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Michael Keiser, PhD

Title(s)Associate Professor, Institute for Neurodegenerative Diseases
SchoolSchool of Medicine
Address675 Nelson Rising Lane
San Francisco CA 94158
Phone415-502-7651
ORCID ORCID Icon0000-0002-1240-2192 Additional info
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


    Collapse Biography 
    Collapse Education and Training
    University of California, San Francisco, CA2020Diversity, Equity, and Inclusion Champion Training
    Collapse Awards and Honors
    Chan Zuckerberg Initiative2018Ben Barres Early Career Acceleration Award
    UCSF Program for Breakthrough Biomedical Research2016New Frontier Research Award
    Paul G. Allen Family Foundation2015Allen Distinguished Investigator
    Glenn Foundation2014Award for Research in Biological Mechanisms of Aging
    SF Business Times201440 Under Forty
    UCSF2010Frank M Goyan Award
    Wired2009Top 10 Scientific Breakthroughs of 2009
    NSF2006  - 2009Graduate Research Fellow
    US Dept. Education2003  - 2004Foreign Languages and Area Studies Fellow

    Collapse Overview 
    Collapse Overview
    Our lab investigates how small molecules perturb protein target networks to biological and therapeutic effect. In a forward polypharmacology campaign, we are using machine learning and computational methods such as the Similarity Ensemble Approach (SEA) to infer new combinations of targets underlying compound-induced phenotypes in cells and broader model systems. Thinking of each target as a musical note, we predict and test entire chords at a time via chemical-genetic epistasis experiments in models of complex diseases such as neurodegeneration.

    These systems pharmacology inquiries tell us where current understanding of drug action is weak, and because we use human pharmacology to mine for mechanisms, we can apply the therapeutic chords we find directly to the prediction of patient drug responses, adverse drug reactions, and personalized medicine.

    Collapse Research 
    Collapse Research Activities and Funding
    Relating GPCRs by biased ligands for enhanced therapeutic efficacy
    NIH/NIMH R43MH099712Jan 18, 2013 - Jan 17, 2015
    Role: Principal Investigator
    Calculating target bias in small molecules for library design
    NIH/NIGMS R43GM097912Sep 15, 2011 - Aug 31, 2013
    Role: Principal Investigator
    A platform to predict side-effect targets for drugs
    NIH/NIGMS R44GM093456Jun 1, 2010 - Jul 31, 2015
    Role: Co-Principal Investigator
    Drug Repurposing using Pharmacological Networks
    NIH/NIGMS R43GM093456Jun 1, 2010 - May 31, 2012
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Faculty Mentoring

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details 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. Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction. J Chem Inf Model. 2020 Nov 27. Cáceres EL, Mew NC, Keiser MJ. PMID: 33245237.
      View in: PubMed   Mentions:    Fields:    
    2. 836 Calibration performance of deep neural networks for image classification declines on real-world, versus curated, test sets. Journal of Investigative Dermatology. 2020 Jul 1; 140(7):s109. A.T. Young, J. Pfau, M.J. Keiser, M. Wei. .
      View in: Publisher Site   Mentions:
    3. 902 Assessing performance of deep neural networks used for image classification by stress testing. Journal of Investigative Dermatology. 2020 Jul 1; 140(7):s119. A.T. Young, J. Pfau, M.J. Keiser, M. Wei. .
      View in: Publisher Site   Mentions:
    4. 383 Assessing deep learning artefact bias using global saliency. Journal of Investigative Dermatology. 2020 Jul 1; 140(7):s49. J. Pfau, A.T. Young, M. Wei, M.J. Keiser. .
      View in: Publisher Site   Mentions:
    5. Learning Molecular Representations for Medicinal Chemistry. J Med Chem. 2020 Aug 27; 63(16):8705-8722. Chuang KV, Gunsalus LM, Keiser MJ. PMID: 32366098.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    6. Validation of machine learning models to detect amyloid pathologies across institutions. Acta Neuropathol Commun. 2020 04 28; 8(1):59. Vizcarra JC, Gearing M, Keiser MJ, Glass JD, Dugger BN, Gutman DA. PMID: 32345363.
      View in: PubMed   Mentions: 1     Fields:    
    7. Artificial Intelligence in Dermatology: A Primer. J Invest Dermatol. 2020 Aug; 140(8):1504-1512. Young AT, Xiong M, Pfau J, Keiser MJ, Wei ML. PMID: 32229141.
      View in: PubMed   Mentions:    Fields:    
    8. Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain. Mol Pain. 2020 Jan-Dec; 16:1744806920936502. Kober KM, Lee MC, Olshen A, Conley YP, Sirota M, Keiser M, Hammer MJ, Abrams G, Schumacher M, Levine JD, Miaskowski C. PMID: 32586194.
      View in: PubMed   Mentions: 2     Fields:    
    9. Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation. Nat Commun. 2019 09 09; 10(1):4078. McCarroll MN, Gendelev L, Kinser R, Taylor J, Bruni G, Myers-Turnbull D, Helsell C, Carbajal A, Rinaldi C, Kang HJ, Gong JH, Sello JK, Tomita S, Peterson RT, Keiser MJ, Kokel D. PMID: 31501447.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    10. Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline. Nat Commun. 2019 05 15; 10(1):2173. Tang Z, Chuang KV, DeCarli C, Jin LW, Beckett L, Keiser MJ, Dugger BN. PMID: 31092819.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    11. Comment on "Predicting reaction performance in C-N cross-coupling using machine learning". Science. 2018 11 16; 362(6416). Chuang KV, Keiser MJ. PMID: 30442776.
      View in: PubMed   Mentions: 4     Fields:    
    12. Adversarial Controls for Scientific Machine Learning. ACS Chem Biol. 2018 10 19; 13(10):2819-2821. Chuang KV, Keiser MJ. PMID: 30336670.
      View in: PubMed   Mentions: 3     Fields:    
    13. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 07 26; 174(3):505-520. Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. PMID: 30053424.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    14. THE USE OF CONVOLUTIONAL NEURAL NETWORKS TO QUANTIFY AMYLOID PLAQUES IN POSTMORTEM HUMAN BRAIN. Alzheimer's & Dementia. 2018 Jul 1; 14(7):p1446. Kangway Chuang, Ziqi Tang, Michael Keiser, Laurel Beckett, Charlie S. DeCarli, Lee-Way Jin, Brittany N. Dugger. .
      View in: Publisher Site   Mentions:
    15. Predicted Biological Activity of Purchasable Chemical Space. J Chem Inf Model. 2018 01 22; 58(1):148-164. Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ. PMID: 29193970.
      View in: PubMed   Mentions: 2     Fields:    
    16. Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior. Cell Rep. 2017 Oct 31; 21(5):1304-1316. Hindle SJ, Munji RN, Dolghih E, Gaskins G, Orng S, Ishimoto H, Soung A, DeSalvo M, Kitamoto T, Keiser MJ, Jacobson MP, Daneman R, Bainton RJ. PMID: 29091768.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    17. A Simple Representation of Three-Dimensional Molecular Structure. J Med Chem. 2017 09 14; 60(17):7393-7409. Axen SD, Huang XP, Cáceres EL, Gendelev L, Roth BL, Keiser MJ. PMID: 28731335.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    18. Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds. Nat Chem Biol. 2016 07; 12(7):559-66. Bruni G, Rennekamp AJ, Velenich A, McCarroll M, Gendelev L, Fertsch E, Taylor J, Lakhani P, Lensen D, Evron T, Lorello PJ, Huang XP, Kolczewski S, Carey G, Caldarone BJ, Prinssen E, Roth BL, Keiser MJ, Peterson RT, Kokel D. PMID: 27239787.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    19. Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. Lancet Psychiatry. 