@article{Devkota2024,
  author = {Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen},
  title = {Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {990--1007},
  year = {2024},
  doi = {10.1089/cmb.2024.0673},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 1-16, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {1--16},
  proceedings_doi = {10.1007/978-1-0716-3989-4_1},
  preprint_id = {bioRxiv 2023.03.13.532445},
  preprint_doi = {10.1101/2023.03.13.532445}
}

@inproceedings{Huang2024,
  author = {Kexin Huang, Romain Lopez, Jan-Christian Hütter, Takamasa Kudo, Antonio Rios, Aviv Regev},
  title = {Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 17-37, Springer, Cham.},
  pages = {17--37},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_2},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 17-37, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {17--37},
  proceedings_doi = {10.1007/978-1-0716-3989-4_2},
  preprint_id = {bioRxiv 2023.12.12.571389},
  preprint_doi = {10.1101/2023.12.12.571389}
}

@article{Gafurov2024,
  author = {Askar Gafurov, Tomáš Vinař, Paul Medvedev, Broňa Brejová},
  title = {Fast Context-Aware Analysis of Genome Annotation Colocalization},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {946--964},
  year = {2024},
  doi = {10.1089/cmb.2024.0667},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 38-53, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {38--53},
  proceedings_doi = {10.1007/978-1-0716-3989-4_3},
  preprint_id = {bioRxiv 2023.11.22.568259},
  preprint_doi = {10.1101/2023.11.22.568259}
}

@inproceedings{Leighton2024,
  author = {Alexander T. Leighton, Yun William Yu},
  title = {Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 54-67, Springer, Cham.},
  pages = {54--67},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_4},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 54-67, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {54--67},
  proceedings_doi = {10.1007/978-1-0716-3989-4_4},
  preprint_id = {bioRxiv 2021.11.10.468090},
  preprint_doi = {10.1101/2021.11.10.468090}
}

@inproceedings{Yalabadi2024,
  author = {Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Ozlem Ozmen Garibay},
  title = {FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 68-85, Springer, Cham.},
  pages = {68--85},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_5},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 68-85, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {68--85},
  proceedings_doi = {10.1007/978-1-0716-3989-4_5},
  preprint_id = {arXiv:2311.02326},
  preprint_doi = {10.48550/arXiv.2311.02326}
}

@inproceedings{Jacobson2024,
  author = {Shani Jacobson, Roded Sharan},
  title = {An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 86-98, Springer, Cham.},
  pages = {86--98},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_6},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 86-98, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {86--98},
  proceedings_doi = {10.1007/978-1-0716-3989-4_6}
}

@article{Du2024,
  author = {Yuxuan Du, Wenxuan Zuo, Fengzhu Sun},
  title = {Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Ra...},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {1008--1021},
  year = {2024},
  doi = {10.1089/cmb.2024.0663},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 99-114, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {99--114},
  proceedings_doi = {10.1007/978-1-0716-3989-4_7},
  preprint_id = {bioRxiv 2023.12.06.570492},
  preprint_doi = {10.1101/2023.12.06.570492}
}

@inproceedings{Shen2024,
  author = {Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford},
  title = {Graph-Based Genome Inference from Hi-C Data},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 115-130, Springer, Cham.},
  pages = {115--130},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_8},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 115-130, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {115--130},
  proceedings_doi = {10.1007/978-1-0716-3989-4_8},
  preprint_id = {bioRxiv 2023.11.08.566275},
  preprint_doi = {10.1101/2023.11.08.566275}
}

@article{Campanelli2024,
  author = {Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro},
  title = {Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {1022--1044},
  year = {2024},
  doi = {10.1089/cmb.2024.0714},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 131-146, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {131--146},
  proceedings_doi = {10.1007/978-1-0716-3989-4_9},
  preprint_id = {bioRxiv 2023.07.21.550101},
  preprint_doi = {10.1101/2023.07.21.550101}
}

@inproceedings{Yacoub2024,
  author = {Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty},
  title = {Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 147-163, Springer, Cham.},
  pages = {147--163},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_10},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 147-163, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {147--163},
  proceedings_doi = {10.1007/978-1-0716-3989-4_10},
  preprint_id = {hal-03816423v3},
  preprint_url = {https://hal.science/hal-03816423v3}
}

