Harvard Catalyst Profiles

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John Ata Bachman, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Todorov PV, Gyori BM, Bachman JA, Sorger PK. INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinformatics. 2019 Nov 01; 35(21):4501-4503. PMID: 31070726.
    Citations:    
  2. Sulahian R, Kwon JJ, Walsh KH, Pailler E, Bosse TL, Thaker M, Almanza D, Dempster JM, Pan J, Piccioni F, Dumont N, Gonzalez A, Rennhack J, Nabet B, Bachman JA, Goodale A, Lee Y, Bagul M, Liao R, Navarro A, Yuan TL, Ng RWS, Raghavan S, Gray NS, Tsherniak A, Vazquez F, Root DE, Firestone AJ, Settleman J, Hahn WC, Aguirre AJ. Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers. Cell Rep. 2019 Oct 01; 29(1):118-134.e8. PMID: 31577942.
    Citations:    
  3. Hoyt CT, Domingo-Fernández D, Aldisi R, Xu L, Kolpeja K, Spalek S, Wollert E, Bachman J, Gyori BM, Greene P, Hofmann-Apitius M. Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database (Oxford). 2019 01 01; 2019. PMID: 31225582.
    Citations:    
  4. Bachman JA, Gyori BM, Sorger PK. FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. BMC Bioinformatics. 2018 06 28; 19(1):248. PMID: 29954318.
    Citations:    Fields:    
  5. Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK. From word models to executable models of signaling networks using automated assembly. Mol Syst Biol. 2017 11 24; 13(11):954. PMID: 29175850.
    Citations: 5     Fields:    Translation:HumansCells
  6. Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ. Fundamental trade-offs between information flow in single cells and cellular populations. Proc Natl Acad Sci U S A. 2017 05 30; 114(22):5755-5760. PMID: 28500273.
    Citations: 6     Fields:    Translation:HumansCells
  7. Sarosiek KA, Chi X, Bachman JA, Sims JJ, Montero J, Patel L, Flanagan A, Andrews DW, Sorger P, Letai A. BID preferentially activates BAK while BIM preferentially activates BAX, affecting chemotherapy response. Mol Cell. 2013 Sep 26; 51(6):751-65. PMID: 24074954.
    Citations: 65     Fields:    Translation:HumansCells
  8. Lopez CF, Muhlich JL, Bachman JA, Sorger PK. Programming biological models in Python using PySB. Mol Syst Biol. 2013; 9:646. PMID: 23423320.
    Citations: 30     Fields:    Translation:Cells
  9. Deeds EJ, Bachman JA, Fontana W. Optimizing ring assembly reveals the strength of weak interactions. Proc Natl Acad Sci U S A. 2012 Feb 14; 109(7):2348-53. PMID: 22308356.
    Citations: 10     Fields:    Translation:Cells
  10. Bachman JA, Sorger P. New approaches to modeling complex biochemistry. Nat Methods. 2011 Feb; 8(2):130-1. PMID: 21278724.
    Citations: 10     Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.