Jon Kleen, MD, PhD

Photo of Jon Kleen, MD, PhD
Title(s)Associate Professor, Neurology
SchoolSchool of Medicine
ORCID ORCID Icon0000-0003-2622-3205 Additional info
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    Other Positions
    Title(s)Lip-Bu Tan Endowed Professor

    Title(s)UCSF Weill Institute for Neurosciences


    Collapse Overview 
    Collapse overview
    Dr. Jon Kleen is a neurologist, epilepsy specialist, and the Lip-Bu Tan Endowed Professor at the University of California, San Francisco. An Associate Professor of Neurology and a UCSF Chen Scholar, he is dedicated to improving the lives of patients with epilepsy by stopping seizures and finding new ways to overcome epilepsy-related memory problems. He is also a neuroscientist with expertise in signal processing and computational approaches. He applies this to cutting-edge diagnostic approaches and emerging therapies for epilepsy, including brain stimulation. His lab investigates how memory circuits work in the human brain and why they are disrupted in many people with epilepsy. He also develops technology that integrates brainwave recordings with brain images to help pinpoint where seizures start, with the goal of increasing the chance for future curative surgery in patients whose prior treatments failed. Dr. Kleen is originally from rural Minnesota. He earned a doctorate in neuroscience from Dartmouth College and his medical degree from Dartmouth Medical School. At UCSF, he completed a residency in neurology, a fellowship in epilepsy, and postdoctoral training in human brain neurophysiology at UCSF. He enjoys mentoring research and clinical trainees at all levels, and he was elected by UCSF's medical student chapter of Alpha Omega Alpha Honor Medical Society for excellence in teaching.

    Collapse Biography 
    Collapse education and training
    UCSF Medical CenterFellowship2019Epilepsy
    UCSF Medical CenterResidency2017Neurology
    Dartmouth Medical SchoolM.D.2013Medicine
    Dartmouth Medical SchoolPh.D.2011Neuroscience
    Collapse awards and honors
    Tianqiao and Chrissy Chen Institute2025UCSF Chen Scholar Award
    American Epilepsy Society2024AES Junior Investigator Award
    UCSF Department of Neurology2024Lip-Bu Tan Endowed Professorship
    American Academy of Neurology20232023 Dreifuss-Penry Epilepsy Award
    National Science Foundation (NSF)2022  - 2025CogNeuro Award
    American Neurological Association (AAN)2022Emerging Scholar Award
    UCSF Medical School2022Bridges Curriculum Award for Inspirational Teaching
    2022NIH BRAIN Initiative Photo & Video Contest (2nd Place)
    Weill Institute for Neurosciences2020Weill Pilot Award for Junior Investigators in the Neurosciences
    NINDS / National Institutes of Health2019  - 2024K23 Career Development Award
    San Francisco Neurological Society (SFNS)2019Boldrey Young Investigator Award
    American Epilepsy Society (AES)2018Young Investigator Award
    Alpha Omega Alpha (AOA) Honor Medical Society2017Resident Physician Inductee

    Collapse Research 
    Collapse research activities and funding
    Understanding mechanisms of semantic memory through intracranial recording and stimulation
    NSF CogNeuro 2148753Sep 1, 2022 - Aug 30, 2025
    Novel cinematic technology to localize intracranial seizure activity in medically-refractory epilepsy
    Weill Institute for Neurosciences Weill Pilot Award for Junior InvestigatorsFeb 1, 2020 - Jul 31, 2021
    Role: Principle Investigator
    Hippocampal-cortical networks underlying memory retrieval of linguistic knowledge
    NIH K23NS110920Jul 1, 2019 - Jun 30, 2024
    Role: Principal Investigator
    Cognitive impact of iterictal spikes in temporal lobe epilepsy
    NIH F30NS064624Jan 1, 2009 - Jun 30, 2014
    Role: Principal Investigator

    Collapse Featured Content 

    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. Disease detection and classification in temporal lobe epilepsy: step-wise versus simultaneous AI decision models in a multisite neuroimaging study. Brain Commun. 2026; 8(4):fcag253. Kaestner E, Sawant J, Arienzo D, Hasenstab KA, Gleichgerrcht E, Gholipour T, Abrol A, Hassanzadeh R, Thomopoulos SI, Yasuda CL, Silva LS, Alvim MKM, Moloney P, Altmann A, Martins Custodio H, Heide EC, Sinha N, Ballerini A, Absil J, Larivière S, Schubert KM, Ferreira-Atuesta C, Duma GM, Christin R, Barbi E, Guerrini R, Rüber T, Bauer T, Sinclair B, Bunyamin J, Courtney MR, Law M, Labate A, Striano P, Vivash L, O'Brien TJ, Lenge M, Saba L, Kleen JK, Bonanni P, Sepeta LN, Galovic M, Bartolini E, Ives-Deliperi V, Bernhardt BC, Martin P, Depondt C, Stoub T, Vaudano AE, Meletti S, Kuzniecky R, Concha L, Bagic AI, Davis KA, Staba RJ, Focke NKN, Pardoe H, Dugan PC, Devinsky O, Drane DL, Zhang Z, Gambardella A, Parashos A, Cendes F, Thompson PM, Sisodiya SM, Calhoun VD, Bonilha L, McDonald CR. PMID: 42534493; PMCID: PMC13421366.
