William Allen weallen@fas.harvard.edu

I am a Junior Fellow in the Harvard Society of Fellows.


From 2013-2019, I was a Ph.D. student at Stanford University in the Neurosciences program, supported by an NSF Graduate Research Fellowship and a Hertz Fellowship. I was co-advised by Prof. Karl Deisseroth in the Departments of Bioengineering and Psychiatry and Prof. Liqun Luo in Department of Biology.

During my PhD, I developed new techniques to perform large-scale, spatially-resolved measurements of neuronal activity [1, 2, 3] and gene expression [4] in the brain and applied these techniques to understand the neural basis of thirst motivation [3, 5]. I was awarded the Harold Weintraub Graduate Student Award for this work.

In 2013, I received an M.Phil. in Computational Biology at the University of Cambridge on a Churchill Scholarship, studying neural circuits in Drosophila in Dr. Gregory Jefferis's group at the MRC Laboratory of Molecular Biology.

In May 2012, I graduated from Brown University with an Sc.B. in Applied Mathematics-Biology. While at Brown, I pursued research in synthetic biology, neurobiology, genomics, molecular genetics, and machine learning. The majority of my research focused on gene regulation in the mouse olfactory system, advised by Professor Gilad Barnea at Brown and Professor Stavros Lomvardas at UCSF (now at Columbia University). The summer of 2012, I also worked in Professor Kristin Scott's lab at UC Berkeley.

  1. 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). [PDF]
  2. 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). [PDF]
  3. 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). [PDF]
  4. 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. [PDF]
  5. 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). [PDF]
  6. 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). [PDF | Science Perspective]
  7. 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) [PDF].
  8. 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) [PDF | Science Perspective | Nature Highlight].
  9. 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) [PDF | Neuron Preview]
  10. 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). * = equal contribution. Cover article. [PDF | Stanford news | Cell Preview]
  11. 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) [PDF]
  12. Allen WE, Luo L. "Intersectional Illumination of Neural Circuit Function" Neuron 85, 889-892 (2015) [PDF]
  13. 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) [PDF]
  14. 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) [PDF]
  15. 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) [PDF]
  16. 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) [PDF]

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