@article{Bohnenkämper2021,
  author = {Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye},
  title = {Computing the rearrangement distance of natural genomes},
  journal = {Journal of Computational Biology},
  volume = {28},
  number = {4},
  pages = {410--431},
  year = {2021},
  doi = {10.1089/cmb.2020.0434},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 3-18, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {3--18},
  proceedings_doi = {10.1007/978-3-030-45257-5_1},
  preprint_id = {arXiv:2001.02139},
  preprint_doi = {10.48550/arXiv.2001.02139}
}

@article{Dizaji2021,
  author = {Kamran Ghasedi Dizaji, Wei Chen, Heng Huang},
  title = {Deep Large-Scale Multitask Learning Network for Gene Expression Inference},
  journal = {Journal of Computational Biology},
  volume = {28},
  number = {5},
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  year = {2021},
  doi = {10.1089/cmb.2020.0438},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 19-36, Springer, Cham.},
  proceedings_volume = {12874},
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  proceedings_doi = {10.1007/978-3-030-45257-5_2}
}

@inproceedings{Ekim2020,
  author = {Barış Ekim, Bonnie Berger, Yaron Orenstein},
  title = {A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 37-53, Springer, Cham.},
  pages = {37--53},
  year = {2020},
  doi = {10.1007/978-3-030-45257-5_3},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 37-53, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {37--53},
  proceedings_doi = {10.1007/978-3-030-45257-5_3},
  preprint_id = {bioRxiv 2020.01.17.910513},
  preprint_doi = {10.1101/2020.01.17.910513}
}

@article{Luo2023,
  author = {Dong Luo, Arya Ebadi, Kristen Emery, Yilun He, William Stafford Noble, Uri Keich},
  title = {Competition-based control of the false discovery proportion},
  journal = {Biometrics},
  volume = {79},
  number = {4},
  pages = {3472--3484},
  year = {2023},
  doi = {10.1111/biom.13830},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 54-71, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {54--71},
  proceedings_doi = {10.1007/978-3-030-45257-5_4},
  preprint_id = {arXiv:1907.01458},
  preprint_doi = {10.48550/arXiv.1907.01458}
}

@article{Ge2021,
  author = {Songwei Ge, Haohan Wang, Amir Alavi, Eric Xing, Ziv Bar-Joseph},
  title = {Supervised Adversarial Alignment of Single-Cell RNA-seq Data},
  journal = {Journal of Computational Biology},
  volume = {28},
  number = {5},
  pages = {501--513},
  year = {2021},
  doi = {10.1089/cmb.2020.0439},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 72-87, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {72--87},
  proceedings_doi = {10.1007/978-3-030-45257-5_5},
  preprint_id = {bioRxiv 2020.01.06.896621},
  preprint_doi = {10.1101/2020.01.06.896621}
}

