*  Application of Atlas of Cancer Signalling Network in preclinical studies, Briefings in Bioinformatics | 10.1093/bib/bby031 |...
Regions of the map having high density of differentially expressed genes/proteins were identified and scored by GSEA [23]. The ... This approach helps to understand the interplay between molecular mechanisms in cancer and to decipher how gene and protein ... call-out with links to external databases, citations and ACSN maps of and functional modules where MYC protein is found); (C) ... In addition, pathway browsing interfaces are becoming more important for cancer researchers and clinicians but require further ...
  https://www.deepdyve.com/lp/ou_press/application-of-atlas-of-cancer-signalling-network-in-preclinical-md5Mc9SJJO
*  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 ... In the human genome alone there are approximately 100,000 genes, encoding a like number of proteins (i.e., each of which may ... multi-view databases. The plural public domain databases 38, 40, 42, include such well known public databases such as those ... Knowledge-based molecular retrieval system and method using a hierarchy of molecular structures in the knowledge base. ...
  http://www.google.com/patents/US7356416?dq=KOI-18
*  Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research...
Philippi S. Light-weight integration of molecular biological databases. Bioinformatics. 2003;20(1):51-7.View ArticleGoogle ... correspond to protein-coding genes detected in the mouse brain, according to the original studies (recorded as PubMed ... A small minority of proteins are found in other tissues as well, and have been included due to their mentions in the same ... The tiers of the platform communicate through interfaces. Therefore, as long as the interface remains stable, the internals can ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1068-8
*  dps - DNA protection during starvation protein - Mycobacterium smegmatis - dps gene & protein
Phylogenomic databases. evolutionary genealogy of genes: Non-supervised Orthologous Groups. More...eggNOGi. ENOG4105DPV. ... Protein. Similar proteins. Organisms. Length. Cluster ID. Cluster name. Size. P0C558. A0R692. L8F211. A0A0D6J3C8. A0A0K0X1R0. ... 12 di-nuclear ferroxidase centers are located at the interfaces between subunits related by 2-fold symmetry axes. ... molecular weight,/a>.,p>,a href='/help/sequences_section' target='_top'>More...,/a>,/p>Sequencei. ,p>This subsection of the ,a ...
  http://www.uniprot.org/uniprot/P0C558
*  Biomedical Science - BSc (Hons) - Canterbury - The University of Kent
Protein structure and function prediction. Prediction of binding sites/interfaces with small ligands and with other proteins. ... Biogenesis of proteins destined for organelles or for secretion.- experimental approaches yeast and bacterial sec genes vs ... It then focuses on nuclear, G-protein coupled, and enzyme linked receptors covering in molecular detail these receptors and ... 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
*  UCI Machine Learning Repository: Data Sets
Mice Protein Expression: Expression levels of 77 proteins measured in the cerebral cortex of 8 classes of control and Down ... Molecular Biology (Protein Secondary Structure): From CMU connectionist bench repository; Classifies secondary structure of ... E. Coli Genes: Data giving characteristics of each ORF (potential gene) in the E. coli genome. Sequence, homology (similarity ... Thyroid Disease: 10 separate databases from Garavan Institute. 49. Thoracic Surgery Data: The data is dedicated to ...
  https://archive.ics.uci.edu/ml/datasets.html?format=&task=&att=&area=&numAtt=&numIns=&type=&sort=nameDown&view=list
*  Molecular Biology Databases
The Protein and Nucleotide entries in Entrez come from several databases: GenBank, EMBL, DDBJ, PIR, SWISS-PROT, PRF, and PDB. ... This database is a catalog of human genes and genetic disorders and was developed for the WWW by NCBI. In this database you ... The expanding resources on the WWW in this area include search and analysis tools for: proteins, nucleic acids, multiple ... and even some gopher interfaces. Quick types of searches may be set up to display the results on a web page, whereas more ...
  http://virology.net/Articles/biotechniquessites1.html
*  Dennis F. Kibler
Week 1: Basic structure of DNA, RNA, genes and proteins.. Week 2&3: Methods: Dot Matrices, Local, Global and Multiple Alignment ... 277A Representations and Algorithms for Molecular Biology(4). o The primary goal of this class is to introduce molecular ... As part of the course students will use current tools on existing databases to a) locate genes and determine their function, b ... In particular you will write algorithms for finding genes, determining similarity between DNA and protein sequences, building ...