      View in: PubMed   Mentions:
    2. Mapping the space of dementia with EEG in stained glass. Front Dement. 2026; 5:1820301. O'Kelly M, Lanata SC, Kleen JK. PMID: 42428696; PMCID: PMC13345836.
      View in: PubMed   Mentions:
    3. Virtual Responsive Neurostimulation Implantation: From Intracranial Connectivity to Optimized Lead Placement. medRxiv. 2026 Jun 22. Feys O, Walsh KG, Nix KC, Josyula M, Sinha N, Lavelle SB, Wagenaar J, Michalak A, Morrell MJ, Jeschke J, Khambhati AN, Conrad EC, Kleen JK, Litt B, Rao VR, Friedman D, Davis KA. PMID: 42396343; PMCID: PMC13320936.
      View in: PubMed   Mentions:
    4. Sex-related structural alterations across common epilepsies: a worldwide ENIGMA study. bioRxiv. 2026 Jun 09. Wen H, Wan B, Gholipour T, Xie K, Chen J, Serio B, Hettwer MD, Alvim MKM, Arienzo D, João RB, Bauer T, Bernasconi A, Bernasconi N, Bonanni P, Caligiuri ME, Cendes F, Christin R, Concha L, Dascal A, Boyd ED, Devinsky O, Focke NKN, Fortunato F, Galovic M, Gambardella A, Guerrini R, Hatton SN, Iliza M, Inati S, Ives-Deliperi V, Juster RP, Kleen JK, Koubeissi MZ, Labate A, Larivière S, Law M, Lenge M, Meletti S, Moloney PB, Naish M, Ngo A, O'Brien TJ, Pana R, Panzeri S, Pardoe H, Rauf EHU, Riva A, Rodríguez-Cruces R, Royer J, Rüber T, Sahlas E, Scárdua-Silva L, Schubert KM, Sepeta LN, Severino M, Sinclair B, Soltanian-Zadeh H, Stoub T, Striano P, Thomopoulos SI, Valientes NV, Vaudano AE, Vivash L, Yasuda CL, Thompson PM, Sisodiya SM, McDonald CR, Bernhardt BC, Valk SL. PMID: 42327327; PMCID: PMC13277886.
      View in: PubMed   Mentions:
    5. Global Socioeconomic Context and Brain Ageing in Epilepsy: an ENIGMA-Epilepsy study. medRxiv. 2026 May 01. Pardoe HR, Devinsky O, Bbiomed Hons JR, Ireland M, Absil J, Altmann A, Alvim MK, Arienzo D, Ballerini A, Barbi E, Bartolini E, Bauer T, Bernasconi A, Bernasconi N, Bernhardt B, Blackmon K, Bonanni P, Bonilha L, Bosco P, Bunyamin J, Caligiuri ME, Cendes F, Christin R, Concha L, Courtney MR, Cruces RR, Danieli A, Davis KA, Depondt C, Dugan P, Duma GM, Duncan JS, Engel J, Atuesta CF, Focke NK, Fortunato F, Gagliardo C, Galovic M, Gambardella A, Gholipour T, Gleichgerrcht E, Guerrini R, Gule MV, Heide EC, Inati S, Ives-Deliperi V, Jackson GD, Jacobs S, Jahanshad N, Kleen JK, Kotikalapudi R, Koubeissi MZ, Labate A, Larivère S, Lenge M, Martins H, Mascalchi M, Meletti S, Moloney PB, O'Brien TJ, Owens-Walton C, Parodi C, Riva A, Roth RW, Royer J, Rüber T, Saba L, Sammarra I, Scárdua-Silva L, Schubert KM, Sepeta L, Severino M, Sinclair B, Sinha N, Staba RJ, Stein DJ, Stein JM, Stoub TR, Striano P, Surges R, Terziev R, Thomopoulos SI, Tondelli M, Tortora D, Vacca S, Vaudano AE, Vivash L, Williams KC, Yasuda CL, Zhang Z, Kaestner E, Thompson PM, Sisodiya SM, McDonald CR. PMID: 42388885; PMCID: PMC13317623.
