@inproceedings{Li2025,
  author = {Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas Guibas, Jian Peng, Jianzhu Ma},
  title = {Orientation-Aware Networks for Protein Structure Representation Learning},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 1-16, Springer, Cham.},
  pages = {1--16},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_1},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 1-16, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {1--16},
  proceedings_doi = {10.1007/978-3-031-90252-9_1},
  preprint_id = {arXiv:2201.13299},
  preprint_doi = {10.48550/arXiv.2201.13299}
}

@inproceedings{Xue2025,
  author = {Zexin Xue, Michael Bailey, Abhinav Gupta, Ruijiang Li, Alejandro Corrochano-Navarro, Sizhen Li, Lorenzo Kogler-Anele, Qui Yu, Ziv Bar-Joseph, Sven Jager},
  title = {Active Learning for Protein Structure Prediction},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 17-33, Springer, Cham.},
  pages = {17--33},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_2},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 17-33, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {17--33},
  proceedings_doi = {10.1007/978-3-031-90252-9_2},
  preprint_id = {bioRxiv 2025.04.01.646404},
  preprint_doi = {10.1101/2025.04.01.646404}
}

@inproceedings{Im2025,
  author = {Chiho Im, Ryan Zhao, Scott D. Boyd, Anshul Kundaje},
  title = {Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 34-48, Springer, Cham.},
  pages = {34--48},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_3},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 34-48, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {34--48},
  proceedings_doi = {10.1007/978-3-031-90252-9_3},
  preprint_id = {bioRxiv 2024.10.25.619698},
  preprint_doi = {10.1101/2024.10.25.619698}
}

@inproceedings{Wang2025,
  author = {Shaojun Wang, Hancheng Liu, Weiqi Zhai, Shanfeng Zhu},
  title = {DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 49-67, Springer, Cham.},
  pages = {49--67},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_4},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 49-67, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {49--67},
  proceedings_doi = {10.1007/978-3-031-90252-9_4}
}

@inproceedings{Benz2025,
  author = {Nina Corvelo Benz, Lucas Miranda, Dexiong Chen, Janko Sattler, Karsten Borgwardt},
  title = {Detecting Antimicrobial Resistance Through MALDI-TOF Mass Spectrometry with Statistical Guarantees Using Conformal Prediction},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 68-85, Springer, Cham.},
  pages = {68--85},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_5},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 68-85, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {68--85},
  proceedings_doi = {10.1007/978-3-031-90252-9_5}
}

@inproceedings{Wei2025,
  author = {Yuxiang Wei, Anees Abrol, Vince D. Calhoun},
  title = {Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 86-98, Springer, Cham.},
  pages = {86--98},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_6},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 86-98, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {86--98},
  proceedings_doi = {10.1007/978-3-031-90252-9_6},
  preprint_id = {arXiv:2408.13074},
  preprint_doi = {10.48550/arXiv.2408.13074}
}

@inproceedings{Albors2025,
  author = {Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song},
  title = {A Phylogenetic Approach to Genomic Language Modeling},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 99-117, Springer, Cham.},
  pages = {99--117},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_7},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 99-117, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {99--117},
  proceedings_doi = {10.1007/978-3-031-90252-9_7},
  preprint_id = {arXiv:2503.03773},
  preprint_doi = {10.48550/arXiv.2503.03773}
}

@article{Dai2026,
  author = {Junyan Dai and Erin K. Molloy},
  title = {StarCDP: Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data},
  journal = {Journal of Computational Biology},
  volume = {33},
  number = {1},
  pages = {48--66},
  year = {2026},
  doi = {10.1177/15578666251386082},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 118-133, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {118--133},
  proceedings_doi = {10.1007/978-3-031-90252-9_8},
  preprint_id = {bioRxiv 2024.11.15.623872},
  preprint_doi = {10.1101/2024.11.15.623872}
}

@inproceedings{Boury2025,
  author = {Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao},
  title = {Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 134-152, Springer, Cham.},
  pages = {134--152},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_9},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 134-152, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {134--152},
  proceedings_doi = {10.1007/978-3-031-90252-9_9},
  preprint_id = {hal-04756160},
  preprint_url = {https://hal.science/hal-04756160}
}

