@article{Pazokitoroudi2024,
  author = {Ali Pazokitoroudi, Zhengtong Liu, Andrew Dahl, Noah Zaitlen, Saharon Rosset, Sriram Sankararaman},
  title = {A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits},
  journal = {American Journal of Human Genetics},
  volume = {111},
  number = {7},
  pages = {1462--1480},
  year = {2024},
  doi = {10.1016/j.ajhg.2024.05.015},
  proceedings_volume = {0},
  proceedings_pages = {NONE}
}

@inproceedings{Joudaki2021,
  author = {Amir Joudaki, Gunnar Ratsch, Andre Kahles},
  title = {Fast Alignment-Free Similarity Estimation By Tensor Sketching},
  pages = {NONE},
  year = {2021},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.13.381814},
  preprint_doi = {10.1101/2020.11.13.381814}
}

@article{Bankevich2022,
  author = {Anton Bankevich, Andrey V. Bzikadze, Mikhail Kolmogorov, Dmitry Antipov, Pavel A. Pevzner},
  title = {Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads},
  journal = {Nature Biotechnology},
  volume = {40: 1075–1081},
  year = {2022},
  doi = {10.1038/s41587-022-01220-6},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.12.10.420448},
  preprint_doi = {10.1101/2020.12.10.420448}
}

@article{Orabi2023,
  author = {Baraa Orabi, Ning Xie, Brian McConeghy, Xuesen Dong, Cedric Chauve, Faraz Hach},
  title = {Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing},
  journal = {Nucleic Acids Research},
  volume = {51},
  number = {2},
  pages = {e11},
  year = {2023},
  doi = {10.1093/nar/gkac1112},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.01.20.427493},
  preprint_doi = {10.1101/2021.01.20.427493}
}

@article{Ekim2021,
  author = {Barış Ekim, Bonnie Berger, Rayan Chikhi},
  title = {Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer},
  journal = {Cell Systems},
  volume = {12},
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  pages = {958--968.e6},
  year = {2021},
  doi = {10.1016/j.cels.2021.08.009},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.06.09.447586},
  preprint_doi = {10.1101/2021.06.09.447586}
}

@article{Chidester2023,
  author = {Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma},
  title = {SPICEMIX enables integrative single-cell spatial modeling of cell identity},
  journal = {Nature Genetics},
  volume = {55},
  number = {1},
  pages = {78--88},
  year = {2023},
  doi = {10.1038/s41588-022-01256-z},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.29.383067},
  preprint_doi = {10.1101/2020.11.29.383067}
}

@article{Oliver2022,
  author = {Carlos Oliver, Vincent Mallet, Pericles Philippopoulos, William L Hamilton, Jerome Waldispuhl},
  title = {Vernal: a tool for mining fuzzy network motifs in RNA},
  journal = {Bioinformatics},
  volume = {38},
  number = {4},
  pages = {970--976},
  year = {2022},
  doi = {10.1093/bioinformatics/btab768},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {arXiv:2009.00664},
  preprint_doi = {10.48550/arXiv.2009.00664}
}

@article{Wójtowicz2021,
  author = {Damian Wójtowicz, Jan Hoinka, Bayarbaatar Amgalan, Yoo-Ah Kim, Teresa M Przytycka},
  title = {RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer},
  journal = {Cell Systems},
  volume = {12},
  number = {10},
  pages = {994--1003.e4},
  year = {2021},
  doi = {10.1016/j.cels.2021.07.004},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.21.392878},
  preprint_doi = {10.1101/2020.11.21.392878}
}

@article{Santoro2022,
  author = {Diego Santoro, Leonardo Pellegrina, Matteo Comin, Fabio Vandin},
  title = {SPRISS: approximating frequent k-mers by sampling reads, and applications},
  journal = {Bioinformatics},
  volume = {38},
  number = {13},
  pages = {3343--3350},
  year = {2022},
  doi = {10.1093/bioinformatics/btac180},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {arXiv:2101.07117},
  preprint_doi = {10.48550/arXiv.2101.07117}
}