2016 Apr; 3(4):350-7. Ruderfer DM, Charney AW, Readhead B, Kidd BA, Kähler AK, Kenny PJ, Keiser MJ, Moran JL, Hultman CM, Scott SA, Sullivan PF, Purcell SM, Dudley JT, Sklar P. PMID: 26915512.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    20. Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology. ACS Chem Biol. 2016 Apr 15; 11(4):842-9. McCarroll MN, Gendelev L, Keiser MJ, Kokel D. PMID: 26845413.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    21. Prediction and validation of enzyme and transporter off-targets for metformin. J Pharmacokinet Pharmacodyn. 2015 Oct; 42(5):463-75. Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM. PMID: 26335661.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    22. In Silico Prediction of Drug Side Effects. Antitargets and Drug Safety. 2015 Apr 22; 19-44. Michael J. Keiser. .
      View in: Publisher Site   Mentions:
    23. Systems pharmacology augments drug safety surveillance. Clin Pharmacol Ther. 2015 Feb; 97(2):151-8. Lorberbaum T, Nasir M, Keiser MJ, Vilar S, Hripcsak G, Tatonetti NP. PMID: 25670520.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    24. In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol. 2013 Nov; 11(11):e1001712. Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K. PMID: 24260022.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimals
    25. Large-scale prediction and testing of drug activity on side-effect targets. Nature. 2012 Jun 10; 486(7403):361-7. Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L. PMID: 22722194.
      View in: PubMed   Mentions: 213     Fields:    Translation:HumansCells
    26. Chapter 4. Designing Multi-Target Drugs. 2012 Jan 1; 50-65. Elisabet Gregori-Puigjané, Michael J. Keiser. .
      View in: Publisher Site   Mentions:
    27. Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol. 2011 Dec 18; 8(2):144-6. Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL, Roth BL, Peterson RT, Shoichet BK. PMID: 22179068.
      View in: PubMed   Mentions: 44     Fields:    Translation:Animals
    28. The chemical basis of pharmacology. Biochemistry. 2010 Dec 07; 49(48):10267-76. Keiser MJ, Irwin JJ, Shoichet BK. PMID: 21058655.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    29. The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology. 2011 Feb; 36(3):638-51. Yadav PN, Abbas AI, Farrell MS, Setola V, Sciaky N, Huang XP, Kroeze WK, Crawford LK, Piel DA, Keiser MJ, Irwin JJ, Shoichet BK, Deneris ES, Gingrich J, Beck SG, Roth BL. PMID: 21048700.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    30. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem. 2010 Jul 08; 53(13):4891-905. Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK. PMID: 20540517.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    31. Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs. J Med Chem. 2010 Mar 25; 53(6):2464-71. DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD. PMID: 20180535.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    32. A pilot study of the pharmacodynamic impact of SSRI drug selection and beta-1 receptor genotype (ADRB1) on cardiac vital signs in depressed patients: a novel pharmacogenetic approach. Psychopharmacol Bull. 2010; 43(1):11-22. Thomas KL, Ellingrod VL, Bishop JR, Keiser MJ. PMID: 20581797.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    33. Predicting new molecular targets for known drugs. Nature. 2009 Nov 12; 462(7270):175-81. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KL, Edwards DD, Shoichet BK, Roth BL. PMID: 19881490.
      View in: PubMed   Mentions: 456     Fields:    Translation:HumansAnimals
    34. A mapping of drug space from the viewpoint of small molecule metabolism. PLoS Comput Biol. 2009 Aug; 5(8):e1000474. Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC. PMID: 19701464.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    35. Quantifying biogenic bias in screening libraries. Nat Chem Biol. 2009 Jul; 5(7):479-83. Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. PMID: 19483698.
      View in: PubMed   Mentions: 51     Fields:    Translation:Cells
    36. Off-target networks derived from ligand set similarity. Methods Mol Biol. 2009; 575:195-205. Keiser MJ, Hert J. PMID: 19727616.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    37. ChemInform Abstract: Quantifying the Relationships among Drug Classes. ChemInform. 2008 Jul 15; 39(29). Jerome Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet. .
      View in: Publisher Site   Mentions:
    38. Quantifying the relationships among drug classes. J Chem Inf Model. 2008 Apr; 48(4):755-65. Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. PMID: 18335977.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
    39. Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007 Feb; 25(2):197-206. Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. PMID: 17287757.
      View in: PubMed   Mentions: 389     Fields:    Translation:Cells
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