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*  NIGMS 'Visions of the Future' Meeting
... poorly defined protein interactions, rate equations that are not experimentally grounded, and an understatement of the role of ... Integrated public databases and accessible computational packages should be developed, although there is also a need for ... Several participants agreed that mutants should not be the focus of study; rather, mutant genes should only be used to search ... Synthetics could serve as interfaces between cells, in tissue reconstruction efforts. To accomplish these goals, life ...
  https://www.nigms.nih.gov/News/meetings/Pages/NIGMSVisionsFutureMeeting.aspx
*  NLM Informatics Training Conference 2008: Agenda and Abstracts
Additionally, target genes for selected microRNAs molecules were queried using public databases. A growing body of experimental ... Protein fold recognition is an essential task in understanding protein tertiary structure and protein functions. The fold of a ... In addition, we identified genes relevant to lipid metabolism from the literature even in cases where such knowledge was not ... The experimentally validated residue contacts are then included in the network model to enhance its ability to discriminate the ...
  https://www.nlm.nih.gov/ep/trainingconf2009agenda.html
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... genes and reprograms protein translation. Effects of 25OHC on ISR gene expression were independent of liver X receptors and ... Since 2D MR thermometry was used, very limited information about unintended heating in near-field tissue/bone interfaces could ... Similarities were apparent across all databases: mean demographics were close to the mid-size anthropometry, mean BMI was in ... Kinetic models were developed for the cyclooxygenase (COX) and lipoxygenase branches of arachidonic acid metabolism, and then ...
  https://www.jove.com/visualize?author=Dennis%20C%20Ko%20
*  29 | April | 2017 | Breast Cancer-derived Factors Stimulate Osteoclastogenesis
Comparisons of two protein interfaces can detect similarities in amino acid sequences of protein GDC-0449 interfaces (sequence ... Agonists of liver X receptors (LXR) α and β are important regulators of cholesterol metabolism but agonism of the LXRα subtype ... To be able to determine candidate genes necessary for G2 and G2/M development as potential fresh cancer therapeutic focuses on ... The PFAM [17] and SCOP [18] databases are commonly utilized for classification by sequence and structural alignments ...
  http://cylch.org/2017/04/29/
*  Synechocystis - Wikipedia
"A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet ... as well as interaction networks in graphical web interfaces. CyanoBase: Cyanobacteria carry a complete set of genes for ... 2011 experimentally determined in Synechocystis sp. PCC6803 the ideal concentrations of kanamycin, spectinomycin, streptomycin ... domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides phylogenetic trees ...
  https://en.wikipedia.org/wiki/Synechocystis
*  Frontiers | Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity |...
The presence of a high degree of mobile elements in genes central to Thiomargarita's core metabolism has not been previously ... Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group ... However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps ... However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2016.00603/full
*  Philosophy of Systems and Synthetic Biology (Stanford Encyclopedia of Philosophy)
Omics fields allowed for large-scale measurements of co-expression between vast number of genes or associated protein ... 2002). Numerous databases, bio-ontologies, and software tools have been developed, emphasizing the ideals of Open Data and ... Dupré, John, & Maureen A. O'Malley, 2009, "Varieties of Living Things: Life at the Intersection of Lineage and Metabolism", ... These predicted functions have been experimentally demonstrated in living bacteria (Mangan et al. 2003). Moreover, similar and ...
  https://plato.stanford.edu/entries/systems-synthetic-biology/
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... the mRNA level and protein content of genes involved in the lipids metabolism, mTOR signal pathway, and the cell cycle ... HSYA can attenuate experimentally induced airway remodeling and this attenuation may be attributed to suppression of TGF-?1 ... PubMed and EMBASE databases were searched up to October 2013. All prospective cohort studies of nut consumption and risk of CAD ... ACS Appl Mater Interfaces. PUBLISHED: 05-14-2014. Show Abstract Hide Abstract ...
  https://www.jove.com/visualize?author=Fang%20Fang%20
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Ring finger protein 8 (RNF8) and bromodomain testis-specific (BRDT) are two candidate genes associated with spermatogenesis. ... It has been shown that glycolytic metabolism is increased in malignant cells. Cancer cell growth is an energy-related process ... Based on this strategy, we performed VS on NCI and SPECS databases and successfully discovered 6 novel compounds from 15 hits ... Using the model plant Arabidopsis thaliana, a variety of factors involved in UV-B-specific signaling have been experimentally ...
