TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Neuroscience
AddressOne Baylor Plaza
Houston, TX 77030
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    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. Ling D, Moss EH, Smith CL, Kroeger R, Reimer J, Raman B, Arenkiel BR. Conserved neural dynamics and computations across species in olfaction. bioRxiv. 2023 Apr 24. PMID: 37162844; PMCID: PMC10168254.
    2. Wang EY, Fahey PG, Ponder K, Ding Z, Chang A, Muhammad T, Patel S, Ding Z, Tran D, Fu J, Papadopoulos S, Franke K, Ecker AS, Reimer J, Pitkow X, Sinz FH, Tolias AS. Towards a Foundation Model of the Mouse Visual Cortex. bioRxiv. 2023 Apr 21. PMID: 36993435; PMCID: PMC10055288.
    3. Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B, Papadopoulos C, Kunin AB, Chang A, Fu J, Ding Z, Patel S, Ponder K, Muhammad T, Bae JA, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Froudarakis E, Sinz F, Seung HS, Collman F, da Costa NM, Reid RC, Walker EY, Pitkow X, Reimer J, Tolias AS. Functional connectomics reveals general wiring rule in mouse visual cortex. bioRxiv. 2023 Mar 30. PMID: 36993398; PMCID: PMC10054929.
    4. Celii B, Papadopoulos S, Ding Z, Fahey PG, Wang E, Papadopoulos C, Kunin AB, Patel S, Bae JA, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yu SC, Yin W, Xenes D, Kitchell LM, Rivlin PK, Rose VA, Bishop CA, Wester B, Froudarakis E, Walker EY, Sinz F, Seung HS, Collman F, da Costa NM, Reid RC, Pitkow X, Tolias AS, Reimer J. NEURD: automated proofreading and feature extraction for connectomics. bioRxiv. 2023 Mar 29. PMID: 36993282; PMCID: PMC10055177.
    5. Ding Z, Tran DT, Ponder K, Cobos E, Ding Z, Fahey PG, Wang E, Muhammad T, Fu J, Cadena SA, Papadopoulos S, Patel S, Franke K, Reimer J, Sinz FH, Ecker AS, Pitkow X, Tolias AS. Bipartite invariance in mouse primary visual cortex. bioRxiv. 2023 Mar 16. PMID: 36993218; PMCID: PMC10055119.
    6. Fu J, Shrinivasan S, Ponder K, Muhammad T, Ding Z, Wang E, Ding Z, Tran DT, Fahey PG, Papadopoulos S, Patel S, Reimer J, Ecker AS, Pitkow X, Haefner RM, Sinz FH, Franke K, Tolias AS. Pattern completion and disruption characterize contextual modulation in mouse visual cortex. bioRxiv. 2023 Mar 14. PMID: 36993321; PMCID: PMC10054952.
    7. MICrONS Consortium, Schneider-Mizell CM, Bodor A, Brittain D, Buchanan J, Bumbarger DJ, Elabbady L, Kapner D, Kinn S, Mahalingam G, Seshamani S, Suckow S, Takeno M, Torres R, Yin W, Dorkenwald S, Bae JA, Castro MA, Fahey PG, Froudakis E, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Papadopoulos S, Patel S, Pitkow X, Popovych S, Silversmith W, Sinz FH, Turner NL, Wong W, Wu J, Yu SC, Reimer J, Tolias AS, Seung HS, Reid RC, Collman F, da Costa NM. Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex. bioRxiv. 2023 Feb 14. PMID: 36747710; PMCID: PMC9900837.
    8. Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J, Bodor AL, Bleckert AA, Brittain D, Kemnitz N, Silversmith WM, Ih D, Zung J, Zlateski A, Tartavull I, Yu SC, Popovych S, Wong W, Castro M, Jordan CS, Wilson AM, Froudarakis E, Buchanan J, Takeno MM, Torres R, Mahalingam G, Collman F, Schneider-Mizell CM, Bumbarger DJ, Li Y, Becker L, Suckow S, Reimer J, Tolias AS, Macarico da Costa N, Reid RC, Seung HS. Binary and analog variation of synapses between cortical pyramidal neurons. Elife. 2022 11 16; 11. PMID: 36382887; PMCID: PMC9704804.