@article{Guo2021,
  author = {Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang},
  title = {EPTool: a new enhancing PSSM tool for protein secondary structure prediction},
  journal = {Journal of Computational Biology},
  volume = {28},
  number = {4},
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  doi = {10.1089/cmb.2020.0417},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 88-103, Springer, Cham.},
  proceedings_volume = {12874},
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@inproceedings{Ivanov2020,
  author = {Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, Martin Vechev},
  title = {AStarix: Fast and Optimal Sequence-to-Graph Alignment},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 104-119, Springer, Cham.},
  pages = {104--119},
  year = {2020},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 104-119, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {104--119},
  proceedings_doi = {10.1007/978-3-030-45257-5_7},
  preprint_id = {bioRxiv 2020.01.22.915496},
  preprint_doi = {10.1101/2020.01.22.915496}
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@article{Legried2021,
  author = {Brandon Legried, Erin K. Molloy, Tandy Warnow, Sébastien Roch},
  title = {Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss},
  journal = {Journal of Computational Biology},
  volume = {28},
  number = {5},
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  doi = {10.1089/cmb.2020.0424},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 120-135, Springer, Cham.},
  proceedings_volume = {12874},
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  preprint_id = {bioRxiv 821439},
  preprint_doi = {10.1101/821439}
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@article{Mitra2021,
  author = {Sneha Mitra, Jianling Zhong, TQ Tran, David M. MacAlpine, Alexander J. Hartemink},
  title = {RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data},
  journal = {Nucleic Acids Research},
  volume = {49},
  number = {14},
  pages = {7925--7938},
  year = {2021},
  doi = {10.1093/nar/gkab553},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 136-151, Springer, Cham.},
  proceedings_volume = {12874},
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  proceedings_doi = {10.1007/978-3-030-45257-5_9},
  preprint_id = {bioRxiv 2020.06.03.132001},
  preprint_doi = {10.1101/2020.06.03.132001}
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@article{Rahman2021,
  author = {Amatur Rahman, Paul Medvedev},
  title = {Representation of k-Mer Sets Using Spectrum-Preserving String Sets},
  journal = {Journal of Computational Biology},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 152-168, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {152--168},
  proceedings_doi = {10.1007/978-3-030-45257-5_10},
  preprint_id = {bioRxiv 2020.01.07.896928},
  preprint_doi = {10.1101/2020.01.07.896928}
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@article{Reyna2021,
  author = {Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael},
  title = {NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks},
  journal = {Journal of Computational Biology},
  volume = {28},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 169-185, Springer, Cham.},
  proceedings_volume = {12874},
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  proceedings_doi = {10.1007/978-3-030-45257-5_11},
  preprint_id = {bioRxiv 2020.01.18.911438},
  preprint_doi = {10.1101/2020.01.18.911438}
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@inproceedings{Sarrazin-Gendron2020,
  author = {Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jérôme Waldispühl},
  title = {Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 186-201, Springer, Cham.},
  pages = {186--201},
  year = {2020},
  doi = {10.1007/978-3-030-45257-5_12},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 186-201, Springer, Cham.},
  proceedings_volume = {12874},
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  preprint_id = {bioRxiv 834762},
  preprint_doi = {10.1101/834762}
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@article{Zheng2021,
  author = {Hongyu Zheng, Carl Kingsford, Guillaume Marçais},
  title = {Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length},
  journal = {Journal of Computational Biology},
  volume = {28},
  number = {4},
  pages = {395--409},
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  doi = {10.1089/cmb.2020.0432},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 202-217, Springer, Cham.},
  proceedings_volume = {12874},
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  preprint_id = {arXiv:2001.06550},
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@inproceedings{Baaijens2020,
  author = {Jasmijn A. Baaijens, Leen Stougie, Alexander Schönhuth},
  title = {Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 221-222, Springer, Cham.},
  pages = {221--222},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 221-222, Springer, Cham.},
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@article{Baharav2020,
  author = {Tavor Z. Baharav, Govinda M. Kamath, David N. Tse, Ilan Shomorony},
  title = {Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments},
  journal = {Patterns},
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@inproceedings{Bankevich2020,
  author = {Anton Bankevich, Pavel Pevzner},
  title = {MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 226-228, Springer, Cham.},
  pages = {226--228},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 226-228, Springer, Cham.},
  proceedings_volume = {12874},
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  preprint_id = {bioRxiv 2020.01.15.908285},
  preprint_doi = {10.1101/2020.01.15.908285}
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@article{Borgsmüller2020,
  author = {Nico Borgsmüller, Jose Bonet, Francesco Marass, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Niko Beerenwinkel},
  title = {BnpC: Bayesian non-parametric clustering of single-cell mutation profiles},
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  proceedings_volume = {12874},
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  preprint_id = {bioRxiv 2020.01.15.907345},
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@article{Born2021,
  author = {Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez},
  title = {PaccMannRL: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning},
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@article{Bose2023,
  author = {Aritra Bose, Myson C. Burch, Agniva Chowdhury, Peristera Paschou, Petros Drineas},
  title = {Structure-informed clustering for population stratification in association studies},
