Michael Keiser, PhD

Assistant Professor

Michael joined the UCSF faculty in the Dept. of Pharmaceutical Chemistry and the Institute for Neurodegenerative Diseases as an Assistant Professor in 2014, with joint appointments in the Dept. of Bioengineering & Therapeutic Sciences and the Institute for Computational Health Sciences. Before this, he co-founded a startup bringing systems pharmacology methods to pharma and the US FDA. During his bioinformatics Ph.D. at UCSF as a NSF Fellow, Michael developed techniques to relate drugs and proteins from the statistical similarity of their ligands, such as the Similarity Ensemble Approach (SEA). He also holds B.Sc., B.A., and M.A. degrees from Stanford University.

Lab papers

  1. Comment on "Predicting reaction performance in C-N cross-coupling using machine learning".

    Science. 2018 Nov 16. Chuang KV, Keiser MJ.

  2. Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline.

    bioRxiv. 2018 Oct 29. Tang Z, Chuang KV, DeCarli C, Jin L-W, Beckett L, Keiser MJ, Dugger BN.

  3. Adversarial Controls for Scientific Machine Learning.

    ACS Chem Biol. 2018 Oct 19. Chuang KV, Keiser MJ.

  4. The Psychiatric Cell Map Initiative- A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.

    Cell. 2018 Jul 26. 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.

  5. Predicted Biological Activity of Purchasable Chemical Space.

    J Chem Inf Model. 2018 Jan 22. Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ.

  6. Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior.

    Cell Rep. 2017 Oct 31. 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.

  7. A Simple Representation of Three-Dimensional Molecular Structure.

    J Med Chem. 2017 Sep 14. Axen SD, Huang XP, Caceres EL, Gendelev L, Roth BL, Keiser MJ.

  8. Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds.

    Nat Chem Biol. 2016 Jul. 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.

  9. Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology.

    ACS Chem Biol. 2016 Apr 15. McCarroll MN, Gendelev L, Keiser MJ, Kokel D.

  10. Polygenic overlap between schizophrenia risk and antipsychotic response- a genomic medicine approach.

    Lancet Psychiatry. 2016 Apr. Ruderfer DM, Charney AW, Readhead B, Kidd BA, Kahler AK, Kenny PJ, Keiser MJ, Moran JL, Hultman CM, Scott SA, Sullivan PF, Purcell SM, Dudley JT, Sklar P.

  11. Prediction and validation of enzyme and transporter off-targets for metformin.

    J Pharmacokinet Pharmacodyn. 2015 Oct. Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM.

  12. Systems pharmacology augments drug safety surveillance.

    Clin Pharmacol Ther. 2015 Feb. Lorberbaum T, Nasir M, Keiser MJ, Vilar S, Hripcsak G, Tatonetti NP.

  13. In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding.

    PLoS Biol. 2013 Nov. Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K.

  14. Large-scale prediction and testing of drug activity on side-effect targets.

    Nature. 2012 Jun 10. Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Cote S, Shoichet BK, Urban L.

  15. Chemical informatics and target identification in a zebrafish phenotypic screen.

    Nat Chem Biol. 2011 Dec 18. Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL Jr, Roth BL, Peterson RT, Shoichet BK.

  16. The presynaptic component of the serotonergic system is required for clozapine's efficacy.

    Neuropsychopharmacology. 2011 Feb. 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.

  17. The chemical basis of pharmacology.

    Biochemistry. 2010 Dec 7. Keiser MJ, Irwin JJ, Shoichet BK.

  18. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.

    J Med Chem. 2010 Jul 8. Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK.

  19. Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs.

    J Med Chem. 2010 Mar 25. DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD.

  20. 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. Thomas KL, Ellingrod VL, Bishop JR, Keiser MJ.

  21. Predicting new molecular targets for known drugs.

    Nature. 2009 Nov 12. 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.

  22. A mapping of drug space from the viewpoint of small molecule metabolism.

    PLoS Comput Biol. 2009 Aug. Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC.

  23. Quantifying biogenic bias in screening libraries.

    Nat Chem Biol. 2009 Jul. Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK.

  24. Off-target networks derived from ligand set similarity.

    Methods Mol Biol. 2009. Keiser MJ, Hert J.

  25. Quantifying the relationships among drug classes.

    J Chem Inf Model. 2008 Apr. Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK.

  26. Relating protein pharmacology by ligand chemistry.

    Nat Biotechnol. 2007 Feb. Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK.