An, Sugyun Cho, Si-Young Kang, Junsoo Lee, Soobeom Kim, Hyung-Su Min, Dae-Jin Son, EuiDong Cho, Kwang-Hyun
Published in
Proceedings of the National Academy of Sciences of the United States of America
Cellular senescence is defined as a stable, persistent arrest of cell proliferation. Here, we examine whether senescent cells can lose senescence hallmarks and reenter a reversible state of cell-cycle arrest (quiescence). We constructed a molecular regulatory network of cellular senescence based on previous experimental evidence. To infer the regul...
Aburatani, Sachiyo Ishiya, Koji Itoh, Toshikazu Hayashi, Toshihiro Taniguchi, Takeaki Takaku, Hiroaki
Published in
Bioengineering
Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we applied our network modeling method to infer the regulatory system for triacylglyceride (TAG) biosyn...
Yatabe, Tadaishi Martínez-López, Beatriz Díaz-Cao, José Manuel Geoghegan, Fiona Ruane, Neil M. Morrissey, Teresa McManus, Catherine Hill, Ashley E. More, Simon J.
Published in
Frontiers in Veterinary Science
Cardiomyopathy syndrome (CMS) is a severe cardiac disease of Atlantic salmon caused by the piscine myocarditis virus (PMCV), which was first reported in Ireland in 2012. In this paper, we describe the use of data-driven network modeling as a framework to evaluate the transmission of PMCV in the Irish farmed Atlantic salmon population and the impact...
Nelson, Kristin N Gandhi, Neel R Mathema, Barun Lopman, Benjamin A Brust, James C M Auld, Sara C Ismail, Nazir Omar, Shaheed Vally Brown, Tyler S Allana, Salim
...
Published in
American journal of epidemiology
Patterns of transmission of drug-resistant tuberculosis (TB) remain poorly understood, despite over half a million incident cases worldwide in 2017. Modeling TB transmission networks can provide insight into drivers of transmission, but incomplete sampling of TB cases can pose challenges for inference from individual epidemiologic and molecular dat...
Tal, Ofir Selvaraj, Gopinath Medina, Shlomit Ofaim, Shany Freilich, Shiri
Published in
Microorganisms
Metabolic conversions allow organisms to produce a set of essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Genomic-based metabolic simulations are being increasingly applied for exploring metabolic capacities, considering different environments and differen...
van der Schaft, Arjan
Published in
Annual Review of Control, Robotics, and Autonomous Systems
This article provides a concise summary of the basic ideas and concepts in port-Hamiltonian systems theory and its use in analysis and control of complex multiphysics systems. It gives special attention to new and unexplored research directions and relations with other mathematical frameworks. Emergent control paradigms and open problems are indica...
Ramirez, Daniel Kohar, Vivek Lu, Mingyang
Published in
Frontiers in Molecular Biosciences
Epithelial-mesenchymal transition (EMT) is well established as playing a crucial role in cancer progression and being a potential therapeutic target. To elucidate the gene regulation that drives the decision making of EMT, many previous studies have been conducted to model EMT gene regulatory circuits (GRCs) using interactions from the literature. ...
schilling, jannik tränckner, jens
For the optimization of sewer networks and integration of water management in urban planning, estimations of wastewater discharges at a high spatial resolution are a key boundary condition. In many cases, these data are not available or, for reasons of data protection and company secrecy, the data are not accessible for research purposes. Therefore...
Cao, Xuan Ding, Lili Mersha, Tesfaye B.
Published in
Statistical Applications in Genetics and Molecular Biology
In this study, we conduct a comparison of three most recent statistical methods for joint variable selection and covariance estimation with application of detecting expression quantitative trait loci (eQTL) and gene network estimation, and introduce a new hierarchical Bayesian method to be included in the comparison. Unlike the traditional univaria...
Yatabe, Tadaishi Martínez-López, Beatriz Díaz-Cao, José Manuel Geoghegan, Fiona Ruane, Neil M Morrissey, Teresa McManus, Catherine Hill, Ashley E More, Simon J
Cardiomyopathy syndrome (CMS) is a severe cardiac disease of Atlantic salmon caused by the piscine myocarditis virus (PMCV), which was first reported in Ireland in 2012. In this paper, we describe the use of data-driven network modeling as a framework to evaluate the transmission of PMCV in the Irish farmed Atlantic salmon population and the impact...
