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JACOB REIMER

TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Neuroscience
AddressOne Baylor Plaza
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    Collapse Research 
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    U01NS137250     (RIVLIN, PATRICIA K)Aug 15, 2024 - Jul 31, 2027
    NIH
    BRAIN CONNECTS: A Scalable Automated Proofreading Framework for Connectomics
    Role: Co-Principal Investigator
    R01NS136027     (ST-PIERRE, FRANCOIS)Apr 17, 2024 - Mar 31, 2029
    NIH
    Red-shifted voltage indicators for two-photon all-optical physiology and multi-spectral imaging
    Role: Co-Principal Investigator
    R56AG080735     (REIMER, JACOB)Sep 15, 2023 - Aug 31, 2024
    NIH
    The Dynamic Neuromodulome in Alzheimer's Disease and Aging
    Role: Principal Investigator
    R34NS132045     (REIMER, JACOB)Apr 17, 2023 - Mar 31, 2025
    NIH
    Validation and Optimization of Two-Photon Dendritic Voltage Imaging in Vivo
    Role: Principal Investigator
    F31NS060384     (REIMER, JACOB JACOB)Mar 1, 2008 - Feb 28, 2010
    NIH
    Effect of oscillations on coding and connectivity in monkey sensorimotor cortex
    Role: Principal Investigator

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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. 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, Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B, Papadopoulos C, Chang A, Kunin AB, Tran D, Fu J, Ding Z, Patel S, Ntanavara L, Froebe R, 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, Yatsenko D, Froudarakis E, Sinz F, Josic K, Rosenbaum R, Seung HS, Collman F, da Costa NM, Reid RC, Walker EY, Pitkow X, Reimer J, Tolias AS, Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B, Papadopoulos C, Chang A, Kunin AB, Tran D, Fu J, Ding Z, Patel S, Ntanavara L, Froebe R, Ponder K, Muhammad T, Alexander Bae J, Cobos E, Dorkenwald S, Elabbady L, Kemnitz N, Macrina T, Nehoran B, Schneider-Mizell CM, Silversmith W, Takeno M, Turner NL, Wu J, Yatsenko D, Froudarakis E, Sinz F, Josic K, Rosenbaum R, Sebastian Seung H, Collman F, da Costa NM, Clay Reid R, Walker EY, Pitkow X, Reimer J, Tolias AS. Functional connectomics reveals general wiring rule in mouse visual cortex. bioRxiv. 2024 Oct 14. PMID: 36993398; PMCID: PMC10054929.
      Citations:    
    2. Neyhart E, Zhou N, Munn BR, Law RG, Smith C, Mridha ZH, Blanco FA, Li G, Li Y, Hu M, McGinley MJ, Shine JM, Reimer J. Cortical acetylcholine dynamics are predicted by cholinergic axon activity and behavior state. Cell Rep. 2024 Oct 22; 43(10):114808. PMID: 39383037.
      Citations: 1     Fields:    Translation:AnimalsCells
    3. Pirhayati D, Smith CL, Kroeger R, Navlakha S, Pfaffinger P, Reimer J, Arenkiel BR, Patel A, Moss EH, Pirhayati D, Smith CL, Kroeger R, Navlakha S, Pfaffinger P, Reimer J, Arenkiel BR, Patel A, Moss EH. Dense and Persistent Odor Representations in the Olfactory Bulb of Awake Mice. J Neurosci. 2024 Sep 25; 44(39). PMID: 39187379; PMCID: PMC11426377.
      Citations:    Fields:    Translation:AnimalsCells
    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, Papadopoulos S, Kunin A, Sinz FH. NEURD offers automated proofreading and feature extraction for connectomics. bioRxiv. 2024 Sep 23. PMID: 36993282; PMCID: PMC10055177.
      Citations:    
    5. 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, Wang EY, Fahey PG, Ding Z, Papadopoulos S, Ponder K, Weis MA, Chang A, Muhammad T, Patel S, Ding Z, Tran D, Fu J, Schneider-Mizell CM, Reid RC, Collman F, da Costa NM, Franke K, Ecker AS, Reimer J, Pitkow X, Sinz FH, Tolias AS, Wang EY, Fahey PG, Ding Z, Papadopoulos S, Ponder K, Weis MA, Chang A, Muhammad T, Patel S, Ding Z, Fu J, Schneider-Mizell CM, Reid RC, Collman F, da Costa NM, Franke K, Ecker AS, Reimer J, Pitkow X, Sinz FH, Tolias AS. Foundation model of neural activity predicts response to new stimulus types and anatomy. bioRxiv. 2024 Aug 31. PMID: 36993435; PMCID: PMC10055288.
      Citations:    
    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, Fu J, Shrinivasan S, Baroni L, Ding Z, Fahey PG, Pierzchlewicz P, Ponder K, Froebe R, Ntanavara L, Muhammad T, Willeke KF, Wang E, Ding Z, Tran DT, Papadopoulos S, Patel S, Reimer J, Ecker AS, Pitkow X, Antolik J, Sinz FH, Haefner RM, Tolias AS, Franke K. Pattern completion and disruption characterize contextual modulation in the visual cortex. bioRxiv. 2024 May 09. PMID: 36993321; PMCID: PMC10054952.
      Citations:    
    7. Neyhart E, Zhou N, Munn BR, Law RG, Smith C, Mridha ZH, Blanco FA, Li G, Li Y, McGinley MJ, Shine JM, Reimer J. Cortical acetylcholine dynamics are predicted by cholinergic axon activity and behavior state. bioRxiv. 2024 Feb 01. PMID: 38352527; PMCID: PMC10862699.
      Citations:    
    8. MICrONS Consortium, Brittain D, Bumbarger DJ, Kapner D, Kinn S, Seshamani S, Suckow S, Torres R, Yin W, Castro MA, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Wong W, Wu J, Reimer J, Tolias AS, Schneider-Mizell CM, Bodor AL, Buchanan J, Elabbady L, Gamlin C, Mahalingam G, Takeno M, Dorkenwald S, Bae JA, Macrina T, Turner NL, Seung HS, Reid RC, Collman F, Ma?arico da Costa N. Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex. bioRxiv. 2024 Jan 06. PMID: 36747710; PMCID: PMC9900837.
      Citations:    
    9. 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.
      Citations:    
    10. 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.
      Citations:    
    11. 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
    12. 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
    13. 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
    14. 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.
      Citations:    
    15. 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
    16. 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
    17. 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
    18. 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
    19. 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
    20. 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
    21. 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
    22. 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
    23. 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
    24. 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
    25. 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     
    26. 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
    27. 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
    28. 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
    29. 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
    30. 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
    31. 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
    32. 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
    33. 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
    34. 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
    35. 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
    36. 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
    37. 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
    38. 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
    39. 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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