      Citations: 16     Fields:    Translation:AnimalsCells
    9. Shen S, Jiang X, Scala F, Fu J, Fahey P, Kobak D, Tan Z, Zhou N, Reimer J, Sinz F, Tolias AS. Distinct organization of two cortico-cortical feedback pathways. Nat Commun. 2022 10 27; 13(1):6389. PMID: 36302912; PMCID: PMC9613627.
      Citations: 5     Fields:    Translation:AnimalsCells
    10. Franke K, Willeke KF, Ponder K, Galdamez M, Zhou N, Muhammad T, Patel S, Froudarakis E, Reimer J, Sinz FH, Tolias AS. State-dependent pupil dilation rapidly shifts visual feature selectivity. Nature. 2022 10; 610(7930):128-134. PMID: 36171291; PMCID: PMC10635574.
      Citations: 10     Fields:    Translation:AnimalsCells
    11. Liu Z, Lu X, Villette V, Gou Y, Colbert KL, Lai S, Guan S, Land MA, Lee J, Assefa T, Zollinger DR, Korympidou MM, Vlasits AL, Pang MM, Su S, Cai C, Froudarakis E, Zhou N, Patel SS, Smith CL, Ayon A, Bizouard P, Bradley J, Franke K, Clandinin TR, Giovannucci A, Tolias AS, Reimer J, Dieudonn? S, St-Pierre F. Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell. 2022 09 01; 185(18):3408-3425.e29. PMID: 35985322; PMCID: PMC9563101.
    12. Turner NL, Macrina T, Bae JA, Yang R, Wilson AM, Schneider-Mizell C, Lee K, Lu R, Wu J, Bodor AL, Bleckert AA, Brittain D, Froudarakis E, Dorkenwald S, Collman F, Kemnitz N, Ih D, Silversmith WM, Zung J, Zlateski A, Tartavull I, Yu SC, Popovych S, Mu S, Wong W, Jordan CS, Castro M, Buchanan J, Bumbarger DJ, Takeno M, Torres R, Mahalingam G, Elabbady L, Li Y, Cobos E, Zhou P, Suckow S, Becker L, Paninski L, Polleux F, Reimer J, Tolias AS, Reid RC, Seung HS, da Costa NM. Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity. Cell. 2022 03 17; 185(6):1082-1100.e24. PMID: 35216674; PMCID: PMC9337909.
      Citations:    Fields:    Translation:AnimalsCells
    13. Schneider-Mizell CM, Bodor AL, Collman F, Brittain D, Bleckert A, Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J, Zhuang J, Nandi A, Hu B, Buchanan J, Takeno MM, Torres R, Mahalingam G, Bumbarger DJ, Li Y, Chartrand T, Kemnitz N, Silversmith WM, Ih D, Zung J, Zlateski A, Tartavull I, Popovych S, Wong W, Castro M, Jordan CS, Froudarakis E, Becker L, Suckow S, Reimer J, Tolias AS, Anastassiou CA, Seung HS, Reid RC, Costa NMD. Structure and function of axo-axonic inhibition. Elife. 2021 12 01; 10. PMID: 34851292; PMCID: PMC8758143.
      Citations: 4     Fields:    Translation:AnimalsCells
    14. Shemesh OA, Linghu C, Piatkevich KD, Goodwin D, Celiker OT, Gritton HJ, Romano MF, Gao R, Yu CJ, Tseng HA, Bensussen S, Narayan S, Yang CT, Freifeld L, Siciliano CA, Gupta I, Wang J, Pak N, Yoon YG, Ullmann JFP, Guner-Ataman B, Noamany H, Sheinkopf ZR, Park WM, Asano S, Keating AE, Trimmer JS, Reimer J, Tolias AS, Bear MF, Tye KM, Han X, Ahrens MB, Boyden ES. Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator. Neuron. 2020 08 05; 107(3):470-486.e11. PMID: 32592656; PMCID: PMC7415598.
