Results 21 to 30 of about 1,232,205 (304)
Studying stochastic systems biology of the cell with single-cell genomics data
bioRxiv, 2023 Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule ...
Gennady Gorin +2 more
semanticscholar +1 more source
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology
IEEE/ACM Transactions on Computational Biology & Bioinformatics, 2022 Biological processes are often modelled using ordinary differential equations. The unknown parameters of these models are estimated by optimizing the fit of model simulation and experimental data. The resulting parameter estimates inevitably possess some
A. F. Villaverde +3 more
semanticscholar +1 more source
iScience, 2021 Summary: Nanoneuromedicine investigates nanotechnology to target the brain and treat neurological diseases. In this work, we biofabricated heterocellular spheroids comprising human brain microvascular endothelial cells, brain vascular pericytes and ...
Murali Kumarasamy, Alejandro Sosnik
doaj +1 more source
Tiglon enables accurate transcriptome assembly via integrating mappings of different aligners
iScience, 2022 Summary: Full-length transcript reconstruction has a pivotal role in RNA-seq data analysis. In this research, we present a new genome-guided transcriptome assembly algorithm, namely Tiglon, which integrates multiple alignments of different mapping tools ...
Xiaoyu Zhao, Ting Yu
doaj +1 more source
Flexible experimentation in the modeling and simulation framework JAMES II--implications for computational systems biology [PDF]
Briefings in Bioinformatics, 2010 Dry-lab experimentation is being increasingly used to complement wet-lab experimentation. However, conducting dry-lab experiments is a challenging endeavor that requires the combination of diverse techniques. JAMES II, a plug-in-based open source modeling and simulation framework, facilitates the exploitation and configuration of these techniques.
Roland Ewald +4 more
openaire +2 more sources
iScience, 2023 Summary: To gain deeper insights into transcriptomes and epigenomes of organoids, liver organoids from two states (expandable and more differentiated) were subjected to single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) analyses ...
Jong-Hwan Kim +4 more
doaj +1 more source
Reproducibility in systems biology modelling
bioRxiv, 2020 The reproducibility crisis has emerged as an important concern across many fields of science including life science, since many published results failed to reproduce.
Krishna Tiwari +13 more
semanticscholar +1 more source
iScience, 2020 Summary: The derivation of endoderm and descendant organs, such as pancreas, liver, and intestine, impacts disease modeling and regenerative medicine.
Michael A. Bukys +7 more
doaj +1 more source
Frontiers in Pharmacology, 2022 Type 2 diabetes mellitus (T2DM) is a heterogeneous disease with numerous abnormal targets and pathways involved in insulin resistance, low-grade inflammation, oxidative stress, beta cell dysfunction, and epigenetic factors. Botanical drugs provide a large chemical space that can modify various targets simultaneously.
Yassin Ismail +7 more
openaire +3 more sources
The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models [PDF]
, 2012 LetterThis is the final version of the article. Available from SAGE Publications via the DOI in this record.Time-dependent light input is an important feature of computational models of the circadian clock.
Adams, RR +8 more
core +1 more source