Michael Keiser, PhD
Associate Professor
Institute for Neurodegenerative Diseases
School of Medicine

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.

• The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.
  Bioinformatics (Oxford, England) 2023 Morris JH, Soman K, Akbas RE, Zhou X, Smith B, Meng EC, Huang CC, Cerono G, Schenk G, Rizk-Jackson A, Harroud A, Sanders L, Costes SV, Bharat K, Chakraborty A, Pico AR, Mardirossian T, Keiser M, Tang …
• Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels.
  bioRxiv : the preprint server for biology 2023 Wong DR, Magaki SD, Vinters HV, Yong WH, Monuki ES, Williams CK, Martini AC, DeCarli C, Khacherian C, Graff JP, Dugger BN, Keiser MJ
• Prioritizing Virtual Screening with Interpretable Interaction Fingerprints.
  Journal of chemical information and modeling 2022 Fassio AV, Shub L, Ponzoni L, McKinley J, O'Meara MJ, Ferreira RS, Keiser MJ, de Melo Minardi RC
• Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics.
  Nature machine intelligence 2022 Wong DR, Conrad J, Johnson N, Ayers J, Laeremans A, Lee JC, Lee J, Prusiner SB, Bandyopadhyay S, Butte AJ, Paras NA, Keiser MJ
• Deep learning from multiple experts improves identification of amyloid neuropathologies.
  Acta neuropathologica communications 2022 Wong DR, Tang Z, Mew NC, Das S, Athey J, McAleese KE, Kofler JK, Flanagan ME, Borys E, White CL, Butte AJ, Dugger BN, Keiser MJ
• A biomedical open knowledge network harnesses the power of AI to understand deep human biology.
  AI magazine 2022 Baranzini SE, Börner K, Morris J, Nelson CA, Soman K, Schleimer E, Keiser M, Musen M, Pearce R, Reza T, Smith B, Herr BW, Oskotsky B, Rizk-Jackson A, Rankin KP, Sanders SJ, Bove R, Rose PW, Israni S, …
• Stress testing reveals gaps in clinic readiness of image-based diagnostic artificial intelligence models.
  NPJ digital medicine 2021 Young AT, Fernandez K, Pfau J, Reddy R, Cao NA, von Franque MY, Johal A, Wu BV, Wu RR, Chen JY, Fadadu RP, Vasquez JA, Tam A, Keiser MJ, Wei ML
• Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction.
  Journal of chemical information and modeling 2020 Cáceres EL, Mew NC, Keiser MJ
• 383 Assessing deep learning artefact bias using global saliency.
  Journal of Investigative Dermatology 2020 J. Pfau, A.T. Young, M. Wei, M.J. Keiser
• 836 Calibration performance of deep neural networks for image classification declines on real-world, versus curated, test sets.
  Journal of Investigative Dermatology 2020 A.T. Young, J. Pfau, M.J. Keiser, M. Wei
• 902 Assessing performance of deep neural networks used for image classification by stress testing.
  Journal of Investigative Dermatology 2020 A.T. Young, J. Pfau, M.J. Keiser, M. Wei
• Learning Molecular Representations for Medicinal Chemistry.
  Journal of medicinal chemistry 2020 Chuang KV, Gunsalus LM, Keiser MJ
• Validation of machine learning models to detect amyloid pathologies across institutions.
  Acta neuropathologica communications 2020 Vizcarra JC, Gearing M, Keiser MJ, Glass JD, Dugger BN, Gutman DA
• Artificial Intelligence in Dermatology: A Primer.
  The Journal of investigative dermatology 2020 Young AT, Xiong M, Pfau J, Keiser MJ, Wei ML
• 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.
  Molecular pain 2020 Kober KM, Lee MC, Olshen A, Conley YP, Sirota M, Keiser M, Hammer MJ, Abrams G, Schumacher M, Levine JD, Miaskowski C
• Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation.
  Nature communications 2019 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
• Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline.
  Nature communications 2019 Tang Z, Chuang KV, DeCarli C, Jin LW, Beckett L, Keiser MJ, Dugger BN
• Comment on "Predicting reaction performance in C-N cross-coupling using machine learning".
  Science (New York, N.Y.) 2018 Chuang KV, Keiser MJ
• Adversarial Controls for Scientific Machine Learning.
  ACS chemical biology 2018 Chuang KV, Keiser MJ
• The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.
  Cell 2018 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, …
• THE USE OF CONVOLUTIONAL NEURAL NETWORKS TO QUANTIFY AMYLOID PLAQUES IN POSTMORTEM HUMAN BRAIN.
  Alzheimer's & Dementia 2018 Kangway Chuang, Ziqi Tang, Michael Keiser, Laurel Beckett, Charlie S. DeCarli, Lee-Way Jin, Brittany N. Dugger
• Predicted Biological Activity of Purchasable Chemical Space.
  Journal of chemical information and modeling 2017 Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ
• Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior.
  Cell reports 2017 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
• A Simple Representation of Three-Dimensional Molecular Structure.
  Journal of medicinal chemistry 2017 Axen SD, Huang XP, Cáceres EL, Gendelev L, Roth BL, Keiser MJ
• Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds.
  Nature chemical biology 2016 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…
• Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach.
  The lancet. Psychiatry 2016 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
• Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology.
  ACS chemical biology 2016 McCarroll MN, Gendelev L, Keiser MJ, Kokel D
• Prediction and validation of enzyme and transporter off-targets for metformin.
  Journal of pharmacokinetics and pharmacodynamics 2015 Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM
• In Silico Prediction of Drug Side Effects.
  Antitargets and Drug Safety 2015 Michael J. Keiser
• Systems pharmacology augments drug safety surveillance.
  Clinical pharmacology and therapeutics 2014 Lorberbaum T, Nasir M, Keiser MJ, Vilar S, Hripcsak G, Tatonetti NP
• In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding.
  PLoS biology 2013 Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K
• Large-scale prediction and testing of drug activity on side-effect targets.
  Nature 2012 Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L
• Chapter 4.
  Designing Multi-Target Drugs 2012 Elisabet Gregori-Puigjané, Michael J. Keiser
• Chemical informatics and target identification in a zebrafish phenotypic screen.
  Nature chemical biology 2011 Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL, Roth BL, Peterson RT, Shoichet BK
• The chemical basis of pharmacology.
  Biochemistry 2010 Keiser MJ, Irwin JJ, Shoichet BK
• The presynaptic component of the serotonergic system is required for clozapine's efficacy.
  Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2010 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
• Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.
  Journal of medicinal chemistry 2010 Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK
• Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs.
  Journal of medicinal chemistry 2010 DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD
• 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.
  Psychopharmacology bulletin 2010 Thomas KL, Ellingrod VL, Bishop JR, Keiser MJ
• Predicting new molecular targets for known drugs.
  Nature 2009 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
• A mapping of drug space from the viewpoint of small molecule metabolism.
  PLoS computational biology 2009 Adams JC, Keiser MJ, Basuino L, Chambers HF, Lee DS, Wiest OG, Babbitt PC
• Quantifying biogenic bias in screening libraries.
  Nature chemical biology 2009 Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK
• Off-target networks derived from ligand set similarity.
  Methods in molecular biology (Clifton, N.J.) 2009 Keiser MJ, Hert J
• ChemInform Abstract: Quantifying the Relationships among Drug Classes.
  ChemInform 2008 Jerome Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet
• Quantifying the relationships among drug classes.
  Journal of chemical information and modeling 2008 Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK
• Relating protein pharmacology by ligand chemistry.
  Nature biotechnology 2007 Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK