* denotes equal contribution

  • Yang, M., et al. (2020) Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Systems, Aug 26;11(2):186-195.e9. doi:10.1016/j.cels.2020.06.013 (link)
  • Bachman, J.A., Gyori, B.M., Sorger, P.K. (2019) Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining. biorxiv preprint. (link)
  • Kale, J.*, Bachman, J.A.*, Leber, B., Sorger, P.K., Andrews, D.W. Cancer-associated Bax point mutations block apoptotic pore formation by trapping kinetic intermediates. Submitted. (Preprint PDF | Supplement)
  • Steppi, A., Gyori, B.M., Bachman, J.A. (2019) Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. Journal of Open Source Software, 5(45), 1708. doi:10.21105/joss.01708 (link | PDF)
  • Ietswaart, R., Gyori, B.M., Bachman, J.A., Sorger, P.K., Churchman, L.S. (2019) GeneWalk identifies relevant gene functions for a biological context using network representation learning. biorxiv preprint, doi:10.1101/755579 (link)
  • Sulahian, R., Kwon, J.J., Walsh, K.H., Pailler, E., Bosse, T.L., Thaker, M., Almanza, D., Dempster, J.D., Pan, J., Piccioni, F., Dumont, N., Gonzalez, A., Rennhack, J., Nabet, B., Bachman, J.A., Goodale, A., Lee, Y., Bagul, M., Liao, R., Navarro, A., Yuan, T.L., Ng, R.W.S., Raghavan, S., Gray, N.S., Tsherniak, A., Vazquez, F., Root, D.E., Firestone, A.J., Settleman, J., Hahn, W.C., Aguirre, A.J. (2019) Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers, Cell Reports, 29, 118–134. doi:10.1016/j.celrep.2019.08.090 (link | PDF)
  • Noriega-Atala, E., Liang, Z., Bachman, J.A., Morrison, C.T., Surdeanu, M. (2019) Understanding the Polarity of Events in the Biomedical Literature: Deep Learning vs. Linguistically-informed Methods. In Proceedings of the Workshop on Extracting Structured Knowledge from Scientific Publications, 2019, NAACL-HLT. doi:10.18653/v1/W19-2603 (link | PDF)
  • Sharp, R., Pyarelal, A., Gyori, B.M., Alcock, K., Laparra, E., Valenzuela-Escárcega, M.A., Nagesh, A., Yadav, V., Bachman, J.A., Tang Z., Lent, H., Luo, F., Paul, M., Bethard, S., Barnard, K., Morrison, C., Surdeanu, M. (2019) Eidos, INDRA, & Delphi: From Free Text to Executable Causal Models. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics (Demonstrations), N19-4008, 42-47. doi:10.18653/v1/N19-4008 (link | PDF)
  • Hoyt, C.T., Domingo-Fernández, D., Aldisi, R., Xu, L., Kolpeja, K., Spalek, S., Wollert, E., Bachman, J.A., Gyori, B.M., Greene, P., Hofmann-Apitius, M. (2019) Re-curation and rational enrichment of knowledge graphs in Biological Expression Language, Database, 2019, 1–13. doi: doi:10.1093/database/baz068 (link | PDF)
  • Todorov, P.V., Gyori, B.M., Bachman, J.A., Sorger, P.K. (2019) INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinformatics, btz289. doi:10.1093/bioinformatics/btz289 (link | PDF)
  • 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)