      View in: PubMed   Mentions:
    6. Laminar organization of cellular microcircuits modulating human interictal epileptiform discharges. Nat Neurosci. 2026 Jun; 29(6):1462-1475. Silva AB, Marathe SA, Greicius QR, Xu D, Jain S, Chung JE, Yang X, Khambhati AN, Leonard MK, Kleen JK, Chang EF. PMID: 42062597; PMCID: PMC13246451.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. Distance of bipolar re-referencing imparts nonlinear frequency-specific influences on intracranial recording signal measurements. J Neural Eng. 2025 11 26; 22(6). Caldwell DJ, Krish D, Chang EF, Kleen JK. PMID: 41187347; PMCID: PMC12648405.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. Dissociating physiological ripples and epileptiform discharges with vision transformers. bioRxiv. 2025 Apr 18. Zhang D, Kleen JK. PMID: 40364911; PMCID: PMC12073830.
      View in: PubMed   Mentions:
    9. Influences of electrode density on intracranial seizure localisation: a single-blinded randomised crossover study. EBioMedicine. 2025 Mar; 113:105606. Chinedu-Eneh EO, Chiang S, Andrews JP, Tadayon E, Fan JM, Garcia PA, Gonzalez-Giraldo E, Hegde M, Hullett P, Rao VR, Knowlton RC, Chang EF, Kleen JK. PMID: 40037091; PMCID: PMC11925122.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    10. Quantitative evaluation of electrographic response to electroconvulsive therapy in super-refractory status epilepticus. Front Neurol. 2024; 15:1493336. Christin R, Hines H, Hophing L, Khambhati AN, Amorim E, Hegde M, Guterman EL, Kleen JK. PMID: 39744102; PMCID: PMC11688648.
      View in: PubMed   Mentions: 1  
    11. Evaluating the feasibility of prehospital point-of-care EEG: The prehospital implementation of rapid EEG (PHIRE) study. J Am Coll Emerg Physicians Open. 2024 Oct; 5(5):e13303. Guterman EL, Mercer MP, Wood AJ, Amorim E, Kleen JK, Gerard D, Kellison C, Yamashita S, Auerbach B, Joshi N, Sporer KA. PMID: 39281726; PMCID: PMC11393765.
      View in: PubMed   Mentions: 4  
    12. Development and validation of a nonverbal consensus-based semantic memory paradigm in patients with epilepsy. J Int Neuropsychol Soc. 2024 08; 30(7):671-679. Tran EB, Vonk JMJ, Casaletto K, Zhang D, Christin R, Marathe S, Gorno-Tempini ML, Chang EF, Kleen JK. PMID: 38616725; PMCID: PMC11473708.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    13. Interictal epileptiform discharges contribute to word-finding difficulty in epilepsy through multiple cognitive mechanisms. Epilepsia. 2023 12; 64(12):3266-3278. Silva AB, Leonard MK, Oganian Y, D'Esopo E, Krish D, Kopald B, Tran EB, Chang EF, Kleen JK. PMID: 37753856; PMCID: PMC10841419.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    14. Ictal EEG Source Imaging With Supplemental Electrodes. J Clin Neurophysiol. 2024 Sep 01; 41(6):507-514. Loube DK, Tan YL, Yoshii-Contreras J, Kleen J, Rao VR, Chang EF, Knowlton RC. PMID: 37820169.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    15. Clinical Reasoning: A Young Adult With New Seizures and Chapeau de Gendarme. Neurology. 2023 10 31; 101(18):e1821-e1827. Valdrighi A, Douglas AG, Knowlton RC, Shah M, Kleen JK. PMID: 37580161; PMCID: PMC10634645.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    16. The New Era of Automated Electroencephalogram Interpretation. JAMA Neurol. 2023 08 01; 80(8):777-778. Kleen JK, Guterman EL. PMID: 37338899.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    17. Is It Reasonable to Drive When There Is a (Spike) Train? Neurology. 2023 08 29; 101(9):377-379. Kleen JK, Davis KA. PMID: 37414566.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    18. Intact speech perception after resection of dominant hemisphere primary auditory cortex for the treatment of medically refractory epilepsy: illustrative case. J Neurosurg Case Lessons. 2022 Nov 28; 4(22). Hullett PW, Kandahari N, Shih TT, Kleen JK, Knowlton RC, Rao VR, Chang EF. PMID: 36443954; PMCID: PMC9705521.
      View in: PubMed   Mentions: 1  
    19. Bidirectional propagation of low frequency oscillations over the human hippocampal surface. Nat Commun. 2021 05 12; 12(1):2764. Kleen JK, Chung JE, Sellers KK, Zhou J, Triplett M, Lee K, Tooker A, Haque R, Chang EF. PMID: 33980852; PMCID: PMC8115072.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    20. Accuracy of omni-planar and surface casting of epileptiform activity for intracranial seizure localization. Epilepsia. 2021 04; 62(4):947-959. Kleen JK, Speidel BA, Baud MO, Rao VR, Ammanuel SG, Hamilton LS, Chang EF, Knowlton RC. PMID: 33634855; PMCID: PMC8276628.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    21. Measuring synchrony in bio-medical timeseries. Chaos. 2021 Jan; 31(1):013138. Leguia MG, Rao VR, Kleen JK, Baud MO. PMID: 33754758.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    22. Early seizure spread and epilepsy surgery: A systematic review. Epilepsia. 2020 10; 61(10):2163-2172. Andrews JP, Ammanuel S, Kleen J, Khambhati AN, Knowlton R, Chang EF. PMID: 32944952; PMCID: PMC8139824.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    23. Interictal Epileptiform Discharges and the Quality of Human Intracranial Neurophysiology Data. Front Hum Neurosci. 2020; 14:44. Ammanuel SG, Kleen JK, Leonard MK, Chang EF. PMID: 32194384; PMCID: PMC7062638.
      View in: PubMed   Mentions: 6  
    24. Prospective validation study of an epilepsy seizure risk system for outpatient evaluation. Epilepsia. 2020 01; 61(1):29-38. Chiang S, Goldenholz DM, Moss R, Rao VR, Haneef Z, Theodore WH, Kleen JK, Gavvala J, Vannucci M, Stern JM. PMID: 31792970; PMCID: PMC6980278.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    25. Unsupervised Learning of Spatiotemporal Interictal Discharges in Focal Epilepsy. Neurosurgery. 2018 10 01; 83(4):683-691. Baud MO, Kleen JK, Anumanchipalli GK, Hamilton LS, Tan YL, Knowlton R, Chang EF. PMID: 29040672; PMCID: PMC6454796.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    26. Multi-day rhythms modulate seizure risk in epilepsy. Nat Commun. 2018 01 08; 9(1):88. Baud MO, Kleen JK, Mirro EA, Andrechak JC, King-Stephens D, Chang EF, Rao VR. PMID: 29311566; PMCID: PMC5758806.
