Publications

• Ye B. Approaches to vascularizing human brain organoids. PLoS Biology. 2023. doi: 10.1371/journal.pbio.3002141, 2023
• Singh M, Ye B#, Kim JH#. Dual Leucine Zipper Kinase regulates Dscam expression through a noncanonical function of the cytoplasmic poly(A)-binding protein. J Neurosci. 2022. doi: 10.1523/JNEUROSCI.0543-21.2022
• Ye B. The molecular mechanisms that underlie neural network assembly. Medical Review. 2022. doi: 10.1515/mr-2022-0011
• Yang T, Veling MW, Zhao XF, Prin NP, Zhu L, Hergenreder T, Liu H, Liu L, Rane Z, Savelieff MG, Fuerst PG, Li Q, Kwan KY, Giger RJ, Wang Y, Ye B. Migrating pyramidal neurons require DSCAM to bypass the border of the developing cortical plate. J Neurosci. 2022. doi: 10.1523/JNEUROSCI.0997-21.2022
• Chiu SL, Diering GH, Ye B, Takamiya K, Chen CM, Jiang Y, Niranjan T, Schwartz CE, Wang T, Huganir RL. GRASP1 regulates synaptic plasticity and learning through endosomal recycling of AMPA receptors. Neuron. 2017. doi: 10.1016/j.neuron.2017.02.031
• Kaneko T*, Macara AM*, Li R, Hu Y, Iwasaki K, Dunnings Z, Firestone E, Horvatic S, Guntur A, Shafer OT, Yang C-H, Zhou J, Ye B. Serotonergic modulation enables pathway-specific plasticity in a developing sensory circuit in Drosophila. Neuron. 2017. doi: 10.1016/j.neuron.2017.06.034
• Wang X*, Zhang MW*, Kim JH, Macara AM, Sterne G, Yang T, Ye B. The Krüppel-like factor Dar1 determines multipolar neuron morphology. J Neurosci. 2015. doi: 10.1523/JNEUROSCI.1610-15.2015 
• Kaneko T., Ye B. Fine-scale topography in sensory systems: Insights from Drosophila and vertebrates. J Comp Physiol. 2015. doi: 10.1007/s00359-015-1022-7
• Zhou W*, Chang J*, Wang W, Savelieff M, Zhao Y, Ke S, Ye B. GM130 is required for compartmental organization of dendritic Golgi outposts. Current Biology. 2014. doi: 10.1016/j.cub.2014.04.008
• Wang X, Sterne GR, Ye B. Regulatory mechanisms underlying the differential growth of dendrites and axons. Neurosci Bull. 2014. doi: 10.1007/s12264-014-1447-3
• Yang L, Li R, Kaneko T, Takle K, Morikawa RK, Essex L, Wang X, Zhou J, Emoto K, Xiang Y, Ye B. Trim9 regulates activity-dependent fine-scale topography in Drosophila. Current Biology. 2014. doi: 10.1016/j.cub.2014.03.041
• Kim JH*, Wang X*, Coolon R, Ye B. Dscam expression levels determine presynaptic arbor sizes in Drosophila sensory neurons. Neuron. 2013. doi: 10.1016/j.neuron.2013.05.020
• Wang X, Kim JH, Bazzi M, Robinson S, Collins CA, Ye B. Bimodal control of dendritic and axonal growth by the dual leucine zipper kinase pathway. PLoS Biology. 2013. doi: 10.1371/journal.pbio.1001572
• Cáceres A#, Ye B#, Dotti CG#. Neuronal polarity: demarcation, growth and commitment. Current Opinion in Cell Biology. 2012. doi: 10.1016/j.ceb.2012.05.011
• Wang X and Ye B. Transcriptional regulators that differentially control dendrite and axon development. Frontiers in Biology. 2012. doi: 10.1007/s11515-012-1234-y
• Ye B, Kim JH, Yang, L, McLachlan I, Younger S, Jan LY, and Jan YN. Differential regulation of dendritic and axonal development by the novel Krüppel like factor Dar1. J Neurosci. 2011. doi: 10.1523/JNEUROSCI.6307-10.2011

