The coupling of the cell cycle to the circadian clock results in the synchronization of these two important cellular rhythms. Gérard C & Goldbeter A (2009) Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle.
Human brain origin and the evolution of regulatory and coding regions of protein-coding genes expressed in brain
Phylogram representing the evolution of the Hominidae, branch length shows the excess (in %) of evolutionary cases with a decrease in TBP affinity for the TATA box relative to cases with an increase in activity. 2008) A stepwise model of TBP/TATA box binding enables prediction of human hereditary diseases using single nucleotide polymorphism, Dokl.
Evolution of regulatory interactions in bacteria
A quantitative systems biology study on a model bacterium
HOST-PATHOGEN INTERACTIONS
Model based analysis of interferon induced apoptosis
Reverse engineering infection diseases: towards a virtual patient
Homeostasis and adaptation� Towards a trade-offs model
Optimization of combined treatment (interferon, ribavirin, protease or polymerase inhibitors) for hepatitis C virus�
Understanding molecular mechanisms of HCV patients
Type-I Interferon response is controlled by multi-layered stochasticity
Rand et al., Multilayered stochasticity and paracrine signal propagation shape the type I interferon response.
SysPatho: Systems biology of Host-Pathogen Interactions
Modeling and visualization of the spatio-temporal dynamics immune processes in lymphoid organs
The authors thank the financial support of the Russian Foundation for Basic Research and the program \Fundamental Research in Medicine» of the Russian Academy of Sciences.
Tracking and Registration for Live Cell Image Analysis
2009 ) Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection. Reiss S, Rebhan I, Backes P, Romero-Brey I, Erfle H, Matula P, Kaderali L, Poenisch M, Blankenburg M, Hiet MS, Longerich T, Diehl S, Ramirez F, Balla T, Rohr K, Kaul A, Bühler S, Pepperkok R, Lengauer T, Albrecht M, Eils R, Schirmacher P, Lohmann V and Bartenschlager R. 2011) Recruitment and activation of a lipid kinase by NS5A of hepatitis C virus is essential for the integrity of the membranous replication compartment , Cell Host & Microbe 9:1, 32-45.
Robust transcriptomic data analysis across individuals
Computer analysis of 3D chromosome contacts mediated by RNA Pol II in human
Computer analysis of 3D chromosome contacts mediated by RNA Pol II in humans. to chromatin-bound contact sites. Our study reveals the three-dimensional basis of gene transcription activity and raises new bioinformatics challenges for modeling transcriptional regulation.
Computational study of protein-protein interaction networks
High-throughput analysis of human transpositional landscape
Walking pathways” and how promoters can help to find new drugs
Such personalized networks are analyzed to find key nodes – the most important nodes that trigger the disease. Topological modeling of the signal transduction network upstream of these transcription factors revealed key nodes—powerful master regulators of the cell survival program that prevent efficient apoptosis of cancer cells.
COMPUTATIONAL AND ExPERIMENTAL SYSTEMS APPROACHES
Complex molecular interactions as determinants of disease outcome and therapy response
One of the main features of a systems approach is the emphasis on the vertical (both down-top and top-down) causality in the multilevel systems to which all the biological objects belong. Among these two, top-down causation (TDC) is a modern incarnation of the ancient holistic tradition of developmental biology.
Dioxin in regulation of the genes involved in the cytokine
Motivation and Objectives: ChIP-Seq data analysis requires tools to identify transcription factor (TF) binding sites (BS). Identification of TFBS from initial ChIP-Seq data was performed with SiteGA and diPWM models with selected recognition thresholds.
