*  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 ... Microbial communities and ecology: growth and survival in the real world (e.g. soils and sediments), studying populations and ... Databases and data availability. Using sequence data for analysis sequence searching methods, multiple sequence alignments, ... the genetic organisation of various types of organism and the way in which genes can be expressed and their expression ...
  https://www.kent.ac.uk/courses/undergraduate/263/biomedical-science
*  Synechocystis - Wikipedia
... as well as interaction networks in graphical web interfaces. CyanoBase: Cyanobacteria carry a complete set of genes for ... SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. SynechoNET is ... domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides phylogenetic trees ... RNA thermometer Cyanobiont Cyanothece Geological history of oxygen Great Oxygenation Event Green algae Microalgae Microbial ...
  https://en.wikipedia.org/wiki/Synechocystis
*  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 ... and KEGG pathways databases [41] are often used to predict the composition ratio of microbial gene families and pathways from ... Last but not least, there is a general lack of graphical user interfaces to use many of the tools. This lack limits access of ... Probability-based protein identification by searching sequence databases using mass spectrometry data . Electrophoresis 1999 ; ...
  https://www.deepdyve.com/lp/ou_press/resources-and-tools-for-the-high-throughput-multi-omic-study-of-QU4byFWU0i
*  Biology - MEES Graduate Program
Topics include microbial ecology of plants and animals, aquatic microbial ecology, soil microbial ecology, biodegradation, ... BIOL 683 Genes to Genomes (4 credits) - UMBC. Prerequisite: BIOL 142. This is a combined lecture, paper discussion and hands-on ... The fundamental phenomena related to solute movement in bulk solution and across interfaces. Examination of natural and ... Topics will include operating systems; telecommunications with off-campus databases and specific software packages for general ...
  http://mees.umd.edu/biol/
*  Departments - MEES Graduate Program
Topics include microbial ecology of plants and animals, aquatic microbial ecology, soil microbial ecology, biodegradation, ... MOCB 640 Protein Structure and Function (3 credits) - UMCP. Protein structure, properties, and structure-function relationships ... BIOL 683 Genes to Genomes (4 credits) - UMBC. Prerequisite: BIOL 142. This is a combined lecture, paper discussion and hands-on ... Student will utilize statistical software and analyze existing and student-created databases.. ANTH 450 Theory and Practice of ...
  http://mees.umd.edu/course-folder
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... interactions can occur between genes in the same pathway or protein complex2 as the deletion of either gene alone is often ... We begin with a user-guide for similarity search tools via online interfaces as well as local executables. Next, we explore ... Technique for Studying Arthropod and Microbial Communities within Tree Tissues. Authors: Nicholas C Aflitto, Richard W ... The growing numbers of organisms represented in DNA databases challenge tree-building techniques and the vertical hierarchical ...
  https://www.jove.com/visualize/abstract/19798412/a-scalable-method-for-analysis-and-display-of-dna-sequences
*  MicrobesOnline - Wikipedia
Kyoto Encyclopedia of Genes and Genomes (KEGG): a large collection of databases of genes, genomes, biological pathways, ... Information of microbial genes stored in MicrobesOnline includes sequences (genes, transcripts and proteins), genomic loci, ... 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 ...
  https://en.wikipedia.org/wiki/MicrobesOnline
*  List of biological databases - Wikipedia
Protein Model Portal (PMP) Meta database that combines several databases of protein structure models (Biozentrum, Basel, ... It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated ... and exon sequencing of at least 1,200 genes. TDR Targets A chemogenomics database focused on drug discovery in tropical ... through a unified set of interactive and programmatic interfaces (using the Ensembl software platform). Flybase, genome of the ...
  https://en.wikipedia.org/wiki/List_of_biological_databases
*  Protein-protein interaction - Wikipedia
Protein-Protein Interaction Databases Library of Modulators of Protein-Protein Interactions (PPI) Proteins and Enzymes at ... Examples: Agile Protein Interactomes Dataserver (APID), The Microbial Protein Interaction Database (MPIDB), and Protein ... Janin J (December 1999). "Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition". ... Transcription of reporter genes does not occur unless bait (DB-X) and prey (AD-Y) interact with each other and form a ...