@article{Renders2024,
  author = {Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier},
  title = {Lossless approximate pattern matching: Automated design of efficient search schemes},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {975--989},
  year = {2024},
  doi = {10.1089/cmb.2024.0664},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 164-184, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {164--184},
  proceedings_doi = {10.1007/978-1-0716-3989-4_11}
}

@inproceedings{Khwaja2024,
  author = {Emaad Khwaja, Yun S. Song, Bo Huang},
  title = {CELL-E: A Text-to-Image Transformer for Protein Image Prediction},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 185-200, Springer, Cham.},
  pages = {185--200},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_12},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 185-200, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {185--200},
  proceedings_doi = {10.1007/978-1-0716-3989-4_12},
  preprint_id = {bioRxiv 2022.05.27.493774},
  preprint_doi = {10.1101/2022.05.27.493774}
}

@article{Elder2024,
  author = {C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford},
  title = {Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {908--926},
  year = {2024},
  doi = {10.1089/cmb.2024.0661},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 201-216, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {201--216},
  proceedings_doi = {10.1007/978-1-0716-3989-4_13},
  preprint_id = {bioRxiv 2024.02.15.580520},
  preprint_doi = {10.1101/2024.02.15.580520}
}

@article{Schill2024,
  author = {Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel},
  title = {Correcting for Observation Bias in Cancer Progression Modeling},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {927--945},
  year = {2024},
  doi = {10.1089/cmb.2024.0666},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 217-234, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {217--234},
  proceedings_doi = {10.1007/978-1-0716-3989-4_14},
  preprint_id = {bioRxiv 2023.12.03.569824},
  preprint_doi = {10.1101/2023.12.03.569824}
}

@inproceedings{Steach2024,
  author = {Holly R. Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew Hirn, Michael Perlmutter, Smita Krishnaswamy},
  title = {Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 235-252, Springer, Cham.},
  pages = {235--252},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_15},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 235-252, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {235--252},
  proceedings_doi = {10.1007/978-1-0716-3989-4_15},
  preprint_id = {bioRxiv 2023.12.05.570153},
  preprint_doi = {10.1101/2023.12.05.570153}
}

@article{Krieger2024,
  author = {Spencer Krieger, John Kececioglu},
  title = {Robust Optimal Metabolic Factories},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {1045--1086},
  year = {2024},
  doi = {10.1089/cmb.2024.0748},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 253-269, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {253--269},
  proceedings_doi = {10.1007/978-1-0716-3989-4_16}
}

@inproceedings{Zhou2024,
  author = {Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang},
  title = {Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 270-287, Springer, Cham.},
  pages = {270--287},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_17},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 270-287, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {270--287},
  proceedings_doi = {10.1007/978-1-0716-3989-4_17},
  preprint_id = {arXiv:2311.08339},
  preprint_doi = {10.48550/arXiv.2311.08339}
}

@inproceedings{Pellizzoni2024,
  author = {Paolo Pellizzoni, Carlos Oliver, Karsten Borgwardt},
  title = {Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 288-307, Springer, Cham.},
  pages = {288--307},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_18},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 288-307, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {288--307},
  proceedings_doi = {10.1007/978-1-0716-3989-4_18}
}

@article{large-scale2024,
  author = {Secure discovery of genetic relatives across large-scale and distributed genomic data sets},
  title = {Secure discovery of genetic relatives across large-scale and distributed genomic data sets},
  journal = {Genome Research},
  volume = {34},
  number = {9},
  pages = {1312--1323},
  year = {2024},
  doi = {10.1101/gr.279057.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 308-313, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {308--313},
  proceedings_doi = {10.1007/978-1-0716-3989-4_19},
  preprint_id = {bioRxiv 2024.02.16.580613},
  preprint_doi = {10.1101/2024.02.16.580613}
}

