Publications

See also my Google Scholar profile. The complete record - including all conference posters and seminars, with student co-authors - is in my CV.

Publications

Michael G. Lerner in bold; * denotes a student co-author.

  • Bernat Navarro-Serer, Maria F. Wissler, Brandi K. Glover, Michael G. Lerner, Harsh H. Oza, Vania Wang, Hildur Knutsdottir, Fatemeh Shojaeian, Kathleen Noller, Saravana Gowtham Baskaran, Sara Hughes, Alana M. Weaver*, Daniel Wilentz, Oluwatobiloba Olayemi, Joel S. Bader, Elana J. Fertig, Daniele M. Gilkes, Laura D. Wood. “P4HA1 mediates hypoxia-induced invasion in human pancreatic cancer organoids.” Cancer Research Communications, 2025.

  • Matthew C. Perrone, Michael G. Lerner, Matthew Dunworth, Andrew J. Ewald, Joel S. Bader. “Prioritizing drug targets by perturbing biological network response functions.” PLoS Computational Biology 20(6), 2024.

  • David Robert Bruce, James Borrelli, Gennifer Smith, Michael G. Lerner, Anne Raich. “Commonality of Failure Modes in New Engineering Program Development.” 2023 ASEE Annual Conference & Exposition, 2023.

  • Yea Ji Jeong, Hildur Knutsdottir, Fatemeh Shojaeian, Michael G. Lerner, Maria F. Wissler, Elodie Henriet, Tammy Ng, Shalini Datta, Bernat Navarro-Serer, Peter Chianchiano, Benedict Kinny-Köster, Jacquelyn W. Zimmerman, Genevieve Stein-O’Brien, Matthias M. Gaida, James R. Eshleman, Ming-Tseh Lin, Elana J. Fertig, Andrew J. Ewald, Joel S. Bader, Laura D. Wood. “Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion.” The Journal of Clinical Investigation 133(8), 2023.

  • Ling Li, Gilad Halpert, Michael G. Lerner, Haijie Hu, Peter Dimitrion, Matthew J. Weiss, Jin He, Benjamin Philosophe, Richard Burkhart, William R. Burns, Russell N. Wesson, Andrew MacGregor Cameron, Christopher L. Wolfgang, Christos Georgiades, Satomi Kawamoto, Nilofer S. Azad, Mark Yarchoan, Stephen J. Meltzer, Kiyoko Oshima, Laura M. Ensign, Joel S. Bader, Florin M. Selaru. “Protein synthesis inhibitor omacetaxine is effective against hepatocellular carcinoma.” JCI Insight 6(12), 2021.

  • William C. Hahn, Joel S. Bader, Theodore P. Braun, Andrea Califano, Paul A. Clemons, Brian J. Druker, Andrew J. Ewald, Haian Fu, Subhashini Jagu, Christopher J. Kemp, William Kim, Calvin J. Kuo, Michael T. McManus, Gordon B. Mills, Xiulei Mo, Nidhi Sahni, Stuart L. Schreiber, Jessica A. Talamas, Pablo Tamayo, Jeffrey W. Tyner, Bridget K. Wagner, William A. Weiss, Daniela S. Gerhard, … Michael G. Lerner … “An expanded universe of cancer targets.” Cell 184(5), 2021.

  • Richard M. Venable, Helgi I. Ingolfsson, Michael G. Lerner, B. Scott Perrin Jr., Brian A. Camley, Siewert-J. Marrink, Frank L. H. Brown, Richard W. Pastor. “Lipid and peptide diffusion in bilayers: the Saffman-Delbrück model and periodic boundary conditions.” Journal of Physical Chemistry B 121(5), 2017.

  • Brian A. Camley, Michael G. Lerner, Richard W. Pastor, Frank L. H. Brown. “Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes.” Journal of Chemical Physics 143(24), 2015.

  • Zachary Levine, Richard M. Venable, Max C. Watson, Michael G. Lerner, Joan-Emma Shea, Richard W. Pastor, Frank L. H. Brown. “Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations.” Journal of the American Chemical Society 136(39), 2014.

  • Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks. “Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding.” PLoS Computational Biology 10(7), 2014.
    Paper highlighted in the PLoS editorial “Making Biomolecular Simulations Accessible in the Post-Nobel Era,” Ruth Nussinov and Quiang Cui.

  • Jefferson D. Knight, Michael G. Lerner, Joan G. Marcano-Velázquez, Richard W. Pastor, Joseph J. Falke. “Single molecule diffusion of membrane-bound proteins: Window into lipid contacts and bilayer dynamics.” Biophysical Journal 99(9), 2010.

  • Michael G. Lerner, Kristin L. Meagher, Heather A. Carlson. “Automated clustering of probe molecules from solvent mapping of protein surfaces.” Journal of Computer-Aided Molecular Design 10, 2008.

