* denotes equal contribution

  • Todorov, P.V., Gyori, B.M., Bachman, J.A., Sorger, P.K. (2018) INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Submitted.
  • Bachman, J.A.*, Gyori, B.M.*, Sorger, P.K. (2018) FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. BMC Bioinformatics, 19:248. doi:10.1186/s12859-018-2211-5 (link | PDF)
  • Gyori, B.M.*, Bachman, J.A.*, Subramanian, K., Muhlich, J.L., Galescu, L., Sorger, P.K. (2017) From word models to executable models of signaling networks using automated assembly. Molecular Systems Biology, 13, 11. doi:10.15252/msb.20177651 (link | PDF | Supplement)
  • Suderman, R., Bachman, J.A.*, Smith, A., Sorger, P.K., Deeds, E.J. (2017) Fundamental trade-offs between information flow in single cells and cellular populations. Proceedings of the National Academy of Sciences of the United States of America, 114(22), 5755-5760. doi:10.1073/pnas.1615660114 (link | PDF)
  • Sarosiek, K.A., Chi, X., Bachman, J.A., Sims, J.J., Montero, J., Patel, L., Andrews, D.W., Sorger, P.K., Letai, A. (2013) BID preferentially activates BAK while BIM preferentially activates BAX, affecting chemotherapy response. Molecular Cell, 51:6, 751-765. doi:10.1016/j.molcel.2013.08.048. (link | PDF | Supplement)
  • Lopez, C. F.*, Muhlich, J. L.*, Bachman, J. A.*, Sorger, P. K. (2013). Programming biological models in Python using PySB. Molecular Systems Biology, 9, 646. doi:10.1038/msb.2013.1 (link | PDF | Supplement)
  • Deeds, E. J.*, Bachman, J. A.*, Fontana, W. (2012). Optimizing ring assembly reveals the strength of weak interactions. Proceedings of the National Academy of Sciences of the United States of America, 109(7), 2348-2353. doi:10.1073/pnas.1113095109 (link | PDF)
  • Bachman, J. A., Sorger, P.K. (2011). New approaches to modeling complex biochemistry. Nature Methods, 8(2), 130131. doi:10.1038/nmeth0211-130 (link | PDF)

Ph.D. Thesis

Bachman, John A. (2016) Identifying Mechanisms of Apoptotic Pore Formation With Programmatic Ensemble Modeling. Doctoral dissertation, Harvard University, Graduate School of Arts and Sciences. (PDF)