Announcement - Rutgers-UMDNJ Integration: UMDNJ will be transferred to Rutgers, effective July 1, 2013. As a result of this integration, you will see changes to this website. To learn more about how IT services are changing related to the integration, visit the OIT Rutgers-UMDNJ Integration site.
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High performance computing (HPC)

Collaborations

HP&RC is involved in a number of scientific investigations with UMDNJ faculty.  Collaborations underway or completed within the last twelve months are listed here.

• Computational Models for Predicting Cardiotoxicity Using Shape-based Molecular Descriptors; PI: Vlad Kholodovych, PhD – IST/High Performance & Research Computing and Department of Pharmacology, RWJMS; Scientific host: Igor Tetko, PhD- Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Muenchen, Munich, Germany
  
  
• Screening for small molecule TAM receptor antagonists; PI: Prof. Raymond Birge; Department of Biochemistry & Molecular Biology, NJMS, UMDNJ
  
  
• Synthetic Counter-Ligands for Inhibition of Athero-Inflammation; PIs: Prof. Prabhas Moghe – Department of Biomedical Engineering and Department of Chemical and Biochemical Engineering, Rutgers University; Prof. Katherine Ulrich – Dean of Math and Physical Sciences, Department of Chemistry & Chemical Biology, Rutgers University; Prof. William J. Welsh – Department of Pharmacology, RWJMS
  
  
• Studies on topoisomerase II-mediated DNA damage, developing of new inhibitors;PI: Prof. Leroy F. Liu, Department of Pharmacology, RWJMS with assistance of John E. Kerrigan, Ph.D. - Assoc. Director, Bioinformatics, The Cancer Informatics Core, The Cancer Institute of NJ (CINJ)

• Models of functional homodimeric glycoprotein hormones: implications for hormone action and evolution; PI: Prof. William R. Moyle – Department of Obstetrics and Gynecology, Robert Wood Johnson Medical School, UMDNJ
  
  
• Activation of Human PXR by Bisphenol A: Implications for Atherosclerosis; PIs: Prof. Changcheng Zhou - Graduate Center for Nutritional Sciences, Cardiovascular Research Center, University of Kentucky; Prof. William J. Welsh – Department of Pharmacology, Robert Wood Johnson Medical School, UMDNJ

• Development of non-receptor tyrosine kinase (Ack-1) inhibitors, new agents for treatment of prostate cancer; PI: Prof. Alam Nur-e-Kamal – Department of Biology, School of Science, Health and Technology, Medgar Evers College, The City University of New York; Olesya Fedoryak, PhD - Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Kiev, Ukraine; Prof. William J. Welsh, Department of Pharmacology, RWJMS
  
  
• Genome assembly and annotation of periodontal bacteria; Collaborator: Prof.  Daniel Fine, Department of Oral Biology, NJDS
  
  
• Genome assembly and annotation of Staph bacteria and TB;  Collaborator: Prof Barry Kreiswirth PHRI
  
  
• Use of an Ion Torrent sequencer for clinical testing; Collaborators:  Professors Gokce Toruner and Jim Dermody
  
  
• Haploid sperm sequencing; Collaborator; Prof.  Honghua Li; RWJMS
  
  
• Molecular dynamics and electronic structure studies: modulation of soluble guanylyl cyclase, the NO-receptor; Collaborator: Prof Anne Beuve, Department of Physiology and Pharmacology, NJMS
  
  
• Molecular dynamics of connexin channel structure and function; PI: Prof Andrew Harris, Department of Physiology and Pharmacology, NJMS
  
  
• Implementing parallel CHARM to improve turn-around time for solving  new protein structures; Collaborators:  Prof Roman Shirakov and Mr. Thomas Comollo, Department of Physiology and Pharmacoloogy, NJMS
  
  
• Human exome sequencing to find genetic mutations associated with aggressive peridontitis; PI: Prof. Scott Diehl, Department of Oral Biology, Scott Diehl
  
  
• RNA-Seq for Enrichment and Analysis of Single Gene Expression Profiling: Contribution of an IRF5-SLE Risk Haplotype to IRF5 Expression and Alternative Splicing; PI:  Prof. Betsy Barnes, New Jersey Cancer Center, NJMS
  
  
• Germ line de novo sequencing; PI: Prof. Honghua Li, Department of Molecular Genetics and Mircrobiology; RWJMS/CINJ
  
  
• Genetic variations among mycobacterium tuberculosis (TB) strains and gene expression after drug treatment; Collaborator: Prof. David Alland, Department of Medicine, NJMS.
  
  
• Host-pathogen interaction studied using RNA-seq in TB infected mouse lung;  Collaborators:Profs. Maria Gennaro and Richard Pine, PHRI
  
  
• Using CHIP-seq to study how vitamin D affects gene regulation; Collaborator: Prof. Sylvia Christkos, Department of Biochemistry, NJMS