@inproceedings{Zhou2025,
  author = {Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang},
  title = {Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 153-174, Springer, Cham.},
  pages = {153--174},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_10},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 153-174, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {153--174},
  proceedings_doi = {10.1007/978-3-031-90252-9_10},
  preprint_id = {arXiv:2402.17206},
  preprint_doi = {10.48550/arXiv.2402.17206}
}

@inproceedings{Sarnaik2025,
  author = {Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao},
  title = {An Exact and Fast SAT Formulation for the DCJ Distance},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 175-189, Springer, Cham.},
  pages = {175--189},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_11},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 175-189, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {175--189},
  proceedings_doi = {10.1007/978-3-031-90252-9_11},
  preprint_id = {bioRxiv 2024.11.05.622153},
  preprint_doi = {10.1101/2024.11.05.622153}
}

@article{Shivakumar,2025,
  author = {Nathaniel K. Brown, Vikram S. Shivakumar, and Ben Langmead},
  title = {Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification},
  journal = {Journal of Computational Biology},
  volume = {33},
  number = {1},
  pages = {168--183},
  year = {2025},
  doi = {10.1177/15578666251400784},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 190-208, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {190--208},
  proceedings_doi = {10.1007/978-3-031-90252-9_12},
  preprint_id = {bioRxiv 2024.10.29.620953},
  preprint_doi = {10.1101/2024.10.29.620953}
}

@article{Zhi,2025,
  author = {Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang},
  title = {An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data},
  journal = {Journal of Computational Biology},
  volume = {33},
  number = {1},
  pages = {67--89},
  year = {2025},
  doi = {10.1177/15578666251385570},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 209-226, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {209--226},
  proceedings_doi = {10.1007/978-3-031-90252-9_13},
  preprint_id = {bioRxiv 2025.02.04.636479},
  preprint_doi = {10.1101/2025.02.04.636479}
}

@article{Park2026,
  author = {Adam Park and David Koslicki},
  title = {Elucidating Transitions of k-mer-Based Objects Across k-mer Sizes},
  journal = {Journal of Computational Biology},
  volume = {33},
  number = {1},
  pages = {107--133},
  year = {2026},
  doi = {10.1177/15578666251401600},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 227-249, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {227--249},
  proceedings_doi = {10.1007/978-3-031-90252-9_14},
  preprint_id = {bioRxiv 2023.11.21.568151},
  preprint_doi = {10.1101/2023.11.21.568151}
}

@article{Chen,2025,
  author = {Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, and Jianzhu Ma},
  title = {Rag2Mol: structure-based drug design based on retrieval augmented generation},
  journal = {Briefings in Bioinformatics},
  volume = {26},
  number = {3},
  pages = {bbaf265},
  year = {2025},
  doi = {10.1093/bib/bbaf265},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 250-254, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {250--254},
  proceedings_doi = {10.1007/978-3-031-90252-9_15},
  preprint_id = {bioRxiv 2024.10.20.619266},
  preprint_doi = {10.1101/2024.10.20.619266}
}

@inproceedings{Li2025,
  author = {Ziang Li and Yunan Luo},
  title = {Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 255-259, Springer, Cham.},
  pages = {255--259},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_16},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 255-259, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {255--259},
  proceedings_doi = {10.1007/978-3-031-90252-9_16},
  preprint_id = {bioRxiv 2025.02.13.638154},
  preprint_doi = {10.1101/2025.02.13.638154}
}

@inproceedings{Erden2025,
  author = {Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh},
  title = {Learning a CONCISE Language for Small-Molecule Binding},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 260-263, Springer, Cham.},
  pages = {260--263},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_17},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 260-263, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {260--263},
  proceedings_doi = {10.1007/978-3-031-90252-9_17},
  preprint_id = {bioRxiv 2025.01.08.632039},
  preprint_doi = {10.1101/2025.01.08.632039}
}