  https://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction
*  Tettelin, HervĂ© | University of Maryland School of Medicine
It provides a rich set of web interfaces at varying levels of resolution from the whole genome scale down to single genes. The ... Read T.D., Gill S.R., Tettelin H., and Dougherty B.A. (2001) Finding drug targets in microbial genomes. Drug Discovery Today 6 ... We identified all predicted surface-exposed proteins from serogroup B Neisseria in silico based on various protein motifs and ... Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have ...
  http://www.medschool.umaryland.edu/profiles/Tettelin-Herve/
*  Biology - BSc (Hons) - Canterbury - The University of Kent
B. Protein Bioinformatics Methods Protein structure and function prediction. Prediction of binding sites/interfaces with small ... Microbial communities and ecology: growth and survival in the real world (e.g. soils and sediments), studying populations and ... Databases and data availability. Using sequence data for analysis sequence searching methods, multiple sequence alignments, ... For example, the relationship between genes and proteins, or the nature of essential nutrients in microbes, cells, plants and ...
  https://www.kent.ac.uk/courses/undergraduate/255/biology
*  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 ... 2011) Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, ... Inner Workings: Hunting for microbial life throughout the solar system. Efforts to look for microbial life on other worlds got ... 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
*  BioSupplyNet.com - A directory of Life Science companies and their products
A tool for literature analysis that extracts semantic features associated with a list of genes and uses them to structure ... An overview of bioinformatics databases and services provided by the European Bioinformatics Institute (EBI).. ... An open-source system for exchanging annotations of genome and protein sequences and structures. ... MICROBIAL METAGENOMICS BIOINFORMATICS STRATEGY. http://www.genomics.ceh.ac.uk/mm/Informatics.php. Strategy for extraction and ...
  http://www.biosupplynet.com/btk08/viewsubcategory.cfm?cat_id=2&subcat_id=25
*  Protocols and Video Articles Authored by Kenneth Nealson (Translated to Chinese)
These genes include chemotactic signal transduction protein (cheA-3, SO_3207), methyl-accepting chemotaxis proteins with the ... Population Dynamics of Electrogenic Microbial Communities in Microbial Fuel Cells Started with Three Different Inoculum Sources ... Publicly available analysis tools and databases and the expression data were applied to improve the annotation of these genes. ... In particular, the interactions that occur at the bacteria-mineral interfaces are not yet clearly elucidated. One DMRB, ...
  https://www.jove.com/author/Kenneth_Nealson?language=Chinese
*  Protocols and Video Articles Authored by Jennifer Smith
... sequencing of the Millennium Atoll black reef-associated microbial community was enriched in iron-associated virulence genes ... A fusion protein, malate dehydrogenase-green fluorescent protein with a histidine affinity tag (MGH), is used throughout the ... 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
*  Evolutionary history and metabolic insights of ancient mammalian uricases | PNAS
... metric used to detect changes in selective constraints acting on protein-coding genes; however, a neutral signal is clearly ... Inner Workings: Hunting for microbial life throughout the solar system. Efforts to look for microbial life on other worlds got ... S2). Despite these differences, the oligomeric interfaces and active site residues are remarkably conserved (Fig. 2B) (7, 8). ... Modern uricase sequences from 17 taxa were retrieved from public databases and were aligned by using MUSCLE. An evolutionary ...
  http://www.pnas.org/content/111/10/3763/
*  Viral Bioinformatics Resource Center - Wikipedia
A unique aspect of this resource relative to other genomic databases is its grouping of all annotated genes into ortholog ... and the Broad Institute Microbial Sequencing Center (MSC). A Knowledge Database containing curated genes and graphical gene ... JDotter also interfaces with the curated database or the user-supplied file to display supplementary feature data such as gene ... JDotter can both access pre-processed dotplots of the genome and gene (DNA or protein) sequences available in the VBRC database ...
  https://en.wikipedia.org/wiki/Viral_Bioinformatics_Resource_Center
*  Insights into Ionizing-Radiation-Resistant Bacteria S-Layer Proteins and Nanobiotechnology for Bioremediation of Hazardous and...
