Publications

 

• Conner, J. M., et al. (2021). Modulation of tactile feedback for the execution of dexterous movement. BioRxiv, 2021.03.04.433649.

​

• Cui, Q., et al. (2021). Striatal Direct Pathway Targets Npas1+ Pallidal Neurons. Journal of Neuroscience, 41(18), 3966–3987.

​

• Hyun, M., et al. (2021). Social isolation uncovers a circuit underlying context-dependent territory-covering micturition. Proceedings of the National Academy of Sciences, 118(1).

​

• Kay, J. E., et al. (2021). Analysis of mutations in tumor and normal adjacent tissue via fluorescence detection. Environmental and Molecular Mutagenesis, 62(2), 108–123.

 

• Wang, X., et al. (2021). Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain. ELife, 10, e63455.

 

• Whitesell, J. D., et al. (2021). Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network. Neuron, 109(3), 545-559.e8.

 

• Xia, D., et al. (2021). Fibrillar Aβ causes profound microglial metabolic perturbations in a novel APP knock-in mouse model. BioRxiv, 2021.01.19.426731.

 

• Abecassis, Z. A., et al. (2020). Npas1+-Nkx2.1+ Neurons Are an Integral Part of the Cortico-pallido-cortical Loop. Journal of Neuroscience, 40(4), 743–768.

 

• Chen, C.-H., et al. (2020). Homotopic Commissural Projections of Area Prostriata in Rat and Mouse: Comparison With Presubiculum and Parasubiculum. Frontiers in Neural Circuits, 14.

 

• Chon, U., et al. (2020). Topographically Distinct Projection Patterns of Early-Generated and Late-Generated Projection Neurons in the Mouse Olfactory Bulb. ENeuro, 7(6).

 

• Cui, Q., et al. (2020). Parallel Movement-suppressing Striatal Output Pathways. BioRxiv, 2020.09.02.273615.

 

• Ding, S.-L., et al. (2020). Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis. Cell Reports, 31(7), 107648.

 

• Grauel, A. L., et al. (2020). TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts. Nature Communications, 11(1), 6315.

 

• Hu, J.-M., et al. (2020). Afferent Projections to Area Prostriata of the Mouse. Frontiers in Neuroanatomy, 14.

 

• Jefferson, S. J., et al.  (2020). Disinhibition of somatostatin interneurons confers resilience to stress in male but not female mice. Neurobiology of Stress, 13, 100238.

 

• Leyrer-Jackson, J. M., et al. (2020). Ethanol has concentration-dependent effects on hypothalamic POMC neuronal excitability. Alcohol, 86, 103–112.

 

• Li, L. Z., et al. (2020). Two-Photon Autofluorescence Imaging of Fixed Tissues: Feasibility and Potential Values for Biomedical Applications. In P.-D. Ryu, J. C. LaManna, D. K. Harrison, & S.-S. Lee (Eds.), Oxygen Transport to Tissue XLI (pp. 375–381). Springer International Publishing.

 

• Matho, K. S., et al. (2020). Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex. BioRxiv, 2020.04.22.054064.

 

• Muñoz-Castañeda, R., et al.  (2020). Cellular Anatomy of the Mouse Primary Motor Cortex. BioRxiv, 2020.10.02.323154.

 

• Oblak, A. L., et al. (2020). Deep phenotyping of the 5XFAD model: IU/JAX/PITT MODEL-AD center. Alzheimer’s & Dementia, 16(S2), e045981.

 

• Ortega, S. B., et al.  (2020). B cells migrate into remote brain areas and support neurogenesis and functional recovery after focal stroke in mice. Proceedings of the National Academy of Sciences, 117(9), 4983–4993.

 

• Steinman, J. S. (2020). Altered 3D Vascular Architecture and Cerebral Blood Flow in a Mouse Model of TBI [Thesis].

 

• Son, S., et al. (2020). Wiring diagram of the oxytocin system in the mouse brain. BioRxiv, 2020.10.01.320978.

 

• Wang, Q., et al. (2020). The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell, 181(4), 936-953.e20.

 

• Whitesell, J. D., et al. (2020). Regional, layer, and cell-class specific connectivity of the mouse default mode network. BioRxiv, 2020.05.13.094458.

 

• Woodward, A., et al. (2020). The NanoZoomer artificial intelligence connectomics pipeline for tracer injection studies of the marmoset brain. Brain Structure and Function, 225(4), 1225–1243.

