Biomedical NLP

  • Percha B, Altman RB (2018) A global network of biomedical relationships derived from text. Bioinformatics 34(15): 2614–2624.
    Download (PDF); Journal Site; Supplement; Dataset
  • Miotto R, Percha BL, Glicksberg BS, Lee HC, Cruz L, Dudley JT, Nabeel I (2019) Identifying acute low back pain episodes in primary care practice from clinical notes. medRxiv. Jan 1:19010462.
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  • Percha B, Zhang Y, Bozkurt S, Rubin D, Altman RB, Langlotz CP (2018) Expanding a radiology lexicon using contextual patterns in radiology reports. J. Am. Med. Inform. Assoc. 25 (6), 679-685.
    Journal Site (Free Download)
  • Percha B (2016) Biomedical Text Mining from Context. PhD Dissertation, Stanford University. First Prize, AMIA Dissertation Award 2018
    Download (PDF); Press Release
  • Percha B, Altman RB (2015) Learning the structure of biomedical relationships from unstructured text. PLoS Comput. Biol. 11(7): e1004216. Download (PDF)
  • Jung K, LePendu P, Iyer S, Bauer-Mehren A, Percha B, Shah NH (2014) Functional evaluation of out-of-the-box text-mining tools for data-mining tasks. J. Am. Med. Inform. Assoc. 22 (1), 121-131.
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  • Percha B, Lee W-N (2014) Ch. 13: Natural Language Processing: Informatics Techniques and Resources. In A Bioinformatics Guide for Molecular Biologists. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
    Book (Amazon)
  • Percha B, Altman RB (2013) Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. AMIA Annu. Symp. Proc. 2013, 1123. Second prize, AMIA Student Paper Competition 2013.
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  • Lyalina S, Percha B, LePendu P, Iyer SV, Altman RB, Shah NH (2013) Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical records. J. Am. Med. Inform. Assoc. 20 (e2): e297-e305.
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  • Percha B, Nassif H, Lipson J, Burnside E, Rubin D (2012) Automatic classification of mammography reports by BI-RADS breast tissue composition class. J. Am. Med. Inform. Assoc. 19 (5), 913-916.
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Drug-Drug Interactions

  • Percha B, Altman RB (2013) Informatics confronts drug-drug interactions. Trends Pharm. Sci. 34(3): 178-184.
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  • Percha B, Garten Y, Altman RB (2012) Discovery and explanation of drug-drug interactions via text mining. Pacific Symposium on Biocomputing 2012 410-421.
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N-of-1 Studies

  • Percha B, Baskerville EB, Johnson M, Dudley JT, Zimmerman N (2019) Designing robust N-of-1 studies for precision medicine: simulation study and design recommendations. J. Med. Intern. Res. 21 (4), e12641.
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  • Percha B (2016) Redesigning clinical studies for the era of precision medicine. Blog Post #1; Blog Post #2


  • Simon CP, Percha B, Riolo R, Foxman B (2013) Modeling bacterial colonization and infection routes in healthcare settings: analytic and numerical approaches. J. Theoretical Biology 334: 187-199.
    Journal Site
  • Eisenberg JNS, Goldstick J, …, Percha B, …, Trostle J (2011) In-roads to the spread of antibiotic resistance: regional patterns of microbial transmission in northern coastal Ecuador. J. Royal Soc. Interface 9(70): 1029-1039.
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  • Percha B, Newman MEJ, Foxman B (2011) Transmission probabilities and durations of immunity for three Group B Streptococcus serotypes. Infection, Genetics, and Evolution 11(6): 1407-1412.
    Journal Site
  • Foxman B, Newman MEJ, Percha B, Holmes KK, Aral SO (2006) Measures of sexual partnerships: lengths, gaps, overlaps, and sexually transmitted infection. Sexually Trans. Dis. 33(4): 209-214.
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  • Percha B, Dzakpasu R, Żochowski M, Parent J (2005) Transition from local to global phase synchrony in small world neural network and its possible implications for epilepsy. Phys. Rev. E 72(3): 031909.
    Download (Preprint); Journal Site


  • Russak AJ, Johnson KW, Halperin J, Percha B, Dudley JT (2019) Racial and sex differences in stroke risk in patients with atrial fibrillation. J. Am. Col. Cardiol. 74(24): 3069-3070.
    Journal Site
  • Badgeley M, Zech JR, …, Percha B, Snyder TM, Dudley JT (2019) Deep learning predicts hip fracture using confounding patient and healthcare variables. npj Digital Medicine 2(1): 31.
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  • Glicksberg BS, Oskotsky B, …, Percha B, …, Butte A (2019) PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model.
    Journal Site (PDF Available)
  • Daneshjou R, Gamazon ER, …, Percha B, …, Perera MA (2014) Genetic variant in folate homeostasis is associated with lower warfarin dose in African Americans. Blood 124 (14), 2298-2305.
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