8 papers · ranked by Valyu relevance
Namasi G Sankar, Georgios Miliotis, Simon Caton
Genome assembly is important in infectious disease surveillance, antimicrobial resistance monitoring, and cancer genomics. The task of reconstructing full genomic sequences from fragmented reads, can be framed as a large scale combinatorial optimisation problem. Recent advances in quantum computing have introduced new…
Fubo Ma, Kang Li, Yangchao Yu, Lei Zhang + 3 more
Type I interferon (IFN-I) is an important class of cytokines that can inhibit tumuor progression through mechanisms such as immunomodulation of the tumuor microenvironment or targeting cellular components. Although various endogenous and exogenous IFN-I therapeutic strategies have been developed, reports of immune cell…
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…
Jordan Eizenga, Mira Mastoras, Julian K. Lucas, Julian Menendez + 14 more
Centromeres play essential roles in chromosome segregation and genome stability, yet they remain among the least characterized regions of the human genome. Despite advances in long-read sequencing and complete genome assembly, the extreme repetitiveness and structural complexity of these regions still challenge…
Justina Stark, Christophe Godin
Biological transport networks range from tree-like to highly reticulated architectures, which have been proposed to reflect different balances between viscous dissipation and metabolic cost. This balance cannot currently be inferred from structure: available descriptors either discard edge width entirely or preserve it…
Raphael Mostov, Greyson Lewis, Gabriel Sturm, Wallace F. Marshall
This paper addresses the increasing need for comprehensive mathematical descriptions of cell organization by examining the algebraic structure of mitochondrial network dynamics. Mitochondria are cellular structures involved in metabolism that take the form of a network of membrane-based tubes that undergo continuous…
Ana Lúcia Leitão, Francisco J Enguita
The evolution of molecular visualization software represents a pivotal yet often underappreciated dimension of computational structural biology and bioinformatics. As the scale and complexity of structural datasets increase, spanning from cryo-electron microscopy reconstructions to proteome-wide AI-predicted models…
John L. Portwood, Ethalinda K. Cannon, Olivia C. Haley, Laura E. Tibbs-Cortes + 2 more
Genome visualization has existed for as long as assembled genomes, with an array of tools and approaches to meet researchers’ needs. The genome browser is one of these tools, and it has become a critical analytical resource for geneticists, genome biologists, and breeders. The evolution of genome browser capabilities…