Modelling Vascular Morphogenesis
From Targets to Human: Engineering of Biotherapeutics
Application of systems pharmacology modeling in drug development
PK properties optimization for Transglutaminase-2 inhibitor as a potential drug for celiac disease treatment
Exploring ensemble properties of serum antibody binding
Mathematical modeling and analysis of antibody reactivity data
Modeling of celiac disease immune response and therapeutic effect of potential drugs�
Mechanistic modeling approach relating human gut microbial community to physiologically-relevant biomarkers
Therapy of chronic myeloid leukaemia: simulation studies of different treatment combinations and patient-specific risk
Google goes cancer: Improving outcome prediction for cancer patients by network based ranking of marker genes
Dissecting cancer heterogeneity
Combinatorial and Dynamic Control Logic within pathogen- responsive Gene Regulatory Networks
Systems-biology approaches to understanding network functions of the human brain
The microRNA determine the early stage dynamics of the regulation network
Towards understanding of apoptosis regulation by systems biology
Using data-driven models of feedback regulation in EGFR signal transduction to predict optimal targeted therapy in colon cancer
Architecture and Dynamics of the Mitochondrial Reticulum in Healthy Systems and in Age-Related Disorders
Specificity and flexibility of RAS-ERK signalling by slow and fast loops
Designing biocomputing devices based on RNA-RNA interactions
POSTER SESSION
Modeling and analysis of dynamics of the gene networks: automatic generation and storage in a new database
Funding: This work was partially supported by the RFBR а], by the "PATHOSYS" grant [260429] of the Seventh Framework Program, by the Interdisciplinary Integration Projects of the Siberian Department of the Russian Academy of Sciences [80]. This study was also partially supported by the scientific school and the programs of the Presidium RAS "Molecular and cell biology" (6.8) as well as "Biological diversity" (30.29).
Comprehensive analysis and computational modeling of microtubule regulation in neuromorphogenesis
Examples of the use of the system are demonstrated in a modeling of several gene regulatory networks.
The Virtual Liver Network - an overview
Systems Biology of Lung Cancer – Linking Dynamic Properties of Signaling Networks to Migratory Behavior of Lung Carcinoma Cells
To reveal the main regulatory mechanisms that promote early proliferation and to establish a quantitative link of information processing through signaling networks, induction of target genes and migration of lung cancer cells, we examined in monolayer cultures of selected cell lines of NSCLC adenocarinoma HGF-mediated signal transduction and target induction. genes, as well as cellular decisions such as proliferation, migration and apoptosis at the level of the cell population. Quantitative data obtained from quantitative immunoblotting, mass spectrometry, quantitative real-time PCR, and NGSeq were used to create detailed mechanistic models of signaling pathways that will be linked to gene regulatory network models and correlated with responses cellular.
Genetic based method for discrimination of lipoproteins level in citizens of North-West region of Russia
We believe that the use of HDL and LDL level regression model would become the appropriate tool for medical genetic research.
Novel insights into epidermal tissue repair using 3D tissue cultures
Our results clarify a long-standing question by demonstrating for the first time a consistent experimental and theoretical model for epidermal wound closure in 3D. Furthermore, epidermal wound closure appears to be not simply an example of collective cell migration, but is instead a complexly regulated 3D phenomenon.
Model of gap gene expression in Drosophila embryo based on telegraph equation
1Ioffe Physical Technical Institute of the Russian Academy of Sciences, St. The connectionist equations provide a general framework for modeling gene regulation at the mesoscopic level of detail [1]. 2006) Quantitative and predictive model for transcriptional control of the Drosophila melanogaster gene, Nature Genetics.
Integration of protein-protein interactions and RNAI screens for
Most methods in this category identify a series of genes known as Seed or Core genes. Both methods use one of the information sources (PPI or RNAi) as the true information source and try to reconcile the differences by filtering the other source.
Automatic Segmentation of Liver from Computed Tomography Examinations
In the second step, the inner region of the initial estimated area is used to generate a set of seed points for a region-growing algorithm using zero-level sets. Reconstruction of the associative genetic networks based on the integration of automated text-mining methods and protein-ligand.
Reconstruction of the associative genetic networks based on integration of automated text-mining methods and protein-ligand
The aim of this work was a development of the integrated computer system for the reconstruction of associative genetic networks based on interactive analysis of scientific literature and prediction of protein-ligand interactions. Conclusion: Developed system can be used by experts for the acceleration of genetic networks reconstruction process, as well as in the other fields of science related to automated analysis of the scientific texts.
Associative network discovery system (ANDSYSTEM): automated literature mining tool for extracting relationships between diseases,
For example, with the ANDSystem, networks of molecular and genetic interactions of proteins from Helicobacter pylori, differentially expressed in different strains isolated from patients with chronic gastritis and gastric tumors, were reconstructed and analyzed. On the example of establishing interactions between human proteins and proteins of hepatitis C virus, a high accuracy of the method of knowledge extraction from texts was shown.