@article{Ideker,2025,
  author = {Rami Nasser, Leah V. Schaffer, Trey Ideker, and Roded Sharan},
  title = {An adversarial scheme for integrating multi-modal data on protein function},
  journal = {Cell Systems},
  volume = {16},
  number = {11},
  pages = {101444},
  year = {2025},
  doi = {10.1016/j.cels.2025.101444},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 264-267, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {264--267},
  proceedings_doi = {10.1007/978-3-031-90252-9_18},
  preprint_id = {bioRxiv 2025.01.16.633332},
  preprint_doi = {10.1101/2025.01.16.633332}
}

@inproceedings{Sledzieski2025,
  author = {Sam Sledzieski, Charlotte Versavel, Rohit Singh, Faith Ocitti, Kapil Devkota, Lokender Kumar, Polina Shpilker, Liza Roger, Jinkyu Yang, Nastassja Lewinski, Hollie Putnam, Bonnie Berger, Judith Klein-Seetharaman, Lenore Cowen},
  title = {Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 268-272, Springer, Cham.},
  pages = {268--272},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_19},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 268-272, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {268--272},
  proceedings_doi = {10.1007/978-3-031-90252-9_19},
  preprint_id = {bioRxiv 2024.10.25.620267},
  preprint_doi = {10.1101/2024.10.25.620267}
}

@inproceedings{Schmidt2025,
  author = {Henri Schmidt and Benjamin J. Raphael},
  title = {The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 273-276, Springer, Cham.},
  pages = {273--276},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_20},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 273-276, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {273--276},
  proceedings_doi = {10.1007/978-3-031-90252-9_20},
  preprint_id = {bioRxiv 2025.02.14.638328},
  preprint_doi = {10.1101/2025.02.14.638328}
}

@article{Gao,2025,
  author = {Haotian Zhang, Yiming Zhang, Teng Gao, and Yufeng Wu},
  title = {ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2781--2791},
  year = {2025},
  doi = {10.1101/gr.280542.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 277-280, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {277--280},
  proceedings_doi = {10.1007/978-3-031-90252-9_21},
  preprint_id = {bioRxiv 2024.11.08.622704},
  preprint_doi = {10.1101/2024.11.08.622704}
}

@article{Dremsek,2025,
  author = {Siavash Raeisi Dehkordi, Zhaoyang Jia, Joey Estabrook, Jen Hauenstein, Neil Miller, Naz Güleray-Lafci, Jürgen Neesen, Alex Hastie, Alka Chaubey, Andy Wing Chun Pang, Paul Dremsek, and Vineet Bafna},
  title = {OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2671--2681},
  year = {2025},
  doi = {10.1101/gr.280536.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 281-284, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {281--284},
  proceedings_doi = {10.1007/978-3-031-90252-9_22},
  preprint_id = {medRxiv 2025.02.13.25322211},
  preprint_doi = {10.1101/medRxiv 2025.02.13.25322211}
}

@inproceedings{Inecik2025,
  author = {Kemal Inecik, Aleyna Kara, Antony Rose, Muzlifah Haniffa, Fabian J. Theis},
  title = {TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 285-289, Springer, Cham.},
  pages = {285--289},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_23},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 285-289, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {285--289},
  proceedings_doi = {10.1007/978-3-031-90252-9_23},
  preprint_id = {bioRxiv 2024.06.20.599903},
  preprint_doi = {10.1101/2024.06.20.599903}
}

@article{Noyes,2025,
  author = {Jim Shaw, Christina Boucher, Yun William Yu, Noelle Noyes, and Heng Li},
  title = {Long-read reconstruction of many diverse haplotypes with devider},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2637--2649},
  year = {2025},
  doi = {10.1101/gr.280510.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 290-293, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {290--293},
  proceedings_doi = {10.1007/978-3-031-90252-9_24},
  preprint_id = {bioRxiv 2024.11.05.621838},
  preprint_doi = {10.1101/2024.11.05.621838}
}

