Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis

in Acta Neuropathologica Communications (2020)

SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies

in Bioinformatics (2019)

Assessment of network module identification across complex diseases

in Nature Methods (2019)

Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks

in Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks (2019)

Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain

in Cell (2019)

Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapy

in Trends in Biotechnology (2019)

A general computational approach to predicting synergistic transcriptional cores that determine cell subpopulation identities

in Nucleic Acids Research (2019)

Modeling of Cellular Systems: Application in Stem Cell Research and Computational Disease Modeling

Book published by Springer International Publishing (2018)

The large-scale development of high-throughput sequencing technologies has allowed the generation of reliable omics data at different regulatory levels. Integrative computational models enable the ... [more ▼]

The large-scale development of high-throughput sequencing technologies has allowed the generation of reliable omics data at different regulatory levels. Integrative computational models enable the disentangling of a complex interplay between these interconnected levels of regulation by interpreting these large quantities of biomedical information in a systematic way. In the context of human diseases, network modeling of complex gene-gene interactions has been successfully used for understanding disease-related dysregulations and for predicting novel drug targets to revert the diseased phenotype. Furthermore, these computational network models have emerged as a promising tool to dissect the mechanisms of developmental processes such as cellular differentiation, transdifferentiation, and reprogramming. In this chapter, we provide an overview of recent advances in the field of computational modeling of cellular systems and known limitations. A particular attention is paid to highlight the impact of computational modeling on our understanding of stem cell biology and the complex multifactorial nature of human diseases and their treatment. [less ▲]

Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease

in Frontiers in Physiology (2018)

Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift

in Nature Communications (2018)