Publications

Highlighted publications (work done prior to Stanford)

* co-first author, † corresponding author, § lead contact

  1. Saunders RA*, Allen WE*†§, Pan X, Sandhu J, Lu J, Lau TK, Smolyar K, Sullivan Z, Dulac C, Weissman JS†, Zhuang X†. A Platform for Multimodal In Vivo Pooled Genetic Screens Reveals Regulators of Liver Function. bioRxiv, 2024.11.18.624217 (2024).

  2. Allen WE†, Blosser TR, Sullivan ZA, Dulac C†, Zhuang X†. Molecular and Spatial Signatures of Mouse Brain Aging at Single-Cell Resolution. Cell, 186, 194-208 (2023).

  3. Allen WE. Brain Mapping, from Molecules to Networks. Science, 370, 925-925 (2021).

  4. Allen WE, Chen MZ, Pichamoorthy N, Tien RH, Pachitariu M, Luo L, Deisseroth K. Thirst Regulates Motivated Behavior Through Modulation of Brainwide Neural Population Dynamics. Science 364, eaav3932 (2019).

  5. Wang X*, Allen WE*, Wright MA, Sylwestrak EL, Samusik N, Vesuna S, Evans K, Liu C, Ramakrishnan C, Liu J, Nolan GP, Bava FP, Deisseroth K. Three-Dimensional Intact-Tissue Sequencing of Single-Cell Transcriptional States. Science DOI:10.1126/science.aat5691 (2018).

  6. Allen WE*, DeNardo LW*, Chen MZ*, Liu CD, Loh KM, Fenno LE, Ramakrishnan C, Deisseroth K, Luo L. Thirst-Associated Preoptic Neurons Encode an Aversive Motivational Drive. Science 357, 1149-1155 (2017)

  7. Allen WE*, Kauvar IV*, Chen MZ, Richman EB, Yang SJ, Chan K, Gradinaru V, Deverman BE, Luo L, Deisseroth K. Global Representations of Goal-Directed Behavior in Distinct Cell Types of Mouse Neocortex. Neuron 94, 891-907 (2017)

  8. Ye L*, Allen WE*, Thompson KR*, Tian Q, Hsueh B, Ramakrishnan C, Wang A, Jennings J, Adhikari A, Witten IB, Barth AL, Luo L, Halpern CH, McNab J, Deisseroth K. Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences. Cell, 165, 1-13 (2016).

  9. Allen WE, Luo L. Intersectional Illumination of Neural Circuit Function Neuron 85, 889-892 (2015)

Other select publications (prior to Stanford)

  1. Richman EB, Ticea N, Allen WE, Deisseroth K†, Luo L†. Neural Landscape Diffusion Resolves Conflicts Between Needs Across Time. Nature, 623, 571-579 (2023).

  2. Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Singh A, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. A Transcription Factor Atlas of Directed Differentiation. Cell, 186, 209-229 (2023).

  3. Sylwestrak E, Vesuna S, Jo Y, Wang X, Holcomb B, Tien RH, Kim DK, Fenno L, Ramakrishnan C, Allen WE, Chen R, Shenoy KV, Sussillo D, Deisseroth K. Cell-type-specific population dynamics of diverse reward computations. Cell, 185, 3568-3587 (2022).

  4. Trautmann E*, O’Shea DJ*, Sun X*, Marshel JH, Crow A, Hsueh B, Vesuna S, Cofer L, Bohner G, Allen W, Kauvar I, Quirin S, MacDougall M, Chen Y, Whitmire M, Ramakrishnan C, Sahani M, Seidemann E, Ryu SI, Deisseroth K, Shenoy KV. Dendritic Calcium Signals in Rhesus Macaque Motor Cortex Drive an Optical Brain-Computer Interface. Nature Communications 12, 3689 (2021).

  5. Lui JH*, Nguyen ND*, Grutznerii SM, Darmanis S, Peixoto D, Wagner MJ, Allen WE, Kebschull JM, Richman EB, Ren J, Newsome WT, Quake SR, Luo L. Differential Encoding in Prefrontal Cortex Projection Neuron Classes Across Cognitive Tasks. Cell, 184, 489-506 (2021).