 

• Zapiec, B., et al.  (2020). The Zonal Organization of Odorant Receptor Gene Choice in the Main Olfactory Epithelium of the Mouse. Cell Reports, 30(12), 4220-4234.e5.

 

• Yanev, P., et al. (2020). Impaired meningeal lymphatic vessel development worsens stroke outcome. Journal of Cerebral Blood Flow & Metabolism, 40(2), 263–275.

 

• Abdeladim, L., et al. (2019). Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy. Nature Communications, 10(1), 1662.

 

• Abecassis, Z. A., et al. (2019). Npas1+-Nkx2.1+ Neurons Form A Unique Pallidal Neuron Subclass. BioRxiv, 644674.

 

• Chon, U., et al. (2019). Enhanced and unified anatomical labeling for a common mouse brain atlas. Nature Communications, 10(1), 5067.

 

• Dorkenwald, S., et al. (2019). Binary and analog variation of synapses between cortical pyramidal neurons. BioRxiv, 2019.12.29.890319.

 

• Harris, J. A., et al.  (2019). Hierarchical organization of cortical and thalamic connectivity. Nature, 575(7781), 195–202.

 

• Hyun, M., et al.  (2019). Social isolation uncovers a brain-wide circuit underlying context-dependent territory-covering micturition behavior. BioRxiv, 798132.

 

• Lo, L., et al. (2019). Connectional architecture of a mouse hypothalamic circuit node controlling social behavior. Proceedings of the National Academy of Sciences, 116(15), 7503–7512.

 

• Mandelbaum, G. (2019). Basal Ganglia Circuitry Controlling Action Selection.

 

• Mandelbaum, G., et al. (2019). Distinct Cortical-Thalamic-Striatal Circuits through the Parafascicular Nucleus. Neuron, 102(3), 636-652.e7.

 

• Pama, E. (2019). Developmental myelination and myelin plasticity during spatial working memory task acquisition [Ph.D., University of Cambridge].

 

• Poinsatte, K., et al. (2019). Visualization and Quantification of Post-stroke Neural Connectivity and Neuroinflammation Using Serial Two-Photon Tomography in the Whole Mouse Brain. Frontiers in Neuroscience, 13.

 

• Ramirez, D. M. O., et al. (2019). Serial Multiphoton Tomography and Analysis of Volumetric Images of the Mouse Brain. In E. Hartveit (Ed.), Multiphoton Microscopy (pp. 195–224). Springer.

 

• Skibbe, H., et al. (2019). PAT—Probabilistic Axon Tracking for Densely Labeled Neurons in Large 3-D Micrographs. IEEE Transactions on Medical Imaging, 38(1), 69–78.

 

• Skibbe, H., et al. (2019). MarmoNet: A pipeline for automated projection mapping of the common marmoset brain from whole-brain serial two-photon tomography. ArXiv:1908.00876 [Cs, Eess, q-Bio, Stat].

 

• Smith, J. B., et al. (2019). The relationship between the claustrum and endopiriform nucleus: A perspective towards consensus on cross-species homology. Journal of Comparative Neurology, 527(2), 476–499.

 

• Tappan, S. J., et al.  (2019). Automatic navigation system for the mouse brain. Journal of Comparative Neurology, 527(13), 2200–2211.

 

• Wang, Y., et al.  (2019). Complete single neuron reconstruction reveals morphological diversity in molecularly defined claustral and cortical neuron types. BioRxiv, 675280.

 

• Whitesell, J. D., et al. (2019). Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer’s disease. Journal of Comparative Neurology, 527(13), 2122–2145.

 

• Zhao, C., et al. (2019). iSMORE: An Iterative Self Super-Resolution Algorithm. In N. Burgos, A. Gooya, & D. Svoboda (Eds.), Simulation and Synthesis in Medical Imaging (pp. 130–139). Springer International Publishing.

 

• Badura, A., et al.  (2018). Normal cognitive and social development require posterior cerebellar activity. ELife, 7, e36401.

 

• Chatterjee, S., et al. (2018). Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons. Nature Neuroscience, 21(4), 638–646.

 

• Han, Y., et al.  (2018). The logic of single-cell projections from visual cortex. Nature, 556(7699), 51–56.

 

• Kelly, S. M., et al. (2018). Radial Glial Lineage Progression and Differential Intermediate Progenitor Amplification Underlie Striatal Compartments and Circuit Organization. Neuron, 99(2), 345-361.e4.

