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Matthew Kaufman

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentOrganismal Biology and Anatomy
AddressChicago IL 60637
Email
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    My lab studies how populations of neurons implement decision making and motor control. We record and manipulate the activity of hundreds or thousands of neurons in mouse cortex, then use sophisticated analyses to understand how these areas compute variables that the animal needs in order to behave. With calcium imaging, we can identify each neuron's cell type, layer, or projection pattern, and use this information to better understand inter-area communication and the organization of computation within cortex. With optogenetics, we can close the causal loop to determine if the activity is necessary or the roles of cell types in computation. Finally, with pharmacological manipulations, we can begin to understand how psychiatric drugs drive their behavioral effects.
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    Collapse education and training
    Stanford University, Stanford, CABS06/2005Symbolic Systems
    Stanford University, Stanford, CAPhD07/2011Neuroscience
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY02/2018Neuroscience
    Collapse awards and honors
    2006 - 2010NSF GRFP, Stanford University
    2013 - 2015Swartz Postdoctoral Fellowship, Cold Spring Harbor Laboratory
    2015 - 2015McKnight Foundation Allison Doupe Fellowship, Cold Spring Harbor Laboratory
    2015 - 2018Simons Collaboration on the Global Brain postdoctoral fellowship, Cold Spring Harbor Laboratory

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    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    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. Zhu F, Grier HA, Tandon R, Cai C, Agarwal A, Giovannucci A, Kaufman MT, Pandarinath C. A deep learning framework for inference of single-trial neural population dynamics from calcium imaging with subframe temporal resolution. Nat Neurosci. 2022 12; 25(12):1724-1734. PMID: 36424431; PMCID: PMC9825112.
      Citations: 2     Fields:    Translation:Animals
    2. Kaufman MT, Benna MK, Rigotti M, Stefanini F, Fusi S, Churchland AK. The implications of categorical and category-free mixed selectivity on representational geometries. Curr Opin Neurobiol. 2022 Dec; 77:102644. PMID: 36332415.
      Citations: 1     Fields:    Translation:Cells
    3. Huang L, Kebschull JM, Musall S, Kaufman MT, Churchland AK, Zador AM, Fürth D. BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. Cell. 2020 Dec 23; 183(7):2040. PMID: 33357401; PMCID: PMC8830377.
      Citations: 2     Fields:    
    4. Suresh AK, Goodman JM, Okorokova EV, Kaufman M, Hatsopoulos NG, Bensmaia SJ. Neural population dynamics in motor cortex are different for reach and grasp. Elife. 2020 11 17; 9. PMID: 33200745; PMCID: PMC7688308.
      Citations: 24     Fields:    Translation:AnimalsCells
    5. Huang L, Kebschull JM, Musall S, Kaufman MT, Churchland AK, Zador AM, Fürth D. BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. Cell. 2020 07 09; 182(1):177-188.e27. PMID: 32619423; PMCID: PMC7771207.
      Citations: 27     Fields:    Translation:AnimalsCells
    6. O'Shea DJ, Kalanithi P, Ferenczi EA, Hsueh B, Chandrasekaran C, Goo W, Diester I, Ramakrishnan C, Kaufman MT, Ryu SI, Yeom KW, Deisseroth K, Shenoy KV. Publisher Correction: Development of an optogenetic toolkit for neural circuit dissection in squirrel monkeys. Sci Rep. 2019 Dec 05; 9(1):18775. PMID: 31801956; PMCID: PMC6892861.
      Citations:    Fields:    
    7. Musall S, Kaufman MT, Juavinett AL, Gluf S, Churchland AK. Single-trial neural dynamics are dominated by richly varied movements. Nat Neurosci. 2019 10; 22(10):1677-1686. PMID: 31551604; PMCID: PMC6768091.
      Citations: 288     Fields:    Translation:AnimalsCells
    8. Trautmann EM, Stavisky SD, Lahiri S, Ames KC, Kaufman MT, O'Shea DJ, Vyas S, Sun X, Ryu SI, Ganguli S, Shenoy KV. Accurate Estimation of Neural Population Dynamics without Spike Sorting. Neuron. 2019 07 17; 103(2):292-308.e4. PMID: 31171448; PMCID: PMC7002296.