  6. Kebschull JM, Richman EB, Ringach N, Friedman D, Kolluru SS, Jones RC, Allen WE, Wang Y, Zhou H, Cho SW, Chang HY, Deisseroth K, Quake SR, Luo L. Cerebellar Nuclei Evolved by Repeatedly Duplicating a Conserved Cell Type Set. Science, 370, eabd5059 (2020).

  7. Kauvar IV*, Machado TA*, Yuen E, Kochalka J, Choi M, Allen WE, Wetzstein G, Deisseroth K. Cortical Observation by Synchronous Multifocal Optical Sampling Reveals Widespread Population Encoding of Actions. Neuron, 107, 1-17 (2020).

  8. DeNardo LA, Liu CD, Allen WE, Adams EL, Friedmann D, Fu L, Guenthner CJ, Tessier-Lavigne M, Luo L. Temporal Evolution of Cortical Ensembles Promoting Remote Memory Retrieval. Nature Neuroscience 22, 460-469 (2019).

  9. Zhu Y, Nachtrab G, Keyes P, Allen WE, Luo L, Chen X. Dynamic Salience Processing in Paraventricular Thalamus Gates Associative Learning. Science 362, 423-429 (2018).

  10. Huang W, Wang DC, Allen WE, Klope M, Hu H, Shamloo M, Luo L. Early Adolescent Rai1 Reactivation Reverses Transcriptional and Social Interaction Deficits In a Mouse Model of Smith-Magenis Syndrome. Proc. Natl. Acad. Sci. USA 42, 10744-10749.

  11. Kato HK*, Kim YS*, Paggi JM, Evans KE, Allen WE, Richardson C, Inoue K, Ito S, Ramakrishnan C, Fenno LE, Yamashita K, Hilger D, Lee SY, Berndt A, Shen K, Kandori H, Dror RO, Kobilka BK, Deisseroth K. Structural Mechanisms of Selectivity and High-Speed Gating in Anion Channelrodopsins. Nature 561, 349-354 (2018).

  12. Lovett-Barron M, Andalman A, Allen WE, Vesuna S, Kauvar I, Burns WM, Deisseroth K. Ancestral Circuits for the Coordinated Modulation of Brain State. Cell 171, 1411-1423 (2017)

  13. Yang SJ, Allen WE, Kauvar I, Andalman A, Young NP, Kim CK, Marshel JH, Wetzstein G, Deisseroth K. Extended Field-of-View and Increased-signal 3D Holographic Illumination with Time-Division Multiplexing. Optics Express 23, 32573-32581 (2015)

  14. Allen WE, Luo L. Intersectional Illumination of Neural Circuit Function Neuron 85, 889-892 (2015)

  15. Markenscoff-Papadimitriou E, Allen WE, Colquitt BM, Goh T, Murphy KK, Monahan K, Mosely CP, Ahituv N, Lomvardas S. Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression. Cell 159, 543-557 (2014)

  16. Colquitt BM, Allen WE, Barnea G, Lomvardas S. Alteration of Genic 5-hydroxymethylcytosine Levels in Olfactory Neurons Correlates With Changes in Gene Expression and Cell Identity. Proc. Natl. Acad. Sci. USA 110, 14682-14687 (2013)

  17. Lyons DB, Allen WE, Goh T, Tsai L, Barnea G, Lomvardas S. An Epigenetic Trap Stabilizes Singular Olfactory Receptor Expression. Cell 154, 325-336 (2013)

  18. Magklara A, Yen A, Colquitt BM, Clowney EJ, Allen W, Markenscoff-Papadimitriou E, Evans ZA, Kheradpour P, Mountoufaris G, Carey C, Barnea G, Kellis M, Lomvardas S. An Epigenetic Signature for Monoallelic Olfactory Receptor Expression. Cell 145, 555-570 (2011)