A stochastic model for suppression of subgenomic hepatitis C virus replication in Huh-7 cells
Disregarding the stochasticity of viral RNA replication-degradation, the model can still describe the experimental kinetics during the first few days of inhibitor action, when the cellular concentration of viral RNA is quite high (≥ 20 RNA molecules/cell). Computational analysis of the model demonstrates that the stochastic nature of subgenomic HCV replicon and drug-resistant mutant replicon replication in cells is necessary to explain the experimentally observed biphasic reduction of viral RNA in the presence of inhibitors. 2007).
Improved differential evolution entirely parallel method
A descendant replaces its parent if the value of the quality functional for the descendant parameter set is less than the value for the parent. We compared the performance of ImDEEP with the original method and state-of-the-art optimization techniques such as Evolutionary Strategy (ES).
Modeling of gap gene expression in Drosophila Kruppel mutants
Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, so here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants . The successful modeling of the quantitative aspects of gap gene expression in the mutant for the trunk gap gene Kr is a major achievement of this work.
Detecting Non-Uniform Clusters in Large Scale Interaction Graphs
This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for failed attempts at mutant simulations. Role of the Mad2 dimerization interface in supporting the Spindle Assembly Checkpoint independently of kinetochores.
Role of the Mad2 dimerization interface in supporting the Spindle Assembly Checkpoint independently from kinetochores
This dissimilarity function satisfies the triangle inequality which enables the natural embedding of the graph in an n-dimensional metric space. Our results indicate that away from kinetochores, the dimerization surface is required for the stabilization of the final product of the pathway, the Mitotic Checkpoint Complex.
Identifiability analysis and predictive power of the gene circuit model
To analyze the putative pathway downstream of the kinetochore, we used two complementary approaches: we activated the SAC ectopically and independently of the kinetochore, and genetically separated the kinetochore-dependent and -independent groups of Mad2. In addition, the requirement for high values of the measures presented in this work can be used as a necessary condition in finding model solutions to ensure high predictive power.
Multiscale modelling of trail therapy applied to multicellular spheroids
The dynamics of the apoptosis pathway is influenced by the extracellular concentration of TRAIL that is described by a reaction-diffusion equation. TRAIL-induced tumor cell death is initiated if the intracellular concentration of active caspase 3 exceeds a death threshold.
Heuristic optimization method for inverse problem solving
In our simulations, we aim to answer the question of how the interplay of cellular heterogeneity together with spatial heterogeneity affects drug efficacy.
Different models of diffusion, related to the equation of the Jeffreys type
The Jeffreys-type equation was proposed to describe transport in rheological (non-Newtonian) media [3]. In this article, we consider and investigate different transport models related to the Jeffreys-type equation.
Mathematical modeling of metformin influence on oncogenesis in SHR mice
This equation generalizes the diffusion equation, takes into account the non-locality of transport both in time and in space (time delay and inertia of molecules). We show that these models are qualitatively different and describe different modes of transport (diffusion).
FDR is the d-risk
Epidemiological data on the relationship of caloric intake, energy balance and weight gain over life span and morbidity, J Gerontol A Biol Sci Med Sci Overweight, obesity and cancer mortality in a prospectively studied cohort e-mail: tatiana @inm.ras.ru. Although the critical constants of both tests for the α =0.05 level are almost identical, the values of the second type of hazards d are fundamentally different.
MODELING of aggregation of TAU proteins: system pharmacology approach�
Our analysis highlights the multifactorial nature of the disease and provides insight into pathological mechanisms of tau-mediated aggregation diseases, including Alzheimer's.
Quantitative characterization of the segmentation gene expression in Drosophila gap mutants
Novel method of CNV analysis in FcγR locus and its application to immune-related diseases
The power of meta-analysis of RNA-seq datasets for eQTL
Our study shows that different types of RNA-seq datasets can be well combined and that RNA-seq meta-analysis is a logical step forward to gain better insight into the genetic regulation of gene expression variation .
Use of mechanism-based mathematical modeling for biological target selection and antibody drug specifications in pharma
Use of mechanism-based mathematical modeling for biological target selection and antibody drug specifications in pharmacy. Through its application, we demonstrate that mechanism-based PK/PD binding models are useful for predicting human response to biological compounds.
INDEx
Proceedings of the SysPatho workshop
Systems Biology and Medicine»