Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. - Yun William Yu; Deniz Yörükoglu; Bonnie Berger (RECOMB, 2014)

Entropy-scaling search of massive biological data. - Yun William Yu; Noah M. Daniels; David Christian Danko; Bonnie Berger (CoRR, 2015)

Fast genotyping of known SNPs through approximate k-mer matching. - Ariya Shajii; Deniz Yörükoglu; Yun William Yu; Bonnie Berger (Bioinform., 2016)

Approximation hardness of Shortest Common Superstring variants. - Yun William Yu (CoRR, 2016)

HyperMinHash: Jaccard index sketching in LogLog space. - Yun William Yu; Griffin M. Weber (CoRR, 2017)

Total Tetris: Tetris with Monominoes, Dominoes, Trominoes, Pentominoes, ... - Erik D. Demaine; Martin L. Demaine; Sarah Eisenstat; Adam Hesterberg; Andrea Lincoln; Jayson Lynch; Yun William Yu (J. Inf. Process., 2017)

Joker de Bruijn: Covering k-Mers Using Joker Characters. - Yaron Orenstein; Yun William Yu; Bonnie Berger (J. Comput. Biol., 2018)

Metagenomic binning through low-density hashing. - Yunan Luo; Yun William Yu; Jianyang Zeng 001; Bonnie Berger; Jian Peng 001 (Bioinform., 2019)

Contact Tracing Mobile Apps for COVID-19: Privacy Considerations and Related Trade-offs. - Hyunghoon Cho; Daphne Ippolito; Yun William Yu (CoRR, 2020)

COVI White Paper. - Hannah Alsdurf; Yoshua Bengio; Tristan Deleu; Prateek Gupta; Daphne Ippolito; Richard Janda; Max Jarvie; Tyler Kolody; Sekoul Krastev; Tegan Maharaj; Robert Obryk; Dan Pilat; et al. (CoRR, 2020)

Severability of mesoscale components and local time scales in dynamical networks. - Yun William Yu; Jean-Charles Delvenne; Sophia N. Yaliraki; Mauricio Barahona (CoRR, 2020)

Privacy-accuracy trade-offs in noisy digital exposure notifications. - Abbas Hammoud; Yun William Yu (CoRR, 2020)

Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories. - Ziye Tao; Griffin M. Weber; Yun William Yu (Bioinform., 2021)

On minimizers and convolutional filters: a partial justification for the unreasonable effectiveness of CNNs in categorical sequence analysis. - Yun William Yu (CoRR, 2021)

Inherent privacy limitations of decentralized contact tracing apps. - Yoshua Bengio; Daphne Ippolito; Richard Janda; Max Jarvie; Benjamin Prud'homme; Jean-Franois Rousseau; Abhinav Sharma; Yun William Yu (J. Am. Medical Informatics Assoc., 2021)

Levenshtein Distance, Sequence Comparison and Biological Database Search. - Bonnie Berger; Michael S. Waterman; Yun William Yu (IEEE Trans. Inf. Theory, 2021)

Skiing Is Easy, Gymnastics Is Hard: Complexity of Routine Construction in Olympic Sports. - James Koppel; Yun William Yu (FUN, 2022)

flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning. - Jim Shaw; Yun William Yu (J. Comput. Biol., 2022)

HyperMinHash: MinHash in LogLog Space. - Yun William Yu; Griffin M. Weber (IEEE Trans. Knowl. Data Eng., 2022)

Theory of local k-mer selection with applications to long-read alignment. - Jim Shaw; Yun William Yu (Bioinform., 2022)

HyperMinHash: MinHash in LogLog Space (Extended Abstract). - Yun William Yu; Griffin M. Weber (ICDE, 2023)

Reverse-Engineering Decoding Strategies Given Blackbox Access to a Language Generation System. - Daphne Ippolito; Nicholas Carlini; Katherine Lee; Milad Nasr; Yun William Yu (INLG, 2023)

Image-centric compression of protein structures improves space savings. - Luke Staniscia; Yun William Yu (BMC Bioinform., 2023)

Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography. - Alexander T. Leighton; Yun William Yu (RECOMB, 2024)

Floria: fast and accurate strain haplotyping in metagenomes. - Jim Shaw; Jean-Sébastien Gounot; Hanrong Chen; Niranjan Nagarajan; Yun William Yu (Bioinform., 2024)

skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements. - Xiaolei Brian Zhang; Grace Oualline; Jim Shaw; Yun William Yu (Bioinform., 2024)

On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis. - Yun William Yu (J. Comput. Biol., 2024)

Mora: abundance aware metagenomic read re-assignment for disentangling similar strains. - Andrew Zheng; Jim Shaw; Yun William Yu (BMC Bioinform., 2024)

Devider: Long-Read Reconstruction of Many Diverse Haplotypes. - Jim Shaw; Christina Boucher 001; Yun William Yu; Noelle R. Noyes; Heng Li (RECOMB, 2025)