Computational approaches to biomedical research

6aace8fbdd01acb47d57d2e5545ac7f8?s=47 Nathan Baker
September 13, 2013

Computational approaches to biomedical research

Short high-level research overview for our computational biology work.


Nathan Baker

September 13, 2013


  1. Computational approaches to biomedical research NATHAN BAKER March 6, 2014

    1 Computational and Statistical Analytics Division, Pacific Northwest National Laboratory
  2. Biomolecular solvation and electrostatics Model electrostatic properties of biomolecules to

    inform Structural biology, biochemistry, and biophysics Molecular and biomolecular design Many other applications Fundamental theory and mathematics research APBS and PDB2PQR software packages Complete unresolved parts of biomolecular structure Assign protein titration states Solve partial differential equations for electrostatic and solvation properties Works with popular structural biology software Freely available 21,000+ users March 6, 2014 NIH R01 GM069702, R01 GM099450, R01 GM090208, P41 GM103426 2
  3. Nanomedicine simulation and informatics Simulation and design Nanoemulsion interaction with

    biomembranes Analysis of mechanism for improved drug delivery Informatics Ontology and data-sharing standard development Machine learning methods for immune response prediction Community development US-EU Communities of Research National Cancer Informatics Program Nano WG March 6, 2014 NIH U01 NS073457-01, U54 HG004028, U54 CA11934205-CCNE 3
  4. Cholesterol homeostasis: molecular mechanisms and simulation Explore the mechanism by

    which oxysterols regulate cholesterol homeostasis Focus on membrane-mediated phenomenon of cholesterol activation Collaborative undertaking (Washington Univ. St. Louis): Cellular biology Experimental biophysics Molecular simulation March 6, 2014 NIH R01 HL067773 4
  5. Signature Discovery Initiative $16M, 6-year PNNL internal investment Signature: A

    distinguishing collection of features that detects or characterizes a phenomenon of interest Objective: Develop a generalizable process for signature discovery in any domain, transforming it to become More rigorous More efficient More econnomical March 6, 2014 PNNL LDRD 5
  6. Additional information APBS & PDB2PQR Nanoparticle Ontology US-EU

    Nanotechnology Communities of Research research/databases-ontologies/ National Cancer Informatics Program Nanotechnology Working Group Signature Discovery Initiative Full publication list March 6, 2014 6