@article{Seiler2021,
  author = {Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, Knut Reinert},
  title = {Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences},
  journal = {iScience},
  volume = {24},
  number = {7},
  pages = {102782},
  year = {2021},
  doi = {j.isci.2021.102782},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.10.08.330985},
  preprint_doi = {10.1101/2020.10.08.330985}
}

@article{Satas2021,
  author = {Gryte Satas, Simone Zaccaria, Mohammed El-Kebir, Benjamin J Raphael},
  title = {DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution},
  journal = {Cell Systems},
  volume = {12},
  number = {10},
  pages = {1004--1018},
  year = {2021},
  doi = {10.1016/j.cels.2021.07.006},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.02.27.429196},
  preprint_doi = {10.1101/2021.02.27.429196}
}

@article{Li2022,
  author = {Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Dan Zhao, Jianyang Zeng},
  title = {Improving molecular property prediction through a task similarity enhanced transfer learning strategy},
  journal = {iScience},
  volume = {25},
  number = {10},
  pages = {105231},
  year = {2022},
  doi = {10.1016/j.isci.2022.105231},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.01.13.426608},
  preprint_doi = {10.1101/2021.01.13.426608}
}

@article{Shrivastava2022,
  author = {Harsh Shrivastava , Xiuwei Zhang, Le Song, Srinivas Aluru},
  title = {GRNUlar: A deep learning framework for recovering single-cell gene regulatory networks},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {1},
  pages = {27--44},
  year = {2022},
  doi = {10.1089/cmb.2021.0437},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.04.23.058149},
  preprint_doi = {10.1101/2020.04.23.058149}
}

@inproceedings{Yao2021,
  author = {Hua-Ting Yao, Jerome Waldispuhl, Yann Ponty, Sebastian Will},
  title = {Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA},
  pages = {NONE},
  year = {2021},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {hal-02987566},
  preprint_url = {https://hal.science/hal-02987566}
}

@article{Li2021,
  author = {Jin Li, Jinbo Xu},
  title = {Study of real-valued distance prediction for protein structure prediction with deep learning},
  journal = {Bioinformatics},
  volume = {37},
  number = {19},
  pages = {3197--3203},
  year = {2021},
  doi = {10.1093/bioinformatics/btab333},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.26.400523},
  preprint_doi = {10.1101/2020.11.26.400523}
}

@article{Zhu2022,
  author = {Kaiyuan Zhu, Alejandro A. Schäffer, Welles Robinson, Junyan Xu, Eytan Ruppin, A. Funda Ergun, Yuzhen Ye, S. Cenk Sahinalp},
  title = {Strain level microbial detection and quantification with applications to single cell metagenomics},
  journal = {Nature Communications},
  volume = {13},
  number = {1},
  pages = {6430},
  year = {2022},
  doi = {10.1038/s41467-022-33869-7},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.06.12.149245},
  preprint_doi = {10.1101/2020.06.12.149245}
}

@article{Zaharias2022,
  author = {Paul Zaharias, Martin Grosshauser, Tandy Warnow},
  title = {Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {1},
  pages = {74--89},
  year = {2022},
  doi = {10.1089/cmb.2021.0383},
  proceedings_volume = {0},
  proceedings_pages = {NONE}
}

@article{Dokmai2021,
  author = {Natnatee Dokmai, Can Kockan, Kaiyuan Zhu, XiaoFeng Wang, S Cenk Sahinalp, Hyunghoon Cho},
  title = {Privacy-preserving genotype imputation in a trusted execution environment},
  journal = {Cell Systems},
  volume = {12},
  number = {10},
  pages = {983--993.e7},
  year = {2021},
  doi = {10.1016/j.cels.2021.08.001},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.02.02.429428},
  preprint_doi = {10.1101/2021.02.02.429428}
}