      Citations: 19     Fields:    Translation:AnimalsCells
    15. Walker EY, Sinz FH, Cobos E, Muhammad T, Froudarakis E, Fahey PG, Ecker AS, Reimer J, Pitkow X, Tolias AS. Inception loops discover what excites neurons most using deep predictive models. Nat Neurosci. 2019 12; 22(12):2060-2065. PMID: 31686023.
      Citations: 15     Fields:    Translation:AnimalsCells
    16. Pitkow X, Reimer J, Tolias AS, Sinz FH, Bethge M. Engineering a Less Artificial Intelligence. Neuron. 2019 09 25; 103(6):967-979. PMID: 31557461.
      Citations: 25     Fields:    Translation:Humans
    17. Froudarakis E, Fahey PG, Reimer J, Smirnakis SM, Tehovnik EJ, Tolias AS. The Visual Cortex in Context. Annu Rev Vis Sci. 2019 09 15; 5:317-339. PMID: 31525143; PMCID: PMC7485906.
      Citations: 12     Fields:    Translation:HumansAnimals
    18. Egbert JR, Fahey PG, Reimer J, Owen CM, Evsikov AV, Nikolaev VO, Griesbeck O, Ray RS, Tolias AS, Jaffe LA. Follicle-stimulating hormone and luteinizing hormone increase Ca2+ in the granulosa cells of mouse ovarian follicles?. Biol Reprod. 2019 08 01; 101(2):433-444. PMID: 31087036; PMCID: PMC7302518.
      Citations: 6     Fields:    Translation:AnimalsCells
    19. Wang H, Dewell RB, Ehrengruber MU, Segev E, Reimer J, Roukes ML, Gabbiani F. Optogenetic manipulation of medullary neurons in the locust optic lobe. J Neurophysiol. 2018 10 01; 120(4):2049-2058. PMID: 30110231; PMCID: PMC6230808.
      Citations: 3     Fields:    Translation:AnimalsCells
    20. Freeman J, Deneux T, Speiser A, Macke JH, Turaga SC, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, Stone J, Sofroniew NJ, Reimer J, Froudarakis E, Theis L, Tolias AS, Berens P, Chenkov N, McColgan T, Rogerson LE, Euler T, Rom?n Ros?n M, Bethge M. Community-based benchmarking improves spike rate inference from two-photon calcium imaging data. PLoS Comput Biol. 2018 05; 14(5):e1006157. PMID: 29782491; PMCID: PMC5997358.
      Citations: 37     Fields:    Translation:AnimalsCells
    21. Ouzounov DG, Wang T, Wang M, Feng DD, Horton NG, Cheng YT, Reimer J, Tolias AS, Nishimura N, Xu C, Cruz-Hern?ndez JC. In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain. Nat Methods. 2017 Apr; 14(4):388-390. PMID: 28218900; PMCID: PMC6441362.
      Citations: 153     Fields:    Translation:AnimalsCells
    22. Segev E, Reimer J, Moreaux LC, Fowler TM, Chi D, Sacher WD, Lo M, Deisseroth K, Tolias AS, Faraon A, Roukes ML. Patterned photostimulation via visible-wavelength photonic probes for deep brain optogenetics. Neurophotonics. 2017 Jan; 4(1):011002. PMID: 27990451; PMCID: PMC5136672.
      Citations: 23     
    23. Reimer J, McGinley MJ, Liu Y, Rodenkirch C, Wang Q, McCormick DA, Tolias AS. Pupil fluctuations track rapid changes in adrenergic and cholinergic activity in cortex. Nat Commun. 2016 11 08; 7:13289. PMID: 27824036; PMCID: PMC5105162.
      Citations: 228     Fields:    Translation:HumansAnimalsCells
    24. Jiang X, Shen S, Sinz F, Reimer J, Cadwell CR, Patel S, Denfield GH, Froudarakis E, Li S, Walker E, Berens P, Ecker AS, Tolias AS. Response to Comment on "Principles of connectivity among morphologically defined cell types in adult neocortex". Science. 2016 09 09; 353(6304):1108. PMID: 27609883.
      Citations: 8     Fields:    Translation:HumansCells
    25. Denfield GH, Fahey PG, Reimer J, Tolias AS. Investigating the Limits of Neurovascular Coupling. Neuron. 2016 Sep 07; 91(5):954-956. PMID: 27608758.
