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Andrew Hodges, PhD


Andrew Hodges

Research Interests

  • Bioinformatics, machine learning, and systems biology
  • Cancer analysis and large-data mining
  • Microarray-based pathway analysis and visualization
  • Discrete math and logic


  • 2011-Now Sanford-Burnham Medical Research Institute, La Jolla, CA. Postdoctoral Associate.
  • 2004-2011 University of Michigan, Ann Arbor, MI. Ph.D. in Bioinformatics.
  • 2004-2006 University of Michigan, Ann Arbor, MI. M.S. in Bioinformatics.
  • 1999-2004 Manchester College, North Manchester, IN. B.A. in Biology-Chemistry and Mathematics, Cum Laude, Honors Diploma.

Publications and Patents

  • Hodges AP, Woolf P, He Y. Prediction of novel pathway elements and interactions using Bayesian networks. (2011) Book chapter in: “Bioinformatics – Experimental Biology Systems”, ISBN 978-953-307-280-7, publisher: InTech – Open Access Publisher.
  • Vigil PD, Stapleton AE, Johnson JR, Hooton TM, Hodges AP, et al. (2011) Presence of Putative Repeat-in-Toxin Gene tosA in Escherichia coli Predicts Successful Colonization of the Urinary Tract. MBio 2(3): e00066-11.
  • Hodges AP, Woolf P, He Y (2010) BN+ 1 Bayesian network expansion for identifying molecular pathway elements. Communicative & Integrative Biology 3: 59-64.
  • Hodges AP, Dai D, Xiang Z, Woolf P, Xi C, He Y. (2010) Bayesian network expansion identifies new ROS and biofilm regulators. PLoS One 5: e9513.
  • Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B, Colby LA, Rush HG, Gilsdorf JR, Jourdian GW, and He Y. (2008) VIOLIN: vaccine investigation and online information network. Nucleic Acids Res, 36, D923-928.
  • Woolf P, He Y, Hodges A. Methods and systems for identifying molecular pathway elements. Submitted for utility/design patent on 6/16/2008, online publication 4/23/2009 (US Patent Application # 12/139,529; WO Patent WO/2008/157,459). IP disclosure (August 2007): An automated method for building molecular pathways using incremental Bayesian learning. IP Disclosure #3792, University of Michigan.

Teaching Experience

  • Winter 2008. Graduate Student Instructor (GSI), Bioinformatics 551. Proteome Informatics. University of Michigan. Course Master: Alexey Nesvizhskii.
  • Fall 2008, Winter 2007. Graduate Student Instructor (GSI), Bioinformatics 526/527. Introduction to Bioinformatics and Computational Biology. University of Michigan. Course Master: Brian Athey.
  • Spring 2003. Lab Assistant Comparative Vertebrate Physiology. Manchester College. Course Instructor: Al Williams.
  • Fall 2002. Lab Assistant, Comparative Vertebrate Anatomy. Manchester College. Course Instructor: Al Williams.
  • Spring 2001. Lab Assistant, Introduction to Organic Chemistry. Manchester College. Course Instructor: Susan Klein.
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Page last modified on April 12, 2013, at 05:05 PM