      Citations: 81     Fields:    Translation:AnimalsCells
    9. Kaufman MT. Adapting Fine with a Little Help from the Null Space. Neuron. 2018 11 21; 100(4):771-773. PMID: 30465761.
      Citations:    Fields:    
    10. Pandarinath C, O'Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann EM, Kaufman MT, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV, Abbott LF, Sussillo D. Inferring single-trial neural population dynamics using sequential auto-encoders. Nat Methods. 2018 10; 15(10):805-815. PMID: 30224673; PMCID: PMC6380887.
      Citations: 139     Fields:    Translation:HumansAnimalsCells
    11. O'Shea DJ, Kalanithi P, Ferenczi EA, Hsueh B, Chandrasekaran C, Goo W, Diester I, Ramakrishnan C, Kaufman MT, Ryu SI, Yeom KW, Deisseroth K, Shenoy KV. Development of an optogenetic toolkit for neural circuit dissection in squirrel monkeys. Sci Rep. 2018 04 30; 8(1):6775. PMID: 29712920; PMCID: PMC5928036.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    12. Omrani M, Kaufman MT, Hatsopoulos NG, Cheney PD. Perspectives on classical controversies about the motor cortex. J Neurophysiol. 2017 09 01; 118(3):1828-1848. PMID: 28615340; PMCID: PMC5599665.
      Citations: 38     Fields:    Translation:HumansAnimals
    13. Licata AM, Kaufman MT, Raposo D, Ryan MB, Sheppard JP, Churchland AK. Posterior Parietal Cortex Guides Visual Decisions in Rats. J Neurosci. 2017 05 10; 37(19):4954-4966. PMID: 28408414; PMCID: PMC5426183.
      Citations: 69     Fields:    Translation:Animals
    14. Kaufman MT, Churchland AK. Many paths from state to state. Nat Neurosci. 2016 11 29; 19(12):1541-1542. PMID: 27898087.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    15. Seely JS, Kaufman MT, Ryu SI, Shenoy KV, Cunningham JP, Churchland MM. Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1. PLoS Comput Biol. 2016 Nov; 12(11):e1005164. PMID: 27814353; PMCID: PMC5096707.
      Citations: 19     Fields:    Translation:Animals
    16. Elsayed GF, Lara AH, Kaufman MT, Churchland MM, Cunningham JP. Reorganization between preparatory and movement population responses in motor cortex. Nat Commun. 2016 10 27; 7:13239. PMID: 27807345; PMCID: PMC5095296.
      Citations: 128     Fields:    Translation:Animals
    17. Kaufman MT, Seely JS, Sussillo D, Ryu SI, Shenoy KV, Churchland MM. The Largest Response Component in the Motor Cortex Reflects Movement Timing but Not Movement Type. eNeuro. 2016 Jul-Aug; 3(4). PMID: 27761519; PMCID: PMC5069299.
      Citations: 66     Fields:    Translation:AnimalsCells
    18. Sussillo D, Churchland MM, Kaufman MT, Shenoy KV. A neural network that finds a naturalistic solution for the production of muscle activity. Nat Neurosci. 2015 Jul; 18(7):1025-33. PMID: 26075643; PMCID: PMC5113297.
      Citations: 167     Fields:    Translation:AnimalsCells
    19. Kaufman MT, Churchland MM, Ryu SI, Shenoy KV. Vacillation, indecision and hesitation in moment-by-moment decoding of monkey motor cortex. Elife. 2015 May 05; 4:e04677. PMID: 25942352; PMCID: PMC4415122.
      Citations: 46     Fields:    Translation:AnimalsCells
    20. Raposo D, Kaufman MT, Churchland AK. A category-free neural population supports evolving demands during decision-making. Nat Neurosci. 2014 Dec; 17(12):1784-1792. PMID: 25383902; PMCID: PMC4294797.
      Citations: 201     Fields:    Translation:AnimalsCells
    21. Kaufman MT, Churchland MM, Ryu SI, Shenoy KV. Cortical activity in the null space: permitting preparation without movement. Nat Neurosci. 2014 Mar; 17(3):440-8. PMID: 24487233; PMCID: PMC3955357.