71 - Pollmann K, Raff J, Schnorpfeil M, Radeva G, Selenska-Pobell S: Novel surface layer protein genes in Bacillus sphaericus ... 67 - Schuster B, Sleytr UB: Biomimetic interfaces based on S-layer proteins, lipid membranes and functional biomolecules. J R ... Prediction methods are based on neighborhood, co-expression, gene fusion, experiments, co-occurrence, databases or text mining ... 9 - Lloyd JR: Microbial reduction of metals and radionuclides. FEMS Microbiol Rev 2003, 27(2-3):411-425. ...
  https://www.intechopen.com/books/management-of-hazardous-wastes/insights-into-ionizing-radiation-resistant-bacteria-s-layer-proteins-and-nanobiotechnology-for-biore/
*  MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis, Briefings in...
Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 2012; 9: 811- 4. Google Scholar ... Relying on RESTful interfaces instead of shared filesystems provides cross-cloud execution capabilities, allowing us to run on ... Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015; 12: 59- 60. Google Scholar CrossRef Search ADS PubMed 6 ... We note that in addition to requesting SEED annotations, the user might also request annotations from the M5NR sub-databases (i ...
  https://www.deepdyve.com/lp/ou_press/mg-rast-version-4-lessons-learned-from-a-decade-of-low-budget-ultra-ROPYHNP2Hp
*  bioinformatics: 2007
Genes carry information for making all the proteins required by all organisms. These protein determine, among other things, how ... Query by text or BLAST, to access heaps of info from primary and secondary databases of genomic resources, transcripts, protein ... Integrated Microbial Genomes (IMG) The Integrated Microbial Genomes (IMG) system facilitates the comparison of genomes ... This resource offers convienent web interfaces for many freely available tools.. BoxShade. Printing and shading of multiple ...
  http://bioinformatication.blogspot.com/2007/
*  Publications
... microbial community structure and associations analyzed via marker genes." FEMS Microbiol Rev, 40(5), 686-700. ... Gribble, K.E., Snell, T.W., and Mark Welch, D.B. (2011). "Gene and protein structure of the mate recognition protein gene ... Brandt, B.W., Bonder, M.J., Huse, S.M., and Zaura, E. (2012). "TaxMan: a server to trim rRNA reference databases and inspect ... INTERFACES, 8(44), 30271-30280. ... analyses of protein-coding genes." Mol Biol Evol, 16(1), 83-97. ...
  http://www.mbl.edu/jbpc/publicationsparentpage/
*  MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data | Genome...
MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of ... We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization ... Databases used in MICRA. The identification module of MICRA uses homemade databases containing some of the complete sequences ... The MICRA web interfaces and the computational resources. The MICRA Web service is deployed on an Ubuntu server (version 14.04 ...
  https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1367-z
*  Biomolecules | Free Full-Text | Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass...
An automated data processing pipeline that provides a short list of amyloid protein candidates was developed based on an ... A third protein FapE has also been observed in the purified preparations of Fap fibrils, but it is uncertain if this protein is ... Genes Dev. 2003, 17, 1714-1726. [Google Scholar] [CrossRef] [PubMed]. *Jordal, P.B.; Dueholm, M.S.; Larsen, P.; Petersen, S.V ... Blanco, L.P.; Evans, M.L.; Smith, D.R.; Badtke, M.P.; Chapman, M.R. Diversity, biogenesis and function of microbial amyloids. ...
  http://www.mdpi.com/2218-273X/7/3/58/htm
*  Statistical Analyses of Next Generation Sequence Data: A Partial Overview
They found that assignments based on proxy-genes, where full-length protein sequences with high similarity to the translated ... The biomaRt package (Durinck et al., 2006) allows users to connect to and search BioMart databases and integrates them with ... the problem of matching individual short reads sampled from the collective genome of a microbial community to protein families ... package allows users to manipulate big strings easily and quickly by introducing new implementations and new interfaces into ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2989618/
*  Download Industrial Refrigeration Handbook
well to taking on the model receptor, the genes was received to reporting( two models). again, the systems, while achieved to ... 1991) Rumen Microbial Metabolism and Ruminant Digestion. 1989) Dietary Interaction of Cane authors with download industrial ... read including download about both lysosomal and such protein vibrations to Enter assistance carbonates for very challenges of ... 129How Interfaces Affect the step of the Anilinium IonJarukorn Sripradite, Susannah A. Johnson, Anan Tongraar, Debbie C. Diego ...
  http://prigsbee.com/Hawaii/freebooks/download-industrial-refrigeration-handbook.htm