@article{Franzese2022,
  author = {Nicholas Franzese, Jason Fan, Roded Sharan, Mark D M Leiserson},
  title = {ScalpelSig: Automated Design of Genomic Panels to Expand Clinical Access to Mutational Signature Analysis},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {1},
  pages = {56--73},
  year = {2022},
  doi = {10.1089/cmb.2021.0453},
  proceedings_volume = {0},
  proceedings_pages = {NONE}
}

@article{Demetci2021,
  author = {Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh},
  title = {Gromov-Wasserstein optimal transport to align single-cell multi-omics data},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {1},
  pages = {3--18},
  year = {2021},
  doi = {10.1089/cmb.2021.0446},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.04.28.066787},
  preprint_doi = {10.1101/2020.04.28.066787}
}

@article{Nasser2022,
  author = {Rami Nasser, Yonina C. Eldar, Roded Sharan},
  title = {Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {1},
  pages = {45--55},
  year = {2022},
  doi = {10.1089/cmb.2021.0438},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {arXiv:2108.09138},
  preprint_doi = {10.48550/arXiv.2108.09138}
}

@article{Zeira2022,
  author = {Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J Raphael},
  title = {Alignment and integration of spatial transcriptomics data},
  journal = {Nature Methods},
  volume = {19},
  number = {5},
  pages = {567--575},
  year = {2022},
  doi = {10.1038/s41592-022-01459-6},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.03.16.435604},
  preprint_doi = {10.1101/2021.03.16.435604}
}

@article{Zhang2025,
  author = {Ruochi Zhang, Jianzhu Ma, Jian Ma},
  title = {Towards the prediction of higher-order genetic interactions},
  journal = {Cell Systems},
  volume = {to appear},
  year = {2025},
  doi = {10.1016},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.26.400739},
  preprint_doi = {10.1101/2020.11.26.400739}
}

@article{Sledzieski2021,
  author = {Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger},
  title = {D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions},
  journal = {Cell Systems},
  volume = {12},
  number = {10},
  pages = {969--982.e6},
  year = {2021},
  doi = {10.1016/j.cels.2021.08.010},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.01.22.427866},
  preprint_doi = {10.1101/2021.01.22.427866}
}

@article{Yılmaz2021,
  author = {Serhan Yılmaz, Marzieh Ayati, Daniela Schlatzer, A Ercument Cicek, Mark Chance, Mehmet Koyuturk},
  title = {Robust inference of kinase activity using functional networks},
  journal = {Nature Communications},
  volume = {12},
  number = {1},
  pages = {1177},
  year = {2021},
  doi = {10.1038/s41467-021-21211-6},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.05.01.062802},
  preprint_doi = {10.1101/2020.05.01.062802}
}

@article{Sarmashghi2021,
  author = {Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna},
  title = {Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT},
  journal = {PLOS Computational Biology},
  volume = {17},
  number = {11},
  pages = {e1009449},
  year = {2021},
  doi = {10.1371/journal.pcbi.1009449},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.01.28.428636},
  preprint_doi = {10.1101/2021.01.28.428636}
}

@article{Dehkordi2021,
  author = {Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna},
  title = {FaNDOM: Fast nested distance-based seeding of optical maps},
  journal = {Patterns},
  volume = {2},
  number = {5},
  pages = {100248},
  year = {2021},
  doi = {10.1016/j.patter.2021.100248},
  proceedings_volume = {0},
  proceedings_pages = {NONE}
}

@article{Sun2021,
  author = {Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li},
  title = {scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured},
  journal = {Genome Biology},
  volume = {22: 163},
  year = {2021},
  doi = {10.1186/s13059-021-02367-2},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.17.387795},
  preprint_doi = {10.1101/2020.11.17.387795}
}

@article{Li2021,
  author = {Wei Vivian Li, Yanzeng Li},
  title = {scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data},
  journal = {Genomics, Proteomics & Bioinformatics},
  volume = {19},
  number = {3},
  pages = {475--492},
  year = {2021},
  doi = {10.1016/j.gpb.2020.11.006},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.09.19.304956},
  preprint_doi = {10.1101/2020.09.19.304956}
}

@article{Zhou2021,
  author = {Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang},
  title = {scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species},
  journal = {Briefings in Bioinformatics},
  volume = {22},
  number = {6},
  pages = {bbab281},
  year = {2021},
  doi = {10.1093/bib/bbab281},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.01.18.427083},
  preprint_doi = {10.1101/2021.01.18.427083}
}

@article{Liu2021,
  author = {Xinhao Liu, Huw A Ogilvie, Luay Nakhleh},
  title = {Variational inference using approximate likelihood under the coalescent with recombination},
  journal = {Genome Research},
  volume = {31},
  number = {11},
  pages = {2107--2119},
  year = {2021},
  doi = {10.1101/gr.273631.120},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.08.19.258137},
  preprint_doi = {10.1101/2020.08.19.258137}
}

@inproceedings{Jiang2021,
  author = {Yuepeng Jiang, Stefano Rensi, Sheng Wang, Russ Altman},
  title = {DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning},
  pages = {NONE},
  year = {2021},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.17.385757},
  preprint_doi = {10.1101/2020.11.17.385757}
}

@article{Jiang2023,
  author = {Yueyu Jiang, Metin Balaban, Qiyun Zhu, Siavash Mirarab},
  title = {DEPP: Deep Learning Enables Extending Species Trees using Single Genes},
  journal = {Systematic Biology},
  volume = {72},
  number = {1},
  pages = {17},
  year = {2023},
  doi = {10.1093/sysbio/syac031},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.01.22.427808},
  preprint_doi = {10.1101/2021.01.22.427808}
}

@article{Kong2022,
  author = {Lupeng Kong, Fusong Ju, Wei-mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu},
  title = {ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {2},
  pages = {92--105},
  year = {2022},
  doi = {10.1089/cmb.2021.0430},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.12.28.424539},
  preprint_doi = {10.1101/2020.12.28.424539}
}

@article{Du2022,
  author = {Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, Fengzhu Sun},
  title = {Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {2},
  pages = {106--120},
  year = {2022},
  doi = {10.1089/cmb.2021.0439},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.03.01.433489},
  preprint_doi = {10.1101/2021.03.01.433489}
}

@article{Zheng2022,
  author = {Hongyu Zheng, Cong Ma, Carl Kingsford},
  title = {Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {2},
  pages = {121--139},
  year = {2022},
  doi = {10.1089/cmb.2021.0444},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2019.12.13.875625},
  preprint_doi = {10.1101/2019.12.13.875625}
}

@article{Shibuya2022,
  author = {Yoshihiro Shibuya, Djamal Belazzougui, Gregory Kucherov},
  title = {Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k-Mer Annotation},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {2},
  pages = {140--154},
  year = {2022},
  doi = {10.1089/cmb.2021.0429},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.14.382713},
  preprint_doi = {10.1101/2020.11.14.382713}
}

@article{Blanca2022,
  author = {Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev},
  title = {The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {2},
  pages = {155--168},
  year = {2022},
  doi = {10.1089/cmb.2021.0431},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.01.15.426881},
  preprint_doi = {10.1101/2021.01.15.426881}
}

@article{Rossi2022,
  author = {Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher},
  title = {MONI: A Pangenomic Index for Finding Maximal Exact Matches},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {2},
  pages = {169--187},
  year = {2022},
  doi = {10.1089/cmb.2021.0290},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2021.07.06.451246},
  preprint_doi = {10.1101/2021.07.06.451246}
}

@article{Shaw2022,
  author = {Jim Shaw, Yun William Yu},
  title = {flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning},
  journal = {Journal of Computational Biology},
  volume = {29},
  number = {2},
  pages = {195--211},
  year = {2022},
  doi = {10.1089/cmb.2021.0436},
  proceedings_volume = {0},
  proceedings_pages = {NONE},
  preprint_id = {bioRxiv 2020.11.06.371799},
  preprint_doi = {10.1101/2020.11.06.371799}
}