      Citations: 260     Fields:    Translation:AnimalsCells
    22. Cowley BR, Kaufman MT, Butler ZS, Churchland MM, Ryu SI, Shenoy KV, Yu BM. DataHigh: graphical user interface for visualizing and interacting with high-dimensional neural activity. J Neural Eng. 2013 Dec; 10(6):066012. PMID: 24216250; PMCID: PMC3950756.
      Citations: 19     Fields:    Translation:Cells
    23. Kaufman MT, Churchland MM, Shenoy KV. The roles of monkey M1 neuron classes in movement preparation and execution. J Neurophysiol. 2013 Aug; 110(4):817-25. PMID: 23699057; PMCID: PMC3742981.
      Citations: 38     Fields:    Translation:AnimalsCells
    24. Kaufman MT, Churchland AK. Cognitive neuroscience: sensory noise drives bad decisions. Nature. 2013 Apr 11; 496(7444):172-3. PMID: 23579673.
      Citations: 3     Fields:    Translation:HumansAnimals
    25. Gilja V, Nuyujukian P, Chestek CA, Cunningham JP, Yu BM, Fan JM, Churchland MM, Kaufman MT, Kao JC, Ryu SI, Shenoy KV. A high-performance neural prosthesis enabled by control algorithm design. Nat Neurosci. 2012 Dec; 15(12):1752-7. PMID: 23160043; PMCID: PMC3638087.
      Citations: 164     Fields:    Translation:Animals
    26. Churchland MM, Cunningham JP, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV. Neural population dynamics during reaching. Nature. 2012 Jul 05; 487(7405):51-6. PMID: 22722855; PMCID: PMC3393826.
      Citations: 507     Fields:    Translation:AnimalsCells
    27. Cowley BR, Kaufman MT, Churchland MM, Ryu SI, Shenoy KV, Yu BM. DataHigh: graphical user interface for visualizing and interacting with high-dimensional neural activity. Annu Int Conf IEEE Eng Med Biol Soc. 2012; 2012:4607-10. PMID: 23366954; PMCID: PMC3745770.
      Citations: 2     Fields:    Translation:Humans
    28. Chestek CA, Gilja V, Nuyujukian P, Foster JD, Fan JM, Kaufman MT, Churchland MM, Rivera-Alvidrez Z, Cunningham JP, Ryu SI, Shenoy KV. Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex. J Neural Eng. 2011 Aug; 8(4):045005. PMID: 21775782; PMCID: PMC3644617.
      Citations: 144     Fields:    Translation:AnimalsCells
    29. Diester I, Kaufman MT, Mogri M, Pashaie R, Goo W, Yizhar O, Ramakrishnan C, Deisseroth K, Shenoy KV. An optogenetic toolbox designed for primates. Nat Neurosci. 2011 Mar; 14(3):387-97. PMID: 21278729; PMCID: PMC3150193.
      Citations: 187     Fields:    Translation:HumansAnimalsCells
    30. Shenoy KV, Kaufman MT, Sahani M, Churchland MM. A dynamical systems view of motor preparation: implications for neural prosthetic system design. Prog Brain Res. 2011; 192:33-58. PMID: 21763517; PMCID: PMC3665515.
      Citations: 35     Fields:    Translation:HumansAnimalsCells
    31. Churchland MM, Cunningham JP, Kaufman MT, Ryu SI, Shenoy KV. Cortical preparatory activity: representation of movement or first cog in a dynamical machine? Neuron. 2010 Nov 04; 68(3):387-400. PMID: 21040842; PMCID: PMC2991102.
      Citations: 200     Fields:    Translation:AnimalsCells
    32. Kaufman MT, Churchland MM, Santhanam G, Yu BM, Afshar A, Ryu SI, Shenoy KV. Roles of monkey premotor neuron classes in movement preparation and execution. J Neurophysiol. 2010 Aug; 104(2):799-810. PMID: 20538784; PMCID: PMC2934936.
      Citations: 67     Fields:    Translation:AnimalsCells
    33. Knutson B, Taylor J, Kaufman M, Peterson R, Glover G. Distributed neural representation of expected value. J Neurosci. 2005 May 11; 25(19):4806-12. PMID: 15888656; PMCID: PMC6724773.
      Citations: 391     Fields:    Translation:Humans
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