Selected Publications

Please find here a link to a list of all publications on pubmed.
 

  • Tillman DE, Durak O, Veeraraghavan P, Froberg JE, Wheeler G, Budnik B, Macklis JD. Sequestration of growth cone surface proteins by cytoplasmic Lrrtm2 introduces de novo amydgala innervation by cerebral cortex associative neurons. BioRxiv preprint. 9 April 2026. DOI:10.64898/2026.04.08.716720
  • Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh S, Basak AN, Macklis JD. 2026. Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors. eLife. DOI:10.7554/eLife.100340
  • Veeraraghavan P, Engmann AK, Hatch JJ, Itoh Y, Nguyen D, Addison T, Macklis JD. 2025. Dynamic subtype- and context-specific subcellular RNA regulation in growth cones of developing neurons of the cerebral cortex. Nature Neuroscience. DOI:10.1038/s41593-025-02173-0
  • Durak, O*, Kim, JY*, Tillman, DE, Itoh, Y, Wettstein, M, Greig, LC, Macklis, JD. 2022. ASD gene Bcl11a regulates subcellular RNA localization, associative circuitry, and social behavior. bioRxiv. DOI:10.1101/2022.10.06.511159
  • Tran TP, Budnik B, Froberg JE, Macklis JD. 2025. Cortical projection neurons with distinct axonal connectivity employ ribosomal complexes with distinct protein compositions. eLife. DOI:10.7554/eLife.107488.1
  • Veeraraghavan P, Tillman DE, Ross MI, Macklis JD. 2025. Developmental dynamics and axonal transport of cerebral cortex projection neuron mRNAs in vivo. bioRxiv. DOI:10.1101/2025.04.23.650263
  • Poulopoulos A, Davis P, Brandenburg C, Itoh Y, Galazo MJ, Greig LC, Romanowski AJ, Budnik B, Macklis JD. 2024. Symmetry in levels of axon-axon homophilic adhesion establishes topography in the corpus callosum and development of connectivity between brain hemispheres. bioRxiv. Pubmed: 38585721 DOI:10.1101/2024.03.28.587108
  • Itoh Y, Woodworth MB, Greig LC, Engmann AK, Tillman DE, Hatch JJ, Macklis JD. 2025. Bcl11b orchestrates subcerebral projection neuron axon development via cell-autonomous, non-cell-autonomous, and subcellular mechanisms. eLife. DOI:10.7554/eLife.105678.1
  • Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD. 2024. BEAM: A combinatorial recombinase toolbox for binary gene expression and mosaic genetic analysis. Cell reports. 43(8):114650. Pubmed: 39159043 DOI:S2211-1247(24)01001-5
  • Froberg JE, Durak O, Macklis JD. 2023. Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes. Cell reports. 42(9):112995. Pubmed: 37624698 DOI:S2211-1247(23)01006-9
  • Galazo MJ, Sweetser DA, Macklis JD. 2023. Tle4 controls both developmental acquisition and early post-natal maturation of corticothalamic projection neuron identity. Cell reports. 42(8):112957. Pubmed: 37561632 DOI:S2211-1247(23)00968-3
  • Itoh Y, Sahni V, Shnider SJ, McKee H, Macklis JD. 2023. Inter-axonal molecular crosstalk via Lumican proteoglycan sculpts murine cervical corticospinal innervation by distinct subpopulations. Cell reports. 42(3):112182. Pubmed: 36934325 DOI:S2211-1247(23)00193-6
  • Song JHT, Ruven C, Patel P, Ding F, Macklis JD*, Sahni V*. 2022. Cbln1 directs axon targeting by corticospinal neurons specifically toward thoraco-lumbar spinal cord. bioRxiv. DOI:https://doi.org/10.1101/2022.04.06.487184
  • Engmann AK, Hatch JJ, Nanda P, Veeraraghavan P, Ozkan A, Poulopoulos A, Murphy AJ, Macklis JD. 2022. Neuronal subtype-specific growth cone and soma purification from mammalian CNS via fractionation and fluorescent sorting for subcellular analyses and spatial mapping of local transcriptomes and proteomes. Nature protocols. 17(2):222-251. Pubmed: 35022617 DOI:10.1038/s41596-021-00638-7
  • Sahni V, Itoh Y, Shnider SJ, Macklis JD. 2021. Crim1 and Kelch-like 14 exert complementary dual-directional developmental control over segmentally specific corticospinal axon projection targeting. Cell reports. 37(3):109842. Pubmed: 34686337 DOI:S2211-1247(21)01306-1
  • Sahni V, Shnider SJ, Jabaudon D, Song JHT, Itoh Y, Greig LC, Macklis JD. 2021. Corticospinal neuron subpopulation-specific developmental genes prospectively indicate mature segmentally specific axon projection targeting. Cell reports. 37(3):109843. Pubmed: 34686320 DOI:S2211-1247(21)01307-3
  • Diaz JL, Siththanandan VB, Lu V, Gonzalez-Nava N, Pasquina L, MacDonald JL, Woodworth MB, Ozkan A, Nair R, He Z, Sahni V, Sarnow P, Palmer TD, Macklis JD, Tharin S. 2020. An evolutionarily acquired microRNA shapes development of mammalian cortical projections. Proceedings of the National Academy of Sciences of the United States of America. 117(46):29113-29122. Pubmed: 33139574 DOI:10.1073/pnas.2006700117
  • Poulopoulos A, Murphy AJ, Ozkan A, Davis P, Hatch J, Kirchner R, Macklis JD. 2019. Subcellular transcriptomes and proteomes of developing axon projections in the cerebral cortex. Nature. 565(7739):356-360. Pubmed: 30626971 DOI:10.1038/s41586-018-0847-y
  • Wuttke TV, Markopoulos F, Padmanabhan H, Wheeler AP, Murthy VN, Macklis JD. 2018. Developmentally primed cortical neurons maintain fidelity of differentiation and establish appropriate functional connectivity after transplantation. Nature neuroscience. 21(4):517-529. Pubmed: 29507412 DOI:10.1038/s41593-018-0098-0
  • Galazo MJ, Emsley JG, Macklis JD. 2016. Corticothalamic Projection Neuron Development beyond Subtype Specification: Fog2 and Intersectional Controls Regulate Intraclass Neuronal Diversity. Neuron. 91(1):90-106. Pubmed: 27321927 DOI:S0896-6273(16)30203-3
  • Greig LC, Woodworth MB, Greppi C, Macklis JD. 2016. Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex. Neuron. 90(2):261-77. Pubmed: 27100196 DOI:S0896-6273(16)00187-2
  • Woodworth MB, Greig LC, Liu KX, Ippolito GC, Tucker HO, Macklis JD. 2016. Ctip1 Regulates the Balance between Specification of Distinct Projection Neuron Subtypes in Deep Cortical Layers. Cell reports. 15(5):999-1012. Pubmed: 27117402 DOI:S2211-1247(16)30335-7
  • Greig LC, Woodworth MB, Galazo MJ, Padmanabhan H, Macklis JD. 2013. Molecular logic of neocortical projection neuron specification, development and diversity. Nature reviews. Neuroscience. 14(11):755-69. Pubmed: 24105342 DOI:10.1038/nrn3586
  • Czupryn A, Zhou YD, Chen X, McNay D, Anderson MP, Flier JS, Macklis JD. 2011. Transplanted hypothalamic neurons restore leptin signaling and ameliorate obesity in db/db mice. Science (New York, N.Y.). 334(6059):1133-7. Pubmed: 22116886 DOI:10.1126/science.1209870