@inproceedings{Fan2024,
  author = {Yimin Fan, Yu Li, Jun Ding, Yue Li},
  title = {GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 314-319, Springer, Cham.},
  pages = {314--319},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_20},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 314-319, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {314--319},
  proceedings_doi = {10.1007/978-1-0716-3989-4_20},
  preprint_id = {bioRxiv 2023.11.09.566403},
  preprint_doi = {10.1101/2023.11.09.566403}
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@article{Yang2024,
  author = {Jianyu Yang, Kuangyu Yen, Shaun Mahony},
  title = {Size-based expectation maximization for characterizing nucleosome positions and subtypes},
  journal = {Genome Research},
  volume = {34},
  number = {9},
  pages = {1334--1343},
  year = {2024},
  doi = {10.1101/gr.279138.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 320-323, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {320--323},
  proceedings_doi = {10.1007/978-1-0716-3989-4_21},
  preprint_id = {bioRxiv 2023.10.17.562727},
  preprint_doi = {10.1101/2023.10.17.562727}
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@article{Song2024,
  author = {Li Song, Ben Langmead},
  title = {Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification},
  journal = {Genome Biology},
  volume = {25},
  number = {1},
  pages = {106},
  year = {2024},
  doi = {10.1186/s13059-024-03244-4},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 324-327, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {324--327},
  proceedings_doi = {10.1007/978-1-0716-3989-4_22},
  preprint_id = {bioRxiv 2023.11.15.567129},
  preprint_doi = {10.1101/2023.11.15.567129}
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@article{Saha2024,
  author = {Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Dawn L. DeMeo, Camila M. Lopes-Ramos, John Quackenbush},
  title = {Bayesian Inference of Sample-Specific Coexpression Networks},
  journal = {Genome Research},
  volume = {34:1397–1410},
  year = {2024},
  doi = {10.1101/gr.279117.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 328-331, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {328--331},
  proceedings_doi = {10.1007/978-1-0716-3989-4_23},
  preprint_id = {bioRxiv 2023.11.16.567119},
  preprint_doi = {10.1101/2023.11.16.567119}
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@article{Lal2024,
  author = {Avantika Lal, David Garfield, Tommaso Biancalani, Gokcen Eraslan},
  title = {Designing realistic regulatory DNA with autoregressive language models},
  journal = {Genome Research},
  volume = {34},
  number = {9},
  pages = {1411--1420},
  year = {2024},
  doi = {10.1101/gr.279142.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 332-335, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {332--335},
  proceedings_doi = {10.1007/978-1-0716-3989-4_24},
  preprint_id = {bioRxiv 2024.02.14.580373},
  preprint_doi = {10.1101/2024.02.14.580373}
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@article{Childs2024,
  author = {Henry Childs, Nathan Guerin, Pei Zhou, Bruce R. Donald},
  title = {Protocol for Designing De Novo Noncanonical Peptide Binders in OSPREY},
  journal = {Journal of Computational Biology},
  volume = {31},
  number = {10},
  pages = {965--974},
  year = {2024},
  doi = {10.1089/cmb.2024.0669},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 336-339, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {336--339},
  proceedings_doi = {10.1007/978-1-0716-3989-4_25},
  preprint_id = {bioRxiv 2024.02.12.579944},
  preprint_doi = {10.1101/2024.02.12.579944}
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@article{Şapcı2024,
  author = {Ali Osman Berk Şapcı and Siavash Mirarab},
  title = {Memory-Bound k-Mer Selection for Large and Evolutionary Diverse Reference Libraries},
  journal = {Genome Research},
  volume = {34},
  number = {9},
  pages = {1455--1467},
  year = {2024},
  doi = {10.1101/gr.279339.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 340-343, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {340--343},
  proceedings_doi = {10.1007/978-1-0716-3989-4_26},
  preprint_id = {bioRxiv 2024.02.12.580015},
  preprint_doi = {10.1101/2024.02.12.580015}
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@article{Schrod2024,
  author = {Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Dennis Völkl, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger},
  title = {Spatial Cellular Networks from omics data with SpaCeNet},
  journal = {Genome Research},
  volume = {34},
  number = {9},
  pages = {1371--1383},
  year = {2024},
  doi = {10.1101/gr.279125.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 344-347, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {344--347},
  proceedings_doi = {10.1007/978-1-0716-3989-4_27},
  preprint_id = {bioRxiv 2022.09.01.506219},
  preprint_doi = {10.1101/2022.09.01.506219}
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@inproceedings{Zhang2024,
  author = {Ziting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang},
  title = {Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 348-351, Springer, Cham.},
  pages = {348--351},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_28},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 348-351, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {348--351},
  proceedings_doi = {10.1007/978-1-0716-3989-4_28},
  preprint_id = {bioRxiv 2024.02.07.579420},
  preprint_doi = {10.1101/2024.02.07.579420}
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@article{Burch2024,
  author = {Myson Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas},
  title = {Matrix sketching framework for linear mixed models in association studies},
  journal = {Genome Research},
  volume = {34},
  number = {9},
  pages = {1304--1311},
  year = {2024},
  doi = {10.1101/gr.279230.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 352-355, Springer, Cham.},
  proceedings_volume = {14758},
  proceedings_pages = {352--355},
  proceedings_doi = {10.1007/978-1-0716-3989-4_29},
  preprint_id = {bioRxiv 2023.11.13.23298469},
  preprint_doi = {10.1101/2023.11.13.23298469}
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@inproceedings{Mohebbi2024,
  author = {Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums},
  title = {Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 356-359, Springer, Cham.},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 356-359, Springer, Cham.},
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@article{Chu2025,
  author = {Gillian Chu, Uyen Mai, Henri Schmidt, Benjamin J. Raphael},
  title = {Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 360-363, Springer, Cham.},
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@inproceedings{Weber2024,
  author = {Leah L. Weber, Derek Reiman, Mrinmoy S. Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan},
  title = {TRIBAL: Tree Inference of B Cell Clonal Lineages},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 364-367, Springer, Cham.},
  pages = {364--367},
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@article{Chitra2025,
  author = {Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Kohei Sanno, Cong Ma, Sereno Lopez-Darwin, Benjamin J. Raphael},
  title = {Mapping the topography of spatial gene expression with interpretable deep learning},
  journal = {Nature Methods},
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@article{Azizpour2024,
  author = {Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra},
  title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly},
  journal = {Genome Research},
  volume = {34},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 372-376, Springer, Cham.},
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}