      View in: PubMed   Mentions: 245     Fields:    Translation:Humans
    27. The nociferous influence of interictal discharges on memory. Brain. 2017 08 01; 140(8):2072-2074. Kleen JK, Kirsch HE. PMID: 28899025; PMCID: PMC6248646.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    28. Chronic ambulatory electrocorticography from human speech cortex. Neuroimage. 2017 06; 153:273-282. Rao VR, Leonard MK, Kleen JK, Lucas BA, Mirro EA, Chang EF. PMID: 28396294; PMCID: PMC5482367.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    29. Progress in Epilepsy: Latest Waves of Discovery. JAMA Neurol. 2017 02 01; 74(2):139-140. Kleen JK, Lowenstein DH. PMID: 27918766.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    30. Injection Therapy for Headache and Facial Pain. Oral Maxillofac Surg Clin North Am. 2016 Aug; 28(3):423-34. Kleen JK, Levin M. PMID: 27475516.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    31. Oscillation Phase Locking and Late ERP Components of Intracranial Hippocampal Recordings Correlate to Patient Performance in a Working Memory Task. Front Hum Neurosci. 2016; 10:287. Kleen JK, Testorf ME, Roberts DW, Scott RC, Jobst BJ, Holmes GL, Lenck-Santini PP. PMID: 27378885; PMCID: PMC4910536.
      View in: PubMed   Mentions: 12  
    32. Regulatory T cells are not a strong predictor of survival for patients with glioblastoma. Neuro Oncol. 2015 Jun; 17(6):801-9. Thomas AA, Fisher JL, Rahme GJ, Hampton TH, Baron U, Olek S, Schwachula T, Rhodes CH, Gui J, Tafe LJ, Tsongalis GJ, Lefferts JA, Wishart H, Kleen J, Miller M, Whipple CA, de Abreu FB, Ernstoff MS, Fadul CE. PMID: 25618892; PMCID: PMC4483125.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    33. Hippocampal interictal epileptiform activity disrupts cognition in humans. Neurology. 2013 Jul 02; 81(1):18-24. Kleen JK, Scott RC, Holmes GL, Roberts DW, Rundle MM, Testorf M, Lenck-Santini PP, Jobst BC. PMID: 23685931; PMCID: PMC3770206.
      View in: PubMed   Mentions: 139     Fields:    Translation:Humans
    34. Enhanced oscillatory activity in the hippocampal-prefrontal network is related to short-term memory function after early-life seizures. J Neurosci. 2011 Oct 26; 31(43):15397-406. Kleen JK, Wu EX, Holmes GL, Scott RC, Lenck-Santini PP. PMID: 22031886; PMCID: PMC3224083.
      View in: PubMed   Mentions: 39     Fields:    Translation:Animals
    35. Early-life seizures produce lasting alterations in the structure and function of the prefrontal cortex. Epilepsy Behav. 2011 Oct; 22(2):214-9. Kleen JK, Sesqué A, Wu EX, Miller FA, Hernan AE, Holmes GL, Scott RC. PMID: 21873119; PMCID: PMC3185212.
      View in: PubMed   Mentions: 29     Fields:    Translation:Animals
    36. Neuroaminidase reduces interictal spikes in a rat temporal lobe epilepsy model. Epilepsia. 2011 Mar; 52(3):e12-5. Isaev D, Zhao Q, Kleen JK, Lenck-Santini PP, Adstamongkonkul D, Isaeva E, Holmes GL. PMID: 21366554; PMCID: PMC3265164.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    37. Taming TLR4 may ease seizures. Nat Med. 2010 Apr; 16(4):369-70. Kleen JK, Holmes GL. PMID: 20376038.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    38. Hippocampal interictal spikes disrupt cognition in rats. Ann Neurol. 2010 Feb; 67(2):250-7. Kleen JK, Scott RC, Holmes GL, Lenck-Santini PP. PMID: 20225290; PMCID: PMC2926932.
      View in: PubMed   Mentions: 106     Fields:    Translation:Animals
    39. Brain inflammation initiates seizures. Nat Med. 2008 Dec; 14(12):1309-10. Kleen JK, Holmes GL. PMID: 19057551.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    40. Chronic stress impairs spatial memory and motivation for reward without disrupting motor ability and motivation to explore. Behav Neurosci. 2006 Aug; 120(4):842-51. Kleen JK, Sitomer MT, Killeen PR, Conrad CD. PMID: 16893290; PMCID: PMC1578508.
      View in: PubMed   Mentions: 78     Fields:    Translation:AnimalsCells
    41. Combination of high fat diet and chronic stress retracts hippocampal dendrites. Neuroreport. 2005 Jan 19; 16(1):39-43. Baran SE, Campbell AM, Kleen JK, Foltz CH, Wright RL, Diamond DM, Conrad CD. PMID: 15618887; PMCID: PMC1363787.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCells
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