 

• Szelenyi, E., et al. (2018). A brain network basis of Fragile X syndrome behavioral penetrance determined by X chromosome inactivation in female mice. BioRxiv, 458992.

 

• Turcan, S., et al. (2018). Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence. Nature Genetics, 50(1), 62–72.

 

• Abe, H., et al. (2017). 3D reconstruction of brain section images for creating axonal projection maps in marmosets. Journal of Neuroscience Methods, 286, 102–113.

 

• Becker, A. M. (2017). Targeting Cholinergic Neuromodulation in Stroke Recovery [Thesis].

 

• Han, Y., et al. (2017). A single-cell anatomical blueprint for intracortical information transfer from primary visual cortex. BioRxiv, 148031.

 

• Kim, Y., et al. (2017). Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism. Cell, 171(2), 456-469.e22.

 

• Kutten, Kwame Sanwu. (2017). A Large Deformation Diffeomorphic Approach to Inter-modality Registration of Microscopy Images via Mutual Information [Thesis, Johns Hopkins University].

 

• Martersteck, E. M., et al. (2017). Diverse Central Projection Patterns of Retinal Ganglion Cells. Cell Reports, 18(8), 2058–2072.

 

• Niedworok, C. J. (2017). A Pipeline for Automated Assessment of Cell Location in 3D Mouse Brain Image Sets [Doctoral, UCL (University College London)]. In Doctoral thesis, UCL (University College London). UCL.

 

• Quina, L. A., et al. (2017). Specific connections of the interpeduncular subnuclei reveal distinct components of the habenulopeduncular pathway. Journal of Comparative Neurology, 525(12), 2632–2656.

 

• Sharpe, M. J., et al. (2017). Lateral Hypothalamic GABAergic Neurons Encode Reward Predictions that Are Relayed to the Ventral Tegmental Area to Regulate Learning. Current Biology, 27(14), 2089-2100.e5.

 

• Wang, Q., et al. (2017). Organization of the connections between claustrum and cortex in the mouse. Journal of Comparative Neurology, 525(6), 1317–1346.

 

• Amato, S. P., et al. (2016). Whole Brain Imaging with Serial Two-Photon Tomography. Frontiers in Neuroanatomy, 10.

 

• Billeh, Y. N., et al.  (2016). Effects of Chronic Sleep Restriction during Early Adolescence on the Adult Pattern of Connectivity of Mouse Secondary Motor Cortex. ENeuro, 3(2).

 

• Brown, A. P. Y. (2016). Intrinsic and Visually-Evoked Properties of Layer 2/3 Neurons in Mouse Primary Visual Cortex and Their Dependence on Sensory Experience [Doctoral, UCL (University College London)]. In Doctoral thesis, UCL (University College London). UCL (University College London).

 

• Cazemier, J. L., et al.  (2016). Connectomic Analysis of Brain Networks: Novel Techniques and Future Directions. Frontiers in Neuroanatomy, 10.

 

• He, M., et al.  (2016). Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex. Neuron, 91(6), 1228–1243.

 

• Hou, X. H., et al. (2016). Central Control Circuit for Context-Dependent Micturition. Cell, 167(1), 73-86.e12.

 

• Hudry, E., et al.  (2016). Exosome-associated AAV vector as a robust and convenient neuroscience tool. Gene Therapy, 23(4), 380–392.

 

• Jeong, M., et al. (2016). Comparative three-dimensional connectome map of motor cortical projections in the mouse brain. Scientific Reports, 6(1), 20072.

 

• Kim, Y., et al. (2016). Whole-Brain Mapping of Neuronal Activity in the Learned Helplessness Model of Depression. Frontiers in Neural Circuits, 10.

 

• Kutten, Kwame S., et al. (2016). An image registration pipeline for analysis of transsynaptic tracing in mice. Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging, 9788, 978823.

 

• Wang, Q., et al. (2016). Identification of Phosphorylation Consensus Sequences and Endogenous Neuronal Substrates of the Psychiatric Risk Kinase TNIK. Journal of Pharmacology and Experimental Therapeutics, 356(2), 410–423.

 

• Zapiec, B., et al.  (2016). Neuropilin-1 and the Positions of Glomeruli in the Mouse Olfactory Bulb. ENeuro, 3(5).

 

• Quina, L. A., et al. (2015). Efferent Pathways of the Mouse Lateral Habenula. Journal of Comparative Neurology, 523(1), 32–60.

 

• Dance, A. (2015). Connectomes make the map. Nature, 526(7571), 147–149.

 

• Feng, D., et al. (2015). Exploration and visualization of connectivity in the adult mouse brain. Methods, 73, 90–97.

 

• Georgiev, T., et al. (2015). Colocalization properties of elementary Ca2+ release signals with structures specific to the contractile filaments and the tubular system of intact mouse skeletal muscle fibers. Journal of Structural Biology, 192(3), 366–375.

 

• Janke, A. L., et al.  (2015). Robust methods to create ex vivo minimum deformation atlases for brain mapping. Methods, 73, 18–26.

 

• Kuan, L., et al.  (2015). Neuroinformatics of the Allen Mouse Brain Connectivity Atlas. Methods, 73, 4–17.

 

• Magnain, C., et al.  (2015). Optical coherence tomography visualizes neurons in human entorhinal cortex. Neurophotonics, 2(1), 015004.

 

• Vousden, D. A., et al. (2015). Whole-brain mapping of behaviourally induced neural activation in mice. Brain Structure and Function, 220(4), 2043–2057.

 

• Yuan, J., et al.  (2015). Visible rodent brain-wide networks at single-neuron resolution. Frontiers in Neuroanatomy, 9.

 

• Zapiec, B., et al. (2015). Multiplex assessment of the positions of odorant receptor-specific glomeruli in the mouse olfactory bulb by serial two-photon tomography. Proceedings of the National Academy of Sciences, 112(43), E5873–E5882.

 

• Oh, S. W., et al.  (2014). A mesoscale connectome of the mouse brain. Nature, 508(7495), 207–214.

 

• Rubenstein, J. L. R. (2014). Major progress towards elucidating brain wiring diagrams. Journal of Comparative Neurology, 522(9), 1987–1988.

 

• Dos Santos, C. O., et al. (2013). Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells. Proceedings of the National Academy of Sciences of the United States of America, 110(18), 7123–7130.

 

• Ghafaryasl, B., et al. (2013). Cardiac Microstructure Estimation from Multi-photon Confocal Microscopy Images. In S. Ourselin, D. Rueckert, & N. Smith (Eds.), Functional Imaging and Modeling of the Heart (pp. 80–88). Springer. https://doi.org/10.1007/978-3-642-38899-6_10

 

• Gleave, J. A., et al.  (2013). A Method for 3D Immunostaining and Optical Imaging of the Mouse Brain Demonstrated in Neural Progenitor Cells. PLOS ONE, 8(8), e72039.

 

• Osten, P., et al. (2013). Mapping brain circuitry with a light microscope. Nature Methods, 10(6), 515–523.

 

• Pastrana, E. (2013). Focus on Mapping the Brain. Nature Methods, 10(6), 481–481.

 

• Harris, J. A., et al. (2012). Adeno-Associated Viral Vectors for Anterograde Axonal Tracing with Fluorescent Proteins in Nontransgenic and Cre Driver Mice. Current Protocols in Neuroscience, 59(1), 1.20.1-1.20.18.

 

• Helmstaedter, M., et al.  (2012). Computational methods and challenges for large-scale circuit mapping. Current Opinion in Neurobiology, 22(1), 162–169.

 

• Sempeles, S. (2012). Whole-Brain Mapping Enhanced by Automated Imaging. Journal of Clinical Engineering, 37(2), 36–37.

​

• Ragan, T., et al. (2012). Serial two-photon tomography for automated ex vivo mouse brain imaging. Nature Methods, 9(3), 255–258.

 

• Betz Dene M, Becker April M, et al. (n.d.). Abstract TP333: Motor Recovery After Transient Middle Cerebral Artery Occlusion May be Impacted by the Disruption of Nucleus Basalis-Cortical Cholinergic Pathways. Stroke, 50(Suppl_1), ATP333–ATP333.

 

• Morganstern, I., et al. (n.d.). Behavioral Manifestations, Aggression and Plaque Distribution in Transgenic Mouse Models of Alzheimer’s Disease. 1.

 

• Torres Vanessa O, et al. (n.d.). Abstract TP107: B cells Migrate to Remote Areas Supporting Functional Recovery After Stroke. Stroke, 49(Suppl_1), ATP107–ATP107.