  • Michael G. Lerner, Anna L. Bowman, Heather A. Carlson. “Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-based Drug Discovery.” Journal of Chemical Information and Modeling 47, 2007.

  • Anna L. Bowman, Michael G. Lerner, Heather A. Carlson. “Protein flexibility and species specificity in structure-based drug discovery: Dihydrofolate reductase as a test system.” Journal of the American Chemical Society 129(12), 2007.

  • Kristin L. Meagher, Michael G. Lerner, Heather A. Carlson. “Refining the multiple protein structure method: consistency across three independent HIV-1 protease models.” Journal of Medicinal Chemistry 49(12), 2006.

  • Leigi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner, Heather A. Carlson. “Binding MOAD (Mother of All Databases).” Proteins: Structure, Function and Bioinformatics 60, 2005.

Grants

  • Increasing Success of STEM Students through Cohort Building, Mentoring, and Career Discerning Experiences: an Interdisciplinary Collaboration. NSF/DUE (Co-PI), $747,247. August 2022.
  • Computational Prediction of Genetic Drivers of Breast Cancer. NIH/NCI (PI), F33, 1F33CA247344-01, $62,848. February 2020.
  • Training in RNA-Seq analysis and computational network analysis. Burroughs Wellcome Fund (PI), $12,500. May 2019.
  • Modeling Climate Change in New Zealand: Collaborative Faculty-Student Research Project. Earlham College (PI), $9,000. August 2018.
  • Non-Newtonian Physicists: Assessment mini-grants focusing on Diversity. Earlham College (PI), $500. January 2018.
  • Making Molecules Move: Collaborative Faculty-Student Research Project. Earlham College (PI), $10,600. January 2016.
  • Expedited Research Grants: Computational Topology and Drug Design. Earlham College (PI), $850. December 2014.
  • Experiential Learning Fund: Getting Started with Python - Programming for Everyone. Earlham College (PI), $2,000. October 2014.
  • CC*IIE Campus Design: Network Infrastructure for Improved Science Discovery and Education. NSF (Co-PI), $347,228. August 2014.
  • Kickstarter Technology Grant: IPython Notebooks for Computer Science and Physics. Earlham College (PI), $500. August 2013.
  • Pedagogical Incubator Initiative: Science Scholars Seminar. Earlham College (Co-PI), $2,500. February 2012.

Invited Talks

Invited colloquia, seminars, and conference talks where I was the speaker (excludes posters, panels, session-chair roles, and “participant only” entries; the complete list is in my CV).

  • “Patterns of metastasis in human pancreatic cancer.” Invited talk, CTD² Site Visit, Johns Hopkins University and School of Medicine, Baltimore, MD. January 2021.
  • “Diffusion in biological systems: from simulating biomembranes to predicting the drivers of cancer metastasis.” Invited colloquium, Department of Physics, University of Mary Washington, Fredericksburg, VA. February 2020.
  • “Diffusion in biological systems: from simulating biomembranes to predicting the drivers of cancer metastasis.” Invited colloquium, Department of Physics, Cal State Fullerton, Fullerton, CA. February 2020.
  • “Correlated motions and two-point microrheology: calculating diffusion coefficients from membrane simulations.” Invited colloquium, Molecular Dynamics Group, Department of Biological Chemistry, University of Groningen, The Netherlands. July 2018.
  • “Two-point microrheology and correlated motions: a few ways to calculate diffusion coefficients from membrane simulations.” Invited colloquium, Laboratory of Computational Biology, NHLBI, NIH, Bethesda, MD. July 2018.
  • “Diffusion and correlated motions in lipid simulations.” Invited speaker, Biological Membranes and Membrane Proteins: Challenges for Theory and Experiment, Santa Fe, NM. June 2017.
  • “Diffusion, correlated motions and periodic boundary conditions in lipid membranes.” Invited colloquium, Department of Physics, Georgia Tech, Atlanta, GA. April 2017.
  • “Faster, more accurate quantification of diffusion and correlated motions in molecular simulations of lipid bilayers.” Invited colloquium, Department of Chemistry, West Virginia University, Morgantown, WV. November 2015.
  • “Faster, more accurate quantification of diffusion and correlated motions in molecular simulations of lipid bilayers.” Invited colloquium, Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN. October 2015.
  • “Faster, more accurate diffusion constants.” Invited speaker, Biological Membranes and Membrane Proteins: Challenges for Theory and Experiment, Telluride, CO. July 2015.
  • Invited speaker, NIH 2014 Orloff Science Awards, Bethesda, MD. January 2014.
  • “Computational and theoretical studies of protein and lipid dimers and trimers diffusing in lipid membranes.” Invited seminar, South Dakota State University, Brookings, SD. December 2012.
  • “Diffusion of tethered dimer and trimer systems.” Invited speaker, Biological Membranes and Membrane Proteins: Challenges for Theory and Experiment, Snowmass, CO. July 2011.