4 papers · ranked by Valyu relevance
Brett Kiyota, Chaehyeon Lee, Haoyang Yao, Nozomu Yachie
The rapid expansion of single-cell genomic datasets has led to the compilation of biological resources comprising hundreds of millions of cells across tissues, developmental stages, and disease states. This has underscored the need for scalable and interpretable data representations that preserve the complex…
Ivan Specht, Soyoon Park, Seyone Chithrananda, Claudia L. Driscoll + 3 more
Viral mutation forecasting plays a key role in pandemic preparedness by enabling researchers to anticipate novel variants and design proactive interventions. Evolutionary histories, represented as phylogenetic trees, offer key insights into the emergence of past and present strains, yet their role in predicting future…
Fabio Cumbo, Kabir Dhillon, M. Hassan Najafi, Sercan Aygun + 1 more
The exponential growth of genomic databases necessitates alignment-free methods for comparing genomes. While MinHash-based tools have revolutionized this field by efficiently estimating the Average Nucleotide Identity based on k-mer sets, they inherently discard structural genomic information. We introduce HyperSketch…
Luise Häuser, Alexandros Stamatakis
While there exists a plethora of prior research on phylogenetic tree shape indices, a largescale analysis of the behavior of these indices on empirical trees has not yet been conducted. Here, we address this by computing 54 indices on more than 45,000,000 empirical trees retrieved from the EvoNAPS and RAxML Grove…