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@article{Brandes2020,
  author = {Nadav Brandes, Nathan Linial, Michal Linial},
  title = {PWAS: proteome-wide association study—linking genes and phenotypes by functional variation in proteins},
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@article{Caggiano2021,
  author = {Christa Caggiano, Barbara Celona, Fleur Garton, Joel Mefford, Brian Black, Robert Henderson, Catherine Lomen-Hoerth, Andrew Dahl, Noah Zaitlen},
  title = {Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE},
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@article{Tastan,2021,
  author = {Gizem Caylak, Oznur Tastan, and A. Ercument Cicek},
  title = {Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection},
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@article{Cho2020,
  author = {Hyunghoon Cho, Sean Simmons, Ryan Kim, Bonnie Berger},
  title = {Privacy-preserving biomedical database queries with optimal privacy-utility trade-offs},
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@article{Gao2021,
  author = {Chao Gao, Jialin Liu, April R. Kriebel, Sebastian Preissl, Chongyuan Luo, Rosa Castanon, Justin Sandoval, Angeline Rivkin, Joseph R. Nery, Margarita M. Behrens, Joseph R. Ecker, Bing Ren, Joshua D. Welch},
  title = {Iterative single-cell multi-omic integration using online learning},
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@article{Hristov2020,
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  title = {uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes},
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@article{Johnson2021,
  author = {Ruth Johnson, Heather E. Wheeler, Kathryn S. Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc, Sriram Sankararaman},
  title = {Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits},
  journal = {PLOS Computational Biology},
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@article{Joseph2020,
  author = {Tyler A. Joseph, Amey P. Pasarkar, Itsik Pe'er},
  title = {Efficient and Accurate Inference of Mixed Microbial Population Trajectories from Longitudinal Count Data},
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@article{LaPierre2021,
  author = {Nathan LaPierre, Kodi Taraszka, Helen Huang, Rosemary He, Farhad Hormozdiari, Eleazar Eskin},
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@article{Li2020,
  author = {Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng},
  title = {MONN: a Multi-Objective Neural Network for Predicting Compound-Protein Interactions and Affinities},
  journal = {Cell Systems},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 259-260, Springer, Cham.},
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  preprint_id = {bioRxiv 2019.12.30.891515},
  preprint_doi = {10.1101/2019.12.30.891515}
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@article{Luo2021,
  author = {Yunan Luo, G Jiang, T Yu, Y Liu, Lam Vo, Hantian Ding, Yufeng Su, Wesley Wei Qian, Huimin Zhao, Jian Peng},
  title = {ECNet is an evolutionary context-integrated deep learning framework for protein engineering},
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  preprint_id = {bioRxiv 2020.01.16.908509},
  preprint_doi = {10.1101/2020.01.16.908509}
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@article{Mai2021,
  author = {Uyen Mai, Siavash Mirarab},
  title = {Log Transformation Improves Dating of Phylogenies},
  journal = {Molecular Biology and Evolution},
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  number = {3},
  pages = {1151--1167},
  year = {2021},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 264-265, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {264--265},
  proceedings_doi = {10.1007/978-3-030-45257-5_31},
  preprint_id = {bioRxiv 2019.12.20.885582},
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@article{Paige2021,
  author = {Brooks Paige, James Bell, Aurélien Bellet, Adrià Gascón, Daphne Ezer},
  title = {Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores},
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  pages = {435--451},
  year = {2021},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 266-268, Springer, Cham.},
  proceedings_volume = {12874},
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@article{Sanaullah2021,
  author = {Ahsan Sanaullah, Degui Zhi, Shaojie Zhang},
  title = {d-PBWT: dynamic positional Burrows–Wheeler transform},
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  volume = {37},
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  pages = {2390--2397},
  year = {2021},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 269-270, Springer, Cham.},
  proceedings_volume = {12874},
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  preprint_id = {bioRxiv 2020.01.14.906487},
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@article{Sason2021,
  author = {Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan},
  title = {A mixture model for signature discovery from sparse mutation data},
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  year = {2021},
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  proceedings_volume = {12874},
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@article{Satas2020,
  author = {Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael},
  title = {SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses},
  journal = {Cell Systems},
  volume = {10},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 273-273, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {273--273},
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  preprint_id = {bioRxiv 840355},
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@article{Wang2022,
  author = {Yijie Wang, Hangnoh Lee, Justin M. Fear, Isabelle Berger, Brian Oliver, Teresa M. Przytycka},
  title = {NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 274-275, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {274--275},
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  preprint_id = {bioRxiv 2020.01.07.898031},
  preprint_doi = {10.1101/2020.01.07.898031}
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@article{Zhang2020,
  author = {Ruochi Zhang, Jian Ma},
  title = {MATCHA: Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning},
  journal = {Cell Systems},
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  number = {5},
  pages = {397--407},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12874, pp 276-277, Springer, Cham.},
  proceedings_volume = {12874},
  proceedings_pages = {276--277},
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  preprint_id = {bioRxiv 2020.01.22.916171},
  preprint_doi = {10.1101/2020.01.22.916171}
}