Announcing the First Annual Three Rivers Evolution Event (TREE)

We are excited to announce the first annual Three Rivers Evolution Event (TREE), a new regional conference serving Western Pennsylvania and the surrounding areas, sponsored in part by the American Society of Naturalists. Researchers of all stages and institution types are welcome. TREE will take place on Saturday, September 9th, 2017 at the University of Pittsburgh and include multiple sessions of talks, a poster session, and a keynote lecture presented by Dr. Cynthia Beall of Case Western University. The abstract deadline is July 14th, and we encourage those interested in presenting talks or posters to apply. Registration is accepted until September. Please see the website for more information: https://sites.google.com/view/tree2017/home 

We hope to see you in September!

Cheng and Bahar Provide Novel Information About EAATs in eLife Publication

Identifying chloride channeling path in excitatory amino acid transporters

The paper provides novel evidence on the molecular determinants of the dual function, substrate transport and anion permeation, of excitatory amino acid transporters (EAATs).

It opens avenues toward illuminating how EAATs regulate synaptic transmission and neurological conditions.

This is a collaborative study between the Bahar and Amara (NIH) labs, with key contributions from Drs. Delany Torres-Salazar and Mary Cheng

Cheng MH#, Torres-Salazar D #, Gonzalez-Suarez AD, Amara SG & Bahar I*, “Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters”. eLife, (2017).

Takis and Collaborators Receive U01 Grant

Systems Level Causal Discovery in Heterogeneous TOPMed Data

Takis Benos PhD, Frank Sciurba MD, and  Panos Chrysanthis PhD

The team will investigate the mechanism, pathology and pathophysiology of chronic obstructive pulmonary disease (COPD) facilitation and progression by analyzing existing TOPMed clinical and omics datasets. COPD is the third leading cause of death and a major cause of disability and health care costs in the US.  The tools and methods developed through this grant will be made publicly available using cloud services.

Congratulations, Takis!

Carlos Camacho Receives R01

“REAL-TIME DISCOVERY OF INHIBITORS AMONG BILLION COMPOUNDS FOR PREVIEW AND
DOWNLOAD”untitled-2

Innovations in computational techniques have enabled us to advance interactive virtual screening
platforms to speed up the identification of small molecules to disrupt protein function. As a step towards addressing polypharmacology issues, we plan to apply our state-of-the-art methodologies to build efficient tools to perform compound-and-target centric virtual screening of human proteins to discover pre-clinical compounds for hard to treat diseases.

CO-I on the grant is Alexander Dömling (U. of Groningen)

Chromosomal Dynamics using the GNM

From Hi-C maps to Chromosome Dynamics and Cross-Correlations between Gene Loci

This is the first structure-based study of chromosomal dynamics using elastic network models, between the Bahar and Kingsford labs.

zhang-nucl-acid-resIn this study, we constructed Gaussian Network Models (GNM) for chromosome structures based on Hi-C maps. The GNM analysis permits us to predict chromatin mobility profile, identify hierarchical structural domains, and discover cross-correlated distal domains (CCDDs). These biological findings were found consistent with various types of experimental data, including chromatin accessibility (ATAC-seq and DNase-seq), interacting pairs of regulatory elements and gene loci (ChIA-PET), and gene co-expression.

Sauerwald,N.*, Zhang,S.*, Kingsford,C., Bahar, I. (2017) Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Research.