8 papers · ranked by Valyu relevance
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…
Lena Trnovec, Miha Štajdohar, Gad Shaulsky, Blaž Zupan
dictyExpress 3.0 is a React/TypeScript reimplementation of the Dictyostelium discoideum transcriptomics web server, first introduced in 2009, that unifies bulk and single-cell exploration. A long-standing gene-expression resource for the Dictyostelium community, dictyExpress is also accessible through dictyBase, the…
Xuebin Feng, Emma R. Master
Sequence similarity networks (SSNs) are graphical representations of sequence relationship frequently used for exploring protein sequence space. Conventional SSN workflows typically use BLAST to calculate sequence similarities and rely on external visualization tools to generate the final networks. Consequently, raw…
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…
Huihai Wu, Ashleigh Lister, Iain Macaulay, Katie Long + 10 more
Single-cell and spatial transcriptomics are transforming our understanding of cellular heterogeneity and tissue organization, yet their analytical complexity remains a major bottleneck. Here, we present EISCA and EISTA, two standardized, end-to-end pipelines for single-cell RNA- seq and imaging-based spatial…
Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga + 2 more
Although cell type annotation has become an integral part of single-cell analysis workflows, the assessment of computational annotations remains challenging. Many annotation tools transfer labels from an annotated reference dataset to a new query dataset of interest, but blindly transferring labels from one dataset to…
Farsai Taemaitree, Jinwoo Sung, Yutaro Miki, Ryuju Suzuki + 15 more
Many nanoscale materials, ranging from environmental particulates to carrier-free nanomedicine platforms, enter the human body, yet their metabolic fates remain poorly understood. This process involves complex physical changes and molecular transformations within lysosomes; however, the particle-to-molecule…
Cheryl Kim, Denise Hinz, Aaron Middlebrook, Aaron J Tyznik + 4 more
Circulating cell-cell complexes (doublets) provide critical insights into in vivo immune interactions. Here, we leverage high-dimensional imaging spectral cytometry to systematically map the landscape of immune doublets in human peripheral blood. By integrating morphometric imaging features with a 22-color spectral…