A5007497613- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Neuroscience and Neuropharmacology Research
- Microbial Metabolic Engineering and Bioproduction
- Advanced Database Systems and Queries
- Photoreceptor and optogenetics research
- Data Management and Algorithms
- Cardiomyopathy and Myosin Studies
- Distributed and Parallel Computing Systems
- Advanced Computational Techniques and Applications
- Thyroid Cancer Diagnosis and Treatment
- Parallel Computing and Optimization Techniques
- Retinal Development and Disorders
- T-cell and B-cell Immunology
- Genomics and Chromatin Dynamics
- Ferroptosis and cancer prognosis
- Signaling Pathways in Disease
- Alzheimer's disease research and treatments
- Semantic Web and Ontologies
- Photochromic and Fluorescence Chemistry
- Cell Image Analysis Techniques
- Medicinal Plants and Neuroprotection
- Microtubule and mitosis dynamics
- Escherichia coli research studies
- Salmonella and Campylobacter epidemiology
University of Michigan–Ann Arbor
2021
Central China Normal University
2021
Allen Institute
2015-2020
Babraham Institute
2017-2020
Zhejiang University
2019-2020
Allen Institute for Brain Science
2015-2020
Sun Yat-sen Memorial Hospital
2020
Sun Yat-sen University
2020
Shanghai Center for Brain Science and Brain-Inspired Technology
2020
University of Wisconsin–Madison
2019
Abstract Background Quantitative models of biochemical and cellular systems are used to answer a variety questions in the biological sciences. The number published quantitative is growing steadily thanks increasing interest use as well development improved software availability better, cheaper computer hardware. To maximise benefits this body models, field needs centralised model repositories that will encourage, facilitate promote dissemination reuse. Ideally, stored these should be...
Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), repository for mathematical models, was established 2005. The current allows submission of models encoded diverse formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. submitted are curated verify the computational...
Summary To understand how the brain processes sensory information to guide behavior, we must know stimulus representations are transformed throughout visual cortex. Here report an open, large-scale physiological survey of neural activity in awake mouse cortex: Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical from nearly 60,000 neurons collected 6 areas, 4 layers, and 12 transgenic lines 221 adult mice, response a systematic set stimuli. Using...
NMDA receptor dependent long-term potentiation (LTP) and depression (LTD) are two prominent forms of synaptic plasticity, both which triggered by post-synaptic calcium elevation. To understand how selectively stimulates opposing processes, we developed a detailed computational model performed simulations with different input frequencies, amplitudes, durations. We show that total amount ions kept constant, high frequencies pulses stimulate calmodulin more efficiently. Calcium activates...
Abstract Neurons have complex dendritic trees, receiving numerous inputs at various distances from the cell body. Yet rules of molecular signal propagation dendrites to nuclei are unknown. DARPP-32 is a phosphorylation-regulated signalling hub in striatal output neurons. We combine diffusion-reaction modelling and live imaging investigate cAMP-activated nucleus. The model predicts maximal effects on nucleus cAMP production secondary dendrites, due segmental decrease dendrite diameter....
Anaplastic thyroid carcinoma (ATC) is one of the most aggressive and rapidly lethal tumors. However, limited advances have been made to prolong survival reduce mortality over last decades. Therefore, identifying master regulators underlying ATC progression desperately needed. In our present study, three datasets including GSE33630, GSE29265, GSE65144 were retrieved from Gene Expression Omnibus with a total 32 samples 78 normal tissues. A 1804 consistently changed differentially expressed...
ARPP-16, ARPP-19, and ENSA are inhibitors of protein phosphatase PP2A. ARPP-19 phosphorylated by Greatwall kinase inhibit PP2A during mitosis. ARPP-16 is expressed in striatal neurons where basal phosphorylation MAST3 inhibits regulates key components signaling. The ARPP-16/19 proteins were discovered as substrates for PKA, but the function PKA unknown. We find that or mutually suppresses ability other to act on ARPP-16. Phosphorylation also acts prevent inhibition MAST3. Moreover,...
Calmodulin sits at the center of molecular mechanisms underlying learning and memory. Its complex sometimes opposite influences, mediated via binding to various proteins, are yet be fully understood. Calcium/calmodulin-dependent protein kinase II (CaMKII) calcineurin (CaN) both bind open calmodulin, favoring Long-Term Potentiation (LTP) or Depression (LTD) respectively. Neurogranin binds closed conformation calmodulin its impact on synaptic plasticity is less clear. We set up a mechanistic...
CellML and SBML are XML-based languages for storage exchange of molecular biological physiological reaction models. They use very similar subsets MathML to specify the mathematical aspects CellML2SBML is implemented as a suite XSLT stylesheets that, when applied consecutively, convert models expressed in into without significant loss information. The converter based on most recent stable versions (CellML version 1.1; Level 2 Version 1), used adheres 1.0 specification. Of all 306 repository...
This paper discussed a rarely touched topic for XML database: how to control the size of index. Compared relational database and object- oriented database, has relatively larger index due recording element address structure information. A solution is proposed: granular
We present XPDL, a modular, extensible platform description language for heterogeneous multicore systems and clusters. XPDL specifications provide metadata about hardware installed system software that are relevant the adaptive static dynamic optimization of application programs settings improved performance energy efficiency. is based on XML uses hyperlinks to create distributed libraries specifications. also first components retarget able tool chain browses processes specifications,...
Background Unlike papillary thyroid cancer (PTC), anaplastic carcinoma (ATC) is extremely aggressive and rapidly lethal without effective therapies. However, the differences of master regulators regulatory networks between PTC ATC remain unclear. Methods: Three representative datasets comprising 32 ATC, 69 PTC, 78 normal tissue samples were combined to form a large dataset. Differentially expressed genes (DEGs) identified enriched by limma package gene set enrichment analysis, respectively....
Background: The human body has natural defenses against viruses. During the virus infection, as a self-protective mechanism, immune cells and other will secrete amount of antiviral cytokines to promote host clear microorganism, with multiple mechanisms such alteration major histocompatibility complex (MHC) molecules, activation cellular responses involving killer (NK cells) cytotoxic lymphocytes (CTLs), production proteins antibodies. Natural products traditional pharmaceutical sources for...
Abstract Calmodulin sits at the centre of molecular mechanisms underlying learning and memory. Its complex, sometimes opposite influences, via binding to various proteins, are yet be fully understood. Calcium/calmodulin-dependent protein kinase II (CaMKII) calcineurin (CaN) both bind open calmodulin, favouring Long-term potentiation (LTP) or depression (LTD) respectively. Neurogranin binds closed conformation calmodulin its impact on synaptic plasticity is less clear. We set up a mechanistic...
XPDL is a modular, extensible platform description language for heterogeneous multicore systems and clusters. models provide metadata about hardware installed system software that are relevant adaptive static dynamic optimizations of application programs settings improved performance energy efficiency. based on XML uses hyperlinks inheritance to create distributed libraries models. We also retargetable toolchain browses processes generates driver code microbenchmarking bootstrap empirical at...
In view of the current problems in credit evaluation systems provided by C2C E-commerce, this paper analyzes three main aspects that influence seller's credit, and then build a new seller index system. On basis this, multi-index linguistic method based on assessment information is proposed using LWD operator LOWA operator. Finally, an example used to illustrate use method.
Abstract The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability formats recurring issue in Systems Biology. Although there are various tools available convert models from one format another, most of them have been independently developed and cannot easily be combined, specially support for more written Java can used as standalone executable. This collaborative project we hope developers...