Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching. Paolo Pellizzoni, Carlos G. Oliver, Karsten M. Borgwardt |
| 2024 | TRIBAL: Tree Inference of B Cell Clonal Lineages. Leah L. Weber, Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan |
| 2024 | Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition. Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang |
| 2024 | VICTree - A Variational Inference Method for Clonal Tree Reconstruction. Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren |
| 2024 | regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models. Avantika Lal, David Garfield, Tommaso Biancalani, Gökcen Eraslan |
| 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 |