  https://www.jove.com/visualize?author=Jin+Xiao
*  Search | re3data.org
Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the ... InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways ... interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. In each ... Metabolism, Biochemistry and Genetics of Microorganisms (2) * Virology (1) * Medicine (11) * Epidemiology, Medical Biometry, ...
  https://www.re3data.org/search?query=&subjects%5B%5D=201%20Basic%20Biological%20and%20Medical%20Research&keywords%5B%5D=genes
*  TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis | PNAS
Genetic Analysis in Arabidopsis Defines a TIR-Containing, Truncated NLR Protein That Encodes RBA1.. To determine what genes are ... To date, we have been unable to purify RBA1 protein and determine its structure experimentally. To put RBA1 into the context of ... 2011) Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, ... RBA1 was not supported by Col-0 cDNA data and is not expressed in public Affymetrix databases, as is consistent with ...
  http://www.pnas.org/content/114/10/E2053
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
The mitogenome is 16,790?bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 ... Coupling efficiency of 29% for SWG coupler is experimentally achieved. Propagation loss of 11??dB/cm has been experimentally ... In conclusion, adhesives containing DMADDM inhibited the growth, lactic acid production and EPS metabolism of S. mutans biofilm ... Candidate lncRNAs were searched in authorized databases. The significant lncRNAs were identified and confirmed through high- ...
  https://www.jove.com/visualize?author=Cheng-Zhi+Xu
*  FAIRsharing: bsg-s000228: FASTA
Diving into the structure and evolution of protein complex interfaces Evolution of protein-protein Interfaces InterEvol is a ... Eukaryotic Genes euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including ... MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. ... Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of ...
  https://fairsharing.org/bsg-s000228/
*  A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function...
Importantly, analyses of all features from transcript metabolism to functional protein domains were integrated in a highly ... In addition to identifying the transcripts produced by human and mouse genes, fast DB http://www.fast-db.com provides tools for ... Nevertheless, owing to the diversity of the transcriptome, there is a need for interactive databases that provide information ... Therefore, fast DB has achieved an advance in alternative splicing databases by providing resources for the functional ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-180
*  IEEE Computer Society Bioinformatics Conference
Identifying gene and protein names from literature is a critical step for mining functional information of genes and proteins. ... information with existing gene and protein databases. Evaluation on two different corpuses shows that our method achieves ... The first step in the process is to experimentally determine a subset of the probes that have a high affinity to the antibody. ... We have also designed command line, web and custom interfaces for the system. We have named our system HyBrow (from Hypothesis ...
  http://conferences.computer.org/bioinformatics/CSB2003/SectA.html
*  Protocols and Video Articles Authored by Grady E. Carlson (Translated to Chinese)
The protein encoded by one of these genes, YP_003504839, clustered with respiratory arsenate reductases on a phylogenetic tree ... C, Nanomaterials and Interfaces. Feb, 2013 , Pubmed ID: 23814632 We report an electrochemical method for measuring the activity ... Sphingosine kinases (SphKs) catalyze a key step in sphingomyelin metabolism that leads to the production of S1P. There are two ... Literature searches of PubMed, the Cochrane Library, and congress databases were carried out to identify economic evaluations ...
  https://www.jove.com/author/Grady+E._Carlson?language=Chinese
*  Protocols and Video Articles Authored by Peter Nagy (Translated to Norwegian)
Sep, 2014 , Pubmed ID: 25333068 Pathogenic mutations in the three known genes - the amyloid precursor protein (APP), presenilin ... In this review, we discuss how Tomato bushy stunt virus (TBSV) co-opts lipid transfer proteins and modulates lipid metabolism ... The results of the model are experimentally validated and the simulations are further used to study the dependence of ... Two cohorts of patients aged 50-84 years were identified from UK primary care databases: individuals with a first prescription ...