@article{Li2025,
  author = {Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang},
  title = {Modeling gene interactions in polygenic prediction via geometric deep learning},
  journal = {Genome Research},
  volume = {35},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 377-380, Springer, Cham.},
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@article{Gibney,2024,
  author = {Ghanshyam Chandra, Daniel Gibney, and Chirag Jain},
  title = {Haplotype-aware sequence alignment to pangenome graphs},
  journal = {Genome Research},
  volume = {34},
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@article{Sens2024,
  author = {Daniel Sens, Liubov Shilova, Ludwig Gräf, Maria Grebenshchikova, Bjoern M. Eskofier, Francesco Paolo Casale},
  title = {Genetics-driven risk predictions leveraging the Mendelian randomization framework},
  journal = {Genome Research},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 385-389, Springer, Cham.},
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@article{Park2024,
  author = {Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Teddy Huang, Shuqiang Li, Satyen Gohil, Kenneth J. Livak, David A. Knowles, Catherine J. Wu, Elham Azizi},
  title = {A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data},
  journal = {Genome Research},
  volume = {34},
  number = {9},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 390-395, Springer, Cham.},
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  preprint_id = {bioRxiv 2023.11.14.566956},
  preprint_doi = {10.1101/2023.11.14.566956}
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@article{Li2024,
  author = {Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao},
  title = {A best-match approach for gene set analyses in embedding spaces},
  journal = {Genome Research},
  volume = {34},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 396-399, Springer, Cham.},
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  preprint_id = {bioRxiv 2023.11.21.568145},
  preprint_doi = {10.1101/2023.11.21.568145}
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@article{Zeng2024,
  author = {Shuai Zeng, Duolin Wang, Lei Jiang, Dong Xu},
  title = {Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction},
  journal = {Genome Research},
  volume = {34},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 400-405, Springer, Cham.},
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  preprint_id = {bioRxiv 2023.11.04.565642},
  preprint_doi = {10.1101/2023.11.04.565642}
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@article{Giurgiu2024,
  author = {Mădălina 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},
  title = {Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil},
  journal = {Genome Research},
  volume = {34},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 406-411, Springer, Cham.},
  proceedings_volume = {14758},
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  preprint_id = {bioRxiv 2023.11.15.567169},
  preprint_doi = {10.1101/2023.11.15.567169}
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@article{Goldenberg2024,
  author = {Meir Goldenberg, Loay Mualem, Amit Shahar, Sagi Snir, Adi Akavia},
  title = {Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption},
  journal = {Genome Research},
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  doi = {10.1101/gr.279071.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 412-416, Springer, Cham.},
  proceedings_volume = {14758},
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  preprint_id = {bioRxiv 2024.02.15.580590},
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@article{Gu2025,
  author = {Yichen Gu, Jialin Liu, Kun H. Lee, Chen Li, Lu Lu, Jaimee Moline, Renxiang Guan, Joshua D. Welch},
  title = {Topological velocity inference from spatial transcriptomic data},
  journal = {Nature Biotechnology},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 417-420, Springer, Cham.},
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@article{Iovino2024,
  author = {Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye},
  title = {Protein domain embeddings for fast and accurate similarity search},
  journal = {Genome Research},
  volume = {34},
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  year = {2024},
  doi = {10.1101/gr.279127.124},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 421-424, Springer, Cham.},
  proceedings_volume = {14758},
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  proceedings_doi = {10.1007/978-1-0716-3989-4_44},
