A5081629005- Bioinformatics and Genomic Networks
- Fungal and yeast genetics research
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- Computational Drug Discovery Methods
- Fermentation and Sensory Analysis
- Metabolism and Genetic Disorders
- Cellular transport and secretion
- Protein Kinase Regulation and GTPase Signaling
- Plant Disease Resistance and Genetics
- Enzyme Structure and Function
- Microbial Natural Products and Biosynthesis
- Amino Acid Enzymes and Metabolism
- RNA and protein synthesis mechanisms
- Streptococcal Infections and Treatments
- Machine Learning in Bioinformatics
- Grief, Bereavement, and Mental Health
- Physical Education and Training Studies
- Neurobiology and Insect Physiology Research
- Advanced Proteomics Techniques and Applications
- Protist diversity and phylogeny
- Plant Gene Expression Analysis
- Plant-Microbe Interactions and Immunity
Broad Institute
2017-2022
Harvard University
1988-2022
Dana-Farber Cancer Institute
2022
Princeton University
2007-2016
Stanford University
2004-2011
University of Massachusetts Chan Medical School
1997-1999
University of Massachusetts Amherst
1996
University of California, Davis
1984-1985
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular cellular biology are freely available for community use in the annotation genes, gene products sequences. Many model organism databases genome groups GO contribute their sets to resource. database integrates contributed annotations full access this information formats. Members Consortium continually work collectively,...
The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for budding yeast cerevisiae. SGD project provides highest-quality manually curated information from peer-reviewed literature. experimental results reported in literature are extracted and integrated within a well-developed database. These data combined with quality high-throughput provided through Locus Summary pages, powerful query engine rich genome browser. acquisition, integration retrieval of...
The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature all major model organism species humans. As of September 2014, BioGRID contains 749 912 as drawn 43 149 publications represent 30 organisms. This interaction count represents a 50% increase compared to our previous 2013 update. data are freely distributed through partner databases...
In enteric bacteria the products of two nitrogen regulatory genes, ntrA and ntrC, activate transcription glnA, structural gene encoding glutamine synthetase, both in vivo vitro. The ntrC product (gpntrC) is a DNA-binding protein, which binds to five sites glnA promoter-regulatory region appears initiation. Using as an assay stimulation coupled vitro transcription-translation system, we have partially purified (gpntrA). following evidence consistent with view that gpntrA sigma subunit for RNA...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features gene products of budding yeast cerevisiae. Although published data from traditional experimental methods are primary sources evidence supporting Gene Ontology (GO) annotations for a product, high-throughput experiments computational predictions can also provide valuable insights in absence an extensive body literature. Therefore, GO available at...
We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which disrupt the function of disease-associated genes. Both experimental and computational methods exist predict pathogenicity genetic variation. However, a systematic performance comparison between them has been lacking. Therefore, we developed exploited panel 26 yeast-based functional complementation assays measure impact 179 (101 disease- 78 non-disease-associated variants)...
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of yeast cerevisiae, which commonly known as baker's or budding yeast. information in SGD includes functional annotations, mapping sequence information, protein domains structure, expression data, mutant phenotypes, physical genetic interactions primary literature from these data are derived. Here we describe how published phenotypes interaction annotated displayed SGD.
SUMMARY We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs and disease states are connected by virtue common gene-expression signatures. Here, we report more than 1,000-fold scale-up CMap as part NIH LINCS Consortium, made possible new, low-cost, high throughput reduced representation expression profiling method that term L1000. show L1000 is highly reproducible, comparable to RNA sequencing, suitable for computational inference levels 81% non-measured...
Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes gene products. To make this information available an ongoing basis, Genome Database (SGD) (http://www.yeastgenome.org/) created Snapshot (http://db.yeastgenome.org/cgi-bin/genomeSnapShot.pl). The summarizes current state knowledge about chromosomal features S.cerevisiae. is organized into two categories: (i) number each type feature annotated in (ii)...
The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein genetic interaction data. Structured experimental evidence codes, an intuitive search interface, visualization tools enable discovery of individual gene, protein, or network function. BioGRID houses data major model organism species—including yeast, nematode, fly, zebrafish, mouse, human—with...
The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available information prompted Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance depth accessibility annotations. In particular, we have ongoing improve integration experimental sequence-based predictions redesigned web pages. A key feature this redesign is development a GBrowse-derived interactive Proteome...
The his4-912 delta mutation is an insertion of the long terminal repeat (delta) yeast retrotransposon Ty into HIS4 promoter region, such that 97 base pairs upstream transcription initiation site. Strains carrying allele are His- at 23 degrees C; this phenotype can be reversed either by growth 37 C or mutations in trans-acting SPT genes. Under conditions which confers a phenotype. initiates site, rather than producing longer, nonfunctional transcript. strain His+, wild-type To understand how...
The pheromone response in the yeast Saccharomyces cerevisiae is mediated by a heterotrimeric G protein. Gβγ subunit (a complex of Ste4p and Ste18p) associated with both internal plasma membranes, portion not stably either membrane fraction. Like Ras, Ste18p contains farnesyl-directing CaaX box motif (C-terminal residues 107 to 110) cysteine residue (Cys 106) that potential site for palmitoylation. Mutant containing serine at position 106 (mutation ste18-C106S) migrated more rapidly than...
The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae , fission Schizosaccharomyces pombe Candida albicans SC5314 as well several other model organisms humans. This protocol describes how to use website query or any gene interest, visualize associated using embedded interactive network viewer, download data files either selected entire interaction set.
Genetic evidence suggests that the yeast STE4 and STE18 genes encode Gβ Gγ subunits, respectively, Gβγ complex plays a positive role in pheromone response pathway, its activity is subject to negative regulation by Gα subunit (product of GPA1 gene) cell-surface receptors. However, as yet there no direct biochemical for protein associated with plasma membrane. We found products are stably membrane well internal membranes 30% pool not tightly either fraction. A slower-migrating, presumably...
Curation of biological data is a multi-faceted task whose goal to create structured, comprehensive, integrated, and accurate resource current knowledge. These structured facilitate the work scientific community by providing knowledge about genes or genomes generating validated connections between that yield new information stimulate research approaches. For model organism databases (MODs), an important source publications. Every published paper containing experimental particular candidate...
Abstract Analysis of genomic data requires access to software tools that place the sequence‐derived information in context biology. The Saccharomyces Genome Database (SGD) integrates functional about budding yeast genes and their products with a set analysis facilitate exploring biological details. This unit describes how various types available at SGD can be searched, retrieved, analyzed. Starting guided tour Home page Locus Summary page, this highlights retrieve using YeastMine, visualize...
The his4-912 delta mutation is an insertion of the long terminal repeat (delta) yeast retrotransposon Ty into HIS4 promoter region, such that 97 base pairs upstream transcription initiation site. Strains carrying allele are His- at 23 degrees C; this phenotype can be reversed either by growth 37 C or mutations in trans-acting SPT genes. Under conditions which confers a phenotype. initiates site, rather than producing longer, nonfunctional transcript. strain His+, wild-type To understand how...