  https://www.jove.com/author/Peter_Nagy?language=Norwegian
*  UW Genome Sciences: past GS Seminars
The majority of current genome annotations is heavily protein coding gene centric. This focus on protein coding genes ... "TDP-43, RNA metabolism, and ALS" October 21 - Dr. Susan Rosenberg. Baylor College of Medicine "How bacteria and cancer cells ... Designing and Mining Pathogen Genome Databases' website. Wed, November 6 - Dr. Anthony Blau, Medicine & Hematology, UW ' ... Molecular engineering of optical and chemical interfaces with biology' flier October 5 - Dr. Alice Berger. Fred Hutchinson ...
  http://www.gs.washington.edu/news/pastseminars.htm
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... osmotic stress genes and ion transport protein genes such as SOS1, AtP5CS1 and AtGSTU5. Overall, our results suggest that ... Positive correlation between variants of lipid metabolism?related genes and coronary heart disease. ... We searched eligible studies in Pubmed, Embase, and Web of Science databases. Six studies with a total of 556 patients were ... In this Letter, we propose and experimentally demonstrate a novel access network architecture using hybrid integrated W-band ...
  https://www.jove.com/visualize?author=Yuan+Fang
*  Laboratory of Functional and Structural Genomics
Protein-protein interaction and pathway databases, a graphical review in Briefings in Bioinformatics ... Abstract: The physico-chemical properties of interaction interfaces have a crucial role in characterization of protein-protein ... The selection of experimentally confirmed modifications is acquired from the latest UniProt and Phospho.ELM databases for ... genes used by viral immune escape mechanisms, and genes particularly expressed after vaccination, since they are more likely to ...
  http://nucleus3d.cent.uw.edu.pl/papers
*  Protocols and Video Articles Authored by Yu-Ju Chen
... with 757 protein-coding genes. A number of marker genes for many diseases have been found in this chromosome, including genetic ... indicating a role of copper ions in the expression of the genes associated with the metabolism of the organism downstream of ... the Journal of Biological Databases and Curation. 2014 , Pubmed ID: 24771658 Protein phosphorylation catalyzed by kinases plays ... The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and ...
  https://www.jove.com/author/Yu-Ju_Chen
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... including 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and 2 control regions. All genes ... This code, experimentally tested in 17 ARPs, predicts the nuclear-cytoplasmic localization of over 150 annotated human ARPs ... and enhancing energy metabolism. The expression level of DsbA-L is negatively correlated with obesity in mice and humans, but ... databases, and Wanfang database by October 2013. We included studies that reported odds ratio (OR) or hazard ratio (HR) with ...
  https://www.jove.com/visualize?author=Shuo-Lin%20Wu%20
*  Protocols and Video Articles Authored by Gaoqing Yang
Importantly, tagSNPs of the selected genes are retrieved for genotyping analyses. All drug-based and protein-protein ... Collectively, we identify Pin1 as a novel PRDX1 binding protein and propose a mechanism for Pin1 in regulating the metabolism ... An experimentally generated, pancreas-specific gene expression signature of Wnt/β-catenin transcriptional activation was used ... Methods: We searched the Cochrane Library, PubMed, Embase, Web of Science and Chinese databases (Chinese BioMedical Literature ...
  https://www.jove.com/author/Gaoqing_Yang
*  Macromolecular crystallography and structural biology databases at NIST. - Free Online Library
Macromolecular crystallography and structural biology databases at NIST.(National Institute of Standards and Technology) by ' ... The protein is likely to be an ATP-dependent regulator of peptidoglycan metabolism given the distribution of conserved residues ... and at both interfaces, were constructed. At [[alpha].sub.1][[beta].sub.2]/[[alpha].sub.2][[beta].sub.1]-interface [beta]Cys93 ... in the absence of cAMP it is able to express genes that normally require cAMP. The structural analysis revealed the two alanine ...
  https://www.thefreelibrary.com/Macromolecular+crystallography+and+structural+biology+databases+at+...-a086041906
*  Protocols and Video Articles Authored by Jianrong Li (Translated to Arabic)
... genes: biological functions (BP), protein interaction modeling, and protein domain implicated in the disease-associated ... An experimentally validated two-dimensional finite element model representing the adult male human head was used. The model ... Integration of Curated Databases to Identify Genotype-phenotype Associations BMC Genomics. 2006 , Pubmed ID: 17038185 The ... Ceramide, a bioactive sphingolipid pivotal to sphingolipid metabolism pathways, regulates cell death in response to diverse ...
  https://www.jove.com/author/Jianrong_Li?language=Arabic