10 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…
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…
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…
Atif Khan, Sruti Chandramouli, Hiren M. Joshi
The crystal violet (CV) microtiter plate assay is widely used to compare microbial biofilm formation because it is inexpensive, simple, and readily adapted to 96-well formats. Its high-throughput design enables multiple strains, growth conditions, and treatments to be tested in parallel, but increasing experimental…
Nancy Hom, Connor Weidle, Marie Pancera, Kelly K. Lee
The circumsporozoite protein (CSP) on the surface of the sporozoite stage of Plasmodium falciparum parasites is one of the major malaria antigens recognized by the adaptive immune system. Antibodies against CSP can provide protection from malaria infection following mosquito bite of the human host. Recent studies have…
Braden Charles DeMattei, Stephanie E. Hampton
Understanding species interactions is integral to understanding ecosystem function and predicting how disturbances may affect the services provided to society. Analysis of trophic interactions, however, requires a significant investment of time and resources. Using a simple predator-prey pairing of a semi-sessile…
Florencia Anunziata, Julie A. Kable, Marla C. Castañeda, Melanie H. Koslosky + 5 more
2.1### Study Design and Setting The main cross-sectional study was designed to examine clinical and subclinical indicators of current or future chronic disease among children and adolescents aged 3-17 years with and without confirmed PAE. The study is conducted as part of the Collaborative Initiative on Fetal Alcohol…