@article{Ochoa,2026,
  author = {Leah L. Weber, Anna Hart, Idoia Ochoa, and Mohammed El-Kebir},
  title = {Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors},
  journal = {Journal of Computational Biology},
  volume = {33},
  number = {1},
  pages = {2--18},
  year = {2026},
  doi = {10.1177/15578666251374694},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 294-298, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {294--298},
  proceedings_doi = {10.1007/978-3-031-90252-9_25},
  preprint_id = {bioRxiv 2024.11.17.623950},
  preprint_doi = {10.1101/2024.11.17.623950}
}

@inproceedings{Park2025,
  author = {Gyeongsik Park, Andrew J. Lee, Inkyung Jung},
  title = {GEM-Finder: Dissecting GWAS Variants via Long-Range Interacting Cis-Regulatory Elements with Differentiationspecific Genes},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 299-302, Springer, Cham.},
  pages = {299--302},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_26},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 299-302, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {299--302},
  proceedings_doi = {10.1007/978-3-031-90252-9_26},
  preprint_id = {medRxiv 2025.03.02.25323165},
  preprint_doi = {10.1101/medRxiv 2025.03.02.25323165}
}

@inproceedings{Liu2025,
  author = {Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang, Minsheng Hao, Hector Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg},
  title = {Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 303-306, Springer, Cham.},
  pages = {303--306},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_27},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 303-306, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {303--306},
  proceedings_doi = {10.1007/978-3-031-90252-9_27},
  preprint_id = {bioRxiv 2024.11.18.624166},
  preprint_doi = {10.1101/2024.11.18.624166}
}

@inproceedings{Wang2025,
  author = {Yixuan Wang, Jiayi Li, Jingqi Li, Shen Yang, Yuhan Huang, Xinyuan Liu, Yimin Fan, Irwin King, Yumei Li, Yu Li},
  title = {cfDecon: Accurate and Interpretable Methylation-Based Cell Type Deconvolution for Cell-Free DNA},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 307-311, Springer, Cham.},
  pages = {307--311},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_28},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 307-311, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {307--311},
  proceedings_doi = {10.1007/978-3-031-90252-9_28},
  preprint_id = {bioRxiv 2025.02.11.637663},
  preprint_doi = {10.1101/2025.02.11.637663}
}

@article{Chan,2025,
  author = {Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, and Benjamin J. Raphael},
  title = {Inferring cell differentiation maps from lineage tracing data},
  journal = {Nature Methods},
  volume = {33},
  number = {1},
  pages = {107--133},
  year = {2025},
  doi = {10.1038/s41592-025-02903-z},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 312-315, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {312--315},
  proceedings_doi = {10.1007/978-3-031-90252-9_29},
  preprint_id = {bioRxiv 2024.09.09.611835},
  preprint_doi = {10.1101/2024.09.09.611835}
}

@article{Şapcı2026,
  author = {Ali Osman Berk Şapcı and Siavash Mirarab},
  title = {krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement},
  journal = {Genome Biology},
  volume = {epub},
  year = {2026},
  doi = {10.1186/s13059-026-03999-y},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 316-320, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {316--320},
  proceedings_doi = {10.1007/978-3-031-90252-9_30}
}

@article{Crawford,2025,
  author = {Xiran Liu, Lorin Crawford, and Sohini Ramachandran},
  title = {ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2691--2700},
  year = {2025},
  doi = {10.1101/gr.280440.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 321-324, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {321--324},
  proceedings_doi = {10.1007/978-3-031-90252-9_31},
  preprint_id = {bioRxiv 2025.02.11.637655},
  preprint_doi = {10.1101/2025.02.11.637655}
}

@article{Sahinalp,2025,
  author = {Natnatee Dokmai, Kaiyuan Zhu, S. Cenk Sahinalp, and Hyunghoon Cho},
  title = {Secure phasing of private genomes in a trusted execution environment with TX-Phase},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2626--2636},
  year = {2025},
  doi = {10.1101/gr.280558.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 325-329, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {325--329},
  proceedings_doi = {10.1007/978-3-031-90252-9_32},
  preprint_id = {bioRxiv 2024.09.16.613301},
  preprint_doi = {10.1101/2024.09.16.613301}
}