• Pizzano S*, Sterne GR*, Veling MW*, Xu LA, Hergenreder T, Ye B. The Drosophila homolog of APP promotes Dscam expression to drive axon terminal growth, revealing interaction between Down syndrome genes. Disease Models & Mechanisms. 2023 (in press). 
• Liu H*, Caballero-Florán RN*, Hergenreder T*, Yang T, Hull JM, Pan G, Li R, Veling MW, Isom LL, Kwan KY, Huang ZJ, Fuerst PG, Jenkins PM#, Ye B#. DSCAM gene triplication causes excessive GABAergic synapses in the neocortex in Down syndrome mouse models. PLoS Biology. 2023. doi: 10.1371/journal.pbio.3002078
• Kim JH#, Singh M, Pan G, Lopez A, Zito N, Bosse B, Ye B#: Frameshift mutations of YPEL3 alter the sensory circuit function in Drosophila. Disease Models & Mechanisms. 2020. doi: 10.1242/dmm.042390 
• Sterne GR*, Kim JH*, Ye B. Dysregulated Dscam levels act through Abelson tyrosine kinase to enlarge presynaptic arbors. Elife. 2015. doi: 10.7554/eLife.05196
• Kim JH*, Wang X*, Coolon R, Ye B. Dscam expression levels determine presynaptic arbor sizes in Drosophila sensory neurons. Neuron. 2013. doi: 10.1016/j.neuron.2013.05.020

• Pan G, Li R, Xu G, Weng S, Yang XL, Yang L#, Ye B#. Cross-modal modulation gates nociceptive inputs in Drosophila. Current Biology. 2023. doi: 10.1016/j.cub.2023.02.032
• Manubens-Gil L, et al., BigNeuron: A resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets. Nature Methods. 2023. doi: 10.1038/s41592-023-01848-5
• Hu Y, Ferrario CR, Maitland AD, Ionides RB, Ghimire A, Watson B, Iwasaki K, White H, Xi Y, Zhou J, Ye B. LabGym: Quantification of user-defined animal behaviors using learning-based holistic assessment. Cell Rep Methods. 2023. doi: 10.1016/j.crmeth.2023.100415
• Ye B. The molecular mechanisms that underlie neural network assembly. Medical Review. 2022. doi: 10.1515/mr-2022-0011
• Hu Y*, Wang C*, Yang L, Pan G, Liu H, Yu G#, Ye B#. A neural basis for categorizing sensory stimuli to enhance decision accuracy. Current Biology. 2020. doi: 10.1016/j.cub.2020.09.045
• Kaneko T*, Macara AM*, Li R, Hu Y, Iwasaki K, Dunnings Z, Firestone E, Horvatic S, Guntur A, Shafer OT, Yang C-H, Zhou J, Ye B. Serotonergic modulation enables pathway-specific plasticity in a developing sensory circuit in Drosophila. Neuron. 2017. doi: 10.1016/j.neuron.2017.06.034
• Sanders J, Singh A, Sterne GR, Peng H, Ye B, Zhou J. Learning-guided automatic three dimensional synapse quantification for Drosophila neurons. BMC Bioinformatics. 2015. doi: 10.1186/s12859-015-0616-y
• Smafield T, Pasupuleti V, Sharma K, Huganir RL, Ye B, Zhou J. Automatic dendritic length quantification for high throughput screening of mature neurons. Neuroinformatics. 2015. doi: 10.1007/s12021-015-9267-4
• Zhou J, Lamichhane S, Sterne G, Ye B, Peng H. BIOCAT: A pattern recognition platform for customizable biological image classification and annotation. BMC Bioinformatics. 2013. doi: 10.1186/1471-2105-14-291

• Massengill C, Bayless-Edwards L, Ceballos C, Cebul E, Qin M, Whorton M, Ye B, Mao T, Zhong H. Highly sensitive genetically-encoded sensors for population and subcellular imaging of cAMP in vivo. Nature Methods. 2022. doi: 10.1038/s41592-022-01646-5
• Liu H, Pizzano S, Li R, Zhao W, Veling MW, Hu Y, Yang L, Ye B. isoTarget: A genetic method for analyzing the functional diversity of splicing isoforms in vivo. Cell Reports. 2020. doi: 10.1038/s41592-022-01646-5
• Veling MW*, Li Y*, Veling MT, Michki N, Liu H, Litts C, Ye B#†, Cai D#. Identification of neuronal lineages in the Drosophila peripheral nervous system with a "digital" multi-spectral lineage tracing system. Cell Reports. 2019. doi: 10.1016/j.celrep.2019.10.124 (†lead contact)
• Mohr SE, Hu Y, Rudd K, Buckner M, Gilly Q, Foster B, Sierzputowska K, Comjean A, Ye B, Perrimon N. Reagent and data resources for investigation of RNA binding protein functions in Drosophila melanogaster cultured cells. G3 (Bethesda). 2015. doi: 10.1534/g3.115.019364
• Mishra B, Ghannad-Rezaie M, Li J, Wang X, Hao Y, Ye B, Chronis N, and Collins CA. Using microfluidics chips for live imaging and study of injury response in Drosophila larvae. Journal of Visualized Experiments. 2014. doi: 10.3791/50998

*Co-first authors
#Co-corresponding authors