Published in eLife
Mapping all the cells and nerve connections in the mouse brain is a major goal of the neuroscience community, as this will provide new insights into how the brain works and what happens during disease. To achieve this, researchers must first capture three-dimensional images of the brain. These images are then processed using computational tools tha...
Published in Briefings in bioinformatics
Biological systems function through dynamic interactions among genes and their products, regulatory circuits and metabolic networks. Our development of the Pathway Tools software was motivated by the need to construct biological knowledge resources that combine these many types of data, and that enable users to find and comprehend data of interest ...
Published in Antibiotics
Clavulanic acid (CA) is an irreversible β-lactamase enzyme inhibitor with a weak antibacterial activity produced by Streptomyces clavuligerus ( S. clavuligerus ). CA is typically co-formulated with broad-spectrum β‑lactam antibiotics such as amoxicillin, conferring them high potential to treat diseases caused by bacteria that possess β‑lactam resis...
Published in Frontiers in Genetics
Background: Prostate cancer (PCa) is occurred with increasing incidence and heterogeneous pathogenesis. Although clinical strategies are accumulated for PCa prevention, there is still a lack of sensitive biomarkers for the holistic management in PCa occurrence and progression. Based on systems biology and artificial intelligence, translational info...
Published in Frontiers in Immunology
The Pediatric Acute Liver Failure (PALF) study is a multicenter, observational cohort study of infants and children diagnosed with this complex clinical syndrome. Outcomes in PALF reflect interactions among the child’s clinical condition, response to supportive care, disease severity, potential for recovery, and, if needed, availability of a suitab...
Biomedical data are usually analyzed at the univariate level, focused on a single primary outcome measure to provide insight into systems biology, complex disease states, and precision medicine opportunities. More broadly, these complex biological and disease states can be detected as common factors emerging from the relationships among measured va...
Published in Frontiers in Cell and Developmental Biology
B-cells are the poster child for cellular diversity and heterogeneity. The diverse repertoire of B lymphocytes, each expressing unique antigen receptors, provides broad protection against pathogens. However, B-cell diversity goes beyond unique antigen receptors. Side-stepping B-cell receptor (BCR) diversity through BCR-independent stimuli or engine...
Published in Patterns
Tomic et al. developed SIMON, an open-source software for application of machine learning algorithms to high-dimensional biomedical data ranging from the transcriptome to flow cytometry to the microbiome. Using a graphical user interface, standardized pipelines for predictive modeling, and automated machine learning, SIMON empowers non-technical bi...
Published in Frontiers in Genetics
Dynamics of cell fate decisions are commonly investigated by inferring temporal sequences of gene expression states by assembling snapshots of individual cells where each cell is measured once. Ordering cells according to minimal differences in expression patterns and assuming that differentiation occurs by a sequence of irreversible steps, yields ...
Published in Frontiers in Microbiology
Present in many industrial effluents and as common degradation product of organic matter, phenol is a widespread compound which may cause serious environmental problems, due to its toxicity to animals and humans. Degradation of phenol from the environment by mesophilic bacteria has been studied extensively over the past decades, but only little is ...