@inproceedings{Martayan2025,
  author = {Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset},
  title = {Hyper-k-mers: Efficient Streaming k-mers Representation},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 330-335, Springer, Cham.},
  pages = {330--335},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_33},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 330-335, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {330--335},
  proceedings_doi = {10.1007/978-3-031-90252-9_33},
  preprint_id = {bioRxiv 2024.11.06.620789},
  preprint_doi = {10.1101/2024.11.06.620789}
}

@inproceedings{Roddur2025,
  author = {Mrinmoy S. Roddur, Vikram Ramavarapu, Abigail Bunkum, Ariana Huebner, Roman Mineyev, Nicholas McGranahan, Simone Zaccaria, Mohammed El-Kebir},
  title = {Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 336-339, Springer, Cham.},
  pages = {336--339},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_34},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 336-339, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {336--339},
  proceedings_doi = {10.1007/978-3-031-90252-9_34},
  preprint_id = {bioRxiv 2024.11.19.624301},
  preprint_doi = {10.1101/2024.11.19.624301}
}

@inproceedings{An2025,
  author = {Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan},
  title = {Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual Inference},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 340-344, Springer, Cham.},
  pages = {340--344},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_35},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 340-344, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {340--344},
  proceedings_doi = {10.1007/978-3-031-90252-9_35},
  preprint_id = {bioRxiv 2024.12.11.628077},
  preprint_doi = {10.1101/2024.12.11.628077}
}

@inproceedings{Litinetskaya2025,
  author = {Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, Fabian Theis},
  title = {Integration and Querying of Multimodal Single-Cell Data with PoE-VAE},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 345-348, Springer, Cham.},
  pages = {345--348},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_36},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 345-348, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {345--348},
  proceedings_doi = {10.1007/978-3-031-90252-9_36},
  preprint_id = {bioRxiv 2022.03.16.484643},
  preprint_doi = {10.1101/2022.03.16.484643}
}

@article{Berger,2025,
  author = {Enzo Battistella, Anant Maheshwari, Barış Ekim, Bonnie Berger, and Victoria Popic},
  title = {Graph-based deep reinforcement learning for haplotype assembly with Ralphi},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2617--2625},
  year = {2025},
  doi = {10.1101/gr.280569.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 349-353, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {349--353},
  proceedings_doi = {10.1007/978-3-031-90252-9_37},
  preprint_id = {bioRxiv 2025.02.17.638151},
  preprint_doi = {10.1101/2025.02.17.638151}
}

@article{Geman,2025,
  author = {An Wang, Stephanie Hicks, Donald Geman, and Laurent Younes},
  title = {Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2744--2755},
  year = {2025},
  doi = {10.1101/gr.280539.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 354-357, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {354--357},
  proceedings_doi = {10.1007/978-3-031-90252-9_38},
  preprint_id = {bioRxiv 2024.10.30.621151},
  preprint_doi = {10.1101/2024.10.30.621151}
}

@article{Sarkar,2025,
  author = {Hongyu Zheng, Hirak Sarkar, and Benjamin J. Raphael},
  title = {Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2734--2743},
  year = {2025},
  doi = {10.1101/gr.280555.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 358-361, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {358--361},
  proceedings_doi = {10.1007/978-3-031-90252-9_39},
  preprint_id = {bioRxiv 2025.02.17.638195},
  preprint_doi = {10.1101/2025.02.17.638195}
}

@article{Al-Abri2025,
  author = {Rashid Al-Abri and Gamze Gürsoy},
  title = {Estimating the size of long tandem repeat expansions from short reads with ScatTR},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2701--2713},
  year = {2025},
  doi = {10.1101/gr.280563.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 362-366, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {362--366},
  proceedings_doi = {10.1007/978-3-031-90252-9_40},
  preprint_id = {bioRxiv 2025.02.15.638440},
  preprint_doi = {10.1101/2025.02.15.638440}
}