  https://www.ics.uci.edu/~kibler/
*  Gene Designer: a synthetic biology tool for constructing artificial DNA segments | BMC Bioinformatics | Full Text
More recently, protein and DNA sequences have become easier to obtain electronically through databases than physically from ... thereby creating designed non-natural genes, proteins, biological processes and organisms[1]. Gene synthesis was conceived as a ... and protein engineering[6].. Synthetic Biology is the convergence of molecular biology and engineering principles that is ... Current commercial sequence manipulation packages are typically very feature rich with graphic user interfaces and multiple ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-285
*  Resources and tools for the high-throughput, multi-omic study of intestinal microbiota, Briefings in Bioinformatics | 10.1093...
... or translated protein database searches [30]. That is, the assignment may be based on full protein-coding genes (CDSs) by means ... understanding of the molecular mechanisms of host-bacteria interaction through extracellular and surface-associated proteins/ ... Probability-based protein identification by searching sequence databases using mass spectrometry data . Electrophoresis 1999 ; ... Last but not least, there is a general lack of graphical user interfaces to use many of the tools. This lack limits access of ...
  https://www.deepdyve.com/lp/ou_press/resources-and-tools-for-the-high-throughput-multi-omic-study-of-QU4byFWU0i
*  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 ... As noted above in RNA Polymerase and Sigma Factors, the beta clamp proteins within the RNAP complex have a higher initial ... domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides phylogenetic trees ...
  https://en.wikipedia.org/wiki/Synechocystis
*  Primer on the Gene Ontology | SpringerLink
... but there are only approximately 20,000 recognised human protein-coding genes (20,187 reviewed human proteins in the UniProt ... A wealth of tools-web-based services, stand-alone software, and programing interfaces-has been developed for applying the GO to ... Field 5 specifies the GO term, while field 9 denotes the sub-ontology of GO, either Molecular Function, Biological Process, or ... The GO Consortium consists of a number of large databases working together to define standardised ontologies and provide ...
  https://link.springer.com/protocol/10.1007/978-1-4939-3743-1_3
*  Departments - MEES Graduate Program
These include Ecology, Environmental Science, Environmental Molecular Biology/Biotechnology, Environmental Chemistry, Fisheries ... Protein structure, properties, and structure-function relationships.. MOCB 708 Advanced Topics in Molecular and Cell Biology (1 ... Translation of mRNA to make proteins.. BCHM 671 Protein Chemistry and Enzyme Catalysis (3 credits) - UMCP. Prerequisite: BCHM ... BIOL 683 Genes to Genomes (4 credits) - UMBC. Prerequisite: BIOL 142. This is a combined lecture, paper discussion and hands-on ...
  http://mees.umd.edu/course-folder
*  Computer Science Course Descriptions - 2010-2012 Graduate Catalog - UT Dallas
... and text databases in the real world; finding patterns (motifs) in genes and proteins; differentiating between valid patterns ... Comprehensive introduction to molecular biology and molecular genetics for a program of study in bioinformatics. Discussion of ... Device drivers and streams as interfaces to hardware features. TCP/IP and other UNIX inter-machine communication facilities. ... The major topics include: computational inference of biological networks (regulatory, protein interactions, and metabolic) and ...
  http://www.utdallas.edu/ogs/CAT2010/ECS/CS/coursedescriptions_cs.htm
*  Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into...
These genes might represent true orphan genes, representing species- or lineage-specific adaptive innovations or non-protein- ... Gene family sizes in P. patens proteins from several Viridiplantae were clustered using OrthoMCL. Depicted are all protein ... "molecular function" (MF) by 2702, the number of genes with a "cellular component" (CC) term has increased by 10,065. A ... knowledge on moss genes to the digital representations scattered across several databases. ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-498
*  Protocols and Video Articles Authored by Gregor Rot
Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution' ... Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive ... and the decreased nuclear abundance of NOVA proteins. As expected, a dramatic down-regulation of neuronal genes was associated ... Apr, 2011 , Pubmed ID: 21358640 TDP-43 is a predominantly nuclear RNA-binding protein that forms inclusion bodies in ...
