Publications
The volume and diversity of data in biomedical research has been rapidly increasing in recent years. While such data hold significant promise for accelerating discovery, their use entails many challenges including: Read more “Developing a Framework for Digital Objects in the Big Data to Knowledge (BD2K) Commons”
Events - Past
Join Mark Musen (Stanford), Janice Kranz and Stephan Schürer (University of Miami) for CDD’s Q3 Town Hall Webinar, “Human vs. Machine-Enhanced Scientific Discovery.” We’re seeing ‘Big Data’ everywhere: healthcare, business, sports, traffic control, biology, drug discovery. The ‘behind-the-scenes’ tool enabling the power of Big Data – searching, sharing, visualizing, querying, analyzing – is the Semantic Web (aka ‘Web 3.0’ a term coined by Tim Berners-Lee in a Scientific American article (http://www.scientificamerican.com/article/the-semantic-web/) in 2001 to describe a web of data that can be processed by machines.) . The major advancement brought about by the Semantic Web is the treatment of data and metadata on the internet as one giant graph of knowledge. Instead of the disjointed islands of knowledge we are used to, with the Semantic Web, databases will be more naturally connected to one other (except where privacy prevents openness). Read more “Human vs. Machine-Enhanced Discovery”
Grants
Stephan Schürer, PhD, Associate Professor of Molecular and Cellular Pharmacology at the Miller School, and Chemoinformatics program leader at IDSC, is the head of the team of University of Miami researchers funded through the National Institutes of Health (NIH) who are creating a Data Coordination and Integration Center for the Library of Integrated Network-based Cellular Signatures (LINCS) program. Read more “NIH Big Data to Knowledge (BD2K) Grant”
Publications
Depending on endoplasmic reticulum (ER) stress levels, the ER transmembrane multidomain protein IRE1α promotes either adaptation or apoptosis. Unfolded ER proteins cause IRE1α lumenal domain homo-oligomerization, inducing trans autophosphorylation that further drives homo-oligomerization of its cytosolic kinase/endoribonuclease (RNase) domains to activate mRNA splicing of adaptive XBP1 transcription factor. Read more “Allosteric Inhibition of the IRE1α RNase Preserves Cell Viability and Function during Endoplasmic Reticulum Stress”
News - Archived
A new version of the LIFE search engine has been released. LIFE makes it possible to search across data generated at the LINCS project. This new release includes recent data releases from the LINCS Consortium. It has improved search functionality and several new data visualization features. Read more “New Release of the LIFE Search Engine”
Awards & Honors
Collaborative Drug Discovery (CDD) and researchers at the Center for Computational Science of the University of Miami received a National Institutes of Health (NIH) (Small Business Innovation Research) SBIR Award to develop novel assay annotation technology for the CDD Vault leveraging our BioAssay Ontology (BAO). Read more “CDD and IDSC receive NIH SBIR Award”
Grants
With the ultimate goal of accelerating the discovery of drugs to regenerate or protect nerves after spinal cord injury, UM Miller School researchers have received a $2.5 million grant to develop a novel database via the Center for Computational Science to enable neuroscientists to search the voluminous and growing number of studies related to nervous system repair, and link relevant data from those studies to other resources. Read more “Researchers to Create World Database for Nervous System Repair”
News - Archived
Congratulations to Drs. Stephan Schurer, Vance Lemmon, Ubbo Visser, and the Cheminformatics Group, recipients of NIH funding for their proposal entitled “LINCS Information FramEwork (LIFE) to Integrate and Analyze Diverse Data set”. This project proposes to develop a novel information system that will help scientists to access and use information generated by the NIH LINCS project and other public data sources. Read more “NIH funds “LIFE””
Publications
PPARγ is the functioning receptor for the thiazolidinedione (TZD) class of anti-diabetes drugs including rosiglitazone and pioglitazone. These drugs are full classical agonists for this nuclear receptor, but recent data have shown that many PPARγ-based drugs have a separate biochemical activity, blocking the obesity-linked phosphorylation of PPARγ by Cdk5. Read more “Anti-Diabetic Actions of a Non-Agonist PPARγ Ligand Blocking Cdk5-Mediated Phosphorylation”
News - Archived
For chemists and other scientists who, like Stephan Schürer, Ph.D., are immersed in the early phases of new drug discovery, PubChem is a treasure trove. The largest public database of small molecule screening data accessible to anyone in the world contains thousands of experiments on hundreds of thousands of compounds with millions of values.