*  Application of Atlas of Cancer Signalling Network in preclinical studies, Briefings in Bioinformatics | 10.1093/bib/bby031 |...
... call-out with links to external databases, citations and ACSN maps of and functional modules where MYC protein is found); (C) ... 5) Components of the Wnt and Notch pathways are negatively regulated by miRNAs induced by the p53 family (p53, p63 and p73). ... In addition, pathway browsing interfaces are becoming more important for cancer researchers and clinicians but require further ... For this purpose, comprehensive signalling network maps covering simultaneously multiple cellular processes are more suitable ...
  https://www.deepdyve.com/lp/ou_press/application-of-atlas-of-cancer-signalling-network-in-preclinical-md5Mc9SJJO
*  MetNet Online: a novel integrated resource for plant systems biology | BMC Bioinformatics | Full Text
Pathways are enriched with known or predicted information on sub cellular location. MetNet Online enables pathways, ... interactions and entities to be browsed or searched by multiple categories such as sub cellular compartment, pathway ontology, ... The study of plant biological pathways is advanced by easy access to integrated data sources. Today, various plant data sources ... obtained via manual curation and/or information from external databases) overlays the pathways. Third, a protein-protein ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-267
*  Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research...
... protein interactions or cellular pathways [49]. BRIDE supports access via a web browser client [50]. This type of integration ... Philippi S. Light-weight integration of molecular biological databases. Bioinformatics. 2003;20(1):51-7.View ArticleGoogle ... The tiers of the platform communicate through interfaces. Therefore, as long as the interface remains stable, the internals can ... Protein biosynthesis in low dose ionizing radiation-adapted human melanoma cells. J Radiat Res. 1996;37(3):161-9.View Article ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1068-8
*  Frontiers | Expression, Localization of SUMO-1, and Analyses of Potential SUMOylated Proteins in Bubalus bubalis Spermatozoa |...
Protein sumoylation was recently demonstrated in human and rodent spermatozoa, with potential consequences for sperm motility ... Protein sumoylation was recently demonstrated in human and rodent spermatozoa, with potential consequences for sperm motility ... The details of the TPR PPIs (Figure 10A) and pathways reported by STRING are described in Table 3. The second protein reported ... Plot describing the distribution of protein Sub-cellular localization [SCL] predicted by iLoc-Animal and iLoc-Euk tools. [C]: ...
  https://www.frontiersin.org/articles/10.3389/fphys.2017.00354/full
*  ISMB 2008
InterPro integrates data from ten signature databases and five structural databases, providing information on protein families ... and NCBI EntrezGene and PubMed to form a network of applications linking protein interactions, pathways data and literature ... It integrates the context (e.g., modular activity) and the hierarchical organization of cellular agents (e.g., molecules and ... different research centres have been exposed with a variety of programmatic interfaces. The unified presentation and ...
  http://www.iscb.org/cms_addon/conferences/ismb2008/techtrack.php
*  Abhishek Tiwari:INTERACTOMICS - OpenWetWare
... and protein interactions play a key role in many cellular processes; in particular, the distortion of protein interfaces may ... Modularity exists in a variety of biological contexts, including protein complexes, metabolic pathways, signaling pathways, and ... this review we describe different experimental techniques of protein interaction identification together with various databases ... Deciphering Protein-Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners ...
  https://openwetware.org/wiki/Abhishek_Tiwari:INTERACTOMICS
*  Patent US7356416 - Method and system for automated inference creation of physico-chemical ... - Google Patents
Methods and system for automated inference of physico-chemical interaction knowledge from databases of term co-occurrence data ... interactions with co-occurrence analysis of indexed literature databases that can be used to determine biological pathways. ... A number of well-established protein-protein interactions are included; and (3) American Association for the Advancement of ... ions and other cellular components. New compounds that may look promising at a nucleotide level may be toxic at a cellular ...
  http://www.google.com/patents/US7356416?dq=KOI-18
*  Cover Pages: CellML
... while Physiome developed XML-based descriptions of cellular and subcellular process, including biochemical pathways." ... In Silico Cell interfaces with powerful software tools to create a unique software environment that enables the rapid ... CellML is expected to enable scientists to more effectively manage and interpret gene and protein data and apply it to study ... At its core is the proprietary In Silico Cell system, which links mathematical tools, annotated biological databases and an XML ...
  http://xml.coverpages.org/cellML.html
*  FGF9 Gene - GeneCards | FGF9 Protein | FGF9 Antibody
Protein Coding), Fibroblast Growth Factor 9, including: function, proteins, disorders, pathways, orthologs, and expression. ... Structure of fibroblast growth factor 9 shows a symmetric dimer with unique receptor- and heparin-binding interfaces. (PMID: ... Search for latest publications for FGF9 gene in PubMed and other databases ... Molecular and cellular biology 1993) 2 3 4 22 60 ... Genes that share pathways with FGF9: view Pathways by source ...