  preprint_id = {bioRxiv 2023.11.27.567555},
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@article{Austin2025,
  author = {George I. Austin, Aya Brown Kav, Shahd ElNaggar, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Itsik Pe’er, Tal Korem},
  title = {Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models},
  journal = {Nature Microbiology},
  volume = {10: 897–911},
  year = {2025},
  doi = {10.1038/s41564-025-01954-4},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 425-428, Springer, Cham.},
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  preprint_id = {bioRxiv 2024.02.09.579716},
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@inproceedings{Melin2024,
  author = {Harald Melin, Vittorio Zampinetti, Andrew McPherson, Jens Lagergren},
  title = {VICTree - A Variational Inference Method for Clonal Tree Reconstruction},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 429-433, Springer, Cham.},
  pages = {429--433},
  year = {2024},
  doi = {10.1007/978-1-0716-3989-4_46},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 429-433, Springer, Cham.},
  proceedings_volume = {14758},
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  preprint_id = {bioRxiv 2024.02.14.580312},
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@article{Halmos2025,
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  title = {Dest-ot: Alignment of spatiotemporal transcriptomics data},
  journal = {Cell Systems},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 434-437, Springer, Cham.},
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  preprint_id = {bioRxiv 2024.03.05.583575},
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@inproceedings{Wu2024,
  author = {Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, S. Cenk Sahinalp, Salem Malikic},
  title = {Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 438-443, Springer, Cham.},
  pages = {438--443},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 438-443, Springer, Cham.},
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@article{Zahin2024,
  author = {Tasfia Zahin, Qian Shi, Xiaofei Carl Zang, Mingfu Shao},
  title = {Accurate assembly of circular RNAs with TERRACE},
  journal = {Genome Research},
  volume = {34},
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  doi = {10.1101/gr.279106.124},
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@inproceedings{Freestone2024,
  author = {Jack Freestone, Lukas Käll, William Stafford Noble, Uri Keich},
  title = {Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 448-453, Springer, Cham.},
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@article{Zhu2024,
  author = {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},
  title = {CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing},
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  volume = {34},
  number = {9},
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  year = {2024},
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@article{Fu2024,
  author = {Boyang Fu, Prateek Anand, Aakarsh Anand, Joel Mefford, Sriram Sankararaman},
  title = {A Scalable Adaptive Quadratic Kernel Method for Interpretable Epistasis Analysis in Complex Traits},
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  volume = {34},
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@inproceedings{Arasti2024,
  author = {Shayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, Siavash Mirarab},
  title = {Optimal Tree Metric Matching Enables Phylogenomic Branch Length Estimation},
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@article{Ma2024,
  author = {Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Michael J. Wilson, Christopher H. Sun, Li Ding, Benjamin J. Raphael},
  title = {Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics},
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@inproceedings{Zhao2024,
  author = {Junming Zhao, Chao Zhang, Yunan Luo},
  title = {Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 470-474, Springer, Cham.},
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@article{Jeong2024,
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  title = {Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy},
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@inproceedings{Bian2024,
  author = {Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Lei Wei, Xuegong Zhang},
  title = {scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 479-482, Springer, Cham.},
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