      Citations: 1     Fields:    Translation:Animals
    26. Froudarakis E, Reimer J, Theis L, Berens P, Rom?n Ros?n M, Baden T, Euler T, Tolias AS, Bethge M. Benchmarking Spike Rate Inference in Population Calcium Imaging. Neuron. 2016 05 04; 90(3):471-82. PMID: 27151639; PMCID: PMC4888799.
      Citations: 62     Fields:    Translation:AnimalsCells
    27. Cadwell CR, Palasantza A, Jiang X, Berens P, Deng Q, Yilmaz M, Reimer J, Shen S, Tolias KF, Sandberg R, Tolias AS, Bethge M. Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. Nat Biotechnol. 2016 Feb; 34(2):199-203. PMID: 26689543; PMCID: PMC4840019.
      Citations: 183     Fields:    Translation:AnimalsCells
    28. McGinley MJ, Vinck M, Reimer J, Batista-Brito R, Zagha E, Cadwell CR, Tolias AS, Cardin JA, McCormick DA. Waking State: Rapid Variations Modulate Neural and Behavioral Responses. Neuron. 2015 Sep 23; 87(6):1143-1161. PMID: 26402600; PMCID: PMC4718218.
      Citations: 253     Fields:    Translation:HumansAnimalsCells
    29. Reimer J, Froudarakis E, Cadwell CR, Yatsenko D, Denfield GH, Tolias AS. Pupil fluctuations track fast switching of cortical states during quiet wakefulness. Neuron. 2014 Oct 22; 84(2):355-62. PMID: 25374359; PMCID: PMC4323337.
      Citations: 247     Fields:    Translation:AnimalsCells
    30. Stevenson IH, London BM, Oby ER, Sachs NA, Reimer J, Englitz B, David SV, Shamma SA, Blanche TJ, Mizuseki K, Zandvakili A, Hatsopoulos NG, Miller LE, Kording KP. Functional connectivity and tuning curves in populations of simultaneously recorded neurons. PLoS Comput Biol. 2012; 8(11):e1002775. PMID: 23166484; PMCID: PMC3499254.
      Citations: 30     Fields:    Translation:AnimalsCells
    31. Stevenson IH, Cherian A, London BM, Sachs NA, Lindberg E, Reimer J, Slutzky MW, Hatsopoulos NG, Miller LE, Kording KP. Statistical assessment of the stability of neural movement representations. J Neurophysiol. 2011 Aug; 106(2):764-74. PMID: 21613593; PMCID: PMC3154833.
      Citations: 32     Fields:    Translation:AnimalsCells
    32. Reimer J, Hatsopoulos NG. Periodicity and evoked responses in motor cortex. J Neurosci. 2010 Aug 25; 30(34):11506-15. PMID: 20739573; PMCID: PMC2952881.
      Citations: 25     Fields:    Translation:Animals
    33. Saleh M, Reimer J, Penn R, Ojakangas CL, Hatsopoulos NG. Fast and slow oscillations in human primary motor cortex predict oncoming behaviorally relevant cues. Neuron. 2010 Feb 25; 65(4):461-71. PMID: 20188651; PMCID: PMC3199221.
      Citations: 103     Fields:    Translation:HumansCells
    34. Fagg AH, Hatsopoulos NG, London BM, Reimer J, Solla SA, Wang D, Miller LE. Toward a biomimetic, bidirectional, brain machine interface. Annu Int Conf IEEE Eng Med Biol Soc. 2009; 2009:3376-80. PMID: 19963797.
      Citations: 4     Fields:    Translation:HumansCells
    35. Reimer J, Hatsopoulos NG. The problem of parametric neural coding in the motor system. Adv Exp Med Biol. 2009; 629:243-59. PMID: 19227503; PMCID: PMC4480635.
      Citations: 11     Fields:    Translation:AnimalsCells
    36. Tkach D, Reimer J, Hatsopoulos NG. Congruent activity during action and action observation in motor cortex. J Neurosci. 2007 Nov 28; 27(48):13241-50. PMID: 18045918; PMCID: PMC6673404.
      Citations: 100     Fields:    Translation:AnimalsCells
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