  http://www.genecards.org/cgi-bin/carddisp.pl?id_type=entrezgene&id=2254
*  World Community Grid - News & Media
This protein, therefore, would be a possible target for developing drugs with few side effects. About the Proteinworld Database ... This comparison allows scientists to correct errors and fill gaps in the functional annotations in international databases that ... and interfaces for access.. For the Oswaldo Cruz Foundation, participate the Laboratory of Functional Genomics and ... which contain the genetic information for the synthesis of the cellular proteins. The more scientists study and decipher ...
  https://www.worldcommunitygrid.org/newsletter/09Q2/viewProjects.do?utm_source=email&utm_medium=email&utm_campaign=09q2newsletter
*  A convex optimization approach for identification of human tissue-specific interactomes
... which consolidates protein interactions from different databases. Edges in this dataset are weighted using an MI (MINT-Inspired ... However, we observed direct interaction between GSK3B and SNCA, and parallel pathways connecting it to LRRK2 via SNCA and MAPT ... 2015) Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types. Gen. Med ... Perturbations that impact interacting interfaces of proteins are significantly enriched among tissue-specific, disease-causing ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC4908329/
*  From Sight to Insight: Visualization tools yield biomedical success stories | Biomedical Computation Review
Scores of protein-protein and protein-DNA interactions already abound in databases. But sifting through this information is ... MetNet3D can organize the elements into pathways or by sub-cellular compartments, and users can modify their colors and edges ... Because it uses three open-source application program interfaces, MetNet3D can run on a variety of virtual reality and ... particular biochemical pathways or protein complexes in the cell that connect the genes that are upor down-regulated together.' ...
  http://www.bcr.org/content/sight-insight-visualization-tools-yield-biomedical-success-stories
*  Biomedical Science - BSc (Hons) - Canterbury - The University of Kent
B. Protein Bioinformatics Methods Protein structure and function prediction. Prediction of binding sites/interfaces with small ... Intracellular signalling pathways: activation of monomeric G-protein Ras, leading to activation of the mitogen activated ... Roles in specific cellular responses e.g. regulation of protein kinase C. ... Databases and data availability. Using sequence data for analysis sequence searching methods, multiple sequence alignments, ...
  https://www.kent.ac.uk/courses/undergraduate/263/biomedical-science
*  Neuroinformatics - Wikipedia
BIRN allows combining databases, interfaces and tools into a single environment. Budapest Reference Connectome is a web-based ... protein pathways), Data from organs and systems (visual cortex, perception, audition, sensory system, pain, taste, motor system ... Neuroscience provides the following types of data and information on which neuroinformatics operates: Molecular and cellular ... The project involves: Databases: 3D reconstructed model neurons, synapses, synaptic pathways, microcircuit statistics, computer ...
  https://en.wikipedia.org/wiki/Neuroinformatics
*  List of Accepted Software Demos
SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics). Olga Krebs, Scientific Databases and ... Also, synonymous protein entries in other databases are returned. It also contains E-values, similarity scores as the Smith- ... 5] Rives,A.W. and Galitski,T. (2003) Modular organization of cellular networks. Proc. Natl. Acad. Sci. U S A, 100, 1128-1133.. ... REST interfaces for automated database queries, novel functionality for the gene expression warehouse and advanced data ...
  http://www.eccb06.org/new_pages/program/accepted_sw.html
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
A large-scale identification of cellular partners of a pathogen protein is performed by mating-based yeast two-hybrid ... We begin with a user-guide for similarity search tools via online interfaces as well as local executables. Next, we explore ... can be coupled to automated high-throughput small interfering RNA screens in order to characterize cellular signaling pathways ... and unknown features extracted from the mass spectra can be queried in databases. ...
  https://www.jove.com/visualize/abstract/22384000/insights-into-scptaps-proteins-liver-flukes-based-on-large-scale
*  Protein-protein interaction - Wikipedia
Protein-Protein Interaction Databases Library of Modulators of Protein-Protein Interactions (PPI) Proteins and Enzymes at ... Janin J (December 1999). "Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition". ... "Identification of protein interactions involved in cellular signaling". Molecular & Cellular Proteomics. 12 (7): 1752-63. doi: ... The recruitment of signaling pathways through PPIs is called signal transduction and plays a fundamental role in many ...