  https://www.jove.com/author/Gregor_Rot
*  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 ... Phospholipid molecular species are often expressed as isobaric species that are denoted by the phospholipid class and the total ... 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 ...
  https://www.jove.com/visualize?author=Dennis%20C%20Ko%20
*  Computer Science Course Descriptions - 2012-2014 Graduate Catalog - UT Dallas
... and text databases in the real world; finding patterns (motifs) in genes and proteins; differentiating between valid patterns ... Comprehensive introduction to molecular biology and molecular genetics for a program of study in bioinformatics. Discussion of ... Device drivers and streams as interfaces to hardware features. TCP/IP and other UNIX inter-machine communication facilities. ... Novel data mining methods in bioinformatics with an emphasis on protein structure prediction, homology search, genomic sequence ...
  http://www.utdallas.edu/ogs/CAT2012/ECS/CS/coursedescriptions_cs.htm
*  Biomolecules | Free Full-Text | Structure-Dependent Interfacial Properties of Chaplin F from Streptomyces coelicolor | HTML
Linder, M.B. Hydrophobins: Proteins that self assemble at interfaces. Curr. Opin. Colloid Interface Sci. 2009, 14, 356-363. [ ... Self-assembled hydrophobin protein films at the air-water interface: Structural analysis and molecular engineering. ... A family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor. Genes Dev. 2003 ... DICHROWEB includes a wide range of protein spectral databases and various programs [31]. The CDSSTR reference set 1 (optimized ...
  http://www.mdpi.com/2218-273X/7/3/68/html
*  About | NASA GeneLab
The structure of proteins. Molecular signaling processes. On GeneLab we conduct research beyond gravity and search for answers ... GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing ... Combining the study of genes, proteins and fundamental metabolic function, systems biology integrates the analysis of genomics ... In late 2015 GeneLab will link to existing life science databases, expand life science studies through collaboration and ...
  https://genelab.nasa.gov/about/
*  Madison 2008 Retrospective
Molecular biology are filled with proteins affecting cellular process. New causation? Network causation, how do we review these ... Green experimental protein, red experimental protein, could view each. *Bring these together in juxtaposition, look at ... Interconnectiveness of genes, hierarchy in the genome. *See the feedback between the genotype and phenotype to make sure that ... Component-based programming and interfaces. Movable type simple, in biology want interactions. Interesting, but a long ways ...
  http://www.isss.org/world/book/export/html/466
*  Neuroinformatics - Wikipedia
BIRN allows combining databases, interfaces and tools into a single environment. Budapest Reference Connectome is a web-based ... Genes to Cognition Project A neuroscience research programme that studies genes, the brain and behaviour in an integrated ... proteins to learning and memory). Neuroinformatics uses databases, the Internet, and visualization in the storage and analysis ... Methods in Molecular Biology. 401. Totowa, NJ: Humana. ISBN 978-1-58829-720-4. OCLC 123798711. Koslow, Stephen H.; Huerta, ...
  https://en.wikipedia.org/wiki/Neuroinformatics
*  RCSB PDB: Homepage
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex ... Membrane Proteins. *Protein Modification. *Protein Symmetry. *Biological Process, Cell Component, Molecular Function ... This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. ... All human genes have been mapped to representative PDB structure protein chains (selected from sequence clusters at 40% ...
  https://www.rcsb.org/
*  MicrobesOnline - Wikipedia
... which relies on protein sequence comparison for the detection of homology. Functional information of genes and proteins: The ... Kyoto Encyclopedia of Genes and Genomes (KEGG): a large collection of databases of genes, genomes, biological pathways, ... molecular and signaling pathways of genes, and PANTHER for information about molecular and functional pathways, in the context ... which can be accessed through two interfaces. The first one is the Tree Browser, which draws a species tree or a gene tree for ...
  https://en.wikipedia.org/wiki/MicrobesOnline
*  Enhancing navigation in biomedical databases by community voting and database-driven text classification | BMC Bioinformatics |...
... molecular imaging, etc. Ensembles of bagged decision trees met the requirements of our application best. No other algorithm ... The breadth of biological databases and their information content continues to increase exponentially. Unfortunately, our ... protein-protein interactions [41], genetic variants of human proteins [42], and allergen cross-reactivity [43]. In text mining ... identified the need for intuitive and easy-to-use interfaces for the biological end user and an increasing interest in ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-317