Wednesday, May 27, 2015

in vivo RNAi screen for "flyabetes" phenotype reveals insight into mammalian systems

Ugrankar R, Berglund E, Akdemir F, Tran C, Kim MS, Noh J, Schneider R, Ebert B, Graff JM. Drosophila glucome screening identifies Ck1alpha as a regulator of mammalian glucose metabolism. Nat Commun. 2015 May 21;6:7102. PMID: 25994086.

Tuesday, May 26, 2015

IMP integrative tool for functional genomics updated to 2.0 version

Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG. IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 2015 May 12. PMID: 25969450.

From the abstract: "... IMP 2.0 integrates updated prior knowledge and data collections from the last three years in the seven supported organisms (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Caenorhabditis elegans, and Saccharomyces cerevisiae) and extends function prediction coverage to include human disease. ... Additionally, IMP 2.0 implements a new flexible platform for experts to generate custom hypotheses about biological processes or diseases, making sophisticated data-driven methods easily accessible to researchers. IMP does not require any registration or installation and is freely available for use at"

Thursday, May 21, 2015

CRISPRs in flies -- two papers

Protocol recently published:

Gratz SJ, Harrison MM, Wildonger J, O'Connor-Giles KM. Precise Genome Editing of Drosophila with CRISPR RNA-Guided Cas9. Methods Mol Biol. 2015;1311:335-48. PMID: 25981484.

And early online at G3:

Systematic Evaluation of Drosophila CRISPR Tools Reveals Safe and Robust Alternatives to Autonomous Gene Drives in Basic Research
  • Fillip Port,
  • Nadine Muschalik,
  • and Simon L. Bullock
G3 g3.115.019083; Early Online May 20, 2015, doi:10.1534/g3.115.019083

Wednesday, May 13, 2015

Using phylogenetic relationships to predict protein functions--Sadreyev et al. release PhyloGene

In the 'not RNAi (or CRISPR) but might be of interest to blog readers anyway' department:

Sadreyev IR, Ji F, Cohen E, Ruvkun G, Tabach Y. PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles. Nucleic Acids Res. 2015 May 9. pii: gkv452. PMID: 25958392.

From the abstract: "... Analysis of the similarity in patterns of sequence conservation across a large set of eukaryotes can predict functional associations between different proteins, identify new pathway members and reveal the function of previously uncharacterized proteins. We used normalized phylogenetic profiling to predict protein function and identify new pathway members and disease genes. The phylogenetic profiles of tens of thousands conserved proteins in the human, mouse, Caenorhabditis elegans and Drosophila genomes can be queried on our new web server, PhyloGene. ..."

Monday, May 4, 2015

FlyBase announces "Gene Group Reports"

FlyBase's May release includes "Gene Group Reports" (see FlyBase release notes news). I was able to view a list of all gene groups by entering the wild card "*" at the Simple tab on the Quick Search link box on the FlyBase home page.

GenomeRNAi announces data release v.14

The DKFZ's GenomeRNAi recently announced that "The database now contains phenotype data from 217 human RNAi screens and 201 screens in D. melanogaster. The total number of gene-phenotype associations has increased to over 1,2 million." That's a lot of associations!