  https://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction
*  MicrobesOnline - Wikipedia
Kyoto Encyclopedia of Genes and Genomes (KEGG): a large collection of databases of genes, genomes, biological pathways, ... The single-genome data view can also show a protein-protein interaction browser that allows the inspection of interaction ... which can be accessed through two interfaces. The first one is the Tree Browser, which draws a species tree or a gene tree for ... including cellular components, molecular function and biological process. The Genome Selector of the MicrobesOnline homepage ...
  https://en.wikipedia.org/wiki/MicrobesOnline
*  Mike Cherry | Stanford Medicine Profiles
These findings generate testable hypotheses when combined with existing knowledge on signaling pathways and protein-protein ... biological process and cellular location of gene products in genome databases. Shaw, D. R., Ashbumer, M., Blake, J. A., ... The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces ... Curated protein information in the Saccharomyces genome database DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION ...
  https://med.stanford.edu/profiles/j-michael-cherry
*  Frontiers | Adaptation to high salt concentrations in halotolerant/halophilic fungi: a molecular perspective | Microbiology
In contrast, the genome of W. ichthyophaga is very compact, as only 4,884 protein-coding genes are predicted, which cover ... Importantly, there has been a significant increase in their hydrophobins, cell-wall proteins that have multiple cellular ... but there are structural and regulation differences between these pathways in H. werneckii and W. ichthyophaga. We also address ... but there are structural and regulation differences between these pathways in H. werneckii and W. ichthyophaga. We also address ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2014.00199/full
*  Research Fellows - Sys-Mel
Dr Rahman joined Dublin City University in 2008 as a senior post-doctoral fellow and worked extensively in the field of protein ... He is skilled in development of a mathematical model of signaling pathways and kinetic parameter estimation as well as dynamics ... Multiscale modeling of intra-&inter-cellular dynamics. ยง Application of artificial intelligence for combination cancer ... and advanced graphical user interfaces. In 2014 he worked in APO-DECIDE project and developed an improved version of In-house ...
  https://sites.google.com/a/oncomark.com/sysmelproject/home/research-fellows
*  Protocols and Video Articles Authored by Jennifer Smith
Molecular and Cellular Biology. Jul, 2011 , Pubmed ID: 21555454 Bromodomain protein 4 (Brd4) plays critical roles in ... At RGD, users can easily identify genes in pathways, see how pathways relate to each other and visualize pathways in a dynamic ... The user interfaces have been adapted to the work routines of the curators, creating a suite of tools that is intuitive and ... Model Organism Databases in Behavioral Neuroscience International Review of Neurobiology. 2012 , Pubmed ID: 23195310 Model ...
  https://www.jove.com/author/Jennifer_Smith
*  UCI Machine Learning Repository: Data Sets
Ecoli: This data contains protein localization sites. 67. Educational Process Mining (EPM): A Learning Analytics Data Set: ... Yeast: Predicting the Cellular Localization Sites of Proteins. 223. YouTube Multiview Video Games Dataset: This dataset ... sEMG for Basic Hand movements: The "sEMG for Basic Hand movements" includes 2 databases of surface electromyographic signals of ... KEGG Metabolic Reaction Network (Undirected): KEGG Metabolic pathways modeled as un-directed reaction network. Variety of ...
  https://archive.ics.uci.edu/ml/datasets.html?format=mat&task=cla&att=&area=&numAtt=&numIns=&type=&sort=nameUp&view=list
*  PPT - Detection of Protein-Protein Interactions Using the GST Fusion Protein Pull-down Technique PowerPoint Presentation - ID...
... fused proteins are used as probes to perform direct measure of protein-protein interactions and for affinity purification. ... Detection of Protein-Protein Interactions Using the GST Fusion Protein Pull-down Technique. Bacterially expressed glutathione S ... Protein-protein Interactions and Pathways -. june 26, 2014. why ppi?. protein-protein interactions determine outcome of most ... brief introduction to protein-protein interfaces hydrophobicity hydrophilicity morphology amino acid composition. brief ...
  https://www.slideserve.com/kyra-boone/detection-of-protein-protein-interactions-using-the-gst-fusion-protein-pull-down-technique
*  Primer on the Gene Ontology | SpringerLink
The annotation object is the entity associated with a GO term-a gene, a protein, a non-protein-coding RNA, a macromolecular ... A wealth of tools-web-based services, stand-alone software, and programing interfaces-has been developed for applying the GO to ... The GO Consortium consists of a number of large databases working together to define standardised ontologies and provide ... and Cellular Component (CC) [1]. These ontologies are non-redundant and share a common space of identifiers and a well- ...
  https://link.springer.com/protocol/10.1007/978-1-4939-3743-1_3