@inproceedings{Halmos2025,
  author = {Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael},
  title = {Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 367-370, Springer, Cham.},
  pages = {367--370},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_41},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 367-370, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {367--370},
  proceedings_doi = {10.1007/978-3-031-90252-9_41},
  preprint_id = {bioRxiv 2025.02.14.638351},
  preprint_doi = {10.1101/2025.02.14.638351}
}

@article{Ma,2025,
  author = {Ellie Haber, Ajinkya Deshpande, Jian Ma, and Spencer Krieger},
  title = {Unified integration of spatial transcriptomics across platforms with LLOKI},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2722--2733},
  year = {2025},
  doi = {10.1101/gr.280803.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 371-375, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {371--375},
  proceedings_doi = {10.1007/978-3-031-90252-9_42},
  preprint_id = {bioRxiv 2025.03.31.646238},
  preprint_doi = {10.1101/2025.03.31.646238}
}

@inproceedings{Prillo2025,
  author = {Sebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew G. Jones, Yun S. Song, Nir Yosef},
  title = {Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 376-380, Springer, Cham.},
  pages = {376--380},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_43},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 376-380, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {376--380},
  proceedings_doi = {10.1007/978-3-031-90252-9_43},
  preprint_id = {bioRxiv 2024.08.27.610007},
  preprint_doi = {10.1101/2024.08.27.610007}
}

@article{Liu2026,
  author = {Pan Liu and Jingyi Jessica Li},
  title = {mcRigor: A Statistical Software Package for Evaluating and Optimizing Metacell Partitioning in Single-Cell Data Analysis},
  journal = {Journal of Computational Biology},
  volume = {33},
  number = {1},
  pages = {43--47},
  year = {2026},
  doi = {10.1177/15578666251383561},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 381-385, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {381--385},
  proceedings_doi = {10.1007/978-3-031-90252-9_44},
  preprint_id = {bioRxiv 2024.10.30.621093},
  preprint_doi = {10.1101/2024.10.30.621093}
}

@inproceedings{Kambhampati2025,
  author = {Sandeep Kambhampati, Luca D'Alessio, Fedor Grab, Stephen Fleming, Fei Chen, Mehrtash Babadi},
  title = {TissueMosaic Enables Cross-Sample Differential Analysis of Spatial Transcriptomics Datasets Through Self-supervised Representation Learning},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 386-389, Springer, Cham.},
  pages = {386--389},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_45},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 386-389, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {386--389},
  proceedings_doi = {10.1007/978-3-031-90252-9_45},
  preprint_id = {bioRxiv 2024.11.07.622479},
  preprint_doi = {10.1101/2024.11.07.622479}
}

@article{Li,2025,
  author = {Zhezheng Song, Tasfia Zahin, Xiang Li, and Mingfu Shao},
  title = {Accurate detection of tandem repeats from error-prone sequences with EquiRep},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2714--2721},
  year = {2025},
  doi = {10.1101/gr.280750.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 390-394, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {390--394},
  proceedings_doi = {10.1007/978-3-031-90252-9_46},
  preprint_id = {bioRxiv 2024.11.05.621953},
  preprint_doi = {10.1101/2024.11.05.621953}
}

@article{Dannenfelser,2025,
  author = {Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser, and Vicky Yao},
  title = {Interpretable phenotype decoding from multicondition sequencing data with ALPINE},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2756--2769},
  year = {2025},
  doi = {10.1101/gr.280566.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 395-399, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {395--399},
  proceedings_doi = {10.1007/978-3-031-90252-9_47},
  preprint_id = {bioRxiv 2025.02.15.638471},
  preprint_doi = {10.1101/2025.02.15.638471}
}

@inproceedings{Song2025,
  author = {Dongyuan Song, Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge, Jingyi Jessica Li},
  title = {Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 400-404, Springer, Cham.},
  pages = {400--404},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_48},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 400-404, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {400--404},
  proceedings_doi = {10.1007/978-3-031-90252-9_48},
  preprint_id = {bioRxiv 2023.07.21.550107},
  preprint_doi = {10.1101/2023.07.21.550107}
}

