Around the Nucleus

submitted by: ahernk

This video is a surreal presentation of a Metabolic Melody by Kevin Ahern ( for more info). The tune is The Beatle's "Across the Universe." The lyrics and video are by Kevin Ahern and the recording is by David Simmons

Deriving rules and assertions from pharmacogenomics knowledge resources in support of patient drug metabolism efficacy...

submitted by: Jamia
Full title: Deriving rules and assertions from pharmacogenomics knowledge resources in support of patient drug metabolism efficacy predictions Abstract: Objective Pharmacogenomics evaluations of variability in drug metabolic processes may be useful for making individual drug response predictions. We present an approach to deriving ‘phenotype scores’ based on existing pharmacogenomics knowledge and a patient's genomics data. Pharmacogenomics plays an important role in the bioactivation...

Staphylococcus aureus phenotype switching: an effective bacterial strategy to escape host immune response and establish a chronic infection

submitted by: Ben_Norman
Staphylococcus aureus is a frequent cause for serious, chronic and therapy-refractive infections in spite of susceptibility to antibiotics in vitro. In chronic infections, altered bacterial phenotypes, such as small colony variants (SCVs), have been found. Yet, it is largely unclear whether the ability to interconvert from the wild-type to the SCV phenotype is only a rare clinical and/or just laboratory phenomenon or is essential to sustain an infection. Here, we performed different...
Authors: L Tuchscherr, E Medina, M Hussain, W Volker, V Heitmann, S Niemann, D Holzinger, J Roth, R Proctor, K Becker, G Peters, B Loffler

Introduction to Biomedical Ontologies #4: Ontology Term Enrichment Using RatMine

submitted by: jennifer.r.smith
You've done your experiments and you have a list of genes that might be of interest, but…what now? Or you keep seeing the term "ontology term enrichment analysis" in the papers you're reading and, well, you have a vague idea of what that means, but you aren't really sure. Whether you're interested in information about gene functions, diseases, phenotypes or pathways, this video provides an overview of what ontology term enrichment analysis is and how you can use the "widgets" in RatMine...

Introduction to the RGD Phenotypes and Models Portal

submitted by: jennifer.r.smith

Despite what our name might imply, the Rat Genome Database contains much more than just genomic and genetic data for the rat. This video will give you an overview of the RGD Phenotypes and Models portal—a rich resource of information on topics including animal husbandry, identifying what rat strains are good models for certain human diseases, and normal physiological measurements for a variety of rat strains.

Uniqueness, Self Belonging and Intercourse in Nature-New Version

submitted by: hsrikm
Biological organization is discussed within a holistic framework . A new orientation is presented of natural processes with an approach in model construction that is focused strictly on physical form and centered away from abstractions that escape the perceptual senses, lead towards the postulation of non-verifiable and non-witnessible entities. A universal construction composed of first perspective representations of path, witness as unique loci in volumes of space delineated as...

Introduction to Biomedical Ontologies 3: Anatomy of an Ontology Annotation, part 2

submitted by: jennifer.r.smith
Are you missing the added value that you could be getting from ontology annotations? You know what ontologies are—maybe you've even used them on occasion. But if the only part of an ontology annotation that you take into account is the term itself, you could be skipping over valuable information that the other components of annotations supply. This video will give you insight into what that "valuable information" is and how to interpret what you see when you examine ontology annotations.

New Methods from the Berkeley Phylogenomics Group

submitted by: ruchira

Here we present two new algorithms hosted within the PhyloFacts phylogenomic encyclopedias.

Introduction to Biomedical Ontologies 1: What is an Ontology?

submitted by: jennifer.r.smith

While reading an article or looking at a website, have you ever seen the term “ontology” and wondered what that meant? Do you hear people talking about using ontologies and ask yourself what the hubbub is about? This video is designed to help answer those questions. Here is a beginner’s look at what an ontology is and why ontologies are an important tool in the scientist’s toolbox.

"Genomic Encyclopedia of Bacteria and Archaea (GEBA)"- Jonathan Eisen @ '09 DOE JGI User Meeting

submitted by: JGI

Jonathan Eisen, (UC Davis) presentation for DOE JGI '09 User Meeting on March 26, 2009, introduction by Dan Rokhsar (JGI).