9 papers · ranked by Valyu relevance
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…
Yuesong Wu, Haohao Su, Yuehua Cui
Cell-cell communication (CCC) is essential for maintaining tissue organization and driving biological progression, yet its inference from transcriptomic data has long been limited by the absence of spatial context. Advances in spatial transcriptomics (ST) now enable mechanistically grounded analyses of CCC by…
Zichao Jin, Jiaoru Wang, Wenjiang Huang, Jingcheng Zhang + 2 more
Accurate, reliable, large-scale disease predictions are essential to ensure rice production. Existing disease prediction models often face a trade-off between interpretability and predictive capability, necessitating the integration of mechanistic knowledge and data-driven learning within a modelling framework.…
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…
Nazanin Zahra Keshvari, Sara Asl Motaleb Nejad Sarkhab, Tara Shahmoradi, Mohammad Pourashory + 3 more
5.1### Limitations of Biomarkers in Traditional Diagnosis of MDD Standard diagnosis of MDD is only reliable clinically through history taking and psychiatric evaluation. This approach is susceptible to false positives and false negatives in diagnosis. Additionally, precision medicine in MDD pharmacotherapy has not been…
Polina Bombina, Kevin R. Coombes
Comparative studies of trajectory inference (TI) methods evaluate complete computational pipelines, making it impossible to isolate how much distortion is introduced specifically by the dimensionality reduction (DR) step. To our knowledge, no study has directly and systematically evaluated how well DR methods alone…
Mirna El Ghosh, Varvara Kalokyri, Maciej Bobowicz, Melanie Sambres + 11 more
Background Semantic interoperability in health care, essential for seamless integration of information systems, is partially achieved through the use of terminologies and common data standards that define the semantic structure of data. Various complexities arise when using real-world health care data, including…
Marie Drottar, Chan-Mi Kim, Howard J. Cabral, Corinna M. Bauer + 1 more
Twenty-one participants with CVI (10 M, 11 F, mean age: 20.19 years, 8.38 standard deviation [s.d.], range: 10-44 years) and 26 controls (10 M, 16 F, mean age: 19.00 years, 5.82 s.d., range: 10-28 years) were enrolled in the study. Participants were recruited using convenience sampling through ties with the greater…
Maria B. Walter Costa, Rose Brouns, Maria Schreiber, Aristeidis Litos + 5 more
Understanding the adaptations of microorganisms to their environment is key to predicting the stability and dynamics of microbial communities. To uncover molecular mechanisms of environmental response, we extracted genomic features from 13,554 prokaryotic isolates, and trained machine learning models to identify which…