@article{Gibney,2025,
  author = {Ghanshyam Chandra, Md Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, and Chirag Jain},
  title = {Pangenome-based genome inference using integer programming},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2661--2670},
  year = {2025},
  doi = {10.1101/gr.280567.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 405-408, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {405--408},
  proceedings_doi = {10.1007/978-3-031-90252-9_49},
  preprint_id = {bioRxiv 2024.10.27.620212},
  preprint_doi = {10.1101/2024.10.27.620212}
}

@inproceedings{Mehrabadi2025,
  author = {Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, John D. Bridgers, Eva Pérez-Guijarro, Kerrie L. Marie, Howard H. Yang, Charli Gruen, Chih Hao Wu, Welles Robinson, Huaitian Liu, Can Kizilkale, Michael C. Kelly, Cari Smith, Sung Chin, Jessica Ebersole, Sandra Burkett, Aydin Buluc, Maxwell P. Lee, Erin K. Molloy, Teresa M. Przytycka, Glenn Merlino, Chi-Ping Day, Salem Malikić, Funda Ergun, S. Cenk Sahinalp},
  title = {A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 409-413, Springer, Cham.},
  pages = {409--413},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_50},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 409-413, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {409--413},
  proceedings_doi = {10.1007/978-3-031-90252-9_50}
}

@inproceedings{Dvir2025,
  author = {Yoav Dvir and Sagi Snir},
  title = {Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 414-419, Springer, Cham.},
  pages = {414--419},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_51},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 414-419, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {414--419},
  proceedings_doi = {10.1007/978-3-031-90252-9_51},
  preprint_id = {bioRxiv 2025.01.27.634999},
  preprint_doi = {10.1101/2025.01.27.634999}
}

@inproceedings{Luo2025,
  author = {Jiaqi Luo and Yunan Luo},
  title = {Learning Maximally Spanning Representations Improves Protein Function Annotation},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 420-423, Springer, Cham.},
  pages = {420--423},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_52},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 420-423, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {420--423},
  proceedings_doi = {10.1007/978-3-031-90252-9_52},
  preprint_id = {bioRxiv 2025.02.13.638156},
  preprint_doi = {10.1101/2025.02.13.638156}
}

@article{Matijević,2025,
  author = {Bartol Borozan, Tomislav Prusina, Luka Borozan, Domagoj Ševerdija, Francisca Rojas Ringeling, Domagoj Matijević, and Stefan Canzar},
  title = {Optimal marker genes for c-separated cell types with SepSolve},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2770--2780},
  year = {2025},
  doi = {10.1101/gr.280637.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 424-427, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {424--427},
  proceedings_doi = {10.1007/978-3-031-90252-9_53},
  preprint_id = {bioRxiv 2025.02.12.637849},
  preprint_doi = {10.1101/2025.02.12.637849}
}

@article{Cai,2025,
  author = {Antonio Nappi, Liubov Shilova, Theofanis Karaletsos, Na Cai, and Francesco Paolo Casale},
  title = {BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations},
  journal = {Genome Research},
  volume = {35},
  number = {12},
  pages = {2682--2690},
  year = {2025},
  doi = {10.1101/gr.280689.125},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 428-431, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {428--431},
  proceedings_doi = {10.1007/978-3-031-90252-9_54},
  preprint_id = {bioRxiv 2025.03.02.641062},
  preprint_doi = {10.1101/2025.03.02.641062}
}

@inproceedings{Liang2025,
  author = {Shaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma},
  title = {STEAMBOAT: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 432-436, Springer, Cham.},
  pages = {432--436},
  year = {2025},
  doi = {10.1007/978-3-031-90252-9_55},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2025. Lecture Notes in Computer Science, vol 15647, pp 432-436, Springer, Cham.},
  proceedings_volume = {15647},
  proceedings_pages = {432--436},
  proceedings_doi = {10.1007/978-3-031-90252-9_55},
  preprint_id = {bioRxiv 2025.04.06.647437},
  preprint_